@article{pmid29166592,

title = {HIV Envelope Glycoform Heterogeneity and Localized Diversity Govern the Initiation and Maturation of a V2 Apex Broadly Neutralizing Antibody Lineage},

author = {Elise Landais and Ben Murrell and Bryan Briney and Sasha Murrell and Kimmo Rantalainen and Zachary T Berndsen and Alejandra Ramos and Lalinda Wickramasinghe and Melissa Laird Smith and Kemal Eren and Natalia de Val and Mengyu Wu and Audrey Cappelletti and Jeffrey Umotoy and Yolanda Lie and Terri Wrin and Paul Algate and Po-Ying Chan-Hui and Etienne Karita and  and  and Andrew B Ward and Ian A Wilson and Dennis R Burton and Davey Smith and Sergei L Kosakovsky Pond and Pascal Poignard},

doi = {10.1016/j.immuni.2017.11.002},

issn = {1097-4180},

year  = {2017},

date = {2017-11-01},

journal = {Immunity},

volume = {47},

number = {5},

pages = {990--1003.e9},

abstract = {Understanding how broadly neutralizing antibodies (bnAbs) to HIV envelope (Env) develop during natural infection can help guide the rational design of an HIV vaccine. Here, we described a bnAb lineage targeting the Env V2 apex and the Ab-Env co-evolution that led to development of neutralization breadth. The lineage Abs bore an anionic heavy chain complementarity-determining region 3 (CDRH3) of 25 amino acids, among the shortest known for this class of Abs, and achieved breadth with only 10% nucleotide somatic hypermutation and no insertions or deletions. The data suggested a role for Env glycoform heterogeneity in the activation of the lineage germline B cell. Finally, we showed that localized diversity at key V2 epitope residues drove bnAb maturation toward breadth, mirroring the Env evolution pattern described for another donor who developed V2-apex targeting bnAbs. Overall, these findings suggest potential strategies for vaccine approaches based on germline-targeting and serial immunogen design.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid29150603,

title = {Bacterially derived synthetic mimetics of mammalian oligomannose prime antibody responses that neutralize HIV infectivity},

author = {Ralph Pantophlet and Nino Trattnig and Sasha Murrell and Naiomi Lu and Dennis Chau and Caitlin Rempel and Ian A Wilson and Paul Kosma},

doi = {10.1038/s41467-017-01640-y},

issn = {2041-1723},

year  = {2017},

date = {2017-11-01},

journal = {Nat Commun},

volume = {8},

number = {1},

pages = {1601},

abstract = {Oligomannose-type glycans are among the major targets on the gp120 component of the HIV envelope protein (Env) for broadly neutralizing antibodies (bnAbs). However, attempts to elicit oligomannose-specific nAbs by immunizing with natural or synthetic oligomannose have so far not been successful, possibly due to B cell tolerance checkpoints. Here we design and synthesize oligomannose mimetics, based on the unique chemical structure of a recently identified bacterial lipooligosaccharide, to appear foreign to the immune system. One of these mimetics is bound avidly by members of a family of oligomannose-specific bnAbs and their putative common germline precursor when presented as a glycoconjugate. The crystal structure of one of the mimetics bound to a member of this bnAb family confirms the antigenic resemblance. Lastly, immunization of human-antibody transgenic animals with a lead mimetic evokes nAbs with specificities approaching those of existing bnAbs. These results provide evidence for utilizing antigenic mimicry to elicit oligomannose-specific bnAbs to HIV-1.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid28988747,

title = {Structural Insights into VLR Fine Specificity for Blood Group Carbohydrates},

author = {Bernard C Collins and Robin J Gunn and Tanya R McKitrick and Richard D Cummings and Max D Cooper and Brantley R Herrin and Ian A Wilson},

doi = {10.1016/j.str.2017.09.003},

issn = {1878-4186},

year  = {2017},

date = {2017-11-01},

journal = {Structure},

volume = {25},

number = {11},

pages = {1667--1678.e4},

abstract = {High-quality reagents to study and detect glycans with high specificity for research and clinical applications are severely lacking. Here, we structurally and functionally characterize several variable lymphocyte receptor (VLR)-based antibodies from lampreys immunized with O erythrocytes that specifically recognize the blood group H-trisaccharide type II antigen. Glycan microarray analysis and biophysical data reveal that these VLRs exhibit greater specificity for H-trisaccharide compared with the plant lectin UEA-1, which is widely used in blood typing. Among these antibodies, O13 exhibits superior specificity for H-trisaccharide, the basis for which is revealed by comparative analysis of high-resolution VLR:glycan crystal structures. Using a structure-guided approach, we designed an O13 mutant with further enhanced specificity for H-trisaccharide. These insights into glycan recognition by VLRs suggest that lampreys can produce highly specific glycan antibodies, and are a valuable resource for the production of next-generation glycan reagents for biological and biomedical research and as diagnostics and therapeutics.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid28971971,

title = {Potent peptidic fusion inhibitors of influenza virus},

author = {Rameshwar U Kadam and Jarek Juraszek and Boerries Brandenburg and Christophe Buyck and Wim B G Schepens and Bart Kesteleyn and Bart Stoops and Rob J Vreeken and Jan Vermond and Wouter Goutier and Chan Tang and Ronald Vogels and Robert H E Friesen and Jaap Goudsmit and Maria J P van Dongen and Ian A Wilson},

doi = {10.1126/science.aan0516},

issn = {1095-9203},

year  = {2017},

date = {2017-10-01},

journal = {Science},

volume = {358},

number = {6362},

pages = {496--502},

abstract = {Influenza therapeutics with new targets and mechanisms of action are urgently needed to combat potential pandemics, emerging viruses, and constantly mutating strains in circulation. We report here on the design and structural characterization of potent peptidic inhibitors of influenza hemagglutinin. The peptide design was based on complementarity-determining region loops of human broadly neutralizing antibodies against the hemagglutinin (FI6v3 and CR9114). The optimized peptides exhibit nanomolar affinity and neutralization against influenza A group 1 viruses, including the 2009 H1N1 pandemic and avian H5N1 strains. The peptide inhibitors bind to the highly conserved stem epitope and block the low pH-induced conformational rearrangements associated with membrane fusion. These peptidic compounds and their advantageous biological properties should accelerate the development of new small molecule- and peptide-based therapeutics against influenza virus.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid29059230,

title = {A structural explanation for the low effectiveness of the seasonal influenza H3N2 vaccine},

author = {Nicholas C Wu and Seth J Zost and Andrew J Thompson and David Oyen and Corwin M Nycholat and Ryan McBride and James C Paulson and Scott E Hensley and Ian A Wilson},

doi = {10.1371/journal.ppat.1006682},

issn = {1553-7374},

year  = {2017},

date = {2017-10-01},

journal = {PLoS Pathog},

volume = {13},

number = {10},

pages = {e1006682},

abstract = {The effectiveness of the annual influenza vaccine has declined in recent years, especially for the H3N2 component, and is a concern for global public health. A major cause for this lack in effectiveness has been attributed to the egg-based vaccine production process. Substitutions on the hemagglutinin glycoprotein (HA) often arise during virus passaging that change its antigenicity and hence vaccine effectiveness. Here, we characterize the effect of a prevalent substitution, L194P, in egg-passaged H3N2 viruses. X-ray structural analysis reveals that this substitution surprisingly increases the mobility of the 190-helix and neighboring regions in antigenic site B, which forms one side of the receptor binding site (RBS) and is immunodominant in recent human H3N2 viruses. Importantly, the L194P substitution decreases binding and neutralization by an RBS-targeted broadly neutralizing antibody by three orders of magnitude and significantly changes the HA antigenicity as measured by binding of human serum antibodies. The receptor binding mode and specificity are also altered to adapt to avian receptors during egg passaging. Overall, these findings help explain the low effectiveness of the seasonal vaccine against H3N2 viruses, and suggest that alternative approaches should be accelerated for producing influenza vaccines as well as isolating clinical isolates.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid28953867,

title = {Massively parallel de novo protein design for targeted therapeutics},

author = {Aaron Chevalier and Daniel-Adriano Silva and Gabriel J Rocklin and Derrick R Hicks and Renan Vergara and Patience Murapa and Steffen M Bernard and Lu Zhang and Kwok-Ho Lam and Guorui Yao and Christopher D Bahl and Shin-Ichiro Miyashita and Inna Goreshnik and James T Fuller and Merika T Koday and Cody M Jenkins and Tom Colvin and Lauren Carter and Alan Bohn and Cassie M Bryan and D Alejandro Fernández-Velasco and Lance Stewart and Min Dong and Xuhui Huang and Rongsheng Jin and Ian A Wilson and Deborah H Fuller and David Baker},

doi = {10.1038/nature23912},

issn = {1476-4687},

year  = {2017},

date = {2017-10-01},

journal = {Nature},

volume = {550},

number = {7674},

pages = {74--79},

abstract = {De novo protein design holds promise for creating small stable proteins with shapes customized to bind therapeutic targets. We describe a massively parallel approach for designing, manufacturing and screening mini-protein binders, integrating large-scale computational design, oligonucleotide synthesis, yeast display screening and next-generation sequencing. We designed and tested 22,660 mini-proteins of 37-43 residues that target influenza haemagglutinin and botulinum neurotoxin B, along with 6,286 control sequences to probe contributions to folding and binding, and identified 2,618 high-affinity binders. Comparison of the binding and non-binding design sets, which are two orders of magnitude larger than any previously investigated, enabled the evaluation and improvement of the computational model. Biophysical characterization of a subset of the binder designs showed that they are extremely stable and, unlike antibodies, do not lose activity after exposure to high temperatures. The designs elicit little or no immune response and provide potent prophylactic and therapeutic protection against influenza, even after extensive repeated dosing.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid28978475,

title = {Elicitation of Neutralizing Antibodies Targeting the V2 Apex of the HIV Envelope Trimer in a Wild-Type Animal Model},

author = {James E Voss and Raiees Andrabi and Laura E McCoy and Natalia de Val and Roberta P Fuller and Terrence Messmer and Ching-Yao Su and Devin Sok and Salar N Khan and Fernando Garces and Laura K Pritchard and Richard T Wyatt and Andrew B Ward and Max Crispin and Ian A Wilson and Dennis R Burton},

