Scientific Report 2006

Molecular Biology

Structural Biology of Immune Recognition, Molecular Assemblies, and Anticancer Targets

I.A. Wilson, R.L. Stanfield, J. Stevens, X. Zhu, M.A. Adams, Y. An, K. Beis, D.A. Calarese, R.M.F. Cardoso, J.E. Carlson, P.J. Carney, J.-W. Choe, S. Connelly, A.L. Corper, T.H. Cross, X. Dai, E.W. Debler, W.L. Densley, M.-A. Elsliger, S. Ferguson, B.W. Han, G.W. Han, M.J. Jimenez-Dalmaroni, J.G. Luz, J.R. Mikolosko, A. Schiefner, D.A. Shore, R.S. Stefanko, J.A. Vanhnasy, P. Verdino, E. Wise, L. Xu, X. Xu, D.M. Zajonc

We are working toward a better understanding of the structure and function of a variety of immune-related receptors and of other medically relevant proteins. We use x-ray crystallography to determine structures for these molecules in complex with their ligands and coreceptors. This research is instrumental for the design of future drugs and vaccines to target these proteins.

Influenza Virus

Influenza virus is a highly contagious and deadly agent that causes acute respiratory illness. The current H5N1 avian influenza virus has reached epizootic levels in domestic and wild birds, with worldwide debate whether the next influenza pandemic could arise from one of these avian strains. Hemagglutinin is the principal viral surface antigen and is responsible for binding to host receptors through interaction with sialylated glycans. The structure of the hemagglutinin from a highly pathogenic H5N1 influenza virus (A/Vietnam/1203/2004; Fig. 1A) is more closely related to the human 1918 H1 hemagglutinin than to the other human, avian, and swine hemagglutinins. We are also examining crystal structures of (1) various influenza neuraminidases to determine the specificity of the enzymes and their involvement in interaction/escape of the virus from current drugs and (2) influenza viral proteins that interact with components of the apoptosis signaling pathway.

In collaboration with O. Blixt and J. Paulson of the Consortium for Functional Glycomics, La Jolla, California, we used their recently described glycan microarray technology to assess the propensity of the avian receptor H5N1 A/Vietnam/1203/2004 hemagglutinin to change from its avian receptor binding (α2-3-linked sialic acids) to adapt to human receptors (α2-6-linked sialic acids; Fig. 1B) and have elucidated a possible route by which H5 viruses could gain a foothold in the human population.

Fig. 1.A, Structure of the H5 A/Vietnam/1203/2004 (Viet04) hemagglutinin trimer, represented as a ribbon diagram. The receptor binding domain, cleavage, and basic patch sites are highlighted on one monomer. Only 2 of the 9 glycosylation sites per monomer (positions 34 and 169 in the HA1 chain) had interpretable carbohydrates in the electron density maps. B, Glycan microarray analyses of wild-type human Viet04 hemagglutinin and mutations at positions 226 and 228, known to be important for adaptation of H3 viruses from avian α2-3 specificity to human α2-6 receptor specificity. Binding to the different avian and human α2-3 and α2-6 sialosides on the array are highlighted.

IL-2 Receptor

IL-2 is a cytokine that functions as a T-cell growth factor and a central immune system regulator. Its importance is underlined by its broad use as a therapeutic agent against cancers of the immune system, and IL-2 antagonists are used to prevent rejection of transplanted organs. We have determined the structure of the heterotrimeric IL-2 receptor ectodomains (IL-2Rαβγ_c) in complex with IL-2 at 3.0-Å resolution (Fig. 2). Surprisingly, IL-2Rα makes no contacts with IL-2Rβ or IL-2Rγ_c, and only minor changes occur in IL-2 in response to receptor binding. Thus, our findings support the notion that IL-2Rα delivers IL-2 to the signaling complex and acts as a regulator of signal transduction. This research was performed in collaboration with K.A. Smith, Cornell University Weill Medical College, New York, New York.

The Innate Immune System

Toll-like receptors (TLRs) play key roles in activating immune responses during infection. The 2.1-Å structure of the human TLR3 ectodomain revealed a large horseshoe-shaped solenoid structure assembled from 23 leucine-rich repeats. Seven conserved hydrophobic residues in the leucine-rich repeat motif form a tight hydrophobic core, and conserved asparagines contribute extensive hydrogen-bonding networks for solenoid stabilization. TLR3 is largely masked by carbohydrate, but the only glycosylation-free face may provide potential ligand-binding sites and an oligomerization interface. We are doing biochemical analysis of the interaction between the TLR3 ectodomain and various double-stranded RNA oligomers and structural investigations of TLR1, TLR2, TLR6, and the TLR2 coreceptor CD36. These projects are a collaboration with B. Beutler and R. Ulevitch, Department of Immunology.

