Research Topics
| TODD YEATESSummaryAffiliation: University of California Country: USA Publications
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Detail Information
Publications
Equations for determining tetartohedral twin fractionsTodd O Yeates
Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA
Acta Crystallogr D Biol Crystallogr 64:1158-64. 2008..Use of the equations is demonstrated with synthetic intensity data simulated according to given values of the twin fractions...- Racemic protein crystallographyTodd O Yeates
Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, USA
Annu Rev Biophys 41:41-61. 2012..Recent ideas and results in the area of racemic protein crystallography are reviewed... 
The genomics of disulfide bonding and protein stabilization in thermophilesMorgan Beeby
UCLA DOE Institute for Genomics and Proteomics, University of California, Los Angeles, California, USA
PLoS Biol 3:e309. 2005..The findings also motivate continued efforts to sequence genomes from divergent organisms...- A computational method to predict genetically encoded rare amino acids in proteinsBarnali N Chaudhuri
UCLA DOE Institute for Genomics and Proteomics and Department of Chemistry and Biochemistry, University of California, Los Angeles, USA
Genome Biol 6:R79. 2005..A survey across a set of microbial genomes identifies almost all the known cases as well as a number of novel candidate proteins... - Detecting coordinated regulation of multi-protein complexes using logic analysis of gene expressionEinat Sprinzak
UCLA DOE Institute for Genomics and Proteomics, University of California Los Angeles, Los Angeles, CA, USA
BMC Syst Biol 3:115. 2009..However, this type of coordinated regulation between whole complexes is difficult to detect by existing methods for analyzing mRNA co-expression. We propose a new methodology that is able to detect such higher order relationships... - Protein-based organelles in bacteria: carboxysomes and related microcompartmentsTodd O Yeates
UCLA Department of Chemistry and Biochemistry, USA
Nat Rev Microbiol 6:681-91. 2008..Although bacterial microcompartments were first observed more than 40 years ago, a detailed understanding of how they function is only now beginning to emerge... 
Biochemistry. Proteins in a small worldTodd O Yeates
Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA90024-1569, USA
Science 314:1882-3. 2006- Protein structure: evolutionary bridges to new foldsTodd O Yeates
UCLA Department of Chemistry and Biochemistry, 611 Charles Young Drive East, Los Angeles, California 90095 1569, USA
Curr Biol 17:R48-50. 2007..Recent work on cysteine-rich domains in Hydra proteins illuminates how evolutionary transitions between dramatically different structures might occur... - Self-assembly in the carboxysome: a viral capsid-like protein shell in bacterial cellsT O Yeates
UCLA Department of Chemistry and Biochemistry, University of California Los Angeles, 607 Charles E Young Drive East, Los Angeles, CA 90095 1569, USA
Biochem Soc Trans 35:508-11. 2007.... - Knotted and topologically complex proteins as models for studying folding and stabilityTodd O Yeates
UCLA Department of Chemistry and Biochemistry, Los Angeles, CA 90095 1569, USA
Curr Opin Chem Biol 11:595-603. 2007..Also, an approach is described for designing an expanded set of knotted proteins... - Biochemistry. How some pili pullTodd O Yeates
Department of Chemistry and Biochemistry and the Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA
Science 318:1558-9. 2007 - Bacterial microcompartment organelles: protein shell structure and evolutionTodd O Yeates
Department of Chemistry and Biochemistry, Institute of Genomics and Proteomics, University of California, Los Angeles, California 90095, USA
Annu Rev Biophys 39:185-205. 2010..Current structural, evolutionary, and mechanistic ideas are discussed, along with genomic studies for exploring the function and diversity of this family of bacterial organelles... - The protein shells of bacterial microcompartment organellesTodd O Yeates
UCLA Department of Chemistry and Biochemistry, Los Angeles, CA, USA
Curr Opin Struct Biol 21:223-31. 2011..The structural data emphasize a high level of mechanistic sophistication in the protein shell, and point the way for further studies on this fascinating but poorly appreciated class of subcellular structures... - Protein crystals and their evil twinsT O Yeates
UCLA Department of Chemistry and Biochemistry, DOE Laboratory of Structural Biology and Molecular Medicine, 405 Hilgard Avenue, Box 951569, Los Angeles CA 90095 1569, USA
Structure 7:R25-9. 1999..The recent literature and a database survey both serve as reminders to perform routine checks whenever twinning is a possibility... - Structures of SET domain proteins: protein lysine methyltransferases make their markTodd O Yeates