doi = {10.1016/j.celrep.2017.09.024},

issn = {2211-1247},

year  = {2017},

date = {2017-10-01},

journal = {Cell Rep},

volume = {21},

number = {1},

pages = {222--235},

abstract = {Recent efforts toward HIV vaccine development include the design of immunogens that can engage B cell receptors with the potential to affinity mature into broadly neutralizing antibodies (bnAbs). V2-apex bnAbs, which bind a protein-glycan region on HIV envelope glycoprotein (Env) trimer, are among the most broad and potent described. We show here that a rare "glycan hole" at the V2 apex is enriched in HIV isolates neutralized by inferred precursors of prototype V2-apex bnAbs. To investigate whether this feature could focus neutralizing responses onto the apex bnAb region, we immunized wild-type rabbits with soluble trimers adapted from these Envs. Potent autologous tier 2 neutralizing responses targeting basic residues in strand C of the V2 region, which forms the core epitope for V2-apex bnAbs, were observed. Neutralizing monoclonal antibodies (mAbs) derived from these animals display features promising for subsequent broadening of the response.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid28930686,

title = {Antibody 27F3 Broadly Targets Influenza A Group 1 and 2 Hemagglutinins through a Further Variation in V1-69 Antibody Orientation on the HA Stem},

author = {Shanshan Lang and Jia Xie and Xueyong Zhu and Nicholas C Wu and Richard A Lerner and Ian A Wilson},

doi = {10.1016/j.celrep.2017.08.084},

issn = {2211-1247},

year  = {2017},

date = {2017-09-01},

journal = {Cell Rep},

volume = {20},

number = {12},

pages = {2935--2943},

abstract = {Antibodies that target both group 1 and group 2 influenza A viruses are valuable for therapeutic and vaccine development, but only a few have been reported to date. Here, we describe a new V1-69 antibody 27F3 that broadly recognizes heterosubtypic hemagglutinins (HAs) from both group 1 and group 2 influenza A viruses. Structural characterization of 27F3 Fab with A/California/04/2009 (H1N1) hemagglutinin illustrates that 27F3 shares the key binding features observed in other V1-69 antibodies to the HA stem. Compared to other V1-69 antibodies, the 27F3 V domain interacts with the HA stem in a distinct orientation, which alters its epitope and may have influenced its breadth. The diverse rotations of V1-69 antibodies on the HA stem epitope highlight the different ways that this antibody family can evolve to broadly neutralize influenza A viruses. These results have important implications for understanding how to elicit broad antibody responses against influenza virus.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid28847869,

title = {Design and crystal structure of a native-like HIV-1 envelope trimer that engages multiple broadly neutralizing antibody precursors in vivo},

author = {Max Medina-Ramírez and Fernando Garces and Amelia Escolano and Patrick Skog and Steven W de Taeye and Ivan Del Moral-Sanchez and Andrew T McGuire and Anila Yasmeen and Anna-Janina Behrens and Gabriel Ozorowski and Tom L G M van den Kerkhof and Natalia T Freund and Pia Dosenovic and Yuanzi Hua and Alexander D Gitlin and Albert Cupo and Patricia van der Woude and Michael Golabek and Kwinten Sliepen and Tanya Blane and Neeltje Kootstra and Mariëlle J van Breemen and Laura K Pritchard and Robyn L Stanfield and Max Crispin and Andrew B Ward and Leonidas Stamatatos and Per Johan Klasse and John P Moore and David Nemazee and Michel C Nussenzweig and Ian A Wilson and Rogier W Sanders},

doi = {10.1084/jem.20161160},

issn = {1540-9538},

year  = {2017},

date = {2017-09-01},

journal = {J Exp Med},

volume = {214},

number = {9},

pages = {2573--2590},

abstract = {Induction of broadly neutralizing antibodies (bNAbs) by HIV-1 envelope glycoprotein immunogens would be a major advance toward an effective vaccine. A critical step in this process is the activation of naive B cells expressing germline (gl) antibody precursors that have the potential to evolve into bNAbs. Here, we reengineered the BG505 SOSIP.664 glycoprotein to engage gl precursors of bNAbs that target either the trimer apex or the CD4-binding site. The resulting BG505 SOSIP.v4.1-GT1 trimer binds multiple bNAb gl precursors in vitro. Immunization experiments in knock-in mice expressing gl-VRC01 or gl-PGT121 show that this trimer activates B cells in vivo, resulting in the secretion of specific antibodies into the sera. A crystal structure of the gl-targeting trimer at 3.2-Å resolution in complex with neutralizing antibodies 35O22 and 9H+109L reveals a native-like conformation and the successful incorporation of design features associated with binding of multiple gl-bNAb precursors.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid28694323,

title = {A single mutation in Taiwanese H6N1 influenza hemagglutinin switches binding to human-type receptors},

author = {Robert P de Vries and Netanel Tzarum and Wenjie Peng and Andrew J Thompson and Iresha N Ambepitiya Wickramasinghe and Alba T Torrents de la Pena and Marielle J van Breemen and Kim M Bouwman and Xueyong Zhu and Ryan McBride and Wenli Yu and Rogier W Sanders and Monique H Verheije and Ian A Wilson and James C Paulson},

doi = {10.15252/emmm.201707726},

issn = {1757-4684},

year  = {2017},

date = {2017-09-01},

journal = {EMBO Mol Med},

volume = {9},

number = {9},

pages = {1314--1325},

abstract = {In June 2013, the first case of human infection with an avian H6N1 virus was reported in a Taiwanese woman. Although this was a single non-fatal case, the virus continues to circulate in Taiwanese poultry. As with any emerging avian virus that infects humans, there is concern that acquisition of human-type receptor specificity could enable transmission in the human population. Despite mutations in the receptor-binding pocket of the human H6N1 isolate, it has retained avian-type (NeuAcα2-3Gal) receptor specificity. However, we show here that a single nucleotide substitution, resulting in a change from Gly to Asp at position 225 (G225D), completely switches specificity to human-type (NeuAcα2-6Gal) receptors. Significantly, G225D H6 loses binding to chicken trachea epithelium and is now able to bind to human tracheal tissue. Structural analysis reveals that Asp225 directly interacts with the penultimate Gal of the human-type receptor, stabilizing human receptor binding.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid28834745,

title = {Improving the Immunogenicity of Native-like HIV-1 Envelope Trimers by Hyperstabilization},

author = {Alba Torrents de la Peña and Jean-Philippe Julien and Steven W de Taeye and Fernando Garces and Miklos Guttman and Gabriel Ozorowski and Laura K Pritchard and Anna-Janina Behrens and Eden P Go and Judith A Burger and Edith E Schermer and Kwinten Sliepen and Thomas J Ketas and Pavel Pugach and Anila Yasmeen and Christopher A Cottrell and Jonathan L Torres and Charlotte D Vavourakis and Marit J van Gils and Celia LaBranche and David C Montefiori and Heather Desaire and Max Crispin and Per Johan Klasse and Kelly K Lee and John P Moore and Andrew B Ward and Ian A Wilson and Rogier W Sanders},

doi = {10.1016/j.celrep.2017.07.077},

issn = {2211-1247},

year  = {2017},

date = {2017-08-01},

journal = {Cell Rep},

volume = {20},

number = {8},

pages = {1805--1817},

abstract = {The production of native-like recombinant versions of the HIV-1 envelope glycoprotein (Env) trimer requires overcoming the natural flexibility and instability of the complex. The engineered BG505 SOSIP.664 trimer mimics the structure and antigenicity of native Env. Here, we describe how the introduction of new disulfide bonds between the glycoprotein (gp)120 and gp41 subunits of SOSIP trimers of the BG505 and other genotypes improves their stability and antigenicity, reduces their conformational flexibility, and helps maintain them in the unliganded conformation. The resulting next-generation SOSIP.v5 trimers induce strong autologous tier-2 neutralizing antibody (NAb) responses in rabbits. In addition, the BG505 SOSIP.v6 trimers induced weak heterologous NAb responses against a subset of tier-2 viruses that were not elicited by the prototype BG505 SOSIP.664. These stabilization methods can be applied to trimers from multiple genotypes as components of multivalent vaccines aimed at inducing broadly NAbs (bNAbs).},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid28827559,

title = {Selection of nanobodies with broad neutralizing potential against primary HIV-1 strains using soluble subtype C gp140 envelope trimers},

author = {Kathrin Koch and Sarah Kalusche and Jonathan L Torres and Robyn L Stanfield and Welbeck Danquah and Kamal Khazanehdari and Hagen von Briesen and Eric R Geertsma and Ian A Wilson and Ulrich Wernery and Friedrich Koch-Nolte and Andrew B Ward and Ursula Dietrich},

doi = {10.1038/s41598-017-08273-7},

issn = {2045-2322},

year  = {2017},

date = {2017-08-01},

journal = {Sci Rep},

volume = {7},

number = {1},

pages = {8390},

abstract = {Broadly neutralizing antibodies (bnAbs) against HIV-1 protect from infection and reduce viral load upon therapeutic applications. However no vaccine was able so far to induce bnAbs demanding their expensive biotechnological production. For clinical applications, nanobodies (VHH) derived from heavy chain only antibodies from Camelidae, may be better suited due to their small size, high solubility/stability and extensive homology to human VH3 genes. Here we selected broadly neutralizing nanobodies by phage display after immunization of dromedaries with different soluble trimeric envelope proteins derived from HIV-1 subtype C. We identified 25 distinct VHH families binding trimeric Env, of which 6 neutralized heterologous primary isolates of various HIV-1 subtypes in a standardized in vitro neutralization assay. The complementary neutralization pattern of two selected VHHs in combination covers 19 out of 21 HIV-1 strains from a standardized panel of epidemiologically relevant HIV-1 subtypes. The CD4 binding site was preferentially targeted by the broadly neutralizing VHHs as determined by competition ELISAs and 3D models of VHH-Env complexes derived from negative stain electron microscopy. The nanobodies identified here are excellent candidates for further preclinical/clinical development for prophylactic and therapeutic applications due to their potency and their complementary neutralization patterns covering the majority of epidemiologically relevant HIV-1 subtypes.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid28648617,

title = {A Perspective on the Structural and Functional Constraints for Immune Evasion: Insights from Influenza Virus},

author = {Nicholas C Wu and Ian A Wilson},

doi = {10.1016/j.jmb.2017.06.015},

issn = {1089-8638},

year  = {2017},

date = {2017-08-01},

journal = {J Mol Biol},

volume = {429},

number = {17},

pages = {2694--2709},

abstract = {Influenza virus evolves rapidly to constantly escape from natural immunity. Most humoral immune responses to influenza virus target the hemagglutinin (HA) glycoprotein, which is the major antigen on the surface of the virus. The HA is composed of a globular head domain for receptor binding and a stem domain for membrane fusion. The major antigenic sites of HA are located in the globular head subdomain, which is highly tolerant of amino acid substitutions and continual addition of glycosylation sites. Nonetheless, the evolution of the receptor-binding site and the stem region on HA is severely constrained by their functional roles in engaging the host receptor and in mediating membrane fusion, respectively. Here, we review how broadly neutralizing antibodies (bnAbs) exploit these evolutionary constraints to protect against diverse influenza strains. We also discuss the emerging role of other epitopes that are conserved only in subsets of viruses. This rapidly increasing knowledge of the evolutionary biology, immunology, structural biology, and virology of influenza virus is invaluable for development and design of more universal influenza vaccines and novel therapeutics.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid28737940,

