Scientific Report 2005

Molecular Biology

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

I.A. Wilson, R.L. Stanfield, J. Stevens, X. Zhu, Y. An, K. Beis, T.A. Bowden, D.A. Calarese, R.M.F. Cardoso, P.J. Carney, J.-W. Choe, A.L. Corper, M.D.M. Crispin, T.A. Cross, X. Dai, W.L. Densley, E.W. Debler, M.-A. Elsliger, S. Ferguson, G.W. Han, P.A. Horton, S. Ito, M.J. Jimenez-Dalmaroni, M.S. Kelker, J.G. Luz, J.B. Reiser, E.B. Shillington, D.A. Shore, D.J. Stauber, R.S. Stefanko, J.A. Vanhnasy, P. Verdino, E. Wise, D.W. Wolan, L. Xu, M. Yu, D.M. Zajonc, Y. Zhang

Our main research focus is concerned with macromolecules and molecular complexes related to the innate and adaptive immune responses, viral pathogenesis, protein trafficking, purine biosynthesis, and reproductive biology. We use x-ray crystallography to determine atomic structures of key proteins in these systems in order to interpret functional data to probe mechanisms and modes of interaction and to aid in the design of therapeutic agents as potential drugs or vaccines.

The Innate Immune System

Toll-like receptors (TLRs) are important mammalian glycoproteins involved in innate immunity that recognize conserved structures in pathogens called pattern recognition motifs. We recently determined the 2.1-Å crystal structure of the extracellular domain of human TLR3, which is activated by double-stranded viral RNA. TLR3 forms a large horseshoelike structure with an outer diameter of 80 Å. Key features include a hydrophobic core formed by the conserved leucine-rich repeats and a continuous β-sheet that spans 270° of arc. We are also investigating other TLRs and their ligands to understand how microorganisms are initially sensed by the innate immune system. Our goal is to use the data to design novel selective agonists and antagonists of TLR signaling pathways. This research is being done in collaboration with R.J. Ulevitch and B. Beutler, Department of Immunology.

Another family of pattern recognition molecules called peptidoglycan recognition proteins (PGRPs) interacts with peptidoglycans. We have determined the crystal structure of the “recognition” PGRP-SA at 1.56 Å. Comparison of PGRP-SA with a “catalytic” PGRP-LB indicates overall structural conservation and a hydrophilic groove that most likely corresponds to the peptidoglycan core binding site.

Approximately 22,500 intensive care patients across the United States die of septic shock syndrome every year. Recently, researchers found that a newly discovered receptor termed triggering receptor expressed on myeloid cells 1 (TREM-1) mediates septic shock. We determined structures of human and mouse TREM-1 immunoglobulin-type domains to 1.47 Å and 1.76 Å, respectively. These structural results provided insights into the nature of ligand recognition by the TREM family in innate immunity. The studies on TREMs and PGRPs are being done in collaboration with L. Teyton, Department of Immunology.

Classical And Nonclassical Mhc And T-Cell Receptor Signaling

In cellular immunity, T-cell receptors (TCRs) sense invading pathogens by recognizing pathogen-derived peptide fragments presented by MHC molecules. The TCRs then act in concert with CD8 and CD3, which assist in transducing the antigen recognition signal. Aberrant signaling can result in numerous disease states. The αβ TCR coreceptor CD8 is an essential factor in the TCR-mediated activation of cytotoxic T lymphocytes. We are doing structural studies of the CD8αβ and the CD8αα isoforms and of other constituents of the TCR signaling complex.

The CD1 family of nonclassical MHC molecules presents lipid antigens to CD1-restricted TCRs. Our recent crystal structure of mouse CD1d at 2.2 Å in complex with the exceptionally potent short-chain sphingolipid α-galactosyl ceramide (Fig. 1) reveals a precise hydrogen-bonding network that positions the galactose moiety.

Fig. 1. The short-chain sphingolipid α-galactosyl ceramide bound to mouse CD1d. This sphingolipid is a strong agonist of natural killer T cells. Both alkyl chains of the ligand are buried deep inside the binding groove, whereas the galactose headgroup is optimally positioned on top of the binding groove to directly interact with the TCR.

Other CD1 structures determined include those of CD1a with a bound sulfatide and with a lipopeptide that have revealed how dual- and single-chain lipids interact with the same CD1 molecule. Collaborators in this research 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 Wayne Severn, AgResearch, Upper Hut, New Zealand.

