@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}

}

@article{pmid11914501,

title = {Protein engineering for crystallization of the GTPase Sar1 that regulates ER vesicle budding},

author = {Mingdong Huang and Jacques T Weissman and Chenqian Wang and William E Balch and Ian A Wilson},

doi = {10.1107/s090744490200238x},

issn = {0907-4449},

year  = {2002},

date = {2002-04-01},

journal = {Acta Crystallogr D Biol Crystallogr},

volume = {58},

number = {Pt 4},

pages = {700--703},

abstract = {Sar1 is an important and unique GTPase that regulates vesicle budding from the ER membrane. An effort to crystallize full-length hamster Sar1 was unsuccessful owing to the aggregation of Sar1 in solution as indicated by dynamic light-scattering measurements. It was presumed that a patch of hydrophobic residues in the N-terminal region of Sar1 was responsible for the aggregation. To attempt to improve protein crystallizability, the N-terminal residues of Sar1 were progressively truncated and the solution behavior of the resulting Sar1 variants was monitored by dynamic light scattering. Truncation of the first nine residues from the N-terminus led to a Sar1 variant that is monodisperse in solution. This well behaved Sar1 variant yielded crystals in just a few days that were ultimately refined to diffraction quality.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid11875514,

title = {Don C. Wiley},

author = {Ian A Wilson},

doi = {10.1038/nsb0302-164},

issn = {1072-8368},

year  = {2002},

date = {2002-03-01},

journal = {Nat Struct Biol},

volume = {9},

number = {3},

pages = {164--166},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid11790533,

title = {The specificity of TCR/pMHC interaction},

author = {Markus G Rudolph and Ian A Wilson},

doi = {10.1016/s0952-7915(01)00298-9},

issn = {0952-7915},

year  = {2002},

date = {2002-02-01},

journal = {Curr Opin Immunol},

volume = {14},

number = {1},

pages = {52--65},

abstract = {Crystal structures of 11 complexes of TCRs with peptide/MHC (pMHC), that represent 6 independent TCRs, constitute the current structural database for deriving general insights into how alphabeta TCRs recognise peptide-bound MHC class I or class II. The TCRs adopt a roughly diagonal orientation on top of the pMHCs, but the identification of a set of conserved interactions that dictate this orientation is not apparent. Furthermore, the specific interaction of each TCR with its cognate pMHC partner is quite variable and also involves bound water molecules at the TCR/pMHC interface. In two of the systems, the structural basis for binding of altered peptide ligands has illustrated that the only significant conformational changes occur in the TCR/pMHC interface, but their small magnitude is inconsistent with the enormous variation in signalling outcomes. The TCRs adjust to different agonist, partial agonist and antagonist peptides by subtle conformational changes in their complementarity-determining regions, as previously observed in induced-fit mechanisms of antibody/antigen recognition. Alloreactive-complex structures determined or modelled so far indicate increased interactions of the TCR beta-chain with the pMHC compared with their syngeneic counterparts.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid11790098,

title = {Probing ligand recognition in the decarboxylase antibody 21D8: implications for the catalytic mechanism},

author = {Kinya Hotta and Ian A Wilson and Donald Hilvert},

doi = {10.1021/bi0158167},

issn = {0006-2960},

year  = {2002},

date = {2002-01-01},

journal = {Biochemistry},

volume = {41},

number = {3},

pages = {772--779},

abstract = {Antibody 21D8, which was elicited with a naphthalene-1,5-disulfonate hapten, catalyzes the medium-sensitive decarboxylation of 5-nitro-3-carboxybenzisoxazole. Structural studies on the hapten-antibody complex show that the active site contains two anion binding pockets separated by a hydrophobic region. To gain further insight into the ligand binding and catalytic mechanism of 21D8, six site-directed mutants were prepared, four for investigating the role of each of the two hapten sulfonate binding sites and two for examining packing interactions between bound ligands and the binding pocket. With the exception of an Arg(L46)Met substitution in the more deeply buried sulfonate binding pocket, modification of the active site resulted in reductions in catalytic efficiency (k(cat)/k(uncat)), ranging between 3- and 23-fold. Importantly, and contrary to predictions based on computational docking experiments, the differential effects of the individual mutations on the K(m), K(TS), and K(product) parameters suggest that only substrate binding modes which place the carboxylate group in the more solvent-exposed sulfonate binding site are catalytically relevant. Such an orientation would permit a potentially significant interaction between the developing oxyanion in the transition state and the side chain of Arg(L96). Incomplete desolvation of the carboxylate in this orientation may also help explain the modest efficiency of 21D8 compared to the most accelerating aprotic dipolar organic solvents.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid11742345,

