@article{pmid14997579,

title = {Crystal structure of a putative PII-like signaling protein (TM0021) from Thermotoga maritima at 2.5 A resolution},

author = {Robert Schwarzenbacher and Frank von Delft and Polat Abdubek and Eileen Ambing and Tanja Biorac and Linda S Brinen and Jaume M Canaves and Jamison Cambell and Hsui-Ju Chiu and Xiaoping Dai and Ashley M Deacon and Mike DiDonato and Marc-André Elsliger and Said Eshagi and Ross Floyd and Adam Godzik and Carina Grittini and Slawomir K Grzechnik and Eric Hampton and Lukasz Jaroszewski and Cathy Karlak and Heath E Klock and Eric Koesema and John S Kovarik and Andreas Kreusch and Peter Kuhn and Scott A Lesley and Inna Levin and Daniel McMullan and Timothy M McPhillips and Mitchell D Miller and Andrew Morse and Kin Moy and Jie Ouyang and Rebecca Page and Kevin Quijano and Alyssa Robb and Glen Spraggon and Raymond C Stevens and Henry van den Bedem and Jeff Velasquez and Juli Vincent and Xianhong Wang and Bill West and Guenter Wolf and Qingping Xu and Keith O Hodgson and John Wooley and Ian A Wilson},

doi = {10.1002/prot.10647},

issn = {1097-0134},

year  = {2004},

date = {2004-03-01},

journal = {Proteins},

volume = {54},

number = {4},

pages = {810--813},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid14982995,

title = {Probing the antibody-catalyzed water-oxidation pathway at atomic resolution},

author = {Xueyong Zhu and Paul Wentworth and Anita D Wentworth and Albert Eschenmoser and Richard A Lerner and Ian A Wilson},

doi = {10.1073/pnas.0307311101},

issn = {0027-8424},

year  = {2004},

date = {2004-02-01},

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

volume = {101},

number = {8},

pages = {2247--2252},

abstract = {Antibodies can catalyze the generation of hydrogen peroxide (H2O2) from singlet dioxygen (1O2*) and water via the postulated intermediacy of dihydrogen trioxide (H2O3) and other trioxygen species. Nine different crystal structures were determined to elucidate the chemical consequences to the antibody molecule itself of exposure to such reactive intermediates and to provide insights into the location on the antibody where these species could be generated. Herein, we report structural evidence for modifications of two specific antibody residues within the interfacial region of the variable and constant domains of different murine antibody antigen-binding fragments (Fabs) by reactive species generated during the antibody-catalyzed water oxidation process. Crystal structure analyses of murine Fabs 4C6 and 13G5 after UV-irradiation revealed complex oxidative modifications to tryptophan L163 and, in 4C6, hydroxylation of the Cgamma of glutamine H6. These discrete modifications of specific residues add further support for the "active site" of the water-oxidation pathway being located within the interfacial region of the constant and variable domains and highlight the general resistance of the antibody molecule to oxidation by reactive oxygen species generated during the water-oxidation process.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid14966891,

title = {Reactivity-based one-pot synthesis of oligomannoses: defining antigens recognized by 2G12, a broadly neutralizing anti-HIV-1 antibody},

author = {Hing-Ken Lee and Christopher N Scanlan and Cheng-Yuan Huang and Aileen Y Chang and Daniel A Calarese and Raymond A Dwek and Pauline M Rudd and Dennis R Burton and Ian A Wilson and Chi-Huey Wong},

doi = {10.1002/anie.200353105},

issn = {1433-7851},

year  = {2004},

date = {2004-02-01},

journal = {Angew Chem Int Ed Engl},

volume = {43},

number = {8},

pages = {1000--1003},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid14756553,

title = {Structural insights into the human and avian IMP cyclohydrolase mechanism via crystal structures with the bound XMP inhibitor},

author = {Dennis W Wolan and Cheom-Gil Cheong and Samantha E Greasley and Ian A Wilson},

doi = {10.1021/bi030162i},

issn = {0006-2960},

year  = {2004},

date = {2004-02-01},

journal = {Biochemistry},

volume = {43},

number = {5},

pages = {1171--1183},

abstract = {Within de novo purine biosynthesis, the AICAR transformylase and IMP cyclohydrolase activities of the bifunctional enzyme ATIC convert the intermediate AICAR to the final product of the pathway, IMP. Identification of the AICAR transformylase active site and a proposed formyl transfer mechanism have already resulted from analysis of crystal structures of avian ATIC in complex with substrate and/or inhibitors. Herein, we focus on the IMPCH active site and the cyclohydrolase mechanism through comparison of crystal structures of XMP inhibitor complexes of human ATIC at 1.9 A resolution with the previously determined avian enzyme. This first human ATIC structure was also determined to ascertain whether any subtle structural differences, compared to the homologous avian enzyme, should be taken into account for structure-based inhibitor design. These structural comparisons, as well as comparative analyses with other IMP and XMP binding proteins, have enabled a catalytic mechanism to be formulated. The primary role of the IMPCH active site appears to be to induce a reconfiguration of the substrate FAICAR to a less energetically favorable, but more reactive, conformer. Backbone (Arg64 and Lys66) and side chain interactions (Thr67) in the IMPCH active site reorient the 4-carboxamide from the preferred conformer that binds to the AICAR Tfase active site to one that promotes intramolecular cyclization. Other backbone amides (Ile126 and Gly127) create an oxyanion hole that helps orient the formyl group for nucleophilic attack by the 4-carboxamide amine and then stabilize the anionic intermediate. Several other residues, including Lys66, Tyr104, Asp125, and Lys137', provide substrate specificity and likely enhance the catalytic rate through contributions to acid-base catalysis.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid14962380,

title = {Structural rationale for the broad neutralization of HIV-1 by human monoclonal antibody 447-52D},

author = {Robyn L Stanfield and Miroslaw K Gorny and Constance Williams and Susan Zolla-Pazner and Ian A Wilson},

doi = {10.1016/j.str.2004.01.003},

issn = {0969-2126},

year  = {2004},

date = {2004-02-01},

journal = {Structure},

volume = {12},

number = {2},

pages = {193--204},

abstract = {447-52D is a human monoclonal antibody isolated from a heterohybridoma derived from an HIV-1-infected individual. This antibody recognizes the hypervariable gp120 V3 loop, and neutralizes both X4 and R5 primary isolates, making it one of the most effective anti-V3 antibodies characterized to date. The crystal structure of the 447-52D Fab in complex with a 16-mer V3 peptide at 2.5 A resolution reveals that the peptide beta hairpin forms a three-stranded mixed beta sheet with complementarity determining region (CDR) H3, with most of the V3 side chains exposed to solvent. Sequence specificity is conferred through interaction of the type-II turn (residues GPGR) at the apex of the V3 hairpin with the base of CDR H3. This novel mode of peptide-antibody recognition enables the antibody to bind to many different V3 sequences where only the GPxR core epitope is absolutely required.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid14739458,

title = {T cell activation by lipopeptide antigens},

author = {D Branch Moody and David C Young and Tan-Yun Cheng and Jean-Pierre Rosat and Carme Roura-Mir and Peter B O'Connor and Dirk M Zajonc and Andrew Walz and Marvin J Miller and Steven B Levery and Ian A Wilson and Catherine E Costello and Michael B Brenner},

doi = {10.1126/science.1089353},

issn = {1095-9203},

year  = {2004},

date = {2004-01-01},

journal = {Science},

volume = {303},

number = {5657},

pages = {527--531},

abstract = {Unlike major histocompatibility proteins, which bind peptides, CD1 proteins display lipid antigens to T cells. Here, we report that CD1a presents a family of previously unknown lipopeptides from Mycobacterium tuberculosis, named didehydroxymycobactins because of their structural relation to mycobactin siderophores. T cell activation was mediated by the alphabeta T cell receptors and was specific for structure of the acyl and peptidic components of these antigens. These studies identify a means of intracellular pathogen detection and identify lipopeptides as a biochemical class of antigens for T cells, which, like conventional peptides, have a potential for marked structural diversity.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid14715906,

title = {Rapid refinement of crystallographic protein construct definition employing enhanced hydrogen/deuterium exchange MS},

author = {Dennis Pantazatos and Jack S Kim and Heath E Klock and Raymond C Stevens and Ian A Wilson and Scott A Lesley and Virgil L Woods},

doi = {10.1073/pnas.0307204101},

issn = {0027-8424},

year  = {2004},

date = {2004-01-01},

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

volume = {101},

number = {3},

pages = {751--756},

abstract = {Crystallographic efforts often fail to produce suitably diffracting protein crystals. Unstructured regions of proteins play an important role in this problem and considerable advantage can be gained in removing them. We have developed a number of enhancements to amide hydrogen/high-throughput and high-resolution deuterium exchange MS (DXMS) technology that allow rapid identification of unstructured regions in proteins. To demonstrate the utility of this approach for improving crystallization success, DXMS analysis was attempted on 24 Thermotoga maritima proteins with varying crystallization and diffraction characteristics. Data acquisition and analysis for 21 of these proteins was completed in 2 weeks and resulted in the localization and prediction of several unstructured regions within the proteins. When compared with those targets of known structure, the DXMS method correctly localized even small regions of disorder. DXMS analysis was then correlated with the propensity of such targets to crystallize and was further used to define truncations that improved crystallization. Truncations that were defined solely on DXMS analysis demonstrated greatly improved crystallization and have been used for structure determination. This approach represents a rapid and generalized method that can be applied to structural genomics or other targets in a high-throughput manner.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid14705036,

title = {Crystal structure of an iron-containing 1,3-propanediol dehydrogenase (TM0920) from Thermotoga maritima at 1.3 A resolution},