1918 Influenza Virus

Flu is a contagious respiratory disease caused by influenza viruses. Of all the known pandemics in the history of humans, the 1918 influenza outbreak was the most destructive; according to estimates, 40 million persons died. As a member of the “flu consortium” funded by the National Institutes of Health, we are working toward a molecular understanding of why this particular influenza virus was so pathogenic and how it managed to evade the immune system so effectively. We have determined the structure of the hemagglutinin of the 1918 virus, and now we are investigating the other viral proteins. We recently analyzed the receptor specificity of the 1918 hemagglutinin by comparing its binding to a panel of carbohydrates with the binding of more modern human and avian viruses (Fig. 2). For these studies, we are using novel glycan array technology developed by O. Blixt and J. Paulson, Consortium for Functional Glycomics, La Jolla, California.

Fig. 2. Results for carbohydrate array binding of the 2 natural hemagglutinins from the influenza virus that circulated during the 1918 pandemic. Human-adapted viruses preferentially bind to receptors with a terminal sialic acid linked by an α2,6 linkage to a vicinal galactose, whereas avian-adapted viruses recognize an α2,3 linkage. Glycan array results are shown for 18SC (A/South Carolina/1/18; A), and 18NY (A/New York/1/18; B). These 2 hemagglutinins differ by a single point mutation that is sufficient to alter the carbohydrate specificity from exclusively α2,6 to mixed α2,6/α2,3. AGP indicates α1-acid glycoprotein.

HIV Type 1 Neutralizing Antibodies

A vaccine effective against the HIV type 1 must elicit antibodies that neutralize all circulating strains of the virus. However, antibodies with such properties are extremely rare; to date, only a handful have been isolated. Crystal structures for 4 of these rare, potent, broadly neutralizing antibodies (b12, 2G12, 4E10, 447-52D) in complex with their viral antigens have revealed the structural basis for the effectiveness of the antibodies (Fig. 3).

Fig. 3. Antigen binding site of the Fab fragment of 4E10, an antibody to gp41. 4E10 cross-reacts with more viral isolates (clades) than any other known HIV type 1 neutralizing antibody. The crystal structure of Fab 4E10 is shown in complex with a synthetic peptide that encompasses the highly conserved 4E10 epitope. The peptide (ball and stick) binds to the surface of Fab 4E10 (solid surface) in a shallow hydrophobic cavity in a helical conformation. The structure also suggests that the complementarity-determining region H3 loop of 4E10 may contact the cell membrane, because the loop is adjacent to the membrane-proximal epitope.

Our goal is to design compounds on the basis of this structural information (retrovaccinology) for testing as potential vaccines. The research on HIV is being 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; S. Zolla-Pazner, New York University School of Medicine, New York, New York; J. Moore, Cornell University, Ithaca, New York; Repligen Corporation, Waltham, Massachusetts; H. Katinger, R. Kunert, and G. Stiegler, University für Bodenkultur, Vienna, Austria; and R. Wyatt and P. Kwong, Vaccine Research Center, National Institutes of Health, Bethesda, Maryland.

Primitive Immunoglobulins

Cartilaginous fish are the phylogenetically oldest living organisms known to have components of the vertebrate adaptive immune system, such as antibodies, MHC molecules, and TCRs. Key to their immune response are heavy-chain, homodimeric immunoglobulins (“new antigen receptors” or IgNARs) in which the antigen-recognizing variable domains consist of only a single immunoglobulin domain. In collaboration with M. Flajnik, University of Maryland Medical School, Baltimore, Maryland, we determined the crystal structure for an IgNAR variable domain in complex with its lysozyme antigen (Fig. 4). The results revealed that 2 complementarity-determining regions are sufficient for antigen recognition. These and ongoing studies will determine whether the IgNAR variable domains are an evolutionary precursor to mammalian TCR and antibody immunoglobulin domains.

Fig. 4. Nurse shark IgNAR type I variable domain (tubes) bound to its lysozyme antigen (solid surface). The IgNAR variable domains have an unusual antigen-binding site that contains only 2 of the 3 conventional complementarity-determining regions (CDRs), but it still binds antigen with nanomolar affinity via an interface comparable in size to conventional antibodies. Two other regions, HV2 and HV4, are also somatically mutated, suggesting that they may also be involved in antigen recognition for other IgNAR-antigen complexes.