UCLA Molecular Biology Institute and Department of Chemistry and Biochemistry, UCLA DOE Center for Genomics and Proteomics, 611 Charles Young Dr East, Box 951570, Los Angeles, CA 90095, USA
Cell 111:5-7. 2002..The structures reveal novel folds for several new domains, including SET, and provide early insights into mechanisms of catalysis and molecular recognition in this family of enzymes... - The structure of beta-carbonic anhydrase from the carboxysomal shell reveals a distinct subclass with one active site for the price of twoMichael R Sawaya
Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA 90095 1570, USA
J Biol Chem 281:7546-55. 2006..Crystal packing analysis suggests that CsoSCA exists within the carboxysome shell either as a homodimer or as extended filaments... - Structure of the RuBisCO chaperone RbcX from Synechocystis sp. PCC6803Shiho Tanaka
UCLA Department of Chemistry and Biochemistry, 611 Charles Young Drive East, Los Angeles, CA 90095 1569, USA
Acta Crystallogr D Biol Crystallogr 63:1109-12. 2007..PCC6803, is reported, revealing an unusually long protruding C-terminal helix, as well as a bound polyethylene glycol molecule in the protein substrate-binding site... - Crystal structure of human L-isoaspartyl methyltransferaseCarsten Ryttersgaard
Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095 1569, USA
J Biol Chem 277:10642-6. 2002..Finally, the human structure reveals that the known genetic polymorphism at residue 119 (Val/Ile) maps to an exposed region away from the active site... - Protein structures forming the shell of primitive bacterial organellesCheryl A Kerfeld
Molecular Biology Institute, University of California, Los Angeles UCLA, Box 951570, Los Angeles, CA 90095, USA
Science 309:936-8. 2005..The structures suggest how molecular transport across the shell may be controlled and how structural variations might govern the assembly and architecture of these subcellular compartments... - Use of logic relationships to decipher protein network organizationPeter M Bowers
Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
Science 306:2246-9. 2004..These relationships illustrate the complexities that arise in cellular networks because of branching and alternate pathways, and they also facilitate assignment of cellular functions to uncharacterized proteins... - Arrangement of subunits and ordering of beta-strands in an amyloid sheetAhmed A Serag
Molecular Biology Institute and School of Medicine, University of California, Los Angeles, California 90095, USA
Nat Struct Biol 9:734-9. 2002.... - Designing supramolecular protein assembliesTodd O Yeates
UCLA Department of Chemistry and Biochemistry, 611Charles E Young Drive East, University of California, Los Angeles, 90095 1569, USA
Curr Opin Struct Biol 12:464-70. 2002..Recent advances include the design of novel proteins that assemble into filaments, symmetric cages and regular arrays... - Insights from multiple structures of the shell proteins from the beta-carboxysomeShiho Tanaka
Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095 1569, USA
Protein Sci 18:108-20. 2009.... - Structure and mechanisms of a protein-based organelle in Escherichia coliShiho Tanaka
Department of Chemistry and Biochemistry, University of California Los Angeles, 611 Charles Young Drive East, Los Angeles, CA 90095, USA
Science 327:81-4. 2010..Together these structures give mechanistic insight into bacterial microcompartments... - The crystal structure of a cyanobacterial water-soluble carotenoid binding proteinCheryl A Kerfeld
Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
Structure 11:55-65. 2003..The structure reveals several possible ways in which the protein environment influences the spectral properties of the pigment and provides insight into how the OCP carries out its putative functions in photoprotection... - Structure of cytochrome c6 from Arthrospira maxima: an assembly of 24 subunits in a nearly symmetric shellCheryl A Kerfeld
Molecular Biology Institute, University of California, Los Angeles, Box 951570, 90095 1570, USA
Acta Crystallogr D Biol Crystallogr 58:1104-10. 2002..The cytochrome c(6) complex described here is the largest assembly of cytochrome c(6) molecules observed thus far... - Prolinks: a database of protein functional linkages derived from coevolutionPeter M Bowers
Institute for Genomics and Proteomics, University of California, Los Angeles, CA 90095, USA
Genome Biol 5:R35. 2004..The Prolinks database and the Proteome Navigator tool are available for use online at http://dip.doe-mbi.ucla.edu/pronav... - The 1.6 A resolution structure of Fe-superoxide dismutase from the thermophilic cyanobacterium Thermosynechococcus elongatusCheryl A Kerfeld
Molecular Biology Institute, UCLA, Box 951570, Los Angeles, CA 90095 1570, USA
J Biol Inorg Chem 8:707-14. 2003..elongatus FeSOD EPR spectra at pH 5.1, 7.5 and 10.0 are similar. This indicates that no change in the geometry of the Fe(III) site occurs over a wide range of pH. This is in contrast to the other FeSODs described in the literature... - Structural and EPR characterization of the soluble form of cytochrome c-550 and of the psbV2 gene product from the cyanobacterium Thermosynechococcus elongatusCheryl A Kerfeld