title = {Defining the Structural Basis for Allosteric Product Release from E. coli Dihydrofolate Reductase Using NMR Relaxation Dispersion},

author = {David Oyen and R Bryn Fenwick and Phillip C Aoto and Robyn L Stanfield and Ian A Wilson and H Jane Dyson and Peter E Wright},

doi = {10.1021/jacs.7b05958},

issn = {1520-5126},

year  = {2017},

date = {2017-08-01},

journal = {J Am Chem Soc},

volume = {139},

number = {32},

pages = {11233--11240},

abstract = {The rate-determining step in the catalytic cycle of E. coli dihydrofolate reductase is tetrahydrofolate (THF) product release, which can occur via an allosteric or an intrinsic pathway. The allosteric pathway, which becomes accessible when the reduced cofactor NADPH is bound, involves transient sampling of a higher energy conformational state, greatly increasing the product dissociation rate as compared to the intrinsic pathway that obtains when NADPH is absent. Although the kinetics of this process are known, the enzyme structure and the THF product conformation in the transiently formed excited state remain elusive. Here, we use side-chain proton NMR relaxation dispersion measurements, X-ray crystallography, and structure-based chemical shift predictions to explore the structural basis of allosteric product release. In the excited state of the E:THF:NADPH product release complex, the reduced nicotinamide ring of the cofactor transiently enters the active site where it displaces the pterin ring of the THF product. The p-aminobenzoyl-l-glutamate tail of THF remains weakly bound in a widened binding cleft. Thus, through transient entry of the nicotinamide ring into the active site, the NADPH cofactor remodels the enzyme structure and the conformation of the THF to form a weakly populated excited state that is poised for rapid product release.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid28689973,

title = {Structure-based optimization and synthesis of antiviral drug Arbidol analogues with significantly improved affinity to influenza hemagglutinin},

author = {Zoë V F Wright and Nicholas C Wu and Rameshwar U Kadam and Ian A Wilson and Dennis W Wolan},

doi = {10.1016/j.bmcl.2017.06.074},

issn = {1464-3405},

year  = {2017},

date = {2017-08-01},

journal = {Bioorg Med Chem Lett},

volume = {27},

number = {16},

pages = {3744--3748},

abstract = {Influenza is a highly contagious respiratory viral infection responsible for up to 50,000 deaths per annum in the US alone. The need for new therapeutics with novel modes of action is of paramount importance. We determined the X-ray structure of Arbidol with influenza hemagglutinin and found it was located in a distinct binding pocket. Herein, we report a structure-activity relationship study based on the co-complex combined with bio-layer interferometry to assess the binding of our compounds. Addition of a meta-hydroxy group to the thiophenol moiety of Arbidol to replace a structured water molecule in the binding pocket resulted in a dramatic increase in affinity against both H3 (1150-fold) and H1 (98-fold) hemagglutinin subtypes. Our analogues represent novel leads to yield more potent compounds against hemagglutinin that block viral entry.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid28799910,

title = {Diversity of Functionally Permissive Sequences in the Receptor-Binding Site of Influenza Hemagglutinin},

author = {Nicholas C Wu and Jia Xie and Tianqing Zheng and Corwin M Nycholat and Geramie Grande and James C Paulson and Richard A Lerner and Ian A Wilson},

doi = {10.1016/j.chom.2017.07.001},

issn = {1934-6069},

year  = {2017},

date = {2017-08-01},

journal = {Cell Host Microbe},

volume = {22},

number = {2},

pages = {247--248},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid28726771,

title = {Rapid elicitation of broadly neutralizing antibodies to HIV by immunization in cows},

author = {Devin Sok and Khoa M Le and Melissa Vadnais and Karen L Saye-Francisco and Joseph G Jardine and Jonathan L Torres and Zachary T Berndsen and Leopold Kong and Robyn Stanfield and Jennifer Ruiz and Alejandra Ramos and Chi-Hui Liang and Patricia L Chen and Michael F Criscitiello and Waithaka Mwangi and Ian A Wilson and Andrew B Ward and Vaughn V Smider and Dennis R Burton},

doi = {10.1038/nature23301},

issn = {1476-4687},

year  = {2017},

date = {2017-08-01},

journal = {Nature},

volume = {548},

number = {7665},

pages = {108--111},

abstract = {No immunogen to date has reliably elicited broadly neutralizing antibodies to HIV in humans or animal models. Advances in the design of immunogens that antigenically mimic the HIV envelope glycoprotein (Env), such as the soluble cleaved trimer BG505 SOSIP, have improved the elicitation of potent isolate-specific antibody responses in rabbits and macaques, but so far failed to induce broadly neutralizing antibodies. One possible reason for this failure is that the relevant antibody repertoires are poorly suited to target the conserved epitope regions on Env, which are somewhat occluded relative to the exposed variable epitopes. Here, to test this hypothesis, we immunized four cows with BG505 SOSIP. The antibody repertoire of cows contains long third heavy chain complementary determining regions (HCDR3) with an ultralong subset that can reach more than 70 amino acids in length. Remarkably, BG505 SOSIP immunization resulted in rapid elicitation of broad and potent serum antibody responses in all four cows. Longitudinal serum analysis for one cow showed the development of neutralization breadth (20%, n = 117 cross-clade isolates) in 42 days and 96% breadth (n = 117) at 381 days. A monoclonal antibody isolated from this cow harboured an ultralong HCDR3 of 60 amino acids and neutralized 72% of cross-clade isolates (n = 117) with a potent median IC of 0.028 μg ml. Breadth was elicited with a single trimer immunogen and did not require additional envelope diversity. Immunization of cows may provide an avenue to rapidly generate antibody prophylactics and therapeutics to address disease agents that have evolved to avoid human antibody responses.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid28539451,

title = {Reducing V3 Antigenicity and Immunogenicity on Soluble, Native-Like HIV-1 Env SOSIP Trimers},

author = {Rajesh P Ringe and Gabriel Ozorowski and Kimmo Rantalainen and Weston B Struwe and Katie Matthews and Jonathan L Torres and Anila Yasmeen and Christopher A Cottrell and Thomas J Ketas and Celia C LaBranche and David C Montefiori and Albert Cupo and Max Crispin and Ian A Wilson and Andrew B Ward and Rogier W Sanders and P J Klasse and John P Moore},

doi = {10.1128/JVI.00677-17},

issn = {1098-5514},

year  = {2017},

date = {2017-08-01},

journal = {J Virol},

volume = {91},

number = {15},

abstract = {Native-like trimers of the SOSIP design are being developed as immunogens in human immunodeficiency virus type 1 (HIV-1) vaccine development programs. These trimers display the epitopes for multiple broadly neutralizing antibodies (bNAbs) but can also expose binding sites for some types of nonneutralizing antibodies (non-NAbs). Among the latter are epitopes in the gp120 V3 region that are highly immunogenic when SOSIP trimers are evaluated in animal models. It is presently uncertain whether antibodies against V3 can interfere with the induction of NAbs, but there are good arguments in favor of suppressing such "off-target" immune responses. Accordingly, we have assessed how to minimize the exposure of V3 non-NAb epitopes and thereby reduce their immunogenicity by introducing -glycans within the V3 region of BG505 SOSIP trimers. We found that inserting glycans at positions 306 and 314 (termed M1 and M7) markedly reduced V3 antigenicity while improving the presentation of trimer apex bNAb epitopes. Both added glycans were shown to be predominantly of the ManGlcNAc form. The additional introduction of the E64K ground-state stabilizing substitution markedly reduced or ablated soluble CD4 (sCD4) induction of non-NAb epitopes in V3 and/or associated with the coreceptor binding site. When a V3 glycan- and E64K-modified trimer variant, BG505 SOSIP.664-E64K.M1M7, was tested in rabbits, V3 immunogenicity was eliminated while the autologous NAb response was unchanged. Trimeric proteins are being developed for future HIV-1 vaccine trials in humans, with the goal of eliciting broadly active neutralizing antibodies (NAbs) that are active against a wide variety of circulating strains. In animal models, the present generation of native-like trimer immunogens, exemplified by the BG505 SOSIP.664 construct, induces narrow-specificity antibodies against the neutralization-resistant (tier-2), sequence-matched virus and more broadly active antibodies against sequence-divergent atypically neutralization-sensitive (tier-1) viruses. A concern in the trimer immunogen design field has been whether the latter off-target antibodies might interfere with the induction of the more desired responses to tier-2 epitopes. Here, we have inserted two glycans into the dominant site for tier-1 NAbs, the gp120 V3 region, to block the induction of off-target antibodies. We characterized the new trimers, tested them as immunogens in rabbits, and found that the blocking glycans eliminated the induction of tier-1 NAbs to V3-epitopes.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid28604693,

title = {Genetically encoding phosphotyrosine and its nonhydrolyzable analog in bacteria},

author = {Xiaozhou Luo and Guangsen Fu and Rongsheng E Wang and Xueyong Zhu and Claudio Zambaldo and Renhe Liu and Tao Liu and Xiaoxuan Lyu and Jintang Du and Weimin Xuan and Anzhi Yao and Sean A Reed and Mingchao Kang and Yuhan Zhang and Hui Guo and Chunhui Huang and Peng-Yu Yang and Ian A Wilson and Peter G Schultz and Feng Wang},

doi = {10.1038/nchembio.2405},

issn = {1552-4469},

year  = {2017},

date = {2017-08-01},

journal = {Nat Chem Biol},

volume = {13},

number = {8},

pages = {845--849},

abstract = {Tyrosine phosphorylation is a common protein post-translational modification that plays a critical role in signal transduction and the regulation of many cellular processes. Using a propeptide strategy to increase cellular uptake of O-phosphotyrosine (pTyr) and its nonhydrolyzable analog 4-phosphomethyl-L-phenylalanine (Pmp), we identified an orthogonal aminoacyl-tRNA synthetase-tRNA pair that allows site-specific incorporation of both pTyr and Pmp into recombinant proteins in response to the amber stop codon in Escherichia coli in good yields. The X-ray structure of the synthetase reveals a reconfigured substrate-binding site, formed by nonconservative mutations and substantial local structural perturbations. We demonstrate the utility of this method by introducing Pmp into a putative phosphorylation site and determining the affinities of the individual variants for the substrate 3BP2. In summary, this work provides a useful recombinant tool to dissect the biological functions of tyrosine phosphorylation at specific sites in the proteome.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid28625364,