Catalytic Antibodies

Catalytic antibodies can be generated to carry out many difficult and novel chemical reactions, including reactions not catalyzed by naturally occurring enzymes. Examples currently under study include several cocaine-hydrolyzing antibodies that could act as possible therapeutic agents to counter cocaine overdose or addiction, highly efficient but widely acting aldolase antibodies, and antibodies that carry out proton abstraction from carbon (Fig. 5).

Fig. 5. Antibody-combining site of 34E4 bound to hapten. Catalytic antibody 34E4 catalyzes the conversion of benzisoxazoles to salicylonitriles with high rates and multiple turnovers. This reaction is a widely used model system for studies of proton abstraction from carbon. The structure of 34E4 in complex with its hapten has revealed many similarities to biological counterparts that promote proton transfers. Nevertheless, the reliance of 34E4 on a single catalytic residue (GluH50) probably prevents it from achieving the rates of the most efficient enzymes. Two of the active-site water molecules are designated S1 and S21. The 3Fo-2Fc σA-weighted electron density map around the hapten and key active-site residues is contoured at 1.3 σ. Hydrogen bonds are shown as broken lines. TrpL91 forms a cation-π interaction with the guanidinium moiety of the hapten.

The studies on catalytic antibodies are being done in collaboration with R.A. Lerner, C.F. Barbas, K.D. Janda, P.G. Schultz, F. Tanaka, P. Wentworth, and P. Wirsching, Department of Chemistry; D.W. Landry, Columbia University, New York, New York; and D. Hilvert, ETH Zürich, Zürich, Switzerland.

Evolution Of Ligand Recognition And Specificity

The antibodies 1E9 and DB3 share a human germ-line precursor but recognize different ligands. Residues in the Diels-Alderase antibody 1E9 active site have been sequentially mutated by D. Hilvert to change the specificity of 1E9 to that of the steroid-binding DB3. Only 2 key residues in 1E9 are required to switch between the catalytic antibody activity and steroid binding that is 14,000-fold higher than in the original 1E9 antibody. Crystal structures of these steroid-bound 1E9 mutants show that although 1E9 and DB3 share similar steroid-binding properties, they surprisingly accomplish binding and specificity in a structurally distinct manner.

Blue and Purple Fluorescent Antibodies

Antibodies generated against trans-stilbene have an interesting, unexpected photochemistry when bound to that hapten. Several of these antibodies bind stilbene with high affinity, yet have significantly different spectroscopic properties. Crystal structures have now been determined to probe the antibodies’ mechanism of action, and further biophysical and biochemical studies are being performed in the laboratories of our collaborators, R.A. Lerner, Department of Molecular Biology; K.D. Janda and F.E. Romesberg, Department of Chemistry; and H.G. Gray, California Institute of Technology, Pasadena, California.

Protein Trafficking

The Rab family GTPases are ubiquitously involved in regulation of membrane docking and fusion in endocytic and exocytic pathways. The tethering factor p115 is recruited by Rab1 to vesicles of coat protein complex II during budding from the endoplasmic reticulum and subsequently interacts with a set of SNARE proteins associated with the vesicles to promote targeting to the Golgi complex. In collaboration with W.E. Balch, Department of Cell Biology, we determined the crystal structure of p115 at 2.0 Å and localized the binding site on p115 for Rab1 by mutational analysis.

Enzymatic Cancer Targets

The de novo purine biosynthesis pathway is the primary provider of purine nucleotides, which are converted to DNA building blocks. This biosynthesis pathway is a validated target for the development of anticancer drugs because of heavy dependence on it by fast-growing cells, such as tumor cells. We have focused on 2 folate-dependent enzymes in the pathway: glycinamide ribonucleotide transformylase and the bifunctional aminoimidazole carboxamide ribonucleotide transformylase inosine monophosphate cyclohydrolase (ATIC, Fig. 6).

Fig. 6. The active site of ATIC in complex with a novel nonfolate inhibitor identified by virtual ligand screening. The inhibitor is depicted in ball-and-stick representation and is surrounded by 2Fo-Fc electron density contoured at 1σInitiative of the National Institute of General Medical Sciences. Its purpose is the high-throughput structure determination of the complete proteomes of a procaryote, Thermotoga maritima, and a eukaryote, the mouse. To date, members of the consortium have pioneered the development of many novel high-throughput methods, constructed a high-throughput pipeline, and determined more than 200 nonredundant structures, including 100 in the past year.