author = {Robert Schwarzenbacher and Frank von Delft and Jaume M Canaves and Linda S Brinen and Xiaoping Dai and Ashley M Deacon and Marc A Elsliger and Said Eshaghi and Ross Floyd and Adam Godzik and Carina Grittini and Slawomir K Grzechnik and Chittibabu Guda and Lukasz Jaroszewski and Cathy Karlak and Heath E Klock and Eric Koesema and John S Kovarik and Andreas Kreusch and Peter Kuhn and Scott A Lesley and Daniel McMullan and Timothy M McPhillips and Mark A Miller and Mitchell D Miller and Andrew Morse and Kin Moy and Jie Ouyang and Rebecca Page and Alyssa Robb and Kevin Rodrigues and Thomas L Selby and Glen Spraggon and Raymond C Stevens and Henry van den Bedem and Jeff Velasquez and Juli Vincent and Xianhong Wang and Bill West and Guenter Wolf and Keith O Hodgson and John Wooley and Ian A Wilson},

doi = {10.1002/prot.10594},

issn = {1097-0134},

year  = {2004},

date = {2004-01-01},

journal = {Proteins},

volume = {54},

number = {1},

pages = {174--177},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid14705032,

title = {Crystal structure of gamma-glutamyl phosphate reductase (TM0293) from Thermotoga maritima at 2.0 A resolution},

author = {Rebecca Page and Michael S Nelson and Frank von Delft and Marc-André Elsliger and Jaume M Canaves and Linda S Brinen and Xiaoping Dai and Ashley M Deacon and Ross Floyd and Adam Godzik and Carina Grittini and Slawomir K Grzechnik and Lukasz Jaroszewski and Heath E Klock and Eric Koesema and John S Kovarik and Andreas Kreusch and Peter Kuhn and Scott A Lesley and Daniel McMullan and Timothy M McPhillips and Mitchell D Miller and Andrew Morse and Kin Moy and Jie Ouyang and Alyssa Robb and Kevin Rodrigues and Robert Schwarzenbacher and Glen Spraggon and Raymond C Stevens and Henry van den Bedem and Jeff Velasquez and Juli Vincent and Xianhong Wang and Bill West and Guenter Wolf and Keith O Hodgson and John Wooley and Ian A Wilson},

doi = {10.1002/prot.10562},

issn = {1097-0134},

year  = {2004},

date = {2004-01-01},

journal = {Proteins},

volume = {54},

number = {1},

pages = {157--161},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid14592768,

title = {Recurring conformation of the human immunodeficiency virus type 1 gp120 V3 loop},

author = {Robyn L Stanfield and Jayant B Ghiara and Erica Ollmann Saphire and Albert T Profy and Ian A Wilson},

doi = {10.1016/s0042-6822(03)00525-7},

issn = {0042-6822},

year  = {2003},

date = {2003-10-01},

journal = {Virology},

volume = {315},

number = {1},

pages = {159--173},

abstract = {The crystal structure of the human immunodeficiency virus type 1 (HIV-1) neutralizing, murine Fab 83.1 in complex with an HIV-1 gp120 V3 peptide has been determined to 2.57 A resolution. The conformation of the V3 loop peptide in complex with Fab 83.1 is very similar to V3 conformations seen previously with two other neutralizing Fabs, 50.1 and 59.1. The repeated identification of this same V3 conformation in complex with three very different, neutralizing antibodies indicates that it is a highly preferred structure for V3 loops on some strains of the HIV-1 virus.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid12945057,

title = {Crystal structure of uronate isomerase (TM0064) from Thermotoga maritima at 2.85 A resolution},

author = {Robert Schwarzenbacher and Jaume M Canaves and Linda S Brinen and Xiaoping Dai and Ashley M Deacon and Marc A Elsliger and Said Eshaghi and Ross Floyd and Adam Godzik and Carina Grittini and Slawomir K Grzechnik and Chittibabu Guda and Lukasz Jaroszewski and Cathy Karlak and Heath E Klock and Eric Koesema and John S Kovarik and Andreas Kreusch and Peter Kuhn and Scott A Lesley and Daniel McMullan and Timothy M McPhillips and Mark A Miller and Mitchell D Miller and Andrew Morse and Kin Moy and Jie Ouyang and Alyssa Robb and Kevin Rodrigues and Thomas L Selby and Glen Spraggon and Raymond C Stevens and Henry van den Bedem and Jeff Velasquez and Juli Vincent and Xianhong Wang and Bill West and Guenter Wolf and Keith O Hodgson and John Wooley and Ian A Wilson},

doi = {10.1002/prot.10462},

issn = {1097-0134},

year  = {2003},

date = {2003-10-01},

journal = {Proteins},

volume = {53},

number = {1},

pages = {142--145},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid13129587,

title = {Design, synthesis and biological evaluation of 10-CF3CO-DDACTHF analogues and derivatives as inhibitors of GAR Tfase and the de novo purine biosynthetic pathway},

author = {Joel Desharnais and Inkyu Hwang and Yan Zhang and Ali Tavassoli and Justin Baboval and Stephen J Benkovic and Ian A Wilson and Dale L Boger},

doi = {10.1016/s0968-0896(03)00458-9},

issn = {0968-0896},

year  = {2003},

date = {2003-10-01},

journal = {Bioorg Med Chem},

volume = {11},

number = {20},

pages = {4511--4521},

abstract = {The synthesis and evaluation of analogues and key derivatives of 10-CF3CO-DDACTHF as inhibitors of glycinamide ribonucleotide transformylase (GAR Tfase) and aminoimidazole carboxamide transformylase (AICAR Tfase) are reported. Polyglutamate analogues of 1 were evaluated as inhibitors of Escherichia coli and recombinant human (rh) GAR Tfase, and AICAR Tfase. Although the pentaglutamate 6 was found to be the most active inhibitor of the series tested against rhGAR Tfase (Ki=0.004 microM), little distinction between the mono-pentaglutamate derivatives was observed (Ki=0.02-0.004 microM), suggesting that the principal role of the required polyglutamation of 1 is intracellular retention. In contrast, 1 and its defined polyglutamates 3-6 were much less inactive when tested against rhAICAR Tfase (Ki=65-0.120 microM) and very selective (> or =100-fold) for rh versus E. coli GAR Tfase. Additional key analogues of 1 were examined (7 and 8) and found to be much less active (1000-fold) highlighting the exceptional characteristics of 1.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid13129585,

title = {Design, synthesis, and biological evaluation of simplified alpha-keto heterocycle, trifluoromethyl ketone, and formyl substituted folate analogues as potential inhibitors of GAR transformylase and AICAR transformylase},

author = {Thomas H Marsilje and Michael P Hedrick and Joel Desharnais and Ali Tavassoli and Yan Zhang and Ian A Wilson and Stephen J Benkovic and Dale L Boger},

doi = {10.1016/s0968-0896(03)00456-5},

issn = {0968-0896},

year  = {2003},

date = {2003-10-01},

journal = {Bioorg Med Chem},

volume = {11},

number = {20},

pages = {4487--4501},

abstract = {A series of simplified alpha-keto heterocycle, trifluoromethyl ketone, and formyl substituted folate analogues lacking the benzoylglutamate subunit were prepared and examined as potential inhibitors of glycinamide ribonucleotide transformylase (GAR Tfase) and aminoimidazole carboxamide transformylase (AICAR Tfase).},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid13129586,

title = {10-(2-benzoxazolcarbonyl)-5,10-dideaza-acyclic-5,6,7,8-tetrahydrofolic acid: a potential inhibitor of GAR transformylase and AICAR transformylase},

author = {Thomas H Marsilje and Michael P Hedrick and Joel Desharnais and Kevin Capps and Ali Tavassoli and Yan Zhang and Ian A Wilson and Stephen J Benkovic and Dale L Boger},

doi = {10.1016/s0968-0896(03)00457-7},

issn = {0968-0896},

year  = {2003},

date = {2003-10-01},

journal = {Bioorg Med Chem},

volume = {11},

number = {20},

pages = {4503--4509},

abstract = {The design and synthesis of 10-(2-benzoxazolcarbonyl)-DDACTHF (1) as an inhibitor of glycinamide ribonucleotide transformylase (GAR Tfase) and aminoimidazole carboxamide transformylase (AICAR Tfase) are reported. Ketone 1 and the corresponding alcohol 13 were evaluated for inhibition of GAR Tfase and AICAR Tfase and the former was found to be a potent inhibitor of recombinant human (rh) GAR Tfase (Ki=600 nM).},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid12972259,

title = {A humanized aldolase antibody for selective chemotherapy and adaptor immunotherapy},

author = {Christoph Rader and James M Turner and Andreas Heine and Doron Shabat and Subhash C Sinha and Ian A Wilson and Richard A Lerner and Carlos F Barbas},

doi = {10.1016/s0022-2836(03)00992-6},

issn = {0022-2836},

year  = {2003},

date = {2003-09-01},

journal = {J Mol Biol},

volume = {332},

number = {4},

pages = {889--899},

abstract = {Mouse monoclonal antibody 38C2 is the prototype of a new class of catalytic antibodies that were generated by reactive immunization. Through a reactive lysine, 38C2 catalyzes aldol and retro-aldol reactions using the enamine mechanism of natural aldolases. In addition to its remarkable versatility and efficacy in synthetic organic chemistry, 38C2 has been used for the selective activation of prodrugs in vitro and in vivo and thereby emerged as a promising tool for selective chemotherapy. Adding another application with relevance for cancer therapy, designated adaptor immunotherapy, we have recently shown that 38C2 can be chemically programmed to target tumors by formation of a covalent bond of defined stoichiometry with a beta-diketone derivative of an integrin alpha(v)beta(3) targeting RGD peptidomimetic. However, a major limitation for the transition from preclinical to clinical evaluation is the human anti-mouse antibody immune response that mouse 38C2 is likely to elicit in a majority of patients after single administration. Here, we report the humanization of mouse 38C2 based on rational design guided by molecular modeling. In essence, the catalytic center of mouse 38C2, which encompasses a deep hydrophobic pocket with a reactive lysine residue at the bottom, was grafted into a human antibody framework. Humanized 38C2 IgG1 was found to bind to beta-diketone haptens with conserved affinities and revealed strong catalytic activity with identical k(cat) and slightly higher K(M) values compared to the parental mouse antibody. Furthermore, humanized 38C2 IgG1 revealed efficiency in prodrug activation and chemical programming comparable to the parental mouse antibody.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid12974624,