title = {Crystal structure of a bacterial cocaine esterase},

author = {Nicholas A Larsen and James M Turner and James Stevens and Susan J Rosser and Amrik Basran and Richard A Lerner and Neil C Bruce and Ian A Wilson},

doi = {10.1038/nsb742},

issn = {1072-8368},

year  = {2002},

date = {2002-01-01},

journal = {Nat Struct Biol},

volume = {9},

number = {1},

pages = {17--21},

abstract = {Here we report the first structure of a cocaine-degrading enzyme. The bacterial esterase, cocE, hydrolyzes pharmacologically active (-)-cocaine to a non-psychoactive metabolite with a rate faster than any other reported cocaine esterase (kcat = 7.8 s-1 and KM = 640 nM). Because of the high catalytic proficiency of cocE, it is an attractive candidate for novel protein-based therapies for cocaine overdose. The crystal structure of cocE, solved by multiple anomalous dispersion (MAD) methods, reveals that cocE is a serine esterase composed of three domains: (i) a canonical alpha/beta hydrolase fold (ii) an alpha-helical domain that caps the active site and (iii) a jelly-roll-like beta-domain that interacts extensively with the other two domains. The active site was identified within the interface of all three domains by analysis of the crystal structures of transition state analog adduct and product complexes, which were refined at 1.58 A and 1.63 A resolution, respectively. These structural studies suggest that substrate recognition arises partly from interactions between the benzoyl moiety of cocaine and a highly evolved specificity pocket.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid11988465,

title = {Structural and thermodynamic correlates of T cell signaling},

author = {Markus G Rudolph and John G Luz and Ian A Wilson},

doi = {10.1146/annurev.biophys.31.082901.134423},

issn = {1056-8700},

year  = {2002},

date = {2002-01-01},

journal = {Annu Rev Biophys Biomol Struct},

volume = {31},

pages = {121--149},

abstract = {The first crystal structures of intact T cell receptors (TCRs) bound to class I peptide-MHC (pMHCs) antigens were determined in 1996. Since then, further structures of class I TCR/pMHC complexes have explored the degree of structural variability in the TCR-pMHC system and the structural basis for positive and negative selection. The recent determination of class II and allogeneic class I TCR/pMHC structures, as well as those of accessory molecules (e.g., CD3), has pushed our knowledge of TCR/pMHC interactions into new realms, shedding light on clinical pathologies, such as graft rejection and graft-versus-host disease. Furthermore, the determination of coreceptor structures lays the foundation for a more comprehensive structural description of the supramolecular TCR signaling events and those assemblies that arise in the immunological synapse. While these telling photodocumentaries of the TCR/pMHC interaction are composed mainly from static crystal structures, a full description of the biological snapshots in T cell signaling requires additional analytical methods that record the dynamics of the process. To this end, surface plasmon resonance (SPR), isothermal titration calorimetry (ITC), and ultracentrifugation (UC) have furnished both affinities and kinetics of the TCR/pMHC association. In the past year, structural, biochemical, and molecular biological data describing TCR/pMHC interactions have sublimely coalesced into a burgeoning well of understanding that promises to deliver further insights into T cell recognition. The coming years will, through a more intimate union of structural and kinetic data, allow many pressing questions to be addressed, such as how TCR/pMHC ligation is affected by coreceptor binding and what is the mechanism of TCR signaling in both early and late stages of T cell engagement with antigen-presenting cells.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid11739406,

title = {Crystal structure of Sar1-GDP at 1.7 A resolution and the role of the NH2 terminus in ER export},

author = {M Huang and J T Weissman and S Beraud-Dufour and P Luan and C Wang and W Chen and M Aridor and I A Wilson and W E Balch},

