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Director,
X-Ray Crystallography (DOE)
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Professor,
Chemistry and Biochemistry,
Biochemistry
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Member,
ACCESS Program: Depts. of Biochemistry & Molecular Biology,
JCCC Cancer Cell Biology Program Area,
JCCC Basic Research,
NanoBiotechnology and Biomaterials,
Biochemistry & Molecular Biology (BMB) Graduate Program,
California NanoSystems Institute,
Molecular Biology Institute
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Staff,
Computer Core Facility (DOE),
Computer Core Facility (DOE)
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Researcher,
Biochemistry,
Biophysics and Structural Biology,
Proteomics and Bioinformatics
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Honors and Awards: |
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2004 UCLA, Hansen-Dow Award for Excellence in Teaching
1995 UCLA, McCoy Award for Excellence in Research
1993 Pittsburgh Diffraction Society, Sidhu Award
1991 - NSF, Presidential Young Investigator
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Certifications: |
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Professional Societies:
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American Chemical Society, American Chemical Society
American Crystallographic Association, American Crystallographic Association
2002 American Association for the Advancement of Science, Fellow
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Contact Information:
| Laboratory Address: |
Laboratory
Paul Boyer Hall 259
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| Work Address: |
Office
Paul Boyer Hall 255A
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Lab Number:
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1 (310) 825-8901
Laboratory
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Work Phone Number:
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1 (310) 206-4866
Office
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Research Interests:
Protein Structure; Supramolecular Protein Assemblies: Filaments,
Cages, and Layers; Protein Design; Protein Interaction
Networks; Bioinformatics and Comparative Genomics; Computational
Biology; Protein Crystallography; Symmetry.
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Technical Research Interest:
Professor Yeates and his research group work in the areas of
molecular, structural and computational biology. In structural
biology, the emphasis is on supramolecular protein assemblies,
such as self-assembling protein filaments, layers,
and cages. Supramolecular assemblies of interest include
both natural and designed structures. Natural assemblies of
particular interest include the actin filament and the bacterial
microcompartment, a shell-like structure that appears to
serve as a primitive organelle inside bacterial cells. The Yeates
group has recently determined the structures of the proteins
that make up a bacterial microcompartment, providing the
first detailed clues about how they operate. Strategies are also
being developed for designing novel proteins to assemble into
ordered structures on the mid-nanometer scale. In the area of
computational biology, the emphasis is on bioinformatics and
comparative genomics. Current work in comparative genomics
has led to the discovery of unusual microbes that are able to
stabilize their proteins at extreme temperatures through the
use of widespread disulfide bonding. Finally, in the area of
bioinformatics, new methods for deciphering protein function
and protein interactions have been developed by applying
ideas in symbolic logic to genomic data.
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Additional Information:
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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.
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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.
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.
Sawaya, M. R. Kudryashov, D. S. Pashkov, I. Adisetiyo, H. Reisler, E. Yeates, T. O. , Multiple crystal structures of actin dimers and their implications for interactions in the actin filament, Acta Crystallographica Section D-Biological Crystallography, 2008, 64 (number), 454-465.
Crowley, C. S. Sawaya, M. R. Bobik, T. A. Yeates, T. O. , Structure of the PduU shell protein from the Pdu microcompartment of Salmonella, Structure, 2008, 16 ( 9), 1324-1332.
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.
Yeates, T. O., Protein structure: evolutionary bridges to new folds, Curr Biol, 2007, 17 (2), R48-50.
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.
Sawaya MR, Cannon GC, Heinhorst S, Tanaka S, Williams EB, Yeates TO, Kerfeld CA , The Structure of beta-Carbonic Anhydrase from the Carboxysomal Shell Reveals a Distinct Subclass with One Active Site for the Price of Two, J Biol Chem, 2006, 281 (11), 7546-55.
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.
O'Connor BD, Yeates TO , GDAP: a web tool for genome-wide protein disulfide bond prediction, Nucleic Acids Res, 2004, 32 (Web Server issue), W360-4.
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.
Elam JS, Taylor AB, Strange R, Antonyuk S, Doucette PA, Rodriguez JA, Hasnain SS, Hayward LJ, Valentine JS, Yeates TO, Hart PJ, Amyloid-like filaments and water-filled nanotubes formed by SOD1 mutant proteins linked to familial ALS, Nat Struct Biol, 2003, 10 (6), 461-7.