title = {Semi-quantitative models for identifying potent and selective transthyretin amyloidogenesis inhibitors},

author = {Stephen Connelly and David E Mortenson and Sungwook Choi and Ian A Wilson and Evan T Powers and Jeffery W Kelly and Steven M Johnson},

doi = {10.1016/j.bmcl.2017.05.080},

issn = {1464-3405},

year  = {2017},

date = {2017-08-01},

journal = {Bioorg Med Chem Lett},

volume = {27},

number = {15},

pages = {3441--3449},

abstract = {Rate-limiting dissociation of the tetrameric protein transthyretin (TTR), followed by monomer misfolding and misassembly, appears to cause degenerative diseases in humans known as the transthyretin amyloidoses, based on human genetic, biochemical and pharmacologic evidence. Small molecules that bind to the generally unoccupied thyroxine binding pockets in the native TTR tetramer kinetically stabilize the tetramer, slowing subunit dissociation proportional to the extent that the molecules stabilize the native state over the dissociative transition state-thereby inhibiting amyloidogenesis. Herein, we use previously reported structure-activity relationship data to develop two semi-quantitative algorithms for identifying the structures of potent and selective transthyretin kinetic stabilizers/amyloidogenesis inhibitors. The viability of these prediction algorithms, in particular the more robust in silico docking model, is perhaps best validated by the clinical success of tafamidis, the first-in-class drug approved in Europe, Japan, South America, and elsewhere for treating transthyretin aggregation-associated familial amyloid polyneuropathy. Tafamidis is also being evaluated in a fully-enrolled placebo-controlled clinical trial for its efficacy against TTR cardiomyopathy. These prediction algorithms will be useful for identifying second generation TTR kinetic stabilizers, should these be needed to ameliorate the central nervous system or ophthalmologic pathology caused by TTR aggregation in organs not accessed by oral tafamidis administration.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid28700571,

title = {Open and closed structures reveal allostery and pliability in the HIV-1 envelope spike},

author = {Gabriel Ozorowski and Jesper Pallesen and Natalia de Val and Dmitry Lyumkis and Christopher A Cottrell and Jonathan L Torres and Jeffrey Copps and Robyn L Stanfield and Albert Cupo and Pavel Pugach and John P Moore and Ian A Wilson and Andrew B Ward},

doi = {10.1038/nature23010},

issn = {1476-4687},

year  = {2017},

date = {2017-07-01},

journal = {Nature},

volume = {547},

number = {7663},

pages = {360--363},

abstract = {For many enveloped viruses, binding to a receptor(s) on a host cell acts as the first step in a series of events culminating in fusion with the host cell membrane and transfer of genetic material for replication. The envelope glycoprotein (Env) trimer on the surface of HIV is responsible for receptor binding and fusion. Although Env can tolerate a high degree of mutation in five variable regions (V1-V5), and also at N-linked glycosylation sites that contribute roughly half the mass of Env, the functional sites for recognition of receptor CD4 and co-receptor CXCR4/CCR5 are conserved and essential for viral fitness. Soluble SOSIP Env trimers are structural and antigenic mimics of the pre-fusion native, surface-presented Env, and are targets of broadly neutralizing antibodies. Thus, they are attractive immunogens for vaccine development. Here we present high-resolution cryo-electron microscopy structures of subtype B B41 SOSIP Env trimers in complex with CD4 and antibody 17b, or with antibody b12, at resolutions of 3.7 Å and 3.6 Å, respectively. We compare these to cryo-electron microscopy reconstructions of B41 SOSIP Env trimers with no ligand or in complex with either CD4 or the CD4-binding-site antibody PGV04 at 5.6 Å, 5.2 Å and 7.4 Å resolution, respectively. Consequently, we present the most complete description yet, to our knowledge, of the CD4-17b-induced intermediate and provide the molecular basis of the receptor-binding-induced conformational change required for HIV-1 entry into host cells. Both CD4 and b12 induce large, previously uncharacterized conformational rearrangements in the gp41 subunits, and the fusion peptide becomes buried in a newly formed pocket. These structures provide key details on the biological function of the type I viral fusion machine from HIV-1 as well as new templates for inhibitor design.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid28630323,

title = {Role of the CBP catalytic core in intramolecular SUMOylation and control of histone H3 acetylation},

author = {Sangho Park and Robyn L Stanfield and Maria A Martinez-Yamout and H Jane Dyson and Ian A Wilson and Peter E Wright},

doi = {10.1073/pnas.1703105114},

issn = {1091-6490},

year  = {2017},

date = {2017-07-01},

journal = {Proc Natl Acad Sci U S A},

volume = {114},

number = {27},

pages = {E5335--E5342},

abstract = {The histone acetyl transferases CREB-binding protein (CBP) and its paralog p300 play a critical role in numerous cellular processes. Dysregulation of their catalytic activity is associated with several human diseases. Previous work has elucidated the regulatory mechanisms of p300 acetyltransferase activity, but it is not known whether CBP activity is controlled similarly. Here, we present the crystal structure of the CBP catalytic core encompassing the bromodomain (BRD), CH2 (comprising PHD and RING), HAT, and ZZ domains at 2.4-Å resolution. The BRD, PHD, and HAT domains form an integral structural unit to which the RING and ZZ domains are flexibly attached. The structure of the apo-CBP HAT domain is similar to that of acyl-CoA-bound p300 HAT complexes and shows that the acetyl-CoA binding site is stably formed in the absence of cofactor. The BRD, PHD, and ZZ domains interact with small ubiquitin-like modifier 1 (SUMO-1) and Ubc9, and function as an intramolecular E3 ligase for SUMOylation of the cell cycle regulatory domain 1 (CRD1) of CBP, which is located adjacent to the BRD. In vitro HAT assays suggest that the RING domain, the autoregulatory loop (AL) within the HAT domain, and the ZZ domain do not directly influence catalytic activity, whereas the BRD is essential for histone H3 acetylation in nucleosomal substrates. Several lysine residues in the intrinsically disordered AL are autoacetylated by the HAT domain. Upon autoacetylation, acetyl-K1596 (Ac-K1596) binds intramolecularly to the BRD, competing with histones for binding to the BRD and acting as a negative regulator that inhibits histone H3 acetylation.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid28604661,

title = {Computational design of trimeric influenza-neutralizing proteins targeting the hemagglutinin receptor binding site},

author = {Eva-Maria Strauch and Steffen M Bernard and David La and Alan J Bohn and Peter S Lee and Caitlin E Anderson and Travis Nieusma and Carly A Holstein and Natalie K Garcia and Kathryn A Hooper and Rashmi Ravichandran and Jorgen W Nelson and William Sheffler and Jesse D Bloom and Kelly K Lee and Andrew B Ward and Paul Yager and Deborah H Fuller and Ian A Wilson and David Baker},

doi = {10.1038/nbt.3907},

issn = {1546-1696},

year  = {2017},

date = {2017-07-01},

journal = {Nat Biotechnol},

volume = {35},

number = {7},

pages = {667--671},

abstract = {Many viral surface glycoproteins and cell surface receptors are homo-oligomers, and thus can potentially be targeted by geometrically matched homo-oligomers that engage all subunits simultaneously to attain high avidity and/or lock subunits together. The adaptive immune system cannot generally employ this strategy since the individual antibody binding sites are not arranged with appropriate geometry to simultaneously engage multiple sites in a single target homo-oligomer. We describe a general strategy for the computational design of homo-oligomeric protein assemblies with binding functionality precisely matched to homo-oligomeric target sites. In the first step, a small protein is designed that binds a single site on the target. In the second step, the designed protein is assembled into a homo-oligomer such that the designed binding sites are aligned with the target sites. We use this approach to design high-avidity trimeric proteins that bind influenza A hemagglutinin (HA) at its conserved receptor binding site. The designed trimers can both capture and detect HA in a paper-based diagnostic format, neutralizes influenza in cell culture, and completely protects mice when given as a single dose 24 h before or after challenge with influenza.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid28636956,

title = {Elicitation of Robust Tier 2 Neutralizing Antibody Responses in Nonhuman Primates by HIV Envelope Trimer Immunization Using Optimized Approaches},

author = {Matthias Pauthner and Colin Havenar-Daughton and Devin Sok and Joseph P Nkolola and Raiza Bastidas and Archana V Boopathy and Diane G Carnathan and Abishek Chandrashekar and Kimberly M Cirelli and Christopher A Cottrell and Alexey M Eroshkin and Javier Guenaga and Kirti Kaushik and Daniel W Kulp and Jinyan Liu and Laura E McCoy and Aaron L Oom and Gabriel Ozorowski and Kai W Post and Shailendra K Sharma and Jon M Steichen and Steven W de Taeye and Talar Tokatlian and Alba Torrents de la Peña and Salvatore T Butera and Celia C LaBranche and David C Montefiori and Guido Silvestri and Ian A Wilson and Darrell J Irvine and Rogier W Sanders and William R Schief and Andrew B Ward and Richard T Wyatt and Dan H Barouch and Shane Crotty and Dennis R Burton},

doi = {10.1016/j.immuni.2017.05.007},

issn = {1097-4180},

year  = {2017},

date = {2017-06-01},

journal = {Immunity},

volume = {46},

number = {6},

pages = {1073--1088.e6},

abstract = {The development of stabilized recombinant HIV envelope trimers that mimic the virion surface molecule has increased enthusiasm for a neutralizing antibody (nAb)-based HIV vaccine. However, there is limited experience with recombinant trimers as immunogens in nonhuman primates, which are typically used as a model for humans. Here, we tested multiple immunogens and immunization strategies head-to-head to determine their impact on the quantity, quality, and kinetics of autologous tier 2 nAb development. A bilateral, adjuvanted, subcutaneous immunization protocol induced reproducible tier 2 nAb responses after only two immunizations 8 weeks apart, and these were further enhanced by a third immunization with BG505 SOSIP trimer. We identified immunogens that minimized non-neutralizing V3 responses and demonstrated that continuous immunogen delivery could enhance nAb responses. nAb responses were strongly associated with germinal center reactions, as assessed by lymph node fine needle aspiration. This study provides a framework for preclinical and clinical vaccine studies targeting nAb elicitation.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid28617868,

title = {Three mutations switch H7N9 influenza to human-type receptor specificity},