Fig. 2. Architecture of the trimeric human IL-2 receptor (designated IL2R in the figure) signaling complex. View of the quaternary IL-2 signaling assembly composed of α, β, and γc chains of the IL-2R and IL-2, with the C terminus of the β and γ chains close to the membrane. IL-2 binds to the elbow regions of IL-2Rβ and IL-2Rγc, as in other cytokine receptors such as human growth hormone receptor and erythropoietin receptor. The novel IL-2Rα chain docks on top of this assembly but does not form any contacts with the other 2 receptor subunits. Six N-linked carbohydrates (S1–S6) are displayed as ball-and-stick models. S1 is wedged between D1 and D2 of IL-2Rβ and thus contributes to the stabilization of a specific D1/D2 interdomain angle. IL-2Rβ and IL-2Rγ form a 3-way junction with IL-2 at the heart of the quaternary high-affinity IL-2 signaling complex and provide a structural basis for the cooperativity in assembly of the complete IL-2 signaling complex.

Neutrophils and other phagocytes play an important role in innate immunity by serving as a first line of defense against invading pathogens. Generation of superoxide by the phagocyte NADPH oxidase complex initiates this process by catalyzing the transfer of metabolic electrons across the plasma membrane for reduction of molecular oxygen. Individuals deficient in this enzymatic activity have chronic granulomatous disease, characterized by recurrent, life-threatening bacterial and fungal infections. In collaboration with G. Bokoch, Department of Immunology, we are studying the membrane-bound part of the NADPH complex to correlate how mutations in NADPH oxidase can cause chronic granulomatous disease.

The nucleotide oligomerization binding domain 2 is an important intracellular receptor that recognizes bacterial peptidoglycans. Mutations in this receptor are associated with the inflammatory Crohn’s disease. Structural studies are under way on the domains and on full-length protein, in collaboration with R. Ulevitch, Department of Immunology.

Catalytic Antibodies

Abuse of cocaine is a major public health problem; however, no treatments approved by the Food and Drug Administration are available for cocaine abuse, addiction, or overdose. Development of effective treatments for cocaine abuse has been frustrated by the complex neurochemistry of cocaine addiction. Nevertheless, within the past decade, immunotherapy for cocaine abuse has been evaluated in preclinical and clinical trials. In collaboration with K.D. Janda, Department of Chemistry, we determined high-resolution structures for the cocaine catalytic antibody 7A1 for all major steps along the catalytic reaction pathway, through cocrystallization with substrate, products, and transition-state analogs (Fig. 3). On the basis of this comprehensive series of crystal structures, a catalytic mechanism has been proposed, as well as possible mutations to improve catalytic proficiency.

Fig. 3. Crystal structure of the antibody 7A1 Fab′ fragment in complex with cocaine. The secondary structure of the Fab′ and the substrate cocaine are shown. Cocaine is trapped in the active site and is hydrolyzed to nontoxic metabolites.

Cofactor-Containing Antibodies

Although antibodies are generally thought to function without use of cofactors, they are major carrier proteins in human circulation for the biologically important cofactor riboflavin. A riboflavin-containing bright-yellow antibody, IgG GAR, was purified from a patient with multiple myeloma 30 years ago and is the only available material for studies of the structure and function of natural cofactor-containing antibodies. Our recent 3.0-Å crystal structure of GAR reveals the location in the antibody-combining site for the riboflavin potential cofactor (Fig. 4). This research was carried out in collaboration with R.A. Lerner and P. Wentworth, Jr., Department of Chemistry.

Fig. 4. The antigen-binding site of the original yellow antibody IgG GAR. The riboflavin cofactor is inserted into the combining site with its isoalloxazine ring stacked between aromatic residues TyrH33, PheH58, and TyrH100A. Together with hydrogen bonds between the N5 atom of the ring to AsnH50 and the ribityl side chain to ArgH52 and GluH56, these interactions reveal the structural basis for high-affinity riboflavin binding.