Molecular Biology Institute, UCLA, Box 951570, Los Angeles, CA 90095 1570, USA
Plant Cell Physiol 44:697-706. 2003..The UV-visible, EPR and Raman spectra are reported. From the spectroscopic data and from a theoretical structural model based on the cytochrome c-550 structure it is proposed that the 6th ligand of the heme-iron is the Tyr86... - Crystal structure of the apo forms of psi 55 tRNA pseudouridine synthase from Mycobacterium tuberculosis: a hinge at the base of the catalytic cleftBarnali N Chaudhuri
UCLA Department of Energy Institute for Genomics and Proteomics, Los Angeles, California 90095, USA
J Biol Chem 279:24585-91. 2004..Our structural data furthers the previously proposed mechanism of tRNA recognition. The present crystal structure emphasizes the significant role that protein dynamics must play in tRNA recognition, base flipping, and modification... - Visualization and interpretation of protein networks in Mycobacterium tuberculosis based on hierarchical clustering of genome-wide functional linkage mapsMichael Strong
Howard Hughes Medical Institute, University of California at Los Angeles, Box 951570, Los Angeles, CA 90095-1570, USA
Nucleic Acids Res 31:7099-109. 2003.... - The crystal structure of a cross-linked actin dimer suggests a detailed molecular interface in F-actinDmitry S Kudryashov
Department of Chemistry and Biochemistry and Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA
Proc Natl Acad Sci U S A 102:13105-10. 2005..A plausible model of F-actin can be constructed by reintroducing the known filament twist, without disturbing significantly the interface observed in the actin dimer crystal... - Atomic-level models of the bacterial carboxysome shellShiho Tanaka
Department of Chemistry and Biochemistry, University of California at Los Angeles UCLA, Los Angeles, CA 90095, USA
Science 319:1083-6. 2008..Combining these pentamers with the hexamers previously elucidated gives two plausible, preliminary atomic models for the carboxysome shell... - Structures and functional implications of an AMP-binding cystathionine beta-synthase domain protein from a hyperthermophilic archaeonNeil P King
Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
J Mol Biol 380:181-92. 2008..In addition, this work extends previous studies that have suggested that, in certain thermophilic microbes, disulfide bonds play a key role in stabilizing intracellular proteins and protein-protein complexes... - Structure of the PduU shell protein from the Pdu microcompartment of SalmonellaChristopher S Crowley
University of California Los Angeles Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA 90095, USA
Structure 16:1324-32. 2008..In view of the hypothesis that microcompartment metabolites diffuse across the outer shell through these pores, the unique structure of PduU suggests the possibility of a special functional role... - Exploiting genomic patterns to discover new supramolecular protein assembliesMorgan Beeby
UCLA DOE Institute for Genomics and Proteomics, University of California Los Angeles, Los Angeles, California 90095, USA
Protein Sci 18:69-79. 2009..We conclude that cotranscribed paralogs are a common feature of diverse supramolecular assemblies, and a useful genomic signature for discovering new kinds of large protein assemblies from genomic data... - Utilizing logical relationships in genomic data to decipher cellular processesPeter M Bowers
Howard Hughes Medical Institute, University of California, Los Angeles, CA 90095, USA
FEBS J 272:5110-8. 2005.... - Directed evolution and structural characterization of a simvastatin synthaseXue Gao
Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA 90095, USA
Chem Biol 16:1064-74. 2009..Comparisons between the structures reveal that beneficial mutations stabilize the structure of G5 in a more compact conformation that is favorable for catalysis... - An approach to crystallizing proteins by synthetic symmetrizationD Rey Banatao
California NanoSystems Institute, University of California, Boyer Hall 259, P.O. Box 951570, Los Angeles, CA 90095-1570, USA
Proc Natl Acad Sci U S A 103:16230-5. 2006..Six new crystal forms have been characterized. The results suggest that synthetic symmetrization may be a useful approach for enlarging the search space for crystallizing proteins... - Discovery of a thermophilic protein complex stabilized by topologically interlinked chainsDaniel R Boutz
Molecular Biology Institute, University of California at Los Angeles, Los Angeles, CA 90095, USA
J Mol Biol 368:1332-44. 2007..This unusual feature emphasizes the variety and sophistication of the molecular mechanisms that can be achieved by evolution... - Conformational dynamics of the SH1-SH2 helix in the transition states of myosin subfragment-1Lisa K Nitao