Crystal structures of these 2 enzymes in complex with many different classes of inhibitors have provided a valuable platform for development of antineoplastic agents. These investigations are being done in collaboration with D.L. Boger, Department of Chemistry; A.J. Olson, Department of Molecular Biology; G.P. Beardsley, Yale University, New Haven, Connecticut; and S.J. Benkovic, Pennsylvania State University, University Park, Pennsylvania.

GHMP Kinases in Reproductive Biology

XOL-1 is the primary sex-determining signal from Caenorhabditis elegans. The crystal structure of XOL-1 revealed that the protein belongs to the GHMP kinase family of small-molecule kinases, establishing an unanticipated role for this protein family in differentiation and development. In collaboration with B.J. Meyer, University of California, Berkeley, California, we identified XOL-1 homologs in the genomes of Caenorhabditis briggsae and Caenorhabditis remanei and are examining their function by using suppression of gene expression mediated by RNA interference. Although XOL-1 is structurally similar to its GHMP kinase neighbors, its endogenous ligand is unknown. Using the crystal structure of XOL-1 as a template for virtual screening, we identified several potential synthetic XOL-1 ligands, and in collaboration with J.R. Williamson, Department of Molecular Biology, we confirmed their binding by using nuclear magnetic resonance.

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

Publications

Arndt, J.W., Schwarzenbacher, R., Page, R., et al. Crystal structure of an / serine hydrolase (YDR428C) from Saccharomyces cerevisiae at 1.85 Å resolution. Proteins 58:755, 2005.

Bakolitsa, C., Schwarzenbacher, R., McMullan, D., et al. Crystal structure of an orphan protein (TM0875) from Thermotoga maritima at 2.00-Å resolution reveals a new fold. Proteins 56:607, 2004.

Blixt, O., Head, S., Mondala, T., Scanlan, C., Huflejt, M.E., Alvarez, R., Bryan, M.C., Fazio, F., Calarese, D., Stevens, J., Razi, N., Stevens, D.J., Skehel, J.J., van Die, I., Burton, D.R., Wilson, I.A., Cummings, R., Bovin, N., Wong, C.H., Paulson, J.C. Printed covalent glycan array for ligand profiling of diverse glycan binding proteins. Proc. Natl. Acad. Sci. U. S. A. 101:17033, 2004.

Bryan, M.C., Fazio, F., Lee, H.K., Huang, C.Y., Chang, A., Best, M.D., Calarese, D.A., Blixt, O., Paulson, J.C., Burton, D., Wilson, I.A., Wong, C.-H. Covalent display of oligosaccharide arrays in microtiter plates. J. Am. Chem. Soc. 126:8640, 2004.

Canaves, J.M., Page, R., Wilson, I.A., Stevens, R.C. Protein biophysical properties that correlate with crystallization success in Thermotoga maritima: maximum clustering strategy for structural genomics. J. Mol. Biol. 344:977, 2004.

Cardoso, R.M., Zwick, M.B., Stanfield, R.L., Kunert, R., Binley, J.M., Katinger, H., Burton, D.R., Wilson, I.A. Broadly neutralizing anti-HIV antibody 4E10 recognizes a helical conformation of a highly conserved fusion-associated motif in gp41. Immunity 22:163, 2005.

Crispin, M.D., Ritchie, G.E., Critchley, A.J., Morgan, B.P., Wilson, I.A., Dwek, R.A., Sim, R.B., Rudd, P.M. Monoglucosylated glycans in the secreted human complement component C3: implications for protein biosynthesis and structure. FEBS Lett. 566:270, 2004.

Debler, E.W., Ito, S., Seebeck, F.P., Heine, A., Hilvert, D., Wilson, I.A. Structural origins of efficient proton abstraction from carbon by a catalytic antibody. Proc. Natl. Acad. Sci. U. S. A. 102:4984, 2005.

Foss, T.R., Kelker, M.S., Wiseman, R.L., Wilson, I.A., Kelly, J.W. Kinetic stabilization of the native state by protein engineering: implications for inhibition of transthyretin amyloidogenesis. J. Mol. Biol. 347:841, 2005.

