Todd O. Yeates, Ph.D.

Laboratory Address:
Paul Boyer Hall 259
Mail Code: 157005
Los Angeles, CA 90095

Work Address:
Paul Boyer Hall 255A
Mail Code: 157005
Los Angeles, CA 90095

Affiliations
Affiliations
Director, X-Ray Crystallography (DOE)
Professor, Chemistry and Biochemistry, Biochemistry, Molecular Biology
Member, Basic/Translational Research, Jonsson Comprehensive Cancer Center, Biochemistry, Biophysics & Structural Biology GPB Home Area, Bioinformatics GPB Home Area, California NanoSystems Institute, Graduate Program in Biochemistry, Molecular and Structural Biology, JCCC Cancer and Stem Cell Biology Program Area, Molecular Biology Institute
Staff, Computer Core Facility (DOE), Computer Core Facility (DOE)
Researcher, Biochemistry, Biophysics and Structural Biology, Proteomics and Bioinformatics
Research Interests
Research in the Yeates group is in the broad areas of computational and structural biology, and comparative genomics and bioinformatics. In the area of structural biology, our emphasis is on supra-molecular protein assemblies. Much of our recent work has focused on bacterial microcompartments -- extraordinary protein assemblies comprised of thousands of subunits reminiscent of viral capsids. They encapsulate a series of enzymes within a protein shell, which controls the transport of substrates and products into and out of the microcompartment interior. They serve as primitive metabolic organelles in many bacteria. Our structural studies on these systems provided the first three-dimensional views of the shell proteins, and have generated long-needed mechanistic hypotheses for how bacterial microcompartments function. In our synthetic-biology work, we are focusing on synthetically designed protein assemblies as vehicles for understanding the evolution of natural assemblies and as potentially valuable materials for nanotechnology applications. We have developed general strategies for designing proteins that self-assemble into large, highly regular architectures such as molecular cages and extended two and three-dimensional arrays. The successful results of a number of very recent experiments emphasize the exciting long-term potential of these strategies in the nanotechnology field.
Biography

After earning his Bachelor's degree at UCLA, Yeates stayed on to do his PhD research under the direction of Prof. Douglas Rees. There he helped determine the crystal structure of the bacterial photosynthetic reaction center as part of a team racing to determine the first crystal structures of membrane proteins. He then moved to The Scripps Research Institute to do his postdoctoral research on the structure of poliovirus with Prof. James Hogle. Yeates returned to UCLA in 1990 to join the Faculty in the Department of Chemistry and Biochemistry. His interdisciplinary research, combining molecular biology with computing and mathematics, has focused on macromolecular structure and computational genomics. His research findings include: an explanation for why proteins crystallize in certain favored arrangements, the discovery of thermophilic microbes rich in intracellular disulfide bonds, co-development of phylogenetic profile methods in genomics, development of designed protein cages or 'nanohedra', the discovery of novel topological features such as slipknots in thermostable proteins, and the elucidation of the structures of the carboxysome shell proteins. Yeates is a member of the Molecular Biology Institute, the California Nanosystems Institute, the Institute of Genomics and Proteomics, and a Fellow of the American Association for the Advancement of Science. He has published approximately 100 research papers.

Publications
Tanaka Shiho, Sawaya Michael R, Yeates Todd O Structure and mechanisms of a protein-based organelle in Escherichia coli. Science. 2010; 327(5961): 81-4.
Tanaka, S. Sawaya, M. R. Phillips, M. Yeates, T. O. Insights from multiple structures of the shell proteins from the beta-carboxysome. Protein Sci. 2009; 18(1): 108-20.
Dryden Kelly A, Crowley Christopher S, Tanaka Shiho, Yeates Todd O, Yeager Mark Two-dimensional crystals of carboxysome shell proteins recapitulate the hexagonal packing of three-dimensional crystals. Protein science : a publication of the Protein Society. 2009; 18(12): 2629-35.
Tanaka, S. Kerfeld, C. A. Sawaya, M. R. Cai, F. Heinhorst, S. Cannon, G. C. Yeates, T. O. Atomic-level models of the bacterial carboxysome shell. Science. 2008; 319(5866): 1083-1086.
Cheng Shouqiang, Liu Yu, Crowley Christopher S, Yeates Todd O, Bobik Thomas A Bacterial microcompartments: their properties and paradoxes. BioEssays : news and reviews in molecular, cellular and developmental biology. 2008; 30(11-12): 1084-95.
Yeates Todd O, Kerfeld Cheryl A, Heinhorst Sabine, Cannon Gordon C, Shively Jessup M Protein-based organelles in bacteria: carboxysomes and related microcompartments. Nature reviews. Microbiology. 2008; 6(9): 681-91.