title = {Structure of avian AICAR transformylase with a multisubstrate adduct inhibitor beta-DADF identifies the folate binding site},

author = {Dennis W Wolan and Samantha E Greasley and Mark J Wall and Stephen J Benkovic and Ian A Wilson},

doi = {10.1021/bi030106h},

issn = {0006-2960},

year  = {2003},

date = {2003-09-01},

journal = {Biochemistry},

volume = {42},

number = {37},

pages = {10904--10914},

abstract = {The penultimate catalytic step of the purine de novo synthesis pathway is the conversion of aminoimidazole-4-carboxamide ribonucleotide (AICAR) to 5-formyl-AICAR that requires the cofactor N(10)-formyl-tetrahydrofolate as the formyl donor. This reaction is catalyzed by the AICAR transformylase domain of the bifunctional enzyme AICAR transformylase/inosine monophosphate cyclohydrolase (ATIC). Identification of the location of the AICAR transformylase active site was previously elucidated from the crystal structure of the avian ATIC with bound substrate AICAR; however, due to the absence of any bound folate, the folate binding region of the active site could not be identified. Here, we have determined the homodimeric crystal structure of avian ATIC in complex with the ATIC-specific multisubstrate adduct inhibitor beta-DADF to 2.5 A resolution. Beta-DADF encompasses both the AICAR and folate moieties into a single covalently linked entity, thereby allowing for the characterization of the folate binding pocket of the AICAR transformylase active site. Beta-DADF is intimately bound at the dimer interface of the transformylase domains with the majority of AICAR moiety interactions occurring within one subunit, whereas the primary interactions to the folate occur with the opposing subunit. The crystal structure suggests that a buried Lys(267) is transiently protonated during formyl transfer allowing for the stabilization of the oxyanion transition state and subsequent protonation of N10 on the tetrahydrofolate leaving group. Furthermore, the beta-DADF-bound structure provides a more optimal three-dimensional scaffold to improve the design of specific antineoplastic agents.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid12833155,

title = {Crystal structure of CD1a in complex with a sulfatide self antigen at a resolution of 2.15 A},

author = {Dirk M Zajonc and Marc A Elsliger and Luc Teyton and Ian A Wilson},

doi = {10.1038/ni948},

issn = {1529-2908},

year  = {2003},

date = {2003-08-01},

journal = {Nat Immunol},

volume = {4},

number = {8},

pages = {808--815},

abstract = {CD1 antigens bind a variety of self and foreign lipid and glycolipid antigens for presentation to CD1-restricted T cell receptors (TCRs). Here we report the crystal structure of human CD1a in complex with a sulfatide self antigen at a resolution of 2.15 A. The lipid adopts an S-shaped conformation, with the sphingosine chain completely buried in the A' pocket and the fatty acid chain emerging from the interface of the A' pocket into the more exposed F' pocket. The headgroup is anchored in the A'-F' junction and protrudes into the F' pocket for TCR recognition. Because the A' pocket is narrow with a fixed terminus, it can act as a molecular 'ruler' to select alkyl chains of a particular length.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid12829775,

title = {Antibody domain exchange is an immunological solution to carbohydrate cluster recognition},

author = {Daniel A Calarese and Christopher N Scanlan and Michael B Zwick and Songpon Deechongkit and Yusuke Mimura and Renate Kunert and Ping Zhu and Mark R Wormald and Robyn L Stanfield and Kenneth H Roux and Jeffery W Kelly and Pauline M Rudd and Raymond A Dwek and Hermann Katinger and Dennis R Burton and Ian A Wilson},

doi = {10.1126/science.1083182},

issn = {1095-9203},

year  = {2003},

date = {2003-06-01},

journal = {Science},

volume = {300},

number = {5628},

pages = {2065--2071},

abstract = {Human antibody 2G12 neutralizes a broad range of human immunodeficiency virus type 1 (HIV-1) isolates by binding an unusually dense cluster of carbohydrate moieties on the "silent" face of the gp120 envelope glycoprotein. Crystal structures of Fab 2G12 and its complexes with the disaccharide Manalpha1-2Man and with the oligosaccharide Man9GlcNAc2 revealed that two Fabs assemble into an interlocked VH domain-swapped dimer. Further biochemical, biophysical, and mutagenesis data strongly support a Fab-dimerized antibody as the prevalent form that recognizes gp120. The extraordinary configuration of this antibody provides an extended surface, with newly described binding sites, for multivalent interaction with a conserved cluster of oligomannose type sugars on the surface of gp120. The unique interdigitation of Fab domains within an antibody uncovers a previously unappreciated mechanism for high-affinity recognition of carbohydrate or other repeating epitopes on cell or microbial surfaces.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid12652485,

title = {Expression and characterization of a humanized cocaine-binding antibody},

author = {El-Rashdy M Redwan and Nicholas A Larsen and Bin Zhou and Peter Wirsching and Kim D Janda and Ian A Wilson},

doi = {10.1002/bit.10598},

issn = {0006-3592},

year  = {2003},

date = {2003-06-01},

journal = {Biotechnol Bioeng},

volume = {82},

number = {5},

pages = {612--618},

abstract = {The murine immunoglobulin G (IgG) cocaine-binding monoclonal antibody (mAb), GNC92H2, is notable for its exquisite specificity for cocaine, as opposed to chemically-related cocaine metabolites, and for its moderately high affinity (K(d) approximately 200 nM) for cocaine. Recently, we described the crystal structure of a mouse/human chimeric Fab construct at 2.3 A resolution. Herein, we report the successful framework humanization of a single-chain Fv (scFv) GNC92H2 construct without loss of affinity for cocaine. In brief, we compared the mAb GNC92H2 sequence to human antibody sequences, and used structure-based design to incorporate mutations (total = 49) that would humanize the framework region without affecting the overall shape of the binding pocket or the key cocaine-contact residues. The codons of the rationally designed sequence were optimized for E. coli expression, and the gene was synthesized by a de novo PCR reaction using 14 overlapping primers. Expression of the scFv construct was significantly improved in E. coli by fusion to thioredoxin. Intriguingly, this construct apparently refolds to form soluble active antibody in the reducing environment of the cytoplasm. Competitive ELISA and equilibrium dialysis demonstrated comparable binding activity between the humanized scFv and the whole IgG. The successful humanization of mAb GNC92H2 should enhance its potential therapeutic value by reducing its overall. immunogenicity.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid12637583,

title = {Secretory IgA N- and O-glycans provide a link between the innate and adaptive immune systems},

author = {Louise Royle and Anja Roos and David J Harvey and Mark R Wormald and Daniëlle van Gijlswijk-Janssen and El-Rashdy M Redwan and Ian A Wilson and Mohamed R Daha and Raymond A Dwek and Pauline M Rudd},

doi = {10.1074/jbc.M301436200},

issn = {0021-9258},

year  = {2003},

date = {2003-05-01},

journal = {J Biol Chem},

volume = {278},

number = {22},

pages = {20140--20153},

abstract = {Secretory IgA (SIgA) is a multi-polypeptide complex consisting of a secretory component (SC) covalently attached to dimeric IgA containing one joining (J) chain. We present the analysis of both the N- and O-glycans on the individual peptides from this complex. Based on these data, we have constructed a molecular model of SIgA1 with all its glycans, in which the Fab arms form a T shape and the SC is wrapped around the heavy chains. The O-glycan regions on the heavy (H) chains and the SC N-glycans have adhesin-binding glycan epitopes including galactose-linked beta1-4 and beta1-3 to GlcNAc, fucose-linked alpha1-3 and alpha1-4 to GlcNAc and alpha1-2 to galactose, and alpha2-3 and alpha2-6-linked sialic acids. These glycan epitopes provide SIgA with further bacteria-binding sites in addition to the four Fab-binding sites, thus enabling SIgA to participate in both innate and adaptive immunity. We also show that the N-glycans on the H chains of both SIgA1 and SIgA2 present terminal GlcNAc and mannose residues that are normally masked by SC, but that can be unmasked and recognized by mannose-binding lectin, by disrupting the SC-H chain noncovalent interactions.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid12755606,

title = {Rational design, synthesis, evaluation, and crystal structure of a potent inhibitor of human GAR Tfase: 10-(trifluoroacetyl)-5,10-dideazaacyclic-5,6,7,8-tetrahydrofolic acid},

author = {Yan Zhang and Joel Desharnais and Thomas H Marsilje and Chenglong Li and Michael P Hedrick and Lata T Gooljarsingh and Ali Tavassoli and Stephen J Benkovic and Arthur J Olson and Dale L Boger and Ian A Wilson},