Serag AA, Altenbach C, Gingery M, Hubbell WL, Yeates TO , Erratum: Arrangement of subunits and ordering of beta-strands in an amyloid sheet, Nat Struct Biol, 2003, 10 (1), 70.
Kerfeld CA, Sawaya MR, Bottin H, Tran KT, Sugiura M, Cascio D, Desbois A, Yeates TO, Kirilovsky D, Boussac A , 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 Physiol, 2003, 44 (7), 697-706.
Kerfeld CA, Yoshida S, Tran KT, Yeates TO, Cascio D, Bottin H, Berthomieu C, Sugiura M, Boussac A , The 1.6 A resolution structure of Fe-superoxide dismutase from the thermophilic cyanobacterium Thermosynechococcus elongatus, J Biol Inorg Chem, 2003, 8 (7), 707-14.
Kerfeld CA, Sawaya MR, Brahmandam V, Cascio D, Ho KK, Trevithick-Sutton CC, Krogmann DW, Yeates TO, The crystal structure of a cyanobacterial water-soluble carotenoid binding protein, Structure (Cambridge, Mass. : 2001) , 2003, 11 (1), 55-65.
Kerfeld, C. A. Sawaya, M. R. Brahmandam, V. Cascio, D. Ho, K. K. Trevithick-Sutton, C. C. Krogmann, D. W. Yeates, T. O., The crystal structure of a cyanobacterial water-soluble carotenoid binding protein, Structure, 2003, 11 (1), 55-65.
Chaudhuri, B. N. Sawaya, M. R. Kim, C. Y. Waldo, G. S. Park, M. S. Terwilliger, T. C. Yeates, T. O., The crystal structure of the first enzyme in the pantothenate biosynthetic pathway, ketopantoate hydroxymethyltransferase, from M tuberculosis, Structure, 2003, 11 (7), 753-64.
Rudolph MG, Kelker MS, Schneider TR, Yeates TO, Oseroff V, Heidary DK, Jennings PA, Wilson IA , Use of multiple anomalous dispersion to phase highly merohedrally twinned crystals of interleukin-1beta, Acta Crystallogr D Biol Crystallogr, 2003, 59 (Pt 2), 290-8.
Strong M, Graeber TG, Beeby M, Pellegrini M, Thompson MJ, Yeates TO, Eisenberg D , Visualization and interpretation of protein networks in Mycobacterium tuberculosis based on hierarchical clustering of genome-wide functional linkage maps, Nucleic Acids Res, 2003, 31 (24), 7099-109.
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.
Nitao LK, Yeates TO, Reisler E, Conformational dynamics of the SH1-SH2 helix in the transition states of myosin subfragment-1, Biophys J, 2002, 83 (5), 2733-41.
Ryttersgaard C, Griffith SC, Sawaya MR, MacLaren DC, Clarke S, Yeates TO , Crystal structure of human L-isoaspartyl methyltransferase, J Biol Chem, 2002, 277 (12), 10642-6.
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.
Thapar N, Griffith SC, Yeates TO, Clarke S , Protein repair methyltransferase from the hyperthermophilic archaeon Pyrococcus furiosus. Unusual methyl-accepting affinity for D-aspartyl and N-succinyl-containing peptides, J Biol Chem, 2002, 277 (2), 1058-65.
Larsen NA, Heine A, de Prada P, Redwan el R, Yeates TO, Landry DW, Wilson IA , Structure determination of a cocaine hydrolytic antibody from a pseudomerohedrally twinned crystal, Acta Crystallogr D Biol Crystallogr, 2002, 58 (Pt 12), 2055-9.
Kerfeld CA, Sawaya MR, Krogmann DW, Yeates TO , Structure of cytochrome c6 from Arthrospira maxima: an assembly of 24 subunits in a nearly symmetric shell, Acta Crystallogr D Biol Crystallogr, 2002, 58 (Pt 7), 1104-10.
Yeates TO , Structures of SET domain proteins: protein lysine methyltransferases make their mark, Cell, 2002, 111 (1), 5-7.
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