Han, G.W., Schwarzenbacher, R., Page, R., et al. Crystal structure of an alanine- glyoxylate aminotransferase from Anabaena sp at 1.70 Å resolution reveals a noncovalently linked PLP cofactor. Proteins 58:971, 2005.

Hava, D.L., Brigl, M., van den Elzen, P., Zajonc, D.M., Wilson, I.A., Brenner, M.B. CD1 assembly and the formation of CD1-antigen complexes. Curr. Opin. Immunol. 17:88, 2005.

Heine, A., Canaves, J.M., von Delft, F., et al. Crystal structure of O-acetylserine sulfhydrylase (TM0665) from Thermotoga maritima at 1.8 Å resolution. Proteins 56:387, 2004.

Heine, A., Luz, J.G., Wong, C.H., Wilson, I.A. Analysis of the class I aldolase binding site architecture based on the crystal structure of 2-deoxyribose-5-phosphate aldolase at 0.99 Å resolution. J. Mol. Biol. 343:1019, 2004.

Jaroszewski, L., Schwarzenbacher, R., von Delft, F., et al. Crystal structure of a novel manganese-containing cupin (TM1459) from Thermotoga maritima at 1.65 Å resolution. Proteins 56:611, 2004.

Kelker, M.S., Debler, E.W., Wilson, I.A. Crystal structure of mouse triggering receptor expressed on myeloid cells 1 (TREM-1) at 1.76 Å. J. Mol. Biol. 344:1175, 2004.

Kelker, M.S., Foss, T.R., Peti, W., Teyton, L., Kelly, J.W., Wüthrich, K., Wilson, I.A. Crystal structure of human triggering receptor expressed on myeloid cells 1 (TREM-1) at 1.47 Å. J. Mol. Biol. 342:1237, 2004.

Larsen, N.A., de Prada, P., Deng, S.X., Mittal, A., Braskett, M., Zhu, X., Wilson, I.A., Landry, D.W. Crystallographic and biochemical analysis of cocaine-degrading antibody 15A10. Biochemistry 43:8067, 2004.

Levin, I., Miller, M.D., Schwarzenbacher, R., et al. Crystal structure of an indigoidine synthase A (IndA)-like protein (TM1464) from Thermotoga maritima at 1.90 Å resolution reveals a new fold. Proteins 59:864, 2005.

Levin, I., Schwarzenbacher, R., McMullan, D., et al. Crystal structure of a putative NADPH-dependent oxidoreductase (GI: 18204011) from mouse at 2.10 Å resolution. Proteins 56:629, 2004.

Levin, I., Schwarzenbacher, R., Page, R., et al. Crystal structure of a PIN (PilT N-terminus) domain (AF0591) from Archaeoglobus fulgidus at 1.90 Å resolution. Proteins 56:404, 2004.

Li, C., Xu, L., Wolan, D.W., Wilson, I.A., Olson, A.J. Virtual screening of human 5-aminoimidazole-4-carboxamide ribonucleotide transformylase against the NCI diversity set by use of AutoDock to identify novel nonfolate inhibitors. J. Med. Chem. 47:6681, 2004.

Mathews, I., Schwarzenbacher, R., McMullan, D., et al. Crystal structure of
S-adenosylmethionine:tRNA ribosyltransferase-isomerase (QueA) from Thermotoga maritima at 2.0 Å resolution reveals a new fold. Proteins 59:869, 2005.

McMullan, D., Schwarzenbacher, R., Hodgson, K.O., et al. Crystal structure of a novel Thermotoga maritima enzyme (TM1112) from the cupin family at 1.83 Å resolution. Proteins 56:615, 2004.

Miller, M.D., Schwarzenbacher, R., von Delft, F., et al. Crystal structure of a tandem cystathionine-β-synthase (CBS) domain protein (TM0935) from Thermotoga maritima at 1.87 Å resolution. Proteins 57:213, 2004.

Page, R., Peti, W., Wilson, I.A., Stevens, R.C., Wüthrich, K. NMR screening and crystal quality of bacterially expressed prokaryotic and eukaryotic proteins in a structural genomics pipeline. Proc. Natl. Acad. Sci. U. S. A. 102:1901, 2005.

Pantophlet, R., Wilson, I.A., Burton, D.R. Improved design of an antigen with enhanced specificity for the broadly HIV-neutralizing antibody b12. Protein Eng. Des. Sel. 17:749, 2004.