Blue and Purple Fluorescent Antibodies

Catalytic antibodies are designed to accelerate chemical reactions by acting on the electronic ground state. However, antibodies have been generated that can interact with and direct the photochemical behavior of the electronically excited state of stilbene, a model compound for studies in photochemistry and photophysics. We are exploring the structural basis of the diverse fluorescent properties of these complexes by using x-ray crystallography in combination with biophysical and biochemical studies with our collaborators, R.A. Lerner, K.D. Janda, P.G. Schultz, and F.E. Romesberg, Department of Chemistry.

Evolution of Ligand Recognition and Specificity

To enhance our understanding of how recognition and specificity for different ligands can be accomplished by different antibodies that have high levels of sequence homology, we are studying the evolution of ligand-binding properties by site-directed mutagenesis. The most active catalytic Diels-Alder antibody known to date, 1E9, and the steroid-binding antibody DB3 are derived from the same germ line and have 85% sequence identity. Through sequential amino acid exchanges, the specificity of 1E9 was changed to that of DB3. Thus, only a few binding site residues are responsible for achieving either efficient catalysis of the Diels-Alder reaction or, when mutated, a strong steroid binder. In collaboration with D. Hilvert, ETH, Zürich, Switzerland, we are structurally characterizing these 1E9 mutants to show how relatively minor changes can be rationally used to modify antibody specificity and function.

HIV Type 1 Neutralizing Antibodies

The search for an effective HIV type 1 vaccine has prompted the study of the few known broadly neutralizing antibodies to HIV type 1 in complex with their antigens, in order to structurally characterize important viral epitopes. The potent and broadly neutralizing antibodies include 4E10 and Z13, which bind to conserved and overlapping epitopes on the membrane-proximal region of gp41, and 2G12, which binds to a carbohydrate cluster rich in mannose on gp120. These crystal structures are then used as the basis for rational design of immunogens for a candidate vaccine against HIV type 1. This research is done in collaboration with D. Burton, Department of Immunology; P. Dawson, Department of Cell Biology; C.-H. Wong, Department of Chemistry; S. Danishefsky, Sloan-Kettering Institute, New York, New York; J.K. Scott, Simon Fraser University, Burnaby, British Columbia; J. Moore, Cornell University, Ithaca, New York; H. Katinger, R. Kunert, and G. Stiegler, University für Bodenkultur, Vienna, Austria; R. Wyatt and P. Kwong, Vaccine Research Center, National Institutes of Health, Bethesda, Maryland; and the Neutralizing Antibody Consortium of the International AIDS Vaccine Initiative, New York, New York.

Classical and Nonclassical MHC and T-Cell Receptor Signaling

An inflammatory joint disease with many similarities to human rheumatoid arthritis develops spontaneously in KRN T-cell receptor (TCR) transgenic mice (F₁ K/B x N mice). Class II MHC I-A^g7 presentation to KRN of self-peptide derived from glucose-6-phosphate isomerase is a critical step in the initiation of the disease. In collaboration with L. Teyton, Department of Immunology, we determined the crystal structures of I-A^g7–glucose-6-phosphate isomerase peptide and of the TCR KRN. We are attempting to crystallize the KRN–I-A^g7 complex to enhance our understanding of how this autoimmune disease is mediated at the molecular level.

The CD3 TCR coreceptor comprises several distinct cell-surface glycoproteins that associate with TCR to enable intracellular signal transduction upon the formation of complexes consisting of TCR and MHC-peptides. Structural investigation into the interaction between the TCR and CD3 subunits can aid in elucidation of the events that lead to T-cell activation. The CD8 glycoprotein is essential for the class I MHC-restricted T-cell response to peptide antigen, analogous to the CD4 coreceptor of class II–restricted T cells. CD8 is expressed at the cell surface as CD8ααand CD8αβ. We have determined structures for both CD8αα and CD8αβ in complex with antibody Fab fragments. Comparison of both forms of the CD8 coreceptor have provided insight into how the αand β forms contribute to the functionality of CD8. These studies are a collaboration with S. Davis, University of Oxford, Oxford, England, and L. Teyton, Department of Immunology.