doi = {10.1083/jcb.200106039},

issn = {0021-9525},

year  = {2001},

date = {2001-12-01},

journal = {J Cell Biol},

volume = {155},

number = {6},

pages = {937--948},

abstract = {The Sar1 GTPase is an essential component of COPII vesicle coats involved in export of cargo from the ER. We report the 1.7-A structure of Sar1 and find that consistent with the sequence divergence of Sar1 from Arf family GTPases, Sar1 is structurally distinct. In particular, we show that the Sar1 NH2 terminus contains two regions: an NH2-terminal extension containing an evolutionary conserved hydrophobic motif that facilitates membrane recruitment and activation by the mammalian Sec12 guanine nucleotide exchange factor, and an alpha1' amphipathic helix that contributes to interaction with the Sec23/24 complex that is responsible for cargo selection during ER export. We propose that the hydrophobic Sar1 NH2-terminal activation/recruitment motif, in conjunction with the alpha1' helix, mediates the initial steps in COPII coat assembly for export from the ER.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid11724527,

title = {Crystal structure of an isolated V(alpha) domain of the 2C T-cell receptor},

author = {M G Rudolph and M Huang and L Teyton and I A Wilson},

doi = {10.1006/jmbi.2001.5113},

issn = {0022-2836},

year  = {2001},

date = {2001-11-01},

journal = {J Mol Biol},

volume = {314},

number = {1},

pages = {1--8},

abstract = {The T-cell receptor (TCR) is a heterodimeric cell-surface protein consisting of two chains, alpha and beta, each of which is composed of a variable (V) and a constant (C) domain. Crystals of the isolated V(alpha) domain of the murine TCR 2C were grown by serendipity from a solution containing the extracellular domains of the intact TCR 2C and CD3 gamma epsilon-chains. The V(alpha) crystal structure shows how crystal packing can substitute for another V(alpha) domain in a different fashion from that observed in V(alpha)/V(alpha) homodimer and V(alpha)/V(beta) heterodimer structures. Significant conformational changes occur in the CDR3 and beta(3)beta(4) loops that normally form part of the dimer interface. The monomeric V(alpha) domain provides the unique opportunity to study the effect of dimerization on the conformation of the unliganded complementarity-determining regions (CDR) of a TCR. This structure of an individual V(alpha) module has implications for stability and bioengineering of isolated antibody and immunoglobulin domains.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid11724535,

title = {Structural basis for a disfavored elimination reaction in catalytic antibody 1D4},

author = {N A Larsen and A Heine and L Crane and B F Cravatt and R A Lerner and I A Wilson},

doi = {10.1006/jmbi.2001.5112},

issn = {0022-2836},

year  = {2001},

date = {2001-11-01},

journal = {J Mol Biol},

volume = {314},

number = {1},

pages = {93--102},

abstract = {Murine antibody 1D4 selectively catalyzes a highly disfavored beta-elimination reaction. Crystal structures of unliganded 1D4 and 1D4 in complex with a transition-state analog (TSA) have elucidated a possible general base mode of catalysis. The structures of the unliganded and liganded Fabs were determined to 1.80 and 1.85 A resolution, respectively. The structure of the complex reveals a binding pocket with high shape complementarity to the TSA, which is recruited to coerce the substrate into the sterically demanding, eclipsed conformation that is required for catalysis. A histidine residue and two water molecules are likely involved in the catalysis. The structure supports either a concerted E2 or stepwise E1cB-like mechanism for elimination. Finally, the liganded 1D4 structure shows minor conformational rearrangements in CDR H2, indicative of induced-fit binding of the hapten. 1D4 has pushed the boundaries of antibody-mediated catalysis into the realm of disfavored reactions and, hence, represents an important milestone in the development of this technology.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid11695901,

title = {Unexpected formation of an epoxide-derived multisubstrate adduct inhibitor on the active site of GAR transformylase},

author = {S E Greasley and T H Marsilje and H Cai and S Baker and S J Benkovic and D L Boger and I A Wilson},