doi = {10.1021/bi034219c},

issn = {0006-2960},

year  = {2003},

date = {2003-05-01},

journal = {Biochemistry},

volume = {42},

number = {20},

pages = {6043--6056},

abstract = {Glycinamide ribonucleotide transformylase (GAR Tfase) has been the target of anti-neoplastic intervention for almost two decades. Here, we use a structure-based approach to design a novel folate analogue, 10-(trifluoroacetyl)-5,10-dideazaacyclic-5,6,7,8-tetrahydrofolic acid (10-CF(3)CO-DDACTHF, 1), which specifically inhibits recombinant human GAR Tfase (K(i) = 15 nM), but is inactive (K(i) > 100 microM) against other folate-dependent enzymes that have been examined. Moreover, compound 1 is a potent inhibitor of tumor cell proliferation (IC(50) = 16 nM, CCRF-CEM), which represents a 10-fold improvement over Lometrexol, a GAR Tfase inhibitor that has been in clinical trials. Thus, this folate analogue 1 is among the most potent and selective inhibitors known toward GAR Tfase. Contributing to its efficacious activity, compound 1 is effectively transported into the cell by the reduced folate carrier and intracellularly sequestered by polyglutamation. The crystal structure of human GAR Tfase with folate analogue 1 at 1.98 A resolution represents the first structure of any GAR Tfase to be determined with a cofactor or cofactor analogue without the presence of substrate. The folate-binding loop of residues 141-146, which is highly flexible in both Escherichia coli and unliganded human GAR Tfase structures, becomes highly ordered upon binding 1 in the folate-binding site. Computational docking of the natural cofactor into this and other apo or complexed structures provides a rational basis for modeling how the natural cofactor 10-formyltetrahydrofolic acid interacts with GAR Tfase, and suggests that this folate analogue-bound conformation represents the best template to date for inhibitor design.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid12742019,

title = {Structural basis for antibody catalysis of a cationic cyclization reaction},

author = {Xueyong Zhu and Andreas Heine and Frédéric Monnat and K N Houk and Kim D Janda and Ian A Wilson},

doi = {10.1016/s0022-2836(03)00406-6},

issn = {0022-2836},

year  = {2003},

date = {2003-05-01},

journal = {J Mol Biol},

volume = {329},

number = {1},

pages = {69--83},

abstract = {Antibody 4C6 efficiently catalyzes a cationic cyclization reaction. Crystal structures of the antibody 4C6 Fab in complex with benzoic acid and in complex with its eliciting hapten were determined to 1.30A and 2.45A resolution, respectively. These crystal structures, together with computational analysis, have elucidated a possible mechanism for the monocyclization reaction. The hapten complex revealed a combining site pocket with high shape complementarity to the hapten. This active site cleft is dominated by aromatic residues that shield the highly reactive carbocation intermediates from solvent and stabilize the carbocation intermediates through cation-pi interactions. Modeling of an acyclic olefinic sulfonate ester substrate and the transition state (TS) structures shows that the chair-like transition state is favored, and trapping by water directly produces trans-2-(dimethylphenylsilyl)-cyclohexanol, whereas the less favored boat-like transition state leads to cyclohexene. The only significant change observed upon hapten binding is a side-chain rotation of Trp(L89), which reorients to form the base of the combining site. Intriguingly, a benzoic acid molecule was sequestered in the combining site of the unliganded antibody. The 4C6 active site was compared to that observed in a previously reported tandem cyclization antibody 19A4 hapten complex. These cationic cyclization antibodies exhibit convergent structural features with terpenoid cyclases that appear to be important for catalysis.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid12719582,

title = {Hyperglycosylated mutants of human immunodeficiency virus (HIV) type 1 monomeric gp120 as novel antigens for HIV vaccine design},

author = {Ralph Pantophlet and Ian A Wilson and Dennis R Burton},

doi = {10.1128/jvi.77.10.5889-5901.2003},

issn = {0022-538X},

year  = {2003},

date = {2003-05-01},

journal = {J Virol},

volume = {77},

number = {10},

pages = {5889--5901},

abstract = {The ability to induce broadly neutralizing antibodies should be a key component of any forthcoming vaccine against human immunodeficiency virus type 1. One potential vaccine candidate, monomeric gp120, has generally failed to elicit such antibodies. We postulated that gp120 might be a better immunogen if it could be engineered to preferentially bind known broadly neutralizing antibodies. In a first study, we found that four alanine substitutions on the perimeter of the so-called Phe-43 cavity of gp120 could reduce binding of weakly neutralizing CD4-binding site antibodies (R. Pantophlet, E. O. Saphire, P. Poignard, P. W. H. I. Parren, I. A. Wilson, and D. R. Burton, J. Virol. 77:642-658, 2003), while slightly enhancing binding of the potent, broadly neutralizing antibody b12. In the present study, we sought to reduce or abolish the binding of a wider range of nonneutralizing antibodies, by incorporating extra N-glycosylation motifs at select positions into the hypervariable loops and the gp120 core. A hyperglycosylated mutant containing seven extra glycosylation sequons (consensus sequences) and the four alanine substitutions described above did not bind an extensive panel of nonneutralizing and weakly neutralizing antibodies, including a polyclonal immunoglobulin preparation (HIVIG) of low neutralizing potency. Binding of b12, at lowered affinity, and of four antibodies to the C1 and C5 regions was maintained. Removal of N- and C-terminal residues in the C1 and C5 regions, respectively, reduced or abolished binding of the four antibodies, but this also adversely affected b12 binding. The hyperglycosylated mutant and its analogues described here are novel antigens that may provide a new approach to eliciting antibodies with b12-like neutralizing properties.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid12670660,

title = {Directed evolution of N-acetylneuraminic acid aldolase to catalyze enantiomeric aldol reactions},

author = {Masaru Wada and Che-Chang Hsu and Dirk Franke and Michael Mitchell and Andreas Heine and Ian Wilson and Chi-Huey Wong},

doi = {10.1016/s0968-0896(03)00052-x},

issn = {0968-0896},

year  = {2003},

date = {2003-05-01},

journal = {Bioorg Med Chem},

volume = {11},

number = {9},

pages = {2091--2098},

abstract = {Expanding the scope of substrate specificity and stereoselectivity is of current interest in enzyme catalysis. Using error-prone PCR for in vitro directed evolution, the Neu5Ac aldolase from Escherichia coli has been altered to improve its catalytic activity toward enantiomeric substrates including N-acetyl-L-mannosamine and L-arabinose to produce L-sialic acid and L-KDO, the mirror-image sugars of the corresponding naturally occurring D-sugars. The first generation variant containing two mutations (Tyr98His and Phe115Leu) outside the (alpha,beta)(8)-barrel active site exhibits an inversion of enantioselectivity toward KDO and the second generation variant contains an additional amino acid change Val251Ile outside the alpha,beta-barrel active site that improves the enantiomeric formation of L-sialic acid and L-KDO. The X-ray structure of the triple mutant epNanA.2.5 at 2.3A resolution showed no significant difference between the wild-type and the mutant enzymes. We probed the potential structural 'hot spot' of enantioselectivity with saturation mutagenesis at Val251, the mutated residue most proximal to the Schiff base forming Lys165. The selected variant had an increase in k(cat) via replacement with another hydrophobic residue, leucine. Further sampling of a larger sequence space with error-prone PCR selected a third generation variant with significant improvement in L-KDO catalysis and a complete reversal of enantioselectivity.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid12719580,

title = {Molecular features of the broadly neutralizing immunoglobulin G1 b12 required for recognition of human immunodeficiency virus type 1 gp120},

author = {Michael B Zwick and Paul W H I Parren and Erica O Saphire and Sarah Church and Meng Wang and Jamie K Scott and Philip E Dawson and Ian A Wilson and Dennis R Burton},

doi = {10.1128/jvi.77.10.5863-5876.2003},

issn = {0022-538X},

year  = {2003},

date = {2003-05-01},

journal = {J Virol},

volume = {77},

number = {10},

pages = {5863--5876},

abstract = {IgG1 b12 is a broadly neutralizing antibody against human immunodeficiency virus type 1 (HIV-1). The epitope recognized by b12 overlaps the CD4 receptor-binding site (CD4bs) on gp120 and has been a target for vaccine design. Determination of the three-dimensional structure of immunoglobulin G1 (IgG1) b12 allowed modeling of the b12-gp120 interaction in which the protruding third complementarity-determining region (CDR) of the heavy chain (H3) was crucial for antibody binding. In the present study, extensive mutational analysis of the antigen-binding site of Fab b12 was carried out to investigate the validity of the model and to identify residues important for gp120 recognition and, by inference, key to the anti-HIV-1 activity of IgG1 b12. In all, 50 mutations were tested: 40 in H3, 4 each in H2 and L1, and 2 in L3. The results suggest that the interaction of gp120 with H3 of b12 is crucially dependent not only on a Trp residue at the apex of the H3 loop but also on a number of residues at the base of the loop. The arrangement of these residues, including aromatic side chains and side chains that hydrogen bond across the base of the loop, may rigidify H3 for penetration of the recessed CD4-binding cavity. The results further emphasize the importance to gp120 binding of a Tyr residue at the apex of the H2 loop that forms a second finger-like structure and a number of Arg residues in L1 that form a positively charged, shelf-like structure. In general, the data are consistent with the b12-gp120 interaction model previously proposed. At the gene level, somatic mutation is seen to be crucial for the generation of many of the structural features described. The Fab b12 mutants were also tested against the b12 epitope-mimic peptide B2.1, and the reactivity profile had many similarities but also significant differences from that observed for gp120. The paratope map of b12 may facilitate the design of molecules that are able to elicit b12-like activities.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid12672694,

title = {XOL-1, primary determinant of sexual fate in C. elegans, is a GHMP kinase family member and a structural prototype for a class of developmental regulators},

author = {John Gately Luz and Christian A Hassig and Catherine Pickle and Adam Godzik and Barbara J Meyer and Ian A Wilson},