The CD1 family is structurally related to MHC molecules, but members of the family present lipid antigens rather than peptides to CD1-restricted TCRs. We have determined several structures of mouse CD1d in complex with α-galacturonosyl ceramide, cis-tetracosenoyl sulfatide, or mycobacterial phosphatidylinositol dimannoside. For each CD1d-ligand, the lipid tails are embedded in the CD1 hydrophobic binding groove, and a restricted set of CD1d residues orient and stabilize the various different antigenic headgroups for TCR recognition (Fig. 5). Collaborators in research on CD1 and TCRs include D.B. Moody and M.B. Brenner, Harvard Medical School, Boston, Massachusetts; C.-H. Wong, Department of Chemistry; L. Teyton, Department of Immunology; M. Kronenberg, La Jolla Institute for Allergy and Immunology, San Diego, California; V. Kumar, Torrey Pines Institute for Molecular Studies, San Diego, California; and W. Severn and G. Painter, Industrial Research Ltd., Upper Hut, New Zealand.

Protein Trafficking

Molecular tethers play a critical role in the organization of the membrane architecture of the exocytic and endocytic pathways of eukaryotic cells. In collaboration with W. Balch, Department of Cell Biology, we have determined the 2.0-Å structure of the Rab1 GTPase-regulated N-terminal domain of the p115 tether involved in transport and structural organization of the Golgi complex. The structure reveals a dimeric handshakelike assembly consisting of 2 α-solenoid chains, each with 12 novel armadillo-like, tetherin trihelical repeat elements that form a superhelical elliptical cylinder. This structure supports a model for binding of Rab1 on opposing membranes to promote membrane tether assembly for membrane docking and fusion and for understanding the large family of molecular tethers.

Fig. 5. Structure of mouse CD1d with inositol-dimannoside. Close-up view of the binding site shows the hydrogen-bonding network between the glycolipid and CD1d. Both alkyl chains of the ligand are deeply buried inside the binding groove (not shown), whereas the complex inositol-dimannoside headgroup is optimally positioned above the binding groove to directly interact with the TCR.

Joint Center for Structural Genomics

The Joint Center for Structural Genomics is a large consortium of scientists from Scripps Research; the Stanford Synchrotron Radiation Laboratory; the University of California, San Diego; the Burnham Institute; and the Genomics Institute of the Novartis Research Foundation. The center is funded by the Protein Structure Initiative of the National Institute of General Medical Sciences. Its purpose is the high-throughput structure determination of large protein families with no structural representatives, a biologically important group of targets that are conserved in the central machinery of life; the complete proteome from Thermotoga maritima; and targets suggested by the community. To date, members of the consortium have pioneered many novel high-throughput methods, constructed a high-throughput pipeline, and determined more than 270 nonredundant structures.

Publications

Almeida, M.S., Herrmann, T., Peti, W., Wilson, I.A., Wüthrich, K. NMR structure of the conserved hypothetical protein TM0487 from Thermotoga maritima: implications for 216 homologous DUF59 proteins. Protein Sci. 14:2880, 2005.

Brunel, F.M., Zwick, M.B., Cardoso, R.M., Nelson, J.D., Wilson, I.A., Burton, D.R., Dawson, P.E. Structure-function analysis of the epitope for 4E10, a broadly neutralizing human immunodeficiency virus type 1 antibody. J. Virol. 80:1680, 2006.

Burton, D.R., Stanfield, R.L., Wilson, I.A. Antibody vs HIV in a clash of evolutionary titans. Proc. Natl. Acad. Sci. U. S. A. 102:14943, 2005.

Calarese, D.A., Lee, H.K., Huang, C.Y., Best, M.D., Astronomo, R.D., Stanfield, R.L., Katinger, H., Burton, D.R., Wong, C.-H., Wilson, I.A. Dissection of the carbohydrate specificity of the broadly neutralizing anti-HIV-1 antibody 2G12. Proc. Natl. Acad. Sci. U. S. A. 102:13372, 2005.

Cheng, H., Chong, Y., Hwang, I., Tavassoli, A., Zhang, Y., Wilson, I.A., Benkovic, S.J., Boger, D.L. Design, synthesis, and biological evaluation of 10-methanesulfonyl-DDACTHF, 10-methanesulfonyl-5-DACTHF, and 10-methylthio-DDACTHF as potent inhibitors of GAR Tfase and the de novo purine biosynthetic pathway. Bioorg. Med. Chem. 13:3577, 2005.

Cheng, H., Hwang, I., Chong, Y., Tavassoli, A., Webb, M.E., Zhang, Y., Wilson, I.A., Benkovic, S.J., Boger, D.L. Synthesis and biological evaluation of N-[4-[5-(2,4-diamino-6-oxo-1,6-dihydropyrimidin-5-yl)-2-(2,2,2-trifluoroacetyl)pentyl]benzoyl]-L-glutamic acid as a potential inhibitor of GAR Tfase and the de novo purine biosynthetic pathway. Bioorg. Med. Chem. 13:3593, 2005.