author = {Robert P de Vries and Wenjie Peng and Oliver C Grant and Andrew J Thompson and Xueyong Zhu and Kim M Bouwman and Alba T Torrents de la Pena and Marielle J van Breemen and Iresha N Ambepitiya Wickramasinghe and Cornelis A M de Haan and Wenli Yu and Ryan McBride and Rogier W Sanders and Robert J Woods and Monique H Verheije and Ian A Wilson and James C Paulson},

doi = {10.1371/journal.ppat.1006390},

issn = {1553-7374},

year  = {2017},

date = {2017-06-01},

journal = {PLoS Pathog},

volume = {13},

number = {6},

pages = {e1006390},

abstract = {The avian H7N9 influenza outbreak in 2013 resulted from an unprecedented incidence of influenza transmission to humans from infected poultry. The majority of human H7N9 isolates contained a hemagglutinin (HA) mutation (Q226L) that has previously been associated with a switch in receptor specificity from avian-type (NeuAcα2-3Gal) to human-type (NeuAcα2-6Gal), as documented for the avian progenitors of the 1957 (H2N2) and 1968 (H3N2) human influenza pandemic viruses. While this raised concern that the H7N9 virus was adapting to humans, the mutation was not sufficient to switch the receptor specificity of H7N9, and has not resulted in sustained transmission in humans. To determine if the H7 HA was capable of acquiring human-type receptor specificity, we conducted mutation analyses. Remarkably, three amino acid mutations conferred a switch in specificity for human-type receptors that resembled the specificity of the 2009 human H1 pandemic virus, and promoted binding to human trachea epithelial cells.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid28404848,

title = {Unique Structural Features of Influenza Virus H15 Hemagglutinin},

author = {Netanel Tzarum and Ryan McBride and Corwin M Nycholat and Wenjie Peng and James C Paulson and Ian A Wilson},

doi = {10.1128/JVI.00046-17},

issn = {1098-5514},

year  = {2017},

date = {2017-06-01},

journal = {J Virol},

volume = {91},

number = {12},

abstract = {Influenza A H15 viruses are members of a subgroup (H7-H10-H15) of group 2 hemagglutinin (HA) subtypes that include H7N9 and H10N8 viruses that were isolated from humans during 2013. The isolation of avian H15 viruses is, however, quite rare and, until recently, geographically restricted to wild shorebirds and waterfowl in Australia. The HAs of H15 viruses contain an insertion in the 150-loop (loop beginning at position 150) of the receptor-binding site common to this subgroup and a unique insertion in the 260-loop compared to any other subtype. Here, we show that the H15 HA has a high preference for avian receptor analogs by glycan array analyses. The H15 HA crystal structure reveals that it is structurally closest to H7N9 HA, but the head domain of the H15 trimer is wider than all other HAs due to a tilt and opening of the HA1 subunits of the head domain. The extended 150-loop of the H15 HA retains the conserved conformation as in H7 and H10 HAs. Furthermore, the elongated 260-loop increases the exposed HA surface and can contribute to antigenic variation in H15 HAs. Since avian-origin H15 HA viruses have been shown to cause enhanced disease in mammalian models, further characterization and immune surveillance of H15 viruses are warranted. In the last 2 decades, an apparent increase has been reported for cases of human infection by emerging avian influenza A virus subtypes, including H7N9 and H10N8 viruses isolated during 2013. H15 is the other member of the subgroup of influenza A virus group 2 hemagglutinins (HAs) that also include H7 and H10. H15 viruses have been restricted to Australia, but recent isolation of H15 viruses in western Siberia suggests that they could be spread more globally via the avian flyways that converge and emanate from this region. Here we report on characterization of the three-dimensional structure and receptor specificity of the H15 hemagglutinin, revealing distinct features and specificities that can aid in global surveillance of such viruses for potential spread and emerging threat to the human population.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid28381572,

title = {Improving the Expression and Purification of Soluble, Recombinant Native-Like HIV-1 Envelope Glycoprotein Trimers by Targeted Sequence Changes},

author = {Rajesh P Ringe and Gabriel Ozorowski and Anila Yasmeen and Albert Cupo and Victor M Cruz Portillo and Pavel Pugach and Michael Golabek and Kimmo Rantalainen and Lauren G Holden and Christopher A Cottrell and Ian A Wilson and Rogier W Sanders and Andrew B Ward and P J Klasse and John P Moore},

doi = {10.1128/JVI.00264-17},

issn = {1098-5514},

year  = {2017},

date = {2017-06-01},

journal = {J Virol},

volume = {91},

number = {12},

abstract = {Soluble, recombinant native-like envelope glycoprotein (Env) trimers of various human immunodeficiency virus type 1 (HIV-1) genotypes are being developed for structural studies and as vaccine candidates aimed at the induction of broadly neutralizing antibodies (bNAbs). The prototypic design is designated SOSIP.664, but many HIV-1  genes do not yield fully native-like trimers efficiently. One such  gene is CZA97.012 from a neutralization-resistant (tier 2) clade C virus. As appropriately purified, native-like CZA97.012 SOSIP.664 trimers induce autologous neutralizing antibodies (NAbs) efficiently in immunized rabbits, we sought to improve the efficiency with which they can be produced and to better understand the limitations to the original design. By using structure- and antigenicity-guided mutagenesis strategies focused on the V2 and V3 regions and the gp120-gp41 interface, we developed the CZA97 SOSIP.v4.2-M6.IT construct. Fully native-like, stable trimers that display multiple bNAb epitopes could be expressed from this construct in a stable CHO cell line and purified at an acceptable yield using either a PGT145 or a 2G12 bNAb affinity column. We also show that similar mutagenesis strategies can be used to improve the yields and properties of SOSIP.664 trimers of the DU422, 426c, and 92UG037 genotypes. Recombinant trimeric proteins based on HIV-1  genes are being developed for future vaccine trials in humans. A feature of these proteins is their mimicry of the envelope glycoprotein (Env) structure on virus particles that is targeted by neutralizing antibodies, i.e., antibodies that prevent cells from becoming infected. The vaccine concept under exploration is that recombinant trimers may be able to elicit virus-neutralizing antibodies when delivered as immunogens. Because HIV-1 is extremely variable, a practical vaccine may need to incorporate Env trimers derived from multiple different virus sequences. Accordingly, we need to understand how to make recombinant trimers from many different  genes. Here, we show how to produce trimers from a clade C virus, CZA97.012, by using an array of protein engineering techniques to improve a prototypic construct. We also show that the methods may have wider utility for other  genes, thereby further guiding immunogen design.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid28618270,

title = {Diversity of Functionally Permissive Sequences in the Receptor-Binding Site of Influenza Hemagglutinin},

author = {Nicholas C Wu and Jia Xie and Tianqing Zheng and Corwin M Nycholat and Geramie Grande and James C Paulson and Richard A Lerner and Ian A Wilson},

doi = {10.1016/j.chom.2017.05.011},

issn = {1934-6069},

year  = {2017},

date = {2017-06-01},

journal = {Cell Host Microbe},

volume = {21},

number = {6},

pages = {742--753.e8},

abstract = {Influenza A virus hemagglutinin (HA) initiates viral entry by engaging host receptor sialylated glycans via its receptor-binding site (RBS). The amino acid sequence of the RBS naturally varies across avian and human influenza virus subtypes and is also evolvable. However, functional sequence diversity in the RBS has not been fully explored. Here, we performed a large-scale mutational analysis of the RBS of A/WSN/33 (H1N1) and A/Hong Kong/1/1968 (H3N2) HAs. Many replication-competent mutants not yet observed in nature were identified, including some that could escape from an RBS-targeted broadly neutralizing antibody. This functional sequence diversity is made possible by pervasive epistasis in the RBS 220-loop and can be buffered by avidity in viral receptor binding. Overall, our study reveals that the HA RBS can accommodate a much greater range of sequence diversity than previously thought, which has significant implications for the complex evolutionary interrelationships between receptor specificity and immune escape.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid28514686,

title = {Glycine Substitution at Helix-to-Coil Transitions Facilitates the Structural Determination of a Stabilized Subtype C HIV Envelope Glycoprotein},

author = {Javier Guenaga and Fernando Garces and Natalia de Val and Robyn L Stanfield and Viktoriya Dubrovskaya and Brett Higgins and Barbara Carrette and Andrew B Ward and Ian A Wilson and Richard T Wyatt},

doi = {10.1016/j.immuni.2017.04.014},

issn = {1097-4180},

year  = {2017},

date = {2017-05-01},

journal = {Immunity},

volume = {46},

number = {5},

pages = {792--803.e3},

abstract = {Advances in HIV-1 envelope glycoprotein (Env) design generate native-like trimers and high-resolution clade A, B, and G structures and elicit neutralizing antibodies. However, a high-resolution clade C structure is critical, as this subtype accounts for the majority of HIV infections worldwide, but well-ordered clade C Env trimers are more challenging to produce due to their instability. Based on targeted glycine substitutions in the Env fusion machinery, we defined a general approach that disfavors helical transitions leading to post-fusion conformations, thereby favoring the pre-fusion state. We generated a stabilized, soluble clade C Env (16055 NFL) and determined its crystal structure at 3.9 Å. Its overall conformation is similar to SOSIP.664 and native Env trimers but includes a covalent linker between gp120 and gp41, an engineered 201-433 disulfide bond, and density corresponding to 22 N-glycans. Env-structure-guided design strategies resulted in multiple homogeneous cross-clade immunogens with the potential to advance HIV vaccine development.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid28504265,

title = {In vitro evolution of an influenza broadly neutralizing antibody is modulated by hemagglutinin receptor specificity},

author = {Nicholas C Wu and Geramie Grande and Hannah L Turner and Andrew B Ward and Jia Xie and Richard A Lerner and Ian A Wilson},

doi = {10.1038/ncomms15371},

issn = {2041-1723},

year  = {2017},

date = {2017-05-01},

journal = {Nat Commun},

volume = {8},

pages = {15371},

abstract = {The relatively recent discovery and characterization of human broadly neutralizing antibodies (bnAbs) against influenza virus provide valuable insights into antiviral and vaccine development. However, the factors that influence the evolution of high-affinity bnAbs remain elusive. We therefore explore the functional sequence space of bnAb C05, which targets the receptor-binding site (RBS) of influenza haemagglutinin (HA) via a long CDR H3. We combine saturation mutagenesis with yeast display to enrich for C05 variants of CDR H3 that bind to H1 and H3 HAs. The C05 variants evolve up to 20-fold higher affinity but increase specificity to each HA subtype used in the selection. Structural analysis reveals that the fine specificity is strongly influenced by a highly conserved substitution that regulates receptor binding in different subtypes. Overall, this study suggests that subtle natural variations in the HA RBS between subtypes and species may differentially influence the evolution of high-affinity bnAbs.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid28341999,