doi = {10.1101/gad.1082303},

issn = {0890-9369},

year  = {2003},

date = {2003-04-01},

journal = {Genes Dev},

volume = {17},

number = {8},

pages = {977--990},

abstract = {In Caenorhabditis elegans, an X chromosome-counting mechanism specifies sexual fate. Specific genes termed X-signal elements, which are present on the X chromosome, act in a concerted dose-dependent fashion to regulate levels of the developmental switch gene xol-1. In turn, xol-1 levels determine sexual fate and the activation state of the dosage compensation mechanism. The crystal structure of the XOL-1 protein at 1.55 A resolution unexpectedly reveals that xol-1 encodes a GHMP kinase family member, despite sequence identity of 10% or less. Because GHMP kinases, thus far, have only been characterized as small molecule kinases involved in metabolic pathways, for example, amino acid and cholesterol synthesis, XOL-1 is the first member that controls nonmetabolic processes. Biochemical investigations demonstrated that XOL-1 does not bind ATP under standard conditions, suggesting that XOL-1 acts by a mechanism distinct from that of other GHMP kinases. In addition, we have cloned a XOL-1 ortholog from Caenorhabditis briggsae, a related nematode that diverged from C. elegans approximately 50-100 million years ago. These findings demonstrate an unanticipated role for GHMP kinase family members as mediators of sexual differentiation and dosage compensation and, possibly, other aspects of differentiation and development.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid12623022,

title = {Geranylgeranyl switching regulates GDI-Rab GTPase recycling},

author = {Yu An and Ying Shao and Christelle Alory and Jeanne Matteson and Toshiaki Sakisaka and Wei Chen and Richard A Gibbs and Ian A Wilson and William E Balch},

doi = {10.1016/s0969-2126(03)00034-0},

issn = {0969-2126},

year  = {2003},

date = {2003-03-01},

journal = {Structure},

volume = {11},

number = {3},

pages = {347--357},

abstract = {Rab GTPases, key regulators of membrane targeting and fusion, require the covalent attachment of geranylgeranyl lipids to their C terminus for function. To elucidate the role of lipid in Rab recycling, we have determined the crystal structure of Rab guanine nucleotide dissociation inhibitor (alphaGDI) in complex with a geranylgeranyl (GG) ligand (H(2)N-Cys-(S-GG)-OMe). The lipid is bound beneath the Rab binding platform in a shallow hydrophobic groove. Mutation of the binding pocket in the brain-specific alphaGDI leads to mental retardation. Strikingly, lipid binding acts through a conserved allosteric switching mechanism to promote release of the GDI-Rab[GDP] complex from the membrane.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid12589760,

title = {Crystal structure of MHC class II I-Ab in complex with a human CLIP peptide: prediction of an I-Ab peptide-binding motif},

author = {Yuerong Zhu and Alexander Y Rudensky and Adam L Corper and Luc Teyton and Ian A Wilson},

doi = {10.1016/s0022-2836(02)01437-7},

issn = {0022-2836},

year  = {2003},

date = {2003-02-01},

journal = {J Mol Biol},

volume = {326},

number = {4},

pages = {1157--1174},

abstract = {Association between the class II major histocompatibility complex (MHC) and the class II invariant chain-associated peptide (CLIP) occurs naturally as an intermediate step in the MHC class II processing pathway. Here, we report the crystal structure of the murine class II MHC molecule I-A(b) in complex with human CLIP at 2.15A resolution. The structure of I-A(b) accounts, via the peptide-binding groove's unique physicochemistry, for the distinct peptide repertoire bound by this allele. CLIP adopts a similar conformation to peptides bound by other I-A alleles, reinforcing the notion that CLIP is presented as a conventional peptide antigen. When compared to the related HLA-DR3/CLIP complex structure, the CLIP peptide displays a slightly different conformation and distinct interaction pattern with residues in I-A(b). In addition, after examining the published sequences of peptides presented by I-A(b), we discuss the possibility of predicting peptide alignment in the I-A(b) binding groove using a simple scoring matrix.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid12576548,

title = {Evidence for the production of trioxygen species during antibody-catalyzed chemical modification of antigens},

author = {Paul Wentworth and Anita D Wentworth and Xueyong Zhu and Ian A Wilson and Kim D Janda and Albert Eschenmoser and Richard A Lerner},

doi = {10.1073/pnas.0437831100},

issn = {0027-8424},

year  = {2003},

date = {2003-02-01},

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

volume = {100},

number = {4},

pages = {1490--1493},

abstract = {Recent work in our laboratory showed that products formed by the antibody-catalyzed water-oxidation pathway can kill bacteria. Dihydrogen peroxide, the end product of this pathway, was found to be necessary, but not sufficient, for the observed efficiency of bacterial killing. The search for further bactericidal agents that might be formed along the pathway led to the recognition of an oxidant that, in its interaction with chemical probes, showed the chemical signature of ozone. Here we report that the antibody-catalyzed water-oxidation process is capable of regioselectively converting antibody-bound benzoic acid into para-hydroxy benzoic acid as well as regioselectively hydroxylating the 4-position of the phenyl ring of a single tryptophan residue located in the antibody molecule. We view the occurrence of these highly selective chemical reactions as evidence for the formation of a short-lived hydroxylating radical species within the antibody molecule. In line with our previously presented hypothesis according to which the singlet-oxygen ((1)O*(2)) induced antibody-catalyzed water-oxidation pathways proceeds via the formation of dihydrogen trioxide (H(2)O(3)), we now consider the possibility that the hydroxylating species might be the hydrotrioxy radical HO(3)*, and we point to the remarkable potential of this either H(2)O(3)- or O(3)-derivable species to act as a masked hydroxyl radical HO* in a biological environment.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid12486729,

title = {Crystal structure of a zinc-containing glycerol dehydrogenase (TM0423) from Thermotoga maritima at 1.5 A resolution},

author = {Linda S Brinen and Jaume M Canaves and Xiaoping Dai and Ashley M Deacon and Marc A Elsliger and Said Eshaghi and Ross Floyd and Adam Godzik and Carina Grittini and Slawomir K Grzechnik and Chittibabu Guda and Lukasz Jaroszewski and Cathy Karlak and Heath E Klock and Eric Koesema and John S Kovarik and Andreas Kreusch and Peter Kuhn and Scott A Lesley and Daniel McMullan and Timothy M McPhillips and Mark A Miller and Mitchell D Miller and Andrew Morse and Kin Moy and Jie Ouyang and Alyssa Robb and Kevin Rodrigues and Thomas L Selby and Glen Spraggon and Raymond C Stevens and Henry van den Bedem and Jeff Velasquez and Juli Vincent and Xianhong Wang and Bill West and Guenter Wolf and Susan S Taylor and Keith O Hodgson and John Wooley and Ian A Wilson},

doi = {10.1002/prot.10302},

issn = {1097-0134},

year  = {2003},

date = {2003-02-01},

journal = {Proteins},

volume = {50},

number = {2},

pages = {371--374},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid12554939,

title = {Use of multiple anomalous dispersion to phase highly merohedrally twinned crystals of interleukin-1beta},

author = {Markus G Rudolph and Matthew S Kelker and Thomas R Schneider and Todd O Yeates and Vanessa Oseroff and David K Heidary and Patricia A Jennings and Ian A Wilson},

doi = {10.1107/s0907444902021704},

issn = {0907-4449},

year  = {2003},

date = {2003-02-01},

journal = {Acta Crystallogr D Biol Crystallogr},

volume = {59},

number = {Pt 2},

pages = {290--298},

abstract = {The crystal structure at 1.54 A resolution of a double mutant of interleukin-1beta (F42W/W120F), a cytokine secreted by macrophages, was determined by multiple-wavelength anomalous dispersion (MAD) using data from highly twinned selenomethionine-modified crystals. The space group is P4(3), with unit-cell parameters a = b = 53.9, c = 77.4 A. Self-rotation function analysis and various intensity statistics revealed the presence of merohedral twinning in crystals of both the native (twinning fraction alpha approximately 0.35) and SeMet (alpha approximately 0.40) forms. Structure determination and refinement are discussed with emphasis on the possible reasons for successful phasing using untreated twinned MAD data.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid12421810,

title = {Observation of an arsenic adduct in an acetyl esterase crystal structure},

author = {Xueyong Zhu and Nicholas A Larsen and Amrik Basran and Neil C Bruce and Ian A Wilson},

doi = {10.1074/jbc.M210103200},

issn = {0021-9258},

year  = {2003},

date = {2003-01-01},

journal = {J Biol Chem},

volume = {278},

number = {3},

pages = {2008--2014},

abstract = {The crystal structures of an acetyl esterase, HerE, and its complex with an inhibitor dimethylarsinic acid have been determined at 1.30- and 1.45-A resolution, respectively. Although the natural substrate for the enzyme is unknown, HerE hydrolyzes the acetyl groups from heroin to yield morphine and from phenyl acetate to yield phenol. Recently, the activity of the enzyme toward heroin has been exploited to develop a heroin biosensor, which affords higher sensitivity than other currently available detection methods. The crystal structure reveals a single domain with the canonical alpha/beta hydrolase fold with an acyl binding pocket that snugly accommodates the acetyl substituent of the substrate and three backbone amides that form a tripartite oxyanion hole. In addition, a covalent adduct was observed between the active site serine and dimethylarsinic acid, which inhibits the enzyme. This crystal structure provides the first example of an As-containing compound in a serine esterase active site and the first example of covalent modification of serine by arsenic. Thus, the HerE complex reveals the structural basis for the broad scope inhibition of serine hydrolases by As(V)-containing organic compounds.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid12467706,

title = {Structure-based mutagenesis approaches toward expanding the substrate specificity of D-2-deoxyribose-5-phosphate aldolase},

author = {Grace DeSantis and Junjie Liu and David P Clark and Andreas Heine and Ian A Wilson and Chi-Huey Wong},