Choe, J., Kelker, M.S., Wilson, I.A. Crystal structure of human Toll-like receptor 3 (TLR3) ectodomain. Science 309:581, 2005.

Chong, Y., Hwang, I., Tavassoli, A., Zhang, Y., Wilson, I.A., Benkovic, S.J., Boger, D.L. Synthesis and biological evaluation of α- and γ-carboxamide derivatives of 10-CF3CO-DDACTHF. Bioorg. Med. Chem. 13:3587, 2005.

DiDonato, M., Krishna, S.S., Schwarzenbacher, R., et al. Crystal structure of a single-stranded DNA-binding protein (TM0604) from Thermotoga maritima at 2.60 Å resolution. Proteins 63:256, 2006.

Giabbai, B., Sidobre, S., Crispin, M.D., Sanchez-Ruiz, Y., Bachi, A., Kronenberg, M., Wilson, I.A., Degano, M. Crystal structure of mouse CD1d bound to the self ligand phosphatidylcholine: a molecular basis for NKT cell activation. J. Immunol. 175:977, 2005.

Glaser, L., Stevens, J., Zamarin, D., Wilson, I.A., Garcia-Sastre, A., Tumpey, T.M., Basler, C.F., Taubenberger, J.K., Palese, P. A single amino acid substitution in 1918 influenza virus hemagglutinin changes receptor binding specificity. J. Virol. 79:11533, 2005.

Han, G.W., Schwarzenbacher, R., McMullan, D., et al. Crystal structure of an apo mRNA decapping enzyme (DcpS) from mouse at 1.83 Å resolution. Proteins 60:797, 2005.

Huang, C.C., Tang, M., Zhang, M.Y., Majeed, S., Montabana, E., Stanfield, R.L., Dimitrov, D.S., Korber, B., Sodroski, J., Wilson, I.A., Wyatt, R., Kwong, P.D. Structure of a V3-containing HIV-1 gp120 core. Science 310:1025, 2005.

Jaroszewski, L., Schwarzenbacher, R., McMullan, D., et al. Crystal structure of Hsp33 chaperone (TM1394) from Thermotoga maritima at 2.20 Å resolution. Proteins 61:669, 2005.

Jin, K.K., Krishna, S.S., Schwarzenbacher, R., et al. Crystal structure of TM1367 from Thermotoga maritima at 1.90 Å resolution reveals an atypical member of the cyclophilin (peptidylprolyl isomerase) fold. Proteins 63:1112, 2006.

Johnson, M.A., Peti, W., Herrmann, T., Wilson, I.A., Wüthrich, K. Solution structure of Asl1650, an acyl carrier protein from Anabaena sp PCC 7120 with a variant phosphopantetheinylation-site sequence. Protein Sci. 15:1030, 2006.

Klock, H.E., Schwarzenbacher, R., Xu, Q., et al. Crystal structure of a conserved hypothetical protein (gi: 13879369) from mouse at 1.90 Å resolution reveals a new fold. Proteins 61:1132, 2005.

Luz, J.G., Yu, M., Su, Y., Wu, Z., Zhou, Z., Sun, R., Wilson, I.A. Crystal structure of viral macrophage inflammatory protein I encoded by Kaposi’s sarcoma-associated herpesvirus at 1.7 Å. J. Mol. Biol. 352:1019, 2005.

Mathews, I.I., Krishna, S.S., Schwarzenbacher, R., et al. Crystal structure of phosphoribosylformylglycinamidine synthase II (smPurL) from Thermotoga maritima at 2.15 Å resolution. Proteins 63:1106, 2006.

Moody, D.B., Zajonc, D.M., Wilson, I.A. Anatomy of CD1-lipid antigen complexes. Nat. Rev. Immunol. 5:387, 2005.

Peti, W., Page, R., Moy, K., O’Neil-Johnson, M., Wilson, I.A., Stevens, R.C., Wüthrich, K. Towards miniaturization of a structural genomics pipeline using micro-expression and microcoil NMR. J. Struct. Funct. Genomics 6:259, 2005.

Rife, C., Schwarzenbacher, R., McMullan, D., et al. Crystal structure of the global regulatory protein CsrA from Pseudomonas putida at 2.05 Å resolution reveals a new fold. Proteins 61:449, 2005.