title = {Immunological memory to hyperphosphorylated tau in asymptomatic individuals},

author = {Gabriel Pascual and Jehangir S Wadia and Xueyong Zhu and Elissa Keogh and Başak Kükrer and Jeroen van Ameijde and Hanna Inganäs and Berdien Siregar and Gerrard Perdok and Otto Diefenbach and Tariq Nahar and Imke Sprengers and Martin H Koldijk and Els C Brinkman-van der Linden and Laura A Peferoen and Heng Zhang and Wenli Yu and Xinyi Li and Michelle Wagner and Veronica Moreno and Julie Kim and Martha Costa and Kiana West and Zara Fulton and Lucy Chammas and Nancy Luckashenak and Lauren Fletcher and Trevin Holland and Carrie Arnold and R Anthony Williamson and Jeroen J Hoozemans and Adrian Apetri and Frederique Bard and Ian A Wilson and Wouter Koudstaal and Jaap Goudsmit},

doi = {10.1007/s00401-017-1705-y},

issn = {1432-0533},

year  = {2017},

date = {2017-05-01},

journal = {Acta Neuropathol},

volume = {133},

number = {5},

pages = {767--783},

abstract = {Several reports have described the presence of antibodies against Alzheimer's disease-associated hyperphosphorylated forms of tau in serum of healthy individuals. To characterize the specificities that can be found, we interrogated peripheral IgG memory B cells from asymptomatic blood donors for reactivity to a panel of phosphorylated tau peptides using a single-cell screening assay. Antibody sequences were recovered, cloned, and expressed as full-length IgGs. In total, 52 somatically mutated tau-binding antibodies were identified, corresponding to 35 unique clonal families. Forty-one of these antibodies recognize epitopes in the proline-rich and C-terminal domains, and binding of 26 of these antibodies is strictly phosphorylation dependent. Thirteen antibodies showed inhibitory activity in a P301S lysate seeded in vitro tau aggregation assay. Two such antibodies, CBTAU-7.1 and CBTAU-22.1, which bind to the proline-rich and C-terminal regions of tau, respectively, were characterized in more detail. CBTAU-7.1 recognizes an epitope that is similar to that of murine anti-PHF antibody AT8, but has different phospho requirements. Both CBTAU-7.1 and CBTAU-22.1 detect pathological tau deposits in post-mortem brain tissue. CBTAU-7.1 reveals a similar IHC distribution pattern as AT8, immunostaining (pre)tangles, threads, and neuritic plaques. CBTAU-22.1 shows selective detection of neurofibrillary changes by IHC. Taken together, these results suggest the presence of an ongoing antigen-driven immune response against tau in healthy individuals. The wide range of specificities to tau suggests that the human immune repertoire may contain antibodies that can serve as biomarkers or be exploited for therapy.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid28423342,

title = {A Broadly Neutralizing Antibody Targets the Dynamic HIV Envelope Trimer Apex via a Long, Rigidified, and Anionic β-Hairpin Structure},

author = {Jeong Hyun Lee and Raiees Andrabi and Ching-Yao Su and Anila Yasmeen and Jean-Philippe Julien and Leopold Kong and Nicholas C Wu and Ryan McBride and Devin Sok and Matthias Pauthner and Christopher A Cottrell and Travis Nieusma and Claudia Blattner and James C Paulson and Per Johan Klasse and Ian A Wilson and Dennis R Burton and Andrew B Ward},

doi = {10.1016/j.immuni.2017.03.017},

issn = {1097-4180},

year  = {2017},

date = {2017-04-01},

journal = {Immunity},

volume = {46},

number = {4},

pages = {690--702},

abstract = {Broadly neutralizing antibodies (bnAbs) to HIV delineate vaccine targets and are prophylactic and therapeutic agents. Some of the most potent bnAbs target a quaternary epitope at the apex of the surface HIV envelope (Env) trimer. Using cryo-electron microscopy, we solved the atomic structure of an apex bnAb, PGT145, in complex with Env. We showed that the long anionic HCDR3 of PGT145 penetrated between glycans at the trimer 3-fold axis, to contact peptide residues from all three Env protomers, and thus explains its highly trimer-specific nature. Somatic hypermutation in the other CDRs of PGT145 were crucially involved in stabilizing the structure of the HCDR3, similar to bovine antibodies, to aid in recognition of a cluster of conserved basic residues hypothesized to facilitate trimer disassembly during viral entry. Overall, the findings exemplify the creative solutions that the human immune system can evolve to recognize a conserved motif buried under a canopy of glycans.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid28402848,

title = {The 150-Loop Restricts the Host Specificity of Human H10N8 Influenza Virus},

author = {Netanel Tzarum and Robert P de Vries and Wenjie Peng and Andrew J Thompson and Kim M Bouwman and Ryan McBride and Wenli Yu and Xueyong Zhu and Monique H Verheije and James C Paulson and Ian A Wilson},

doi = {10.1016/j.celrep.2017.03.054},

issn = {2211-1247},

year  = {2017},

date = {2017-04-01},

journal = {Cell Rep},

volume = {19},

number = {2},

pages = {235--245},

abstract = {Adaptation of influenza A viruses to new hosts are rare events but are the basis for emergence of new influenza pandemics in the human population. Thus, understanding the processes involved in such events is critical for anticipating potential pandemic threats. In 2013, the first case of human infection by an avian H10N8 virus was reported, yet the H10 hemagglutinin (HA) maintains avian receptor specificity. However, the 150-loop of H10 HA, as well as related H7 and H15 subtypes, contains a two-residue insert that can potentially block human receptor binding. Mutation of the 150-loop on the background of Q226L and G228S mutations, which arose in the receptor-binding site of human pandemic H2 and H3 viruses, resulted in acquisition of human-type receptor specificity. Crystal structures of H10 HA mutants with human and avian receptor analogs, receptor-binding studies, and tissue staining experiments illustrate the important role of the 150-loop in H10 receptor specificity.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid28287405,

title = {T cells control the generation of nanomolar-affinity anti-glycan antibodies},

author = {Zinaida Polonskaya and Shenglou Deng and Anita Sarkar and Lisa Kain and Marta Comellas-Aragones and Craig S McKay and Katarzyna Kaczanowska and Marie Holt and Ryan McBride and Valle Palomo and Kevin M Self and Seth Taylor and Adriana Irimia and Sanjay R Mehta and Jennifer M Dan and Matthew Brigger and Shane Crotty and Stephen P Schoenberger and James C Paulson and Ian A Wilson and Paul B Savage and M G Finn and Luc Teyton},

doi = {10.1172/JCI91192},

issn = {1558-8238},

year  = {2017},

date = {2017-04-01},

journal = {J Clin Invest},

volume = {127},

number = {4},

pages = {1491--1504},

abstract = {Vaccines targeting glycan structures at the surface of pathogenic microbes must overcome the inherent T cell-independent nature of immune responses against glycans. Carbohydrate conjugate vaccines achieve this by coupling bacterial polysaccharides to a carrier protein that recruits heterologous CD4 T cells to help B cell maturation. Yet they most often produce low- to medium-affinity immune responses of limited duration in immunologically fit individuals and disappointing results in the elderly and immunocompromised patients. Here, we hypothesized that these limitations result from suboptimal T cell help. To produce the next generation of more efficacious conjugate vaccines, we have explored a synthetic design aimed at focusing both B cell and T cell recognition to a single short glycan displayed at the surface of a virus-like particle. We tested and established the proof of concept of this approach for 2 serotypes of Streptococcus pneumoniae. In both cases, these vaccines elicited serotype-specific, protective, and long-lasting IgG antibodies of nanomolar affinity against the target glycans in mice. We further identified a requirement for CD4 T cells in the anti-glycan antibody response. Our findings establish the design principles for improved glycan conjugate vaccines. We surmise that the same approach can be used for any microbial glycan of interest.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid28225819,

title = {Lipid interactions and angle of approach to the HIV-1 viral membrane of broadly neutralizing antibody 10E8: Insights for vaccine and therapeutic design},

author = {Adriana Irimia and Andreia M Serra and Anita Sarkar and Ronald Jacak and Oleksandr Kalyuzhniy and Devin Sok and Karen L Saye-Francisco and Torben Schiffner and Ryan Tingle and Michael Kubitz and Yumiko Adachi and Robyn L Stanfield and Marc C Deller and Dennis R Burton and William R Schief and Ian A Wilson},

doi = {10.1371/journal.ppat.1006212},

issn = {1553-7374},

year  = {2017},

date = {2017-02-01},

journal = {PLoS Pathog},

volume = {13},

number = {2},

pages = {e1006212},

abstract = {Among broadly neutralizing antibodies to HIV, 10E8 exhibits greater neutralizing breadth than most. Consequently, this antibody is the focus of prophylactic/therapeutic development. The 10E8 epitope has been identified as the conserved membrane proximal external region (MPER) of gp41 subunit of the envelope (Env) viral glycoprotein and is a major vaccine target. However, the MPER is proximal to the viral membrane and may be laterally inserted into the membrane in the Env prefusion form. Nevertheless, 10E8 has not been reported to have significant lipid-binding reactivity. Here we report x-ray structures of lipid complexes with 10E8 and a scaffolded MPER construct and mutagenesis studies that provide evidence that the 10E8 epitope is composed of both MPER and lipid. 10E8 engages lipids through a specific lipid head group interaction site and a basic and polar surface on the light chain. In the model that we constructed, the MPER would then be essentially perpendicular to the virion membrane during 10E8 neutralization of HIV-1. As the viral membrane likely also plays a role in selecting for the germline antibody as well as size and residue composition of MPER antibody complementarity determining regions, the identification of lipid interaction sites and the MPER orientation with regard to the viral membrane surface during 10E8 engagement can be of great utility for immunogen and therapeutic design.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid28017661,

title = {Recent H3N2 Viruses Have Evolved Specificity for Extended, Branched Human-type Receptors, Conferring Potential for Increased Avidity},

author = {Wenjie Peng and Robert P de Vries and Oliver C Grant and Andrew J Thompson and Ryan McBride and Buyankhishig Tsogtbaatar and Peter S Lee and Nahid Razi and Ian A Wilson and Robert J Woods and James C Paulson},