Reiser, J.B., Teyton, L., Wilson, I.A. Crystal structure of the Drosophila peptidoglycan recognition protein (PGRP)-SA at 1.56 Å resolution. J. Mol. Biol. 340:909, 2004.

Santelli, E., Schwarzenbacher, R., McMullan, D., et al. Crystal structure of a glycerophosphodiester phosphodiesterase (GDPD) from Thermotoga maritima (TM1621) at 1.60 Å resolution. Proteins 56:167, 2004.

Schwarzenbacher, R., Jaroszewski, L., von Delft, F., et al. Crystal structure of an aspartate aminotransferase (TM1255) from Thermotoga maritima at 1.90 Å resolution. Proteins 55:759, 2004.

Schwarzenbacher, R., Jaroszewski, L., von Delft, F., et al. Crystal structure of a type II quinolic acid phosphoribosyltransferase (TM1645) from Thermotoga maritima at 2.50 Å resolution. Proteins 55:768, 2004.

Schwarzenbacher, R., von Delft, F., Jaroszewski, L., et al. Crystal structure of a putative oxalate decarboxylase (TM1287) from Thermotoga maritima at 1.95 Å resolution. Proteins 56:392, 2004.

Spraggon, G., Pantazatos, D., Klock, H.E., Wilson, I.A., Woods, V.L., Jr., Lesley, S.A. On the use of DXMS to produce more crystallizable proteins: structures of the T maritima proteins TM0160 and TM1171 [published correction appears in Protein Sci. 14:1688, 2005]. Protein Sci. 13:3187, 2004.

Spraggon, G., Schwarzenbacher, R., Kreusch, A., et al. Crystal structure of a methionine aminopeptidase (TM1478) from Thermotoga maritima at 1.9 Å resolution. Proteins 56:396, 2004.

Spraggon, G., Schwarzenbacher, R., Kreusch, A., et al. Crystal structure of a Udp-n-acetylmuramate-alanine ligase MurC (TM0231) from Thermotoga maritima at 2.3 Å resolution. Proteins 55:1078, 2004.

Stanfield, R.L., Dooley, H., Flajnik, M.F., Wilson, I.A. Crystal structure of a shark single-domain antibody V region in complex with lysozyme. Science 305:1770, 2004.

Wang, X., Matteson, J., An, Y., Moyer, B., Yoo, J.S., Bannykh, S., Wilson, I.A., Riordan, J.R., Balch, W.E. COPII-dependent export of cystic fibrosis transmembrane conductance regulator from the ER uses a di-acidic exit code. J. Cell Biol. 167:65, 2004.

Xu, L., Li, C., Olson, A.J., Wilson, I.A. Crystal structure of avian aminoimidazole-4-carboxamide ribonucleotide transformylase in complex with a novel non-folate inhibitor identified by virtual ligand screening. J. Biol. Chem. 279:50555, 2004.

Xu, Q., Schwarzenbacher, R., McMullan, D., et al. Crystal structure of a formiminotetrahydrofolate cyclodeaminase (TM1560) from Thermotoga maritima at 2.80 Å resolution reveals a new fold. Proteins 58:976, 2005.

Xu, Q., Schwarzenbacher, R., McMullan, D., et al. Crystal structure of a ribose-5- phosphate isomerase RpiB (TM1080) from Thermotoga maritima at 1.90 Å resolution. Proteins 56:171, 2004.

Xu, Q., Schwarzenbacher, R., Page, R., et al. Crystal structure of an allantoicase (YIR029W) from Saccharomyces cerevisiae at 2.4 Å resolution. Proteins 56:619, 2004.

Zajonc, D.M., Crispin, M.D., Bowden, T.A., Young, D.C., Cheng, T.Y., Hu, J., Costello, C.E., Rudd, P.M., Dwek, R.A., Miller, M.J., Brenner, M.B., Moody, D.B., Wilson, I.A. Molecular mechanism of lipopeptide presentation by CD1a. Immunity 22:209, 2005.

Zhu, X., Tanaka, F., Hu, Y., Heine, A., Fuller, R., Zhong, G., Olson, A.J., Lerner, R.A., Barbas, C.F. III, Wilson, I.A. The origin of enantioselectivity in aldolase antibodies: crystal structure, site-directed mutagenesis, and computational analysis. J. Mol. Biol. 343:1269, 2004.