doi = {10.1021/bi011482+},

issn = {0006-2960},

year  = {2001},

date = {2001-11-01},

journal = {Biochemistry},

volume = {40},

number = {45},

pages = {13538--13547},

abstract = {Multisubstrate adduct inhibitors (MAI) of glycinamide ribonucleotide transformylase (GAR Tfase), which incorporate key features of the folate cofactor and the beta-GAR substrate, typically exhibit K(i)'s in the picomolar range. However, these compounds have reduced bioavailability due to the incorporation of a negatively charged phosphate moiety that prevents effective cellular uptake. Thus, a folate analogue that is capable of adduct formation with the substrate on the enzyme active site could lead to a potent GAR Tfase inhibitor that takes advantage of the cellular folate transport systems. We synthesized a dibromide folate analogue, 10-bromo-10-bromomethyl-5,8,10-trideazafolic acid, that was an intermediate designed to assemble with the substrate beta-GAR on the enzyme active site. We have now determined the crystal structure of the Escherichia coli GAR Tfase/MAI complex at 1.6 A resolution to ascertain the nature and mechanism of its time-dependent inhibition. The high-resolution crystal structure clearly revealed the existence of a covalent adduct between the substrate beta-GAR and the folate analogue (K(i) = 20 microM). However, the electron density map surprisingly indicated a C10 hydroxyl in the adduct rather than a bromide and suggested that the multisubstrate adduct is not formed directly from the dibromide but proceeds via an epoxide. Subsequently, we demonstrated the in situ conversion of the dibromide to the epoxide. Moreover, synthesis of the authentic epoxide confirmed that its inhibitory, time-dependent, and cytotoxic properties are comparable to those of the dibromide. Further, inhibition was strongest when the dibromide or epoxide is preincubated with both enzyme and substrate, indicating that inhibition occurs via the enzyme-dependent formation of the multisubstrate adduct. Thus, the crystal structure revealed the successful formation of an enzyme-assembled multisubstrate adduct and highlighted a potential application for epoxides, and perhaps aziridines, in the design of efficacious GAR Tfase inhibitors.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid11598300,

title = {Observation of covalent intermediates in an enzyme mechanism at atomic resolution},

author = {A Heine and G DeSantis and J G Luz and M Mitchell and C H Wong and I A Wilson},

doi = {10.1126/science.1063601},

issn = {0036-8075},

year  = {2001},

date = {2001-10-01},

journal = {Science},

volume = {294},

number = {5541},

pages = {369--374},

abstract = {In classical enzymology, intermediates and transition states in a catalytic mechanism are usually inferred from a series of biochemical experiments. Here, we derive an enzyme mechanism from true atomic-resolution x-ray structures of reaction intermediates. Two ultra-high resolution structures of wild-type and mutant d-2-deoxyribose-5-phosphate (DRP) aldolase complexes with DRP at 1.05 and 1.10 angstroms unambiguously identify the postulated covalent carbinolamine and Schiff base intermediates in the aldolase mechanism. In combination with site-directed mutagenesis and (1)H nuclear magnetic resonance, we can now propose how the heretofore elusive C-2 proton abstraction step and the overall stereochemical course are accomplished. A proton relay system appears to activate a conserved active-site water that functions as the critical mediator for proton transfer.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid11588249,

title = {Global efforts in structural genomics},

author = {R C Stevens and S Yokoyama and I A Wilson},

doi = {10.1126/science.1066011},

issn = {0036-8075},

year  = {2001},

date = {2001-10-01},

journal = {Science},

volume = {294},

number = {5540},

pages = {89--92},

abstract = {A worldwide initiative in structural genomics aims to capitalize on the recent successes of the genome projects. Substantial new investments in structural genomics in the past 2 years indicate the high level of support for these international efforts. Already, enormous progress has been made on high-throughput methodologies and technologies that will speed up macromolecular structure determinations. Recent international meetings have resulted in the formation of an International Structural Genomics Organization to formulate policy and foster cooperation between the public and private efforts.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid11578952,

title = {Getting into the groove: unusual features of peptide binding to MHC class I molecules and implications in vaccine design},

author = {V Apostolopoulos and I F McKenzie and I A Wilson},

doi = {10.2741/apostol},

issn = {1093-9946},

year  = {2001},

date = {2001-10-01},

journal = {Front Biosci},

volume = {6},

pages = {D1311--D1320},

abstract = {The major histocompatibility complex presents antigenic peptides on the surface of antigen presenting cells to T cell receptors. Recognition of peptide-MHC by T cells initiates a cascade of signals in T cells which maintains a T cell dependent immune response. An understanding of the how peptides bind to MHC class I molecules is an important prerequisite in the design of vaccines. Herein, we will discuss, with special emphasis on MUC1, unusual features of MUC1 peptide binding to MHC class I, obtained from vaccine studies including a MUC1 peptide mimic and the crystal structures of low and high affinity peptides lacking canonical anchor motifs in complex with H-2Kb.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid11546867,