doi = {10.1016/j.chom.2016.11.004},

issn = {1934-6069},

year  = {2017},

date = {2017-01-01},

journal = {Cell Host Microbe},

volume = {21},

number = {1},

pages = {23--34},

abstract = {Human and avian influenza viruses recognize different sialic acid-containing receptors, referred to as human-type (NeuAcα2-6Gal) and avian-type (NeuAcα2-3Gal), respectively. This presents a species barrier for aerosol droplet transmission of avian viruses in humans and ferrets. Recent reports have suggested that current human H3N2 viruses no longer have strict specificity toward human-type receptors. Using an influenza receptor glycan microarray with extended airway glycans, we find that H3N2 viruses have in fact maintained human-type specificity, but they have evolved preference for a subset of receptors comprising branched glycans with extended poly-N-acetyl-lactosamine (poly-LacNAc) chains, a specificity shared with the 2009 pandemic H1N1 (Cal/04) hemagglutinin. Lipid-linked versions of extended sialoside receptors can restore susceptibility of sialidase-treated MDCK cells to infection by both recent (A/Victoria/361/11) and historical (A/Hong Kong/8/1968) H3N2 viruses. Remarkably, these human-type receptors with elongated branches have the potential to increase avidity by simultaneously binding to two subunits of a single hemagglutinin trimer.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid28003465,

title = {Structural basis of influenza virus fusion inhibition by the antiviral drug Arbidol},

author = {Rameshwar U Kadam and Ian A Wilson},

doi = {10.1073/pnas.1617020114},

issn = {1091-6490},

year  = {2017},

date = {2017-01-01},

journal = {Proc Natl Acad Sci U S A},

volume = {114},

number = {2},

pages = {206--214},

abstract = {The broad-spectrum antiviral drug Arbidol shows efficacy against influenza viruses by targeting the hemagglutinin (HA) fusion machinery. However, the structural basis of the mechanism underlying fusion inhibition by Arbidol has remained obscure, thereby hindering its further development as a specific and optimized influenza therapeutic. We determined crystal structures of Arbidol in complex with influenza virus HA from pandemic 1968 H3N2 and recent 2013 H7N9 viruses. Arbidol binds in a hydrophobic cavity in the HA trimer stem at the interface between two protomers. This cavity is distal to the conserved epitope targeted by broadly neutralizing stem antibodies and is ∼16 Å from the fusion peptide. Arbidol primarily makes hydrophobic interactions with the binding site but also induces some conformational rearrangements to form a network of inter- and intraprotomer salt bridges. By functioning as molecular glue, Arbidol stabilizes the prefusion conformation of HA that inhibits the large conformational rearrangements associated with membrane fusion in the low pH of the endosome. This unique binding mode compared with the small-molecule inhibitors of other class I fusion proteins enhances our understanding of how small molecules can function as fusion inhibitors and guides the development of broad-spectrum therapeutics against influenza virus.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid28133813,

title = {The HIV-1 envelope glycoprotein structure: nailing down a moving target},

author = {Andrew B Ward and Ian A Wilson},

doi = {10.1111/imr.12507},

issn = {1600-065X},

year  = {2017},

date = {2017-01-01},

journal = {Immunol Rev},

volume = {275},

number = {1},

pages = {21--32},

abstract = {Structure determination of the HIV-1 envelope glycoprotein (Env) presented a number of challenges, but several high-resolution structures have now become available. In 2013, cryo-EM and x-ray structures of soluble, cleaved SOSIP Env trimers from the clade A BG505 strain provided the first glimpses into the Env trimer fold as well as more the variable regions. A recent cryo-EM structure of a native full-length trimer without any stabilizing mutations had the same core structure, but revealed new insights and features. A more comprehensive and higher resolution understanding of the glycan shield has also emerged, enabling a more complete representation of the Env glycoprotein structure. Complexes of Env trimers with broadly neutralizing antibodies have surprisingly illustrated that most of the Env surface can be targeted in natural infection and that the neutralizing epitopes are almost all composed of both peptide and glycan components. These structures have also provided further evidence of the inherent plasticity of Env and how antibodies can exploit this flexibility by perturbing or even stabilizing the trimer to facilitate neutralization. These breakthroughs have stimulated further design and stabilization of Env trimers as well as other platforms to generate trimers that now span multiple subtypes. These Env trimers when used as immunogens, have led to the first vaccine-induced neutralizing antibodies for structural and functional analyses.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid28004685,

title = {HIV's Achilles' Heel},

author = {Rogier W Sanders and Ian A Wilson and John P Moore},

doi = {10.1038/scientificamerican1216-50},

issn = {0036-8733},

year  = {2016},

date = {2016-11-01},

journal = {Sci Am},

volume = {315},

number = {6},

pages = {50--55},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid27841852,

title = {An HIV-1 antibody from an elite neutralizer implicates the fusion peptide as a site of vulnerability},

author = {Marit J van Gils and Tom L G M van den Kerkhof and Gabriel Ozorowski and Christopher A Cottrell and Devin Sok and Matthias Pauthner and Jesper Pallesen and Natalia de Val and Anila Yasmeen and Steven W de Taeye and Anna Schorcht and Stephanie Gumbs and Inez Johanna and Karen Saye-Francisco and Chi-Hui Liang and Elise Landais and Xiaoyan Nie and Laura K Pritchard and Max Crispin and Garnett Kelsoe and Ian A Wilson and Hanneke Schuitemaker and Per Johan Klasse and John P Moore and Dennis R Burton and Andrew B Ward and Rogier W Sanders},

doi = {10.1038/nmicrobiol.2016.199},

issn = {2058-5276},

year  = {2016},

date = {2016-11-01},

journal = {Nat Microbiol},

volume = {2},

pages = {16199},

abstract = {The induction by vaccination of broadly neutralizing antibodies (bNAbs) capable of neutralizing various HIV-1 viral strains is challenging, but understanding how a subset of HIV-infected individuals develops bNAbs may guide immunization strategies. Here, we describe the isolation and characterization of the bNAb ACS202 from an elite neutralizer that recognizes a new, trimer-specific and cleavage-dependent epitope at the gp120-gp41 interface of the envelope glycoprotein (Env), involving the glycan N88 and the gp41 fusion peptide. In addition, an Env trimer, AMC011 SOSIP.v4.2, based on early virus isolates from the same elite neutralizer, was constructed, and its structure by cryo-electron microscopy at 6.2 Å resolution reveals a closed, pre-fusion conformation similar to that of the BG505 SOSIP.664 trimer. The availability of a native-like Env trimer and a bNAb from the same elite neutralizer provides the opportunity to design vaccination strategies aimed at generating similar bNAbs against a key functional site on HIV-1.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid27791120,

title = {Structural flexibility at a major conserved antibody target on hepatitis C virus E2 antigen},

author = {Leopold Kong and David E Lee and Rameshwar U Kadam and Tong Liu and Erick Giang and Travis Nieusma and Fernando Garces and Netanel Tzarum and Virgil L Woods and Andrew B Ward and Sheng Li and Ian A Wilson and Mansun Law},

doi = {10.1073/pnas.1609780113},

issn = {1091-6490},

year  = {2016},

date = {2016-11-01},

journal = {Proc Natl Acad Sci U S A},

volume = {113},

number = {45},

pages = {12768--12773},

abstract = {Hepatitis C virus (HCV) is a major cause of liver disease, affecting over 2% of the world's population. The HCV envelope glycoproteins E1 and E2 mediate viral entry, with E2 being the main target of neutralizing antibody responses. Structural investigations of E2 have produced templates for vaccine design, including the conserved CD81 receptor-binding site (CD81bs) that is a key target of broadly neutralizing antibodies (bNAbs). Unfortunately, immunization with recombinant E2 and E1E2 rarely elicits sufficient levels of bNAbs for protection. To understand the challenges for eliciting bNAb responses against the CD81bs, we investigated the E2 CD81bs by electron microscopy (EM), hydrogen-deuterium exchange (HDX), molecular dynamics (MD), and calorimetry. By EM, we observed that HCV1, a bNAb recognizing the N-terminal region of the CD81bs, bound a soluble E2 core construct from multiple angles of approach, suggesting components of the CD81bs are flexible. HDX of multiple E2 constructs consistently indicated the entire CD81bs was flexible relative to the rest of the E2 protein, which was further confirmed by MD simulations. However, E2 has a high melting temperature of 84.8 °C, which is more akin to proteins from thermophilic organisms. Thus, recombinant E2 is a highly stable protein overall, but with an exceptionally flexible CD81bs. Such flexibility may promote induction of nonneutralizing antibodies over bNAbs to E2 CD81bs, underscoring the necessity of rigidifying this antigenic region as a target for rational vaccine design.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid27760316,

title = {HMGB1 Activates Proinflammatory Signaling via TLR5 Leading to Allodynia},

author = {Nabanita Das and Varun Dewan and Peter M Grace and Robin J Gunn and Ryo Tamura and Netanel Tzarum and Linda R Watkins and Ian A Wilson and Hang Yin},

doi = {10.1016/j.celrep.2016.09.076},

issn = {2211-1247},

year  = {2016},

date = {2016-10-01},

journal = {Cell Rep},

volume = {17},

number = {4},

pages = {1128--1140},

abstract = {Infectious and sterile inflammatory diseases are correlated with increased levels of high mobility group box 1 (HMGB1) in tissues and serum. Extracellular HMGB1 is known to activate Toll-like receptors (TLRs) 2 and 4 and RAGE (receptor for advanced glycation endproducts) in inflammatory conditions. Here, we find that TLR5 is also an HMGB1 receptor that was previously overlooked due to lack of functional expression in the cell lines usually used for studying TLR signaling. HMGB1 binding to TLR5 initiates the activation of NF-κB signaling pathway in a MyD88-dependent manner, resulting in proinflammatory cytokine production and pain enhancement in vivo. Biophysical and in vitro results highlight an essential role for the C-terminal tail region of HMGB1 in facilitating interactions with TLR5. These results suggest that HMGB1-modulated TLR5 signaling is responsible for pain hypersensitivity.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid27617678,

title = {HIV Vaccine Design to Target Germline Precursors of Glycan-Dependent Broadly Neutralizing Antibodies},

author = {Jon M Steichen and Daniel W Kulp and Talar Tokatlian and Amelia Escolano and Pia Dosenovic and Robyn L Stanfield and Laura E McCoy and Gabriel Ozorowski and Xiaozhen Hu and Oleksandr Kalyuzhniy and Bryan Briney and Torben Schiffner and Fernando Garces and Natalia T Freund and Alexander D Gitlin and Sergey Menis and Erik Georgeson and Michael Kubitz and Yumiko Adachi and Meaghan Jones and Andrew A Mutafyan and Dong Soo Yun and Christian T Mayer and Andrew B Ward and Dennis R Burton and Ian A Wilson and Darrell J Irvine and Michel C Nussenzweig and William R Schief},