doi = {10.1016/s0968-0896(02)00429-7},

issn = {0968-0896},

year  = {2003},

date = {2003-01-01},

journal = {Bioorg Med Chem},

volume = {11},

number = {1},

pages = {43--52},

abstract = {2-Deoxyribose-5-phosphate aldolase (DERA, EC 4.1.2.4) catalyzes the reversible aldol reaction between acetaldehyde and D-glyceraldehyde-3-phosphate to generate D-2-deoxyribose-5-phosphate. It is unique among the aldolases as it catalyzes the reversible asymmetric aldol addition reaction of two aldehydes. In order to expand the substrate scope and stereoselectivity of DERA, structure-based substrate design as well as site-specific mutation has been investigated. Using the 1.05 A crystal structure of DERA in complex with its natural substrate as a guide, five site-directed mutants were designed in order to improve its activity with the unnatural nonphosphorylated substrate, D-2-deoxyribose. Of these, the S238D variant exhibited a 2.5-fold improvement over the wild-type enzyme in the retroaldol reaction of 2-deoxyribose. Interestingly, this S238D mutant enzyme was shown to accept 3-azidopropinaldehyde as a substrate in a sequential asymmetric aldol reaction to form a deoxy-azidoethyl pyranose, which is a precursor to the corresponding lactone and the cholesterol-lowering agent Lipitor. This azidoaldehyde is not a substrate for the wild-type enzyme. Another structure-based design of new nonphosphorylated substrates was focused on the aldol reaction with inversion in enantioselectivity using the wild type or the S238D variant as the catalyst and 2-methyl-substituted aldehydes as substrates. An example was demonstrated in the asymmetric synthesis of a deoxypyranose as a new effective synthon for the total synthesis of epothilones. In addition, to facilitate the discovery of new enzymatic reactions, the engineered E. coli strain SELECT (Deltaace, adhC, DE3) was developed to be used in the future for selection of DERA variants with novel nonphosphorylated acceptor specificity.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid12477867,

title = {Fine mapping of the interaction of neutralizing and nonneutralizing monoclonal antibodies with the CD4 binding site of human immunodeficiency virus type 1 gp120},

author = {Ralph Pantophlet and Erica Ollmann Saphire and Pascal Poignard and Paul W H I Parren and Ian A Wilson and Dennis R Burton},

doi = {10.1128/jvi.77.1.642-658.2003},

issn = {0022-538X},

year  = {2003},

date = {2003-01-01},

journal = {J Virol},

volume = {77},

number = {1},

pages = {642--658},

abstract = {Alanine scanning mutagenesis was performed on monomeric gp120 of human immunodeficiency virus type 1 to systematically identify residues important for gp120 recognition by neutralizing and nonneutralizing monoclonal antibodies (MAbs) to the CD4 binding site (CD4bs). Substitutions that affected the binding of broadly neutralizing antibody b12 were compared to substitutions that affected the binding of CD4 and of two nonneutralizing anti-CD4bs antibodies (b3 and b6) with affinities for monomeric gp120 comparable to that of b12. Not surprisingly, the sensitivities to a number of amino acid changes were similar for the MAbs and for CD4. However, in contrast to what was seen for the MAbs, no enhancing mutations were observed for CD4, suggesting that the virus has evolved toward an optimal gp120-CD4 interaction. Although the epitope maps of the MAbs overlapped, a number of key differences between b12 and the other two antibodies were observed. These differences may explain why b12, in contrast to nonneutralizing antibodies, is able to interact not only with monomeric gp120 but also with functional oligomeric gp120 at the virion surface. Neutralization assays performed with pseudovirions bearing envelopes from a selection of alanine mutants mostly showed a reasonable correlation between the effects of the mutations on b12 binding to monomeric gp120 and neutralization efficacy. However, some mutations produced an effect on b12 neutralization counter to that predicted from gp120 binding data. It appears that these mutations have different effects on the b12 epitope on monomeric gp120 and functional oligomeric gp120. To determine whether monomeric gp120 can be engineered to preferentially bind MAb b12, recombinant gp120s were generated containing combinations of alanine substitutions shown to uniquely enhance b12 binding. Whereas b12 binding was maintained or increased, binding by five nonneutralizing anti-CD4bs MAbs (b3, b6, F105, 15e, and F91) was reduced or completely abolished. These reengineered gp120s are prospective immunogens that may prove capable of eliciting broadly neutralizing antibodies.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid14714897,

title = {The carbohydrate epitope of the neutralizing anti-HIV-1 antibody 2G12},

author = {Christopher N Scanlan and Ralph Pantophlet and Mark R Wormald and Erica Ollmann Saphire and Daniel Calarese and Robyn Stanfield and Ian A Wilson and Hermann Katinger and Raymond A Dwek and Dennis R Burton and Pauline M Rudd},

doi = {10.1007/978-1-4615-0065-0_13},

issn = {0065-2598},

year  = {2003},

date = {2003-01-01},

journal = {Adv Exp Med Biol},

volume = {535},

pages = {205--218},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid14714888,

title = {Crystal structure of an intact human IgG: antibody asymmetry, flexibility, and a guide for HIV-1 vaccine design},

author = {Erica Ollmann Saphire and Robyn L Stanfield and M D Max Crispin and Garrett Morris and Michael B Zwick and Ralph A Pantophlet and Paul W H I Parren and Pauline M Rudd and Raymond A Dwek and Dennis R Burton and Ian A Wilson},

doi = {10.1007/978-1-4615-0065-0_4},

issn = {0065-2598},

year  = {2003},

date = {2003-01-01},

journal = {Adv Exp Med Biol},

volume = {535},

pages = {55--66},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid12501179,

title = {Structural insights into the avian AICAR transformylase mechanism},

author = {Dennis W Wolan and Samantha E Greasley and G Peter Beardsley and Ian A Wilson},

doi = {10.1021/bi020505x},

issn = {0006-2960},

year  = {2002},

date = {2002-12-01},

journal = {Biochemistry},

volume = {41},

number = {52},

pages = {15505--15513},

abstract = {ATIC encompasses both AICAR transformylase and IMP cyclohydrolase activities that are responsible for the catalysis of the penultimate and final steps of the purine de novo synthesis pathway. The formyl transfer reaction catalyzed by the AICAR Tfase domain is substantially more demanding than that catalyzed by the other folate-dependent enzyme of the purine biosynthesis pathway, GAR transformylase. Identification of the AICAR Tfase active site and key catalytic residues is essential to elucidate how the non-nucleophilic AICAR amino group is activated for formyl transfer. Hence, the crystal structure of dimeric avian ATIC was determined as a complex with the AICAR Tfase substrate AICAR, as well as with an IMP cyclohydrolase inhibitor, XMP, to 1.93 A resolution. AICAR is bound at the dimer interface of the transformylase domains and forms an extensive hydrogen bonding network with a multitude of active site residues. The crystal structure suggests that the conformation of the 4-carboxamide of AICAR is poised to increase the nucleophilicity of the C5 amine, while proton abstraction occurs via His(268) concomitant with formyl transfer. Lys(267) is likely to be involved in the stabilization of the anionic formyl transfer transition state and in subsequent protonation of the THF leaving group.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid12470953,

title = {Crystal structures of two rat MHC class Ia (RT1-A) molecules that are associated differentially with peptide transporter alleles TAP-A and TAP-B},

author = {Markus G Rudolph and James Stevens and Jeffrey A Speir and John Trowsdale and Geoffrey W Butcher and Etienne Joly and Ian A Wilson},

doi = {10.1016/s0022-2836(02)01095-1},

issn = {0022-2836},

year  = {2002},

date = {2002-12-01},

journal = {J Mol Biol},

volume = {324},

number = {5},

pages = {975--990},

abstract = {Antigenic peptides are loaded onto class I MHC molecules in the endoplasmic reticulum (ER) by a complex consisting of the MHC class I heavy chain, beta(2)-microglobulin, calreticulin, tapasin, Erp57 (ER60) and the transporter associated with antigen processing (TAP). While most mammalian species transport these peptides into the ER via a single allele of TAP, rats have evolved different TAPs, TAP-A and TAP-B, that are present in different inbred strains. Each TAP delivers a different spectrum of peptides and is associated genetically with distinct subsets of MHC class Ia alleles, but the molecular basis for the conservation (or co-evolution) of the two transporter alleles is unknown. We have determined the crystal structures of a representative of each MHC subset, viz RT1-A(a) and RT1-A1(c), in association with high-affinity nonamer peptides. The structures reveal how the chemical properties of the two different rat MHC F-pockets match those of the corresponding C termini of the peptides, corroborating biochemical data on the rates of peptide-MHC complex assembly. An unusual sequence in RT1-A1(c) leads to a major deviation from the highly conserved beta(3)/alpha(1) loop (residues 40-59) conformation in mouse and human MHC class I structures. This loop change contributes to profound changes in the shape of the A-pocket in the peptide-binding groove and may explain the function of RT1-A1(c) as an inhibitory natural killer cell ligand.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid12450384,

title = {Crystal structures of human GAR Tfase at low and high pH and with substrate beta-GAR},

author = {Yan Zhang and Joel Desharnais and Samantha E Greasley and G Peter Beardsley and Dale L Boger and Ian A Wilson},

doi = {10.1021/bi020522m},

issn = {0006-2960},

year  = {2002},

date = {2002-12-01},

journal = {Biochemistry},

volume = {41},

number = {48},

pages = {14206--14215},

abstract = {Glycinamide ribonucleotide transformylase (GAR Tfase) is a key folate-dependent enzyme in the de novo purine biosynthesis pathway and, as such, has been the target for antitumor drug design. Here, we describe the crystal structures of the human GAR Tfase (purN) component of the human trifunctional protein (purD-purM-purN) at various pH values and in complex with its substrate. Human GAR Tfase exhibits pH-dependent enzyme activity with its maximum around pH 7.5-8. Comparison of unliganded human GAR Tfase structures at pH 4.2 and pH 8.5 reveals conformational differences in the substrate binding loop, which at pH 4.2 occupies the binding cleft and prohibits substrate binding, while at pH 8.5 is permissive for substrate binding. The crystal structure of GAR Tfase with its natural substrate, beta-glycinamide ribonucleotide (beta-GAR), at pH 8.5 confirms this conformational isomerism. Surprisingly, several important structural differences are found between human GAR Tfase and previously reported E. coli GAR Tfase structures, which have been used as the primary template for drug design studies. While the E. coli structure gave valuable insights into the active site and formyl transfer mechanism, differences in structure and inhibition between the bacterial and mammalian enzymes suggest that the human GAR Tfase structure is now the appropriate template for the design of anti-cancer agents.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid12454464,