King, N. P. Lee, T. M. Sawaya, M. R. Cascio, D. Yeates, T. O. Structures and functional implications of an AMP-binding cystathionine beta-synthase domain protein from a hyperthermophilic archaeon. Journal of Molecular Biology. 2008; 380(1): 181-192.
Boutz, D. R. Cascio, D. Whitelegge, J. Perry, L. J. Yeates, T. O. Discovery of a thermophilic protein complex stabilized by topologically interlinked chains. J Mol Biol. 2007; 368(5): 1332-44.
Norcross, T. S. Yeates, T. O. A framework for describing topological frustration in models of protein folding. J Mol Biol. 2006; 362(3): 605-21.
Banatao, D. R. Cascio, D. Crowley, C. S. Fleissner, M. R. Tienson, H. L. Yeates, T. O. An approach to crystallizing proteins by synthetic symmetrization. Proc Natl Acad Sci U S A. 2006; 103(44): 16230-5.
Yeates, T. O. Beeby, M. Biochemistry. Proteins in a small world. Science. 2006; 314(5807): 1882-3.
Laidman, J. Forse, G. J. Yeates, T. O. Conformational change and assembly through edge beta strands in transthyretin and other amyloid proteins. Acc Chem Res. 2006; 39(9): 576-83.
Chaudhuri BN, Yeates TO A computational method to predict genetically encoded rare amino acids in proteins. Genome Biol. 2005; 6(9): R79.
Kerfeld, C. A. Sawaya, M. R. Tanaka, S. Nguyen, C. V. Phillips, M. Beeby, M. Yeates, T. O. Protein structures forming the shell of primitive bacterial organelles. Science. 2005; 309(5736): 936-8.
Kudryashov DS, Sawaya MR, Adisetiyo H, Norcross T, Hegyi G, Reisler E, Yeates TO The crystal structure of a cross-linked actin dimer suggests a detailed molecular interface in F-actin. Proc Natl Acad Sci U S A. 2005; 102(37): 13105-10.
Beeby M, O'Connor BD, Ryttersgaard C, Boutz DR, Perry LJ, Yeates TO The genomics of disulfide bonding and protein stabilization in thermophiles. PLoS Biol. 2005; 3(9): e309.
Bowers PM, O'Connor BD, Cokus SJ, Sprinzak E, Yeates TO, Eisenberg D Utilizing logical relationships in genomic data to decipher cellular processes. Febs J. 2005; 272(20): 5110-8.
Chaudhuri BN, Chan S, Perry LJ, Yeates TO Crystal structure of the apo forms of psi 55 tRNA pseudouridine synthase from Mycobacterium tuberculosis: a hinge at the base of the catalytic cleft. J Biol Chem. 2004; 279(23): 24585-91.
Bowers PM, Pellegrini M, Thompson MJ, Fierro J, Yeates TO, Eisenberg D Prolinks: a database of protein functional linkages derived from coevolution. Genome Biol. 2004; 5(5): R35.
Bowers PM, Cokus SJ, Eisenberg D, Yeates TO Use of logic relationships to decipher protein network organization. Science. 2004; 306(5705): 2246-9.
Padilla JE, Yeates TO A statistic for local intensity differences: robustness to anisotropy and pseudo-centering and utility for detecting twinning. Acta crystallographica. Section D, Biological crystallography. . 2003; 59(Pt 7): 1124-30.
Serag AA, Altenbach C, Gingery M, Hubbell WL, Yeates TO Arrangement of subunits and ordering of beta-strands in an amyloid sheet. Nat Struct Biol. 2002; 9(10): 734-9.
Yeates TO, Padilla JE Designing supramolecular protein assemblies. Curr Opin Struct Biol. 2002; 12(4): 464-70.
Mallick P, Boutz DR, Eisenberg D, Yeates TO Genomic evidence that the intracellular proteins of archaeal microbes contain disulfide bonds. Proc Natl Acad Sci U S A. 2002; 99(15): 9679-84.
Yen-Ting Lai, Duilio Cascio, Todd O. Yeates Structure of a 16-nm Cage Designed by Using Protein Oligomers. Science. 2012; 336: 1129.
Neil P. King, William Sheffler, Michael R. Sawaya, Breanna S. Vollmar, John P. Sumida, Ingemar André, Tamir Gonen, Todd O. Yeates, David Baker Computational Design of Self-Assembling Protein Nanomaterials with Atomic Level Accuracy. Science. 2012; 336: 1171-1174.
Lai Yen-Ting, Tsai Kuang-Lei, Sawaya Michael R, Asturias Francisco J, Yeates Todd O Structure and flexibility of nanoscale protein cages designed by symmetric self-assembly. Journal of the American Chemical Society. 2013; 135(20): 7738-43.