title = {Antibody catalysis of the oxidation of water},

author = {P Wentworth and L H Jones and A D Wentworth and X Zhu and N A Larsen and I A Wilson and X Xu and W A Goddard and K D Janda and A Eschenmoser and R A Lerner},

doi = {10.1126/science.1062722},

issn = {0036-8075},

year  = {2001},

date = {2001-09-01},

journal = {Science},

volume = {293},

number = {5536},

pages = {1806--1811},

abstract = {Recently we reported that antibodies can generate hydrogen peroxide (H2O2) from singlet molecular oxygen (1O2*). We now show that this process is catalytic, and we identify the electron source for a quasi-unlimited generation of H2O2. Antibodies produce up to 500 mole equivalents of H2O2 from 1O2*, without a reduction in rate, and we have excluded metals or Cl- as the electron source. On the basis of isotope incorporation experiments and kinetic data, we propose that antibodies use H2O as an electron source, facilitating its addition to 1O2* to form H2O3 as the first intermediate in a reaction cascade that eventually leads to H2O2. X-ray crystallographic studies with xenon point to putative conserved oxygen binding sites within the antibody fold where this chemistry could be initiated. Our findings suggest a protective function of immunoglobulins against 1O2* and raise the question of whether the need to detoxify 1O2* has played a decisive role in the evolution of the immunoglobulin fold.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid11498595,

title = {Crystal structure of a neutralizing human IGG against HIV-1: a template for vaccine design},

author = {E O Saphire and P W Parren and R Pantophlet and M B Zwick and G M Morris and P M Rudd and R A Dwek and R L Stanfield and D R Burton and I A Wilson},

doi = {10.1126/science.1061692},

issn = {0036-8075},

year  = {2001},

date = {2001-08-01},

journal = {Science},

volume = {293},

number = {5532},

pages = {1155--1159},

abstract = {We present the crystal structure at 2.7 angstrom resolution of the human antibody IgG1 b12. Antibody b12 recognizes the CD4-binding site of human immunodeficiency virus-1 (HIV-1) gp120 and is one of only two known antibodies against gp120 capable of broad and potent neutralization of primary HIV-1 isolates. A key feature of the antibody-combining site is the protruding, finger-like long CDR H3 that can penetrate the recessed CD4-binding site of gp120. A docking model of b12 and gp120 reveals severe structural constraints that explain the extraordinary challenge in eliciting effective neutralizing antibodies similar to b12. The structure, together with mutagenesis studies, provides a rationale for the extensive cross-reactivity of b12 and a valuable framework for the design of HIV-1 vaccines capable of eliciting b12-like activity.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid11469854,

title = {Crystal structure of a cocaine-binding antibody},

author = {N A Larsen and B Zhou and A Heine and P Wirsching and K D Janda and I A Wilson},

doi = {10.1006/jmbi.2001.4839},

issn = {0022-2836},

year  = {2001},

date = {2001-08-01},

journal = {J Mol Biol},

volume = {311},

number = {1},

pages = {9--15},

abstract = {Murine monoclonal antibody GNC92H2 was elicited by active immunization with a cocaine immunoconjugate and binds free cocaine with excellent specificity and moderate affinity. Improvement of affinity, as well as humanization of GNC92H2, would be advantageous in immunopharmacotherapy for cocaine addiction, and for emergency cases of drug overdose. Toward this end, the crystal structure of an engineered murine-human chimeric Fab of GNC92H2 complexed with cocaine was determined at 2.3 A resolution. Structural analysis reveals a binding pocket with high shape and charge complementarity to the cocaine framework, which explains the specificity for cocaine, as opposed to the pharmacologically inactive cocaine metabolites. Importantly, the structure provides a foundation for mutagenesis to enhance the binding affinity for cocaine and potent cocaine derivatives, such as cocaethylene, and for additional humanization of the antibody.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid11463918,

title = {Tech.Sight. Industrializing structural biology},

author = {R C Stevens and I A Wilson},

doi = {10.1126/science.293.5529.519},

issn = {0036-8075},

year  = {2001},

date = {2001-07-01},

journal = {Science},

volume = {293},

number = {5529},

pages = {519--520},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid11323713,