title = {Structure determination of a cocaine hydrolytic antibody from a pseudomerohedrally twinned crystal},

author = {Nicholas A Larsen and Andreas Heine and Paloma de Prada and El-Rashdy Redwan and Todd O Yeates and Donald W Landry and Ian A Wilson},

doi = {10.1107/s0907444902017420},

issn = {0907-4449},

year  = {2002},

date = {2002-12-01},

journal = {Acta Crystallogr D Biol Crystallogr},

volume = {58},

number = {Pt 12},

pages = {2055--2059},

abstract = {Few examples of pseudomerohedrally twinned macromolecular crystals have been described in the literature. This unusual phenomenon arises when a fortuitous unit-cell geometry makes it possible for twinning to occur in a space group that ordinarily does not allow twinning. Here, the crystallization, structure determination and refinement of the cocaine hydrolytic antibody 15A10 at 2.35 A resolution are described. The crystal belongs to space group P2(1), with two molecules in the asymmetric unit and unit-cell parameters a = 37.5, b = 108.4, c = 111.3 A and beta fortuitously near 90 degrees; the refined twinning fraction is alpha = 0.43. Interestingly, the non-crystallographic symmetry (NCS) and twin operators are nearly parallel, which appears to be a relatively frequent situation in protein crystals twinned by merohedry or pseudomerohedry.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid12369817,

title = {Biochemical characterization and structural analysis of a highly proficient cocaine esterase},

author = {James M Turner and Nicholas A Larsen and Amrik Basran and Carlos F Barbas and Neil C Bruce and Ian A Wilson and Richard A Lerner},

doi = {10.1021/bi026131p},

issn = {0006-2960},

year  = {2002},

date = {2002-10-01},

journal = {Biochemistry},

volume = {41},

number = {41},

pages = {12297--12307},

abstract = {The bacterial cocaine esterase, cocE, hydrolyzes cocaine faster than any other reported cocaine esterase. Hydrolysis of the cocaine benzoyl ester follows Michaelis-Menten kinetics with k(cat) = 7.8 s(-1) and K(M) = 640 nM. A similar rate is observed for hydrolysis of cocaethylene, a more potent cocaine metabolite that has been observed in patients who concurrently abuse cocaine and alcohol. The high catalytic proficiency, lack of observable product inhibition, and ability to hydrolyze both cocaine and cocaethylene make cocE an attractive candidate for rapid cocaine detoxification in an emergency setting. Recently, we determined the crystal structure of this enzyme, and showed that it is a serine carboxylesterase, with a catalytic triad formed by S117, H287, and D259 within a hydrophobic active site, and an oxyanion hole formed by the backbone amide of Y118 and the Y44 hydroxyl. The only enzyme previously known to use a Tyr side chain to form the oxyanion hole is prolyl oligopeptidase, but the Y44F mutation of cocE has a more deleterious effect on the specificity rate constant (k(cat)/K(M)) than the analogous Y473F mutation of prolyl oligopeptidase. Kinetic studies on a series of cocE mutants both validate the proposed mechanism, and reveal the relative contributions of active site residues toward substrate recognition and catalysis. Inspired by the anionic binding pocket of the cocaine binding antibody GNC92H2, we found that a Q55E mutation within the active site of cocE results in a modest (2-fold) improvement in K(M), but a 14-fold loss of k(cat). The pH rate profile of cocE was fit to the ionization of two groups (pK(a1) = 7.7; pK(a2) = 10.4) that likely represent titration of H287 and Y44, respectively. We also describe the crystal structures of both S117A and Y44F mutants of cocE. Finally, urea denaturation studies of cocE by fluorescence and circular dichroism show two unfolding transitions (0.5-0.6 M and 3.2-3.7 M urea), with the first transition likely representing pertubation of the active site.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid12211025,

title = {Crystal structure of thy1, a thymidylate synthase complementing protein from Thermotoga maritima at 2.25 A resolution},

author = {Peter Kuhn and Scott A Lesley and Irimpan I Mathews and Jaume M Canaves and Linda S Brinen and Xiaoping Dai and Ashley M Deacon and Marc A Elsliger and Said Eshaghi and Ross Floyd and Adam Godzik and Carina Grittini and Slawomir K Grzechnik and Chittibabu Guda and Keith O Hodgson and Lukasz Jaroszewski and Cathy Karlak and Heath E Klock and Eric Koesema and John M Kovarik and Andreas T Kreusch and Daniel McMullan and Timothy M McPhillips and Mark A Miller and Mitchell Miller and Andrew Morse and Kin Moy and Jie Ouyang and Alyssa Robb and Kevin Rodrigues and Thomas L Selby and Glen Spraggon and Raymond C Stevens and Susan S Taylor and Henry van den Bedem and Jeff Velasquez and Juli Vincent and Xianhong Wang and Bill West and Guenter Wolf and John Wooley and Ian A Wilson},

doi = {10.1002/prot.10202},

issn = {1097-0134},

year  = {2002},

date = {2002-10-01},

journal = {Proteins},

volume = {49},

number = {1},

pages = {142--145},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid12193646,

title = {Structural genomics of the Thermotoga maritima proteome implemented in a high-throughput structure determination pipeline},

author = {Scott A Lesley and Peter Kuhn and Adam Godzik and Ashley M Deacon and Irimpan Mathews and Andreas Kreusch and Glen Spraggon and Heath E Klock and Daniel McMullan and Tanya Shin and Juli Vincent and Alyssa Robb and Linda S Brinen and Mitchell D Miller and Timothy M McPhillips and Mark A Miller and Daniel Scheibe and Jaume M Canaves and Chittibabu Guda and Lukasz Jaroszewski and Thomas L Selby and Marc-Andre Elsliger and John Wooley and Susan S Taylor and Keith O Hodgson and Ian A Wilson and Peter G Schultz and Raymond C Stevens},

doi = {10.1073/pnas.142413399},

issn = {0027-8424},

year  = {2002},

date = {2002-09-01},

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

volume = {99},

number = {18},

pages = {11664--11669},

abstract = {Structural genomics is emerging as a principal approach to define protein structure-function relationships. To apply this approach on a genomic scale, novel methods and technologies must be developed to determine large numbers of structures. We describe the design and implementation of a high-throughput structural genomics pipeline and its application to the proteome of the thermophilic bacterium Thermotoga maritima. By using this pipeline, we successfully cloned and attempted expression of 1,376 of the predicted 1,877 genes (73%) and have identified crystallization conditions for 432 proteins, comprising 23% of the T. maritima proteome. Representative structures from TM0423 glycerol dehydrogenase and TM0449 thymidylate synthase-complementing protein are presented as examples of final outputs from the pipeline.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid12057663,

title = {10-Formyl-5,10-dideaza-acyclic-5,6,7,8-tetrahydrofolic acid (10-formyl-DDACTHF): a potent cytotoxic agent acting by selective inhibition of human GAR Tfase and the de novo purine biosynthetic pathway},

author = {Thomas H Marsilje and Marc A Labroli and Michael P Hedrick and Qing Jin and Joel Desharnais and Stephen J Baker and Lata T Gooljarsingh and Joseph Ramcharan and Ali Tavassoli and Yan Zhang and Ian A Wilson and G Peter Beardsley and Stephen J Benkovic and Dale L Boger},

doi = {10.1016/s0968-0896(02)00102-5},

issn = {0968-0896},

year  = {2002},

date = {2002-08-01},

journal = {Bioorg Med Chem},

volume = {10},

number = {8},

pages = {2739--2749},

abstract = {The synthesis of 10-formyl-DDACTHF (3) as a potential inhibitor of glycinamide ribonucleotide transformylase (GAR Tfase) and aminoimidazole carboxamide ribonucleotide transformylase (AICAR Tfase) is reported. Aldehyde 3, the corresponding gamma- and alpha-pentaglutamates 21 and 25 and related agents were evaluated for inhibition of folate-dependent enzymes including GAR Tfase and AICAR Tfase. The inhibitors were found to exhibit potent cytotoxic activity (CCRF-CEM IC(50) for 3=60nM) that exceeded their enzyme inhibition potency [K(i) (3)=6 and 1 microM for Escherichia coli GAR and human AICAR Tfase, respectively]. Cytotoxicity rescue by medium purines, but not pyrimidines, indicated that the potent cytotoxic activity is derived from selective purine biosynthesis inhibition and rescue by AICAR monophosphate established that the activity is derived preferentially from GAR versus AICAR Tfase inhibition. The potent cytotoxic compounds including aldehyde 3 lost activity against CCRF-CEM cell lines deficient in the reduced folate carrier (CCRF-CEM/MTX) or folylpolyglutamate synthase (CCRF-CEM/FPGS(-)) establishing that their potent activity requires both reduced folate carrier transport and polyglutamation. Unexpectedly, the pentaglutamates displayed surprisingly similar K(i)'s versus E. coli GAR Tfase and only modestly enhanced K(i)'s versus human AICAR Tfase. On the surface this initially suggested that the potent cytotoxic activity of 3 and related compounds might be due simply to preferential intracellular accumulation of the inhibitors derived from effective transport and polyglutamation (i.e., ca. 100-fold higher intracellular concentrations). However, a subsequent examination of the inhibitors against recombinant human GAR Tfase revealed they and the corresponding gamma-pentaglutamates were unexpectedly much more potent against the human versus E. coli enzyme (K(i) for 3, 14nM against rhGAR Tfase versus 6 microM against E. coli GAR Tfase) which also accounts for their exceptional cytotoxic potency.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid12072529,