doi = {10.1016/j.immuni.2016.08.016},

issn = {1097-4180},

year  = {2016},

date = {2016-09-01},

journal = {Immunity},

volume = {45},

number = {3},

pages = {483--496},

abstract = {Broadly neutralizing antibodies (bnAbs) against the N332 supersite of the HIV envelope (Env) trimer are the most common bnAbs induced during infection, making them promising leads for vaccine design. Wild-type Env glycoproteins lack detectable affinity for supersite-bnAb germline precursors and are therefore unsuitable immunogens to prime supersite-bnAb responses. We employed mammalian cell surface display to design stabilized Env trimers with affinity for germline-reverted precursors of PGT121-class supersite bnAbs. The trimers maintained native-like antigenicity and structure, activated PGT121 inferred-germline B cells ex vivo when multimerized on liposomes, and primed PGT121-like responses in PGT121 inferred-germline knockin mice. Design intermediates have levels of epitope modification between wild-type and germline-targeting trimers; their mutation gradient suggests sequential immunization to induce bnAbs, in which the germline-targeting prime is followed by progressively less-mutated design intermediates and, lastly, with native trimers. The vaccine design strategies described could be utilized to target other epitopes on HIV or other pathogens.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid27627672,

title = {Sequential and Simultaneous Immunization of Rabbits with HIV-1 Envelope Glycoprotein SOSIP.664 Trimers from Clades A, B and C},

author = {P J Klasse and Celia C LaBranche and Thomas J Ketas and Gabriel Ozorowski and Albert Cupo and Pavel Pugach and Rajesh P Ringe and Michael Golabek and Marit J van Gils and Miklos Guttman and Kelly K Lee and Ian A Wilson and Salvatore T Butera and Andrew B Ward and David C Montefiori and Rogier W Sanders and John P Moore},

doi = {10.1371/journal.ppat.1005864},

issn = {1553-7374},

year  = {2016},

date = {2016-09-01},

journal = {PLoS Pathog},

volume = {12},

number = {9},

pages = {e1005864},

abstract = {We have investigated the immunogenicity in rabbits of native-like, soluble, recombinant SOSIP.664 trimers based on the env genes of four isolates of human immunodeficiency virus type 1 (HIV-1); specifically BG505 (clade A), B41 (clade B), CZA97 (clade C) and DU422 (clade C). The various trimers were delivered either simultaneously (as a mixture of clade A + B trimers) or sequentially over a 73-week period. Autologous, Tier-2 neutralizing antibody (NAb) responses were generated to the clade A and clade B trimers in the bivalent mixture. When delivered as boosting immunogens to rabbits immunized with the clade A and/or clade B trimers, the clade C trimers also generated autologous Tier-2 NAb responses, the CZA97 trimers doing so more strongly and consistently than the DU422 trimers. The clade C trimers also cross-boosted the pre-existing NAb responses to clade A and B trimers. We observed heterologous Tier-2 NAb responses albeit inconsistently, and with limited overall breath. However, cross-neutralization of the clade A BG505.T332N virus was consistently observed in rabbits immunized only with clade B trimers and then boosted with clade C trimers. The autologous NAbs induced by the BG505, B41 and CZA97 trimers predominantly recognized specific holes in the glycan shields of the cognate virus. The shared location of some of these holes may account for the observed cross-boosting effects and the heterologous neutralization of the BG505.T332N virus. These findings will guide the design of further experiments to determine whether and how multiple Env trimers can together induce more broadly neutralizing antibody responses.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid27610570,

title = {Tailored Immunogens Direct Affinity Maturation toward HIV Neutralizing Antibodies},

author = {Bryan Briney and Devin Sok and Joseph G Jardine and Daniel W Kulp and Patrick Skog and Sergey Menis and Ronald Jacak and Oleksandr Kalyuzhniy and Natalia de Val and Fabian Sesterhenn and Khoa M Le and Alejandra Ramos and Meaghan Jones and Karen L Saye-Francisco and Tanya R Blane and Skye Spencer and Erik Georgeson and Xiaozhen Hu and Gabriel Ozorowski and Yumiko Adachi and Michael Kubitz and Anita Sarkar and Ian A Wilson and Andrew B Ward and David Nemazee and Dennis R Burton and William R Schief},

doi = {10.1016/j.cell.2016.08.005},

issn = {1097-4172},

year  = {2016},

date = {2016-09-01},

journal = {Cell},

volume = {166},

number = {6},

pages = {1459--1470.e11},

abstract = {Induction of broadly neutralizing antibodies (bnAbs) is a primary goal of HIV vaccine development. VRC01-class bnAbs are important vaccine leads because their precursor B cells targeted by an engineered priming immunogen are relatively common among humans. This priming immunogen has demonstrated the ability to initiate a bnAb response in animal models, but recall and maturation toward bnAb development has not been shown. Here, we report the development of boosting immunogens designed to guide the genetic and functional maturation of previously primed VRC01-class precursors. Boosting a transgenic mouse model expressing germline VRC01 heavy chains produced broad neutralization of near-native isolates (N276A) and weak neutralization of fully native HIV. Functional and genetic characteristics indicate that the boosted mAbs are consistent with partially mature VRC01-class antibodies and place them on a maturation trajectory that leads toward mature VRC01-class bnAbs. The results show how reductionist sequential immunization can guide maturation of HIV bnAb responses.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid27545891,

title = {Holes in the Glycan Shield of the Native HIV Envelope Are a Target of Trimer-Elicited Neutralizing Antibodies},

author = {Laura E McCoy and Marit J van Gils and Gabriel Ozorowski and Terrence Messmer and Bryan Briney and James E Voss and Daniel W Kulp and Matthew S Macauley and Devin Sok and Matthias Pauthner and Sergey Menis and Christopher A Cottrell and Jonathan L Torres and Jessica Hsueh and William R Schief and Ian A Wilson and Andrew B Ward and Rogier W Sanders and Dennis R Burton},

doi = {10.1016/j.celrep.2016.07.074},

issn = {2211-1247},

year  = {2016},

date = {2016-08-01},

journal = {Cell Rep},

volume = {16},

number = {9},

pages = {2327--2338},

abstract = {A major advance in the search for an HIV vaccine has been the development of a near-native Envelope trimer (BG505 SOSIP.664) that can induce robust autologous Tier 2 neutralization. Here, potently neutralizing monoclonal antibodies (nAbs) from rabbits immunized with BG505 SOSIP.664 are shown to recognize an immunodominant region of gp120 centered on residue 241. Residue 241 occupies a hole in the glycan defenses of the BG505 isolate, with fewer than 3% of global isolates lacking a glycan site at this position. However, at least one conserved glycan site is missing in 89% of viruses, suggesting the presence of glycan holes in most HIV isolates. Serum evidence is consistent with targeting of holes in natural infection. The immunogenic nature of breaches in the glycan shield has been under-appreciated in previous attempts to understand autologous neutralizing antibody responses and has important potential consequences for HIV vaccine design.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid27560183,

title = {Minimally Mutated HIV-1 Broadly Neutralizing Antibodies to Guide Reductionist Vaccine Design},

author = {Joseph G Jardine and Devin Sok and Jean-Philippe Julien and Bryan Briney and Anita Sarkar and Chi-Hui Liang and Erin A Scherer and Carole J Henry Dunand and Yumiko Adachi and Devan Diwanji and Jessica Hsueh and Meaghan Jones and Oleksandr Kalyuzhniy and Michael Kubitz and Skye Spencer and Matthias Pauthner and Karen L Saye-Francisco and Fabian Sesterhenn and Patrick C Wilson and Denise M Galloway and Robyn L Stanfield and Ian A Wilson and Dennis R Burton and William R Schief},

doi = {10.1371/journal.ppat.1005815},

issn = {1553-7374},

year  = {2016},

date = {2016-08-01},

journal = {PLoS Pathog},

volume = {12},

number = {8},

pages = {e1005815},

abstract = {An optimal HIV vaccine should induce broadly neutralizing antibodies (bnAbs) that neutralize diverse viral strains and subtypes. However, potent bnAbs develop in only a small fraction of HIV-infected individuals, all contain rare features such as extensive mutation, insertions, deletions, and/or long complementarity-determining regions, and some are polyreactive, casting doubt on whether bnAbs to HIV can be reliably induced by vaccination. We engineered two potent VRC01-class bnAbs that minimized rare features. According to a quantitative features frequency analysis, the set of features for one of these minimally mutated bnAbs compared favorably with all 68 HIV bnAbs analyzed and was similar to antibodies elicited by common vaccines. This same minimally mutated bnAb lacked polyreactivity in four different assays. We then divided the minimal mutations into spatial clusters and dissected the epitope components interacting with those clusters, by mutational and crystallographic analyses coupled with neutralization assays. Finally, by synthesizing available data, we developed a working-concept boosting strategy to select the mutation clusters in a logical order following a germline-targeting prime. We have thus developed potent HIV bnAbs that may be more tractable vaccine goals compared to existing bnAbs, and we have proposed a strategy to elicit them. This reductionist approach to vaccine design, guided by antibody and antigen structure, could be applied to design candidate vaccines for other HIV bnAbs or protective Abs against other pathogens.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid27396829,

title = {Dynamic Local Polymorphisms in the Gbx1 Homeodomain Induced by DNA Binding},

author = {Andrew Proudfoot and Michael Geralt and Marc-Andre Elsliger and Ian A Wilson and Kurt Wüthrich and Pedro Serrano},

doi = {10.1016/j.str.2016.05.013},

issn = {1878-4186},

year  = {2016},

date = {2016-08-01},

journal = {Structure},

volume = {24},

number = {8},

pages = {1372--1379},

abstract = {The Gastrulation Brain Homeobox 1 (Gbx1) gene encodes the Gbx1 homeodomain that targets TAATTA motifs in double-stranded DNA (dsDNA). Residues Glu17 and Arg52 in Gbx1 form a salt bridge, which is preserved in crystal structures and molecular dynamics simulations of homologous homeodomain-DNA complexes. In contrast, our nuclear magnetic resonance (NMR) studies show that DNA binding to Gbx1 induces dynamic local polymorphisms, which include breaking of the Glu17-Arg52 salt bridge. To study this interaction, we produced a variant with Glu17Arg and Arg52Glu mutations, which exhibited the same fold as the wild-type protein, but a 2-fold reduction in affinity for dsDNA. Analysis of the NMR structures of the Gbx1 homeodomain in the free form, the Gbx1[E17R,R52E] variant, and a Gbx1 homeodomain-DNA complex showed that stabilizing interactions of the Arg52 side chain with the DNA backbone are facilitated by transient breakage of the Glu17-Arg52 salt bridge in the DNA-bound Gbx1.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}