title = {Crystal structure of a bifunctional transformylase and cyclohydrolase enzyme in purine biosynthesis},

author = {S E Greasley and P Horton and J Ramcharan and G P Beardsley and S J Benkovic and I A Wilson},

doi = {10.1038/87555},

issn = {1072-8368},

year  = {2001},

date = {2001-05-01},

journal = {Nat Struct Biol},

volume = {8},

number = {5},

pages = {402--406},

abstract = {ATIC, the product of the purH gene, is a 64 kDa bifunctional enzyme that possesses the final two activities in de novo purine biosynthesis, AICAR transformylase and IMP cyclohydrolase. The crystal structure of avian ATIC has been determined to 1.75 A resolution by the MAD method using a Se-methionine modified enzyme. ATIC forms an intertwined dimer with an extensive interface of approximately 5,000 A(2) per monomer. Each monomer is composed of two novel, separate functional domains. The N-terminal domain (up to residue 199) is responsible for the IMPCH activity, whereas the AICAR Tfase activity resides in the C-terminal domain (200-593). The active sites of the IMPCH and AICAR Tfase domains are approximately 50 A apart, with no structural evidence of a tunnel connecting the two active sites. The crystal structure of ATIC provides a framework to probe both catalytic mechanisms and to design specific inhibitors for use in cancer chemotherapy and inflammation.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid11269318,

title = {Glycosylation and the immune system},

author = {P M Rudd and T Elliott and P Cresswell and I A Wilson and R A Dwek},

doi = {10.1126/science.291.5512.2370},

issn = {0036-8075},

year  = {2001},

date = {2001-03-01},

journal = {Science},

volume = {291},

number = {5512},

pages = {2370--2376},

abstract = {Almost all of the key molecules involved in the innate and adaptive immune response are glycoproteins. In the cellular immune system, specific glycoforms are involved in the folding, quality control, and assembly of peptide-loaded major histocompatibility complex (MHC) antigens and the T cell receptor complex. Although some glycopeptide antigens are presented by the MHC, the generation of peptide antigens from glycoproteins may require enzymatic removal of sugars before the protein can be cleaved. Oligosaccharides attached to glycoproteins in the junction between T cells and antigen-presenting cells help to orient binding faces, provide protease protection, and restrict nonspecific lateral protein-protein interactions. In the humoral immune system, all of the immunoglobulins and most of the complement components are glycosylated. Although a major function for sugars is to contribute to the stability of the proteins to which they are attached, specific glycoforms are involved in recognition events. For example, in rheumatoid arthritis, an autoimmune disease, agalactosylated glycoforms of aggregated immunoglobulin G may induce association with the mannose-binding lectin and contribute to the pathology.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid11223533,

title = {Preliminary X-ray diffraction studies of the transcriptional inhibitory antibody Fab41.4},

author = {J Mazlo and R L Stanfield and I A Wilson and S H Hinrichs and J J Stezowski},

doi = {10.1107/s0907444901001135},

issn = {0907-4449},

year  = {2001},

date = {2001-03-01},

journal = {Acta Crystallogr D Biol Crystallogr},

volume = {57},

number = {Pt 3},

pages = {462--464},

abstract = {The binding of transcription factor ATF-1 to DNA contributes to gene expression and regulation of cell growth. Antibody Mab41.4, raised against ATF-1, and its derivatives Fab41.4 and scFv41.4 inhibit specific DNA binding in vitro and induce apoptotic death of tumor cells in vivo. Structural studies of Fab41.4 were performed to gain insight into the mechanism of action of this potentially therapeutic antibody. The optimal conditions for crystallization of Fab41.4 were determined. Crystals were needle-like in appearance, displayed C2 space-group symmetry and diffracted to a resolution of 1.6 A. The unit-cell parameters were determined to be a = 186.64, b = 40.22, c = 55.58 A, alpha = gamma = 90, beta = 96.93 degrees. The data set was 97.7% complete. Molecular replacement was performed, resulting in an R value of 44.6%.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid11224525,

title = {Crystal structure of the murine NK cell-activating receptor NKG2D at 1.95 A},

author = {D W Wolan and L Teyton and M G Rudolph and B Villmow and S Bauer and D H Busch and I A Wilson},