Rife, C., Schwarzenbacher, R., McMullan, D., et al. Crystal structure of a putative modulator of DNA gyrase (pmbA) from Thermotoga maritima at 1.95 Å resolution reveals a new fold. Proteins 61:444, 2005.

Shore, D.A., Teyton, L., Dwek, R.A., Rudd, P.M., Wilson, I.A. Crystal structure of the TCR co-receptor CD8αα in complex with monoclonal antibody YTS 105.18 Fab fragment at 2.88 Å resolution. J. Mol. Biol. 358:347, 2006.

Stanfield, R.L., Gorny, M.K., Zolla-Pazner, S., Wilson, I.A. Crystal structures of human immunodeficiency virus type 1 (HIV-1) neutralizing antibody 2219 in complex with three different V3 peptides reveal a new binding mode for HIV-1 cross-reactivity. J. Virol. 80:6093, 2006.

Stanfield, R.L., Zemla, A., Wilson, I.A., Rupp, B. Antibody elbow angles are influenced by their light chain class. J. Mol. Biol. 357:1566, 2006.

Stauber, D.J., Debler, E.W., Horton, P.A., Smith, K.A., Wilson, I.A. Crystal structure of the IL-2 signaling complex: paradigm for a heterotrimeric cytokine receptor. Proc. Natl. Acad. Sci. U. S. A. 10:2788 2006.

Stevens, J., Blixt, O., Glaser, L., Taubenberger, J.K., Palese, P., Paulson, J.C., Wilson, I.A. Glycan microarray analysis of the hemagglutinins from modern and pandemic influenza viruses reveals different receptor specificities. J. Mol. Biol. 355:1143, 2006.

Stevens, J., Blixt, O., Tumpey, T.M., Taubenberger, J.K., Paulson, J.C., Wilson, I.A. Structure and receptor specificity of the hemagglutinin from an H5N1 influenza virus. Science 312:404, 2006.

Van Rhijn, I., Zajonc, D.M., Wilson, I.A., Moody, D.B. T-cell activation by lipopeptide antigens. Curr. Opin. Immunol. 17:222, 2005.

Wilson, I.A., Stanfield, R.L. MHC restriction: slip-sliding away. Nat. Immunol. 6:434, 2005.

Wiseman, R.L., Johnson, S.M., Kelker, M.S., Foss, T., Wilson, I.A., Kelly, J.W. Kinetic stabilization of an oligomeric protein by a single ligand binding event. J. Am. Chem. Soc. 127:5540, 2005.

Wu, D., Zajonc, D.M., Fujio, M., Sullivan, B.A., Kinjo, Y., Kronenberg, M., Wilson, I.A., Wong, C.-H. Design of natural killer T cell activators: structure and function of a microbial glycosphingolipid bound to mouse CD1d. Proc. Natl. Acad. Sci. U. S. A. 103:3972, 2006.

Xu, Q., Schwarzenbacher, R., McMullan, D., et al. Crystal structure of virulence factor CJ0248 from Campylobacter jejuni at 2.25 Å resolution reveals a new fold. Proteins 62:292, 2006.

Zajonc, D.M., Cantu, C. III, Mattner, J., Zhou, D., Savage, P.B., Bendelac, A., Wilson, I.A., Teyton, L. Structure and function of a potent agonist for the semi-invariant natural killer T cell receptor. Nat. Immunol. 6:810, 2005.

Zajonc, D.M., Maricic, I., Wu, D., Halder, R., Roy, K., Wong, C.-H., Kumar, V., Wilson, I.A. Structural basis for CD1d presentation of a sulfatide derived from myelin and its implications for autoimmunity. J. Exp. Med. 202:1517, 2005.

Zhang, Y., Wang, L., Schultz, P.G., Wilson, I.A. Crystal structures of apo wild-type M jannaschii tyrosyl-tRNA synthetase (TyrRS) and an engineered TyrRS specific for O-methyl-L-tyrosine. Protein Sci. 14:1340, 2005.

Zhu, X., Dickerson, T.J., Rogers, C.J., Kaufmann, G.F., Mee, J.M., McKenzie, K.M., Janda, K.D., Wilson, I.A. Complete reaction cycle of a cocaine catalytic antibody at atomic resolution. Structure 14:205, 2006.

Zhu, X., Wentworth, P., Jr., Kyle, R.A., Lerner, R.A., Wilson, I.A. Cofactor-containing antibodies: crystal structure of the original yellow antibody. Proc. Natl. Acad. Sci. U. S. A. 103:3581, 2006.