Thapar Nitika, Griffith Scott C, Yeates Todd O, Clarke Steven Protein repair methyltransferase from the hyperthermophilic archaeon Pyrococcus furiosus. Unusual methyl-accepting affinity for D-aspartyl and N-succinyl-containing peptides. The Journal of biological chemistry. 2002; 277(2): 1058-65.
Forse G Jason, Ram Nina, Banatao D Rey, Cascio Duilio, Sawaya Michael R, Klock Heath E, Lesley Scott A, Yeates Todd O Synthetic symmetrization in the crystallization and structure determination of CelA from Thermotoga maritima. Protein science : a publication of the Protein Society. 2011; 20(1): 168-78.
King Neil P, Jacobitz Alex W, Sawaya Michael R, Goldschmidt Lukasz, Yeates Todd O Structure and folding of a designed knotted protein. Proceedings of the National Academy of Sciences of the United States of America. 2010; 107(48): 20732-7.
Crowley Christopher S, Cascio Duilio, Sawaya Michael R, Kopstein Jeffery S, Bobik Thomas A, Yeates Todd O Structural insight into the mechanisms of transport across the Salmonella enterica Pdu microcompartment shell. The Journal of biological chemistry. 2010; 285(48): 37838-46.
Pentelute Brad L, Mandal Kalyaneswar, Gates Zachary P, Sawaya Michael R, Yeates Todd O, Kent Stephen B H Total chemical synthesis and X-ray structure of kaliotoxin by racemic protein crystallography. Chemical communications (Cambridge, England). 2010; 46(43): 8174-6.
Kerfeld Cheryl A, Yoshida Stephanie, Tran Kimberlee T, Yeates Todd O, Cascio Duilio, Bottin Hervé, Berthomieu Catherine, Sugiura Miwa, Boussac Alain The 1.6 A resolution structure of Fe-superoxide dismutase from the thermophilic cyanobacterium Thermosynechococcus elongatus. Journal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry. 2003; 8(7): 707-14.
Lai Yen-Ting, King Neil P, Yeates Todd O Principles for designing ordered protein assemblies. Trends in cell biology. 2012; 22(12): 653-61.
Kerfeld Cheryl A, Sawaya Michael R, Bottin Hervé, Tran Kimberlee T, Sugiura Miwa, Cascio Duilio, Desbois Alain, Yeates Todd O, Kirilovsky Diana, Boussac Alain Structural and EPR characterization of the soluble form of cytochrome c-550 and of the psbV2 gene product from the cyanobacterium Thermosynechococcus elongatus. Plant & cell physiology. 2003; 44(7): 697-706.
Padilla Jennifer E, Yeates Todd O A statistic for local intensity differences: robustness to anisotropy and pseudo-centering and utility for detecting twinning. Acta crystallographica. Section D, Biological crystallography. 2003; 59(Pt 7): 1124-30.
King Neil P, Sheffler William, Sawaya Michael R, Vollmar Breanna S, Sumida John P, André Ingemar, Gonen Tamir, Yeates Todd O, Baker David Computational design of self-assembling protein nanomaterials with atomic level accuracy. Science (New York, N.Y.). 2012; 336(6085): 1171-4.
Tanaka Shiho, Sawaya Michael R, Phillips Martin, Yeates Todd O Insights from multiple structures of the shell proteins from the beta-carboxysome. Protein science : a publication of the Protein Society. 2009; 18(1): 108-20.
Chaudhuri Barnali N, Sawaya Michael R, Kim Chang Yub, Waldo Geoff S, Park Min S, Terwilliger Thomas C, Yeates Todd O The crystal structure of the first enzyme in the pantothenate biosynthetic pathway, ketopantoate hydroxymethyltransferase, from M tuberculosis. Structure (London, England : 1993). 2003; 11(7): 753-64.
Crowley Christopher S, Sawaya Michael R, Bobik Thomas A, Yeates Todd O Structure of the PduU shell protein from the Pdu microcompartment of Salmonella. Structure (London, England : 1993). 2008; 16(9): 1324-32.
Lai Yen-Ting, Cascio Duilio, Yeates Todd O Structure of a 16-nm cage designed by using protein oligomers. Science (New York, N.Y.). 2012; 336(6085): 1129.
King Neil P, Lee Toni M, Sawaya Michael R, Cascio Duilio, Yeates Todd O Structures and functional implications of an AMP-binding cystathionine beta-synthase domain protein from a hyperthermophilic archaeon. Journal of molecular biology. 2008; 380(1): 181-92.