doi = {10.1038/85311},

issn = {1529-2908},

year  = {2001},

date = {2001-03-01},

journal = {Nat Immunol},

volume = {2},

number = {3},

pages = {248--254},

abstract = {NKG2D, a homodimeric lectin-like receptor, is a unique stimulatory molecule that is found on natural killer cells,T cells and activated macrophages. The natural ligands for murine NKG2D are distant major histocompatibility complex homologs, retinoic acid early transcript (Rae1) and H-60 minor histocompatibility antigen. The crystal structure of the extracellular region of murine NKG2D reveals close homology with other C-type lectin receptors such as CD94, Ly49A, rat MBP-A and CD69. However, the precise mode of dimeric assembly varies among these natural killer receptors, as well as their surface topography and electrostatic properties. The NKG2D structure provides the first structural insights into the role and ligand specificity of this stimulatory receptor in the innate and adaptive immune system.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid11290333,

title = {The crystal structures of K(bm1) and K(bm8) reveal that subtle changes in the peptide environment impact thermostability and alloreactivity},

author = {M G Rudolph and J A Speir and A Brunmark and N Mattsson and M R Jackson and P A Peterson and L Teyton and I A Wilson},

doi = {10.1016/s1074-7613(01)00105-4},

issn = {1074-7613},

year  = {2001},

date = {2001-03-01},

journal = {Immunity},

volume = {14},

number = {3},

pages = {231--242},

abstract = {The K(bm1) and K(bm8) natural mutants of the murine MHC class I molecule H-2K(b) were originally identified by allograft rejection. They also bind viral peptides VSV8 and SEV9 with high affinity, but their peptide complexes have substantially decreased thermostability, and the K(bm1) complexes do not elicit alloreactive T cell responses. Crystal structures of the four mutant complexes at 1.7-1.9 A resolution are similar to the corresponding wild-type K(b) structures, except in the vicinity of the mutated residues, which alter the electrostatic potential, topology, hydrogen bonding, and local water structure of the peptide binding groove. Thus, these natural K(b) mutations define the minimal perturbations in the peptide environment that alter antigen presentation to T cells and abolish alloreactivity.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid11160317,

title = {The A' and F' pockets of human CD1b are both required for optimal presentation of lipid antigens to T cells},

author = {K Niazi and M Chiu and R Mendoza and M Degano and S Khurana and D Moody and A Melián and I Wilson and M Kronenberg and S Porcelli and R Modlin},

doi = {10.4049/jimmunol.166.4.2562},

issn = {0022-1767},

year  = {2001},

date = {2001-02-01},

journal = {J Immunol},

volume = {166},

number = {4},

pages = {2562--2570},

abstract = {CD1 proteins are unique in their ability to present lipid Ags to T cells. Human CD1b shares significant amino acid homology with mouse CD1d1, which contains an unusual putative Ag-binding groove formed by two large hydrophobic pockets, A' and F'. We investigated the function of the amino acid residues that line the A' and F' pockets of CD1b by engineering 36 alanine-substitution mutants and analyzing their ability to present mycobacterial glycolipid Ags. Two lipid Ags presented by CD1b were studied, a naturally occurring glucose monomycolate (GMM) isolated from mycobacteria, which contains two long alkyl chains (C54-C62 and C22-C24) and synthetic GMM (sGMM), which includes two short alkyl chains (C18 and C14). We identified eight residues in both the A' and F' pockets that were involved in the presentation of both GMM and sGMM to T cells. Interestingly, four additional residues located in the distal portion of the A' pocket were required for the optimal presentation of GMM, but not sGMM. Conversely, nine residues located between the center of the groove and the F' pocket were necessary for the optimal presentation of sGMM, but not GMM. These data indicate that both the A' and F' pockets of human CD1b are required for the presentation of lipid Ags to T cells.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid11163232,

title = {Two different, highly exposed, bulged structures for an unusually long peptide bound to rat MHC class I RT1-Aa},