title = {The broadly neutralizing anti-human immunodeficiency virus type 1 antibody 2G12 recognizes a cluster of alpha1-->2 mannose residues on the outer face of gp120},

author = {Christopher N Scanlan and Ralph Pantophlet and Mark R Wormald and Erica Ollmann Saphire and Robyn Stanfield and Ian A Wilson and Hermann Katinger and Raymond A Dwek and Pauline M Rudd and Dennis R Burton},

doi = {10.1128/jvi.76.14.7306-7321.2002},

issn = {0022-538X},

year  = {2002},

date = {2002-07-01},

journal = {J Virol},

volume = {76},

number = {14},

pages = {7306--7321},

abstract = {2G12 is a broadly neutralizing human monoclonal antibody against human immunodeficiency virus type-1 (HIV-1) that has previously been shown to bind to a carbohydrate-dependent epitope on gp120. Here, site-directed mutagenesis and carbohydrate analysis were used to define further the 2G12 epitope. Extensive alanine scanning mutagenesis showed that elimination of the N-linked carbohydrate attachment sequences associated with residues N295, N332, N339, N386, and N392 by N-->A substitution produced significant decreases in 2G12 binding affinity to gp120(JR-CSF). Further mutagenesis suggested that the glycans at N339 and N386 were not critical for 2G12 binding to gp120(JR-CSF). Comparison of the sequences of isolates neutralized by 2G12 was also consistent with a lesser role for glycans attached at these positions. The mutagenesis studies provided no convincing evidence for the involvement of gp120 amino acid side chains in 2G12 binding. Antibody binding was inhibited when gp120 was treated with Aspergillus saitoi mannosidase, Jack Bean mannosidase, or endoglycosidase H, indicating that Man(alpha)1-->2Man-linked sugars of oligomannose glycans on gp120 are required for 2G12 binding. Consistent with this finding, the binding of 2G12 to gp120 could be inhibited by monomeric mannose but not by galactose, glucose, or N-acetylglucosamine. The inability of 2G12 to bind to gp120 produced in the presence of the glucose analogue N-butyl-deoxynojirimycin similarly implicated Man(alpha)1-->2Man-linked sugars in 2G12 binding. Competition experiments between 2G12 and the lectin cyanovirin for binding to gp120 showed that 2G12 only interacts with a subset of available Man(alpha)1-->2Man-linked sugars. Consideration of all the data, together with inspection of a molecular model of gp120, suggests that the most likely epitope for 2G12 is formed from mannose residues contributed by the glycans attached to N295 and N332, with the other glycans playing an indirect role in maintaining epitope conformation.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid12051932,

title = {Contrasting IgG structures reveal extreme asymmetry and flexibility},

author = {Erica Ollmann Saphire and Robyn L Stanfield and M D Max Crispin and Paul W H I Parren and Pauline M Rudd and Raymond A Dwek and Dennis R Burton and Ian A Wilson},

doi = {10.1016/S0022-2836(02)00244-9},

issn = {0022-2836},

year  = {2002},

date = {2002-05-01},

journal = {J Mol Biol},

volume = {319},

number = {1},

pages = {9--18},

abstract = {The crystal structure of IgG1 b12 represents the first visualization of an intact human IgG with a full-length hinge that has all domains ordered and visible. In comparison to intact murine antibodies and hinge-deletant human antibodies, b12 reveals extreme asymmetry, indicative of the extraordinary interdomain flexibility within an antibody. In addition, the structure provides an illustration of the human IgG1 hinge in its entirety and of asymmetry in the composition of the carbohydrate attached to each C(H)2 domain of the Fc. The two separate hinges assume different conformations in order to accommodate the vastly different placements of the two Fab domains relative to the Fc domain. Interestingly, only one of two possible intra-hinge disulfides is formed.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid12083519,

title = {Crystal structure of a non-canonical high affinity peptide complexed with MHC class I: a novel use of alternative anchors},

author = {Vasso Apostolopoulos and Minmin Yu and Adam L Corper and Wenjun Li and Ian F C McKenzie and Luc Teyton and Ian A Wilson and Magdalena Plebanski},

doi = {10.1016/s0022-2836(02)00198-5},

issn = {0022-2836},

year  = {2002},

date = {2002-05-01},

journal = {J Mol Biol},

volume = {318},

number = {5},

pages = {1307--1316},

abstract = {The crystal structure of a non-standard peptide, YEA9, in complex with H-2Kb, at 1.5 A resolution demonstrates how YEA9 peptide can bind with surprisingly high affinity through insertion of alternative, long, non-canonical anchors into the B and E pockets. The use of "alternative pockets" represents a new mode of high affinity peptide binding, that should be considered when predicting peptide epitopes for MHC class I. These novel interactions encountered in this non-canonical high affinity peptide-MHC complex should help predict additional binding peptides from primary protein sequences and aid in the design of alternative approaches for peptide-based vaccines.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid12083518,

title = {Crystal structure of a non-canonical low-affinity peptide complexed with MHC class I: a new approach for vaccine design},

author = {Vasso Apostolopoulos and Minmin Yu and Adam L Corper and Luc Teyton and Geoffrey A Pietersz and Ian F C McKenzie and Ian A Wilson and Magdalena Plebanski},

doi = {10.1016/s0022-2836(02)00196-1},

issn = {0022-2836},

year  = {2002},

date = {2002-05-01},

journal = {J Mol Biol},

volume = {318},

number = {5},

pages = {1293--1305},

abstract = {Peptides bind with high affinity to MHC class I molecules by anchoring certain side-chains (anchors) into specificity pockets in the MHC peptide-binding groove. Peptides that do not contain these canonical anchor residues normally have low affinity, resulting in impaired pMHC stability and loss of immunogenicity. Here, we report the crystal structure at 1.6 A resolution of an immunogenic, low-affinity peptide from the tumor-associated antigen MUC1, bound to H-2Kb. Stable binding is still achieved despite small, non-canonical residues in the C and F anchor pockets. This structure reveals how low-affinity peptides can be utilized in the design of novel peptide-based tumor vaccines. The molecular interactions elucidated in this non-canonical low-affinity peptide MHC complex should help uncover additional immunogenic peptides from primary protein sequences and aid in the design of alternative approaches for T-cell vaccines.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid11994422,

title = {Structural comparison of allogeneic and syngeneic T cell receptor-peptide-major histocompatibility complex complexes: a buried alloreactive mutation subtly alters peptide presentation substantially increasing V(beta) Interactions},

author = {John G Luz and Mingdong Huang and K Christopher Garcia and Markus G Rudolph and Vasso Apostolopoulos and Luc Teyton and Ian A Wilson},

doi = {10.1084/jem.20011644},

issn = {0022-1007},

year  = {2002},

date = {2002-05-01},

journal = {J Exp Med},

volume = {195},

number = {9},

pages = {1175--1186},

abstract = {The crystal structures of the 2C/H-2K(bm3)-dEV8 allogeneic complex at 2.4 A and H-2K(bm3)-dEV8 at 2.15 A, when compared with their syngeneic counterparts, elucidate structural changes that induce an alloresponse. The Asp77Ser mutation that imbues H-2K(bm3)-dEV8 with its alloreactive properties is located beneath the peptide and does not directly contact the T cell receptor (TCR). However, the buried mutation induces local rearrangement of the peptide itself to preserve hydrogen bonding interactions between the peptide and the alpha(1) 77 residue. The COOH terminus of the peptide main chain is tugged toward the alpha(1)-helix such that its presentation to the TCR is altered. These changes increase the stability of the allogeneic peptide-major histocompatibility complex (pMHC) complex and increase complementarity in the TCR-pMHC interface, placing greater emphasis on recognition of the pMHC by the TCR beta-chain, evinced by an increase in shape complementarity, buried surface area, and number of TCR-pMHC contacting residues. A nearly fourfold increase in the number of beta-chain-pMHC contacts is accompanied by a concomitant 64% increase in beta-chain-pMHC shape complementarity. Thus, the allogeneic mutation causes the same peptide to be presented differently, temporally and spatially, by the allogeneic and syngeneic MHCs.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid11937549,

title = {Fine specificity of TCR complementarity-determining region residues and lipid antigen hydrophilic moieties in the recognition of a CD1-lipid complex},

author = {Ethan P Grant and Evan M Beckman and Samuel M Behar and Massimo Degano and Daphney Frederique and Gurdyal S Besra and Ian A Wilson and Steven A Porcelli and Stephen T Furlong and Michael B Brenner},

doi = {10.4049/jimmunol.168.8.3933},

issn = {0022-1767},

year  = {2002},

date = {2002-04-01},

journal = {J Immunol},

volume = {168},

number = {8},

pages = {3933--3940},

abstract = {alphabeta TCR can recognize peptides presented by MHC molecules or lipids and glycolipids presented by CD1 proteins. Whereas the structural basis for peptide/MHC recognition is now clearly understood, it is not known how the TCR can interact with such disparate molecules as lipids. Recently, we demonstrated that the alphabeta TCR confers specificity for both the lipid Ag and CD1 isoform restriction, indicating that the TCR is likely to recognize a lipid/CD1 complex. We hypothesized that lipids may bind to CD1 via their hydrophobic alkyl and acyl chains, exposing the hydrophilic sugar, phosphate, and other polar functions for interaction with the TCR complementarity-determining regions (CDRs). To test this model, we mutated the residues in the CDR3 region of the DN1 TCR beta-chain that were predicted to project between the CD1b alpha helices in a model of the TCR/CD1 complex. In addition, we tested the requirement for the negatively charged and polar functions of mycolic acid for Ag recognition. Our findings indicate that the CDR loops of the TCR form the Ag recognition domain of CD1-restricted TCRs and suggest that the hydrophilic domains of a lipid Ag can form a combinatorial epitope recognized by the TCR.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}