Tanaka Shiho, Kerfeld Cheryl A, Sawaya Michael R, Cai Fei, Heinhorst Sabine, Cannon Gordon C, Yeates Todd O Atomic-level models of the bacterial carboxysome shell. Science (New York, N.Y.). 2008; 319(5866): 1083-6.
Sawaya Michael R, Pentelute Brad L, Kent Stephen B H, Yeates Todd O Single-wavelength phasing strategy for quasi-racemic protein crystal diffraction data. Acta crystallographica. Section D, Biological crystallography. 2012; 68(Pt 1): 62-8.
Kerfeld Cheryl A, Sawaya Michael R, Brahmandam Vishnu, Cascio Duilio, Ho Kwok Ki, Trevithick-Sutton Colleen C, Krogmann David W, Yeates Todd O The crystal structure of a cyanobacterial water-soluble carotenoid binding protein. Structure (London, England : 1993). 2003; 11(1): 55-65.
Boutz Daniel R, Cascio Duilio, Whitelegge Julian, Perry L Jeanne, Yeates Todd O Discovery of a thermophilic protein complex stabilized by topologically interlinked chains. Journal of molecular biology. 2007; 368(5): 1332-44.
Yeates Todd O Protein structure: evolutionary bridges to new folds. Current biology : CB. 2007; 17(2): R48-50.
Pickens Lauren B, Sawaya Michael R, Rasool Huma, Pashkov Inna, Yeates Todd O, Tang Yi Structural and biochemical characterization of the salicylyl-acyltranferase SsfX3 from a tetracycline biosynthetic pathway. The Journal of biological chemistry. 2011; 286(48): 41539-51.
Nitao Lisa K, Yeates Todd O, Reisler Emil Conformational dynamics of the SH1-SH2 helix in the transition states of myosin subfragment-1. Biophysical journal. 2002; 83(5): 2733-41.
Yeates Todd O, Beeby Morgan Biochemistry. Proteins in a small world. Science (New York, N.Y.). 2006; 314(5807): 1882-3.
Laganowsky Arthur, Zhao Minglei, Soriaga Angela B, Sawaya Michael R, Cascio Duilio, Yeates Todd O An approach to crystallizing proteins by metal-mediated synthetic symmetrization. Protein science : a publication of the Protein Society. 2011; 20(11): 1876-90.
Yeates Todd O Structures of SET domain proteins: protein lysine methyltransferases make their mark. Cell. 2002; 111(1): 5-7.
Norcross Todd S, Yeates Todd O A framework for describing topological frustration in models of protein folding. Journal of molecular biology. 2006; 362(3): 605-21.
Banatao D Rey, Cascio Duilio, Crowley Christopher S, Fleissner Mark R, Tienson Heather L, Yeates Todd O An approach to crystallizing proteins by synthetic symmetrization. Proceedings of the National Academy of Sciences of the United States of America. 2006; 103(44): 16230-5.
Laidman Janel, Forse G Jason, Yeates Todd O Conformational change and assembly through edge beta strands in transthyretin and other amyloid proteins. Accounts of chemical research. 2006; 39(9): 576-83.
Yeates Todd O, Padilla Jennifer E Designing supramolecular protein assemblies. Current opinion in structural biology. 2002; 12(4): 464-70.
Sawaya Michael R, Cannon Gordon C, Heinhorst Sabine, Tanaka Shiho, Williams Eric B, Yeates Todd O, Kerfeld Cheryl A The structure of beta-carbonic anhydrase from the carboxysomal shell reveals a distinct subclass with one active site for the price of two. The Journal of biological chemistry. 2006; 281(11): 7546-55.
Kerfeld Cheryl A, Sawaya Michael R, Krogmann David W, Yeates Todd O Structure of cytochrome c6 from Arthrospira maxima: an assembly of 24 subunits in a nearly symmetric shell. Acta crystallographica. Section D, Biological crystallography. 2002; 58(Pt 7): 1104-10.
Kerfeld Cheryl A, Sawaya Michael R, Tanaka Shiho, Nguyen Chau V, Phillips Martin, Beeby Morgan, Yeates Todd O Protein structures forming the shell of primitive bacterial organelles. Science (New York, N.Y.). 2005; 309(5736): 936-8.
Ryttersgaard Carsten, Griffith Scott C, Sawaya Michael R, MacLaren Duncan C, Clarke Steven, Yeates Todd O Crystal structure of human L-isoaspartyl methyltransferase. The Journal of biological chemistry. 2002; 277(12): 10642-6.
Bowers Peter M, Cokus Shawn J, Eisenberg David, Yeates Todd O Use of logic relationships to decipher protein network organization. Science (New York, N.Y.). 2004; 306(5705): 2246-9.