author = {J A Speir and J Stevens and E Joly and G W Butcher and I A Wilson},

doi = {10.1016/s1074-7613(01)00091-7},

issn = {1074-7613},

year  = {2001},

date = {2001-01-01},

journal = {Immunity},

volume = {14},

number = {1},

pages = {81--92},

abstract = {The rat MHC class Ia molecule RT1-Aa has the unusual capacity to bind long peptides ending in arginine, such as MTF-E, a thirteen-residue, maternally transmitted minor histocompatibility antigen. The antigenic structure of MTF-E was unpredictable due to its extraordinary length and two arginines that could serve as potential anchor residues. The crystal structure of RT1-Aa-MTF-E at 2.55 A shows that both peptide termini are anchored, as in other class I molecules, but the central residues in two independent pMHC complexes adopt completely different bulged conformations based on local environment. The MTF-E epitope is fully exposed within the putative T cell receptor (TCR) footprint. The flexibility demonstrated by the MTF-E structures illustrates how different TCRs may be raised against chemically identical, but structurally dissimilar, pMHC complexes.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid11358396,

title = {The hHFE gene of browsing and grazing rhinoceroses: a possible site of adaptation to a low-iron diet},

author = {E Beutler and C West and J A Speir and I A Wilson and M Worley},

doi = {10.1006/bcmd.2001.0386},

issn = {1079-9796},

year  = {2001},

date = {2001-01-01},

journal = {Blood Cells Mol Dis},

volume = {27},

number = {1},

pages = {342--350},

abstract = {When rhinoceros species that are browsers in the wild are fed in captivity they become iron overloaded. Presumably, their iron-absorptive mechanisms have evolved to become highly efficient. In humans, mutations of the HFE gene cause increased iron absorption. To determine whether the HFE gene of rhinoceroses has undergone mutation as an adaptive mechanism to improve iron absorption from iron-poor diets, we have sequenced the entire coding region of the HFE genes of four species of rhinoceros. Two of these were browsing species and two were grazing species. Although the HFE gene has been well preserved across species, numerous nucleotide differences were found between rhinoceros and human or mouse, some of which changed deduced amino acids. Of these mutations, only one found in the black rhinoceros appears to be a viable candidate mutation that might adversely affect HFE function. This mutation, S88T, is in a highly conserved region that is involved in the interaction between transferrin receptor and HFE.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid11134947,

title = {Crystallization and preliminary structure determination of an intact human immunoglobulin, b12: an antibody that broadly neutralizes primary isolates of HIV-1},

author = {E O Saphire and P W Parren and C F Barbas and D R Burton and I A Wilson},

doi = {10.1107/s0907444900017376},

issn = {0907-4449},

year  = {2001},

date = {2001-01-01},

journal = {Acta Crystallogr D Biol Crystallogr},

volume = {57},

number = {Pt 1},

pages = {168--171},

abstract = {An intact human immunoglobulin with a full-length hinge has been crystallized for the first time in a form in which all of the Ig domains are ordered. The IgG1 antibody b12 is one of only three known monoclonal antibodies described that potently neutralize a broad range of HIV-1 primary isolates. It binds to an epitope overlapping the conserved CD4 binding site on the viral surface antigen gp120. Hexagonal crystals corresponding to space group R32 were grown from 0.8 M ammonium sulfate, with unit-cell parameters a = b = 271.3, c = 175.2 A and one molecule per asymmetric unit. The crystals diffract to 2.8 A and a preliminary molecular-replacement solution indicates that all 12 Ig domains of the antibody can be resolved.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid11183784,

title = {Catalysis of decarboxylation by a preorganized heterogeneous microenvironment: crystal structures of abzyme 21D8},

author = {K Hotta and H Lange and D J Tantillo and K N Houk and D Hilvert and I A Wilson},

doi = {10.1006/jmbi.2000.4503},

issn = {0022-2836},

year  = {2000},

date = {2000-10-01},

journal = {J Mol Biol},

volume = {302},

number = {5},

pages = {1213--1225},

abstract = {Antibody 21D8 catalyzes the solvent-sensitive decarboxylation of 3-carboxybenzisoxazoles. The crystal structure of chimeric Fab 21D8 with and without hapten at 1.61 A and 2.10 A, respectively, together with computational analysis, shows how a melange of polar and non-polar sites are exploited to achieve both substrate binding and acceleration of a reaction normally facilitated by purely aprotic dipolar media. The striking similarity of the decarboxylase and a series of unrelated esterase antibodies also highlights the chemical versatility of structurally conserved anion binding sites and the relatively subtle changes involved in fine-tuning the immunoglobulin pocket for recognition of different ligands and catalysis of different reactions.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}