Department of Chemistry and Biochemistry, Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA
Biophys J 83:2733-41. 2002..Thus, the SH1-SH2 helix appears to be destabilized in the post-hydrolysis state... - A framework for describing topological frustration in models of protein foldingTodd S Norcross
UCLA Department of Chemistry and Biochemistry, UCLA DOE Institute for Genomics and Proteomics, Los Angeles, CA 90095-1569, USA
J Mol Biol 362:605-21. 2006..The computational analyses lead to testable models for protein folding... - Conformational change and assembly through edge beta strands in transthyretin and other amyloid proteinsJanel Laidman
Department of Chemistry and Biochemistry, University of California-Los Angeles (UCLA, Post Office Box 951569, Los Angeles, CA 90095-1569, USA
Acc Chem Res 39:576-83. 2006..The models and principles emerging from studies on transthyretin lead to connections to other amyloid systems... - GDAP: a web tool for genome-wide protein disulfide bond predictionTodd O Yeates
UCLA-DOE Institute for Genomics and Proteomics, UCLA Molecular Biology Institute and UCLA Department of Chemistry and Biochemistry, Los Angeles, USA
Nucleic Acids Res 32:W360-4. 2004..The prediction server can be accessed at http://www.doe-mbi.ucla.edu/Services/GDAP... - Rational improvement of simvastatin synthase solubility in Escherichia coli leads to higher whole-cell biocatalytic activityXinkai Xie
Department of Chemical and Biomolecular Engineering, University of California, 5531 Boelter Hall, 420 Westwood Plaza, UCLA, Los Angeles, California 90095, USA
Biotechnol Bioeng 102:20-8. 2009..The high efficiency of the improved whole-cell platform renders the biocatalytic synthesis of SS an attractive substitute over the existing semisynthetic routes... - The crystal structure of the first enzyme in the pantothenate biosynthetic pathway, ketopantoate hydroxymethyltransferase, from M tuberculosisBarnali N Chaudhuri
UCLA Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
Structure 11:753-64. 2003..The apparent conservation of certain detailed structural characteristics suggests that KPHMT is distantly related by divergent evolution to enzymes in unrelated pathways, including isocitrate lyase and phosphoenolpyruvate mutase... - Identification of rare slipknots in proteins and their implications for stability and foldingNeil P King
Department of Chemistry and Biochemistry, University of California Los Angeles, 611 Charles Young Drive East, Los Angeles, CA 90095 1569, USA
J Mol Biol 373:153-66. 2007..The trends and conserved features observed in these proteins provide new insights into mechanisms of protein folding and stability... - Analysis of lattice-translocation disorder in the layered hexagonal structure of carboxysome shell protein CsoS1CYingssu Tsai
Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA, USA
Acta Crystallogr D Biol Crystallogr 65:980-8. 2009..The lattice-translocation treatment described here may be useful in analyzing other cases of disorder in which layers or groups of molecules are shifted in multiple symmetry-related directions... - Multiple crystal structures of actin dimers and their implications for interactions in the actin filamentMichael R Sawaya
UCLA Department of Chemistry and Biochemistry, Los Angeles, CA 90095 1569, USA
Acta Crystallogr D Biol Crystallogr 64:454-65. 2008..Highly conserved atomic interactions involving residues 199-205 and 287-291 are highlighted... - Connecting actin monomers by iso-peptide bond is a toxicity mechanism of the Vibrio cholerae MARTX toxinDmitri S Kudryashov
Department of Chemistry and Biochemistry and Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA
Proc Natl Acad Sci U S A 105:18537-42. 2008.... - Structural analysis of CsoS1A and the protein shell of the Halothiobacillus neapolitanus carboxysomeYingssu Tsai
Molecular Biology Institute, University of California Los Angeles, Los Angeles, California, United States of America
PLoS Biol 5:e144. 2007..Insights into carboxysome function are provided by comparisons of the carboxysome shell to viral capsids, and a comparison of its pores to the pores of transmembrane protein channels... - Genomic evidence that the intracellular proteins of archaeal microbes contain disulfide bondsParag Mallick
Department of Chemistry and Biochemistry and Department of Energy Center for Genomics and Proteomics, Molecular Biology Institute, and Howard Hughes Medical Institute, University of California, Los Angeles, CA 90095-1569, USA
Proc Natl Acad Sci U S A 99:9679-84. 2002..These unexpected results illustrate the wealth of biochemical insights available from the growing reservoir of genomic data... - Protein repair methyltransferase from the hyperthermophilic archaeon Pyrococcus furiosus. Unusual methyl-accepting affinity for D-aspartyl and N-succinyl-containing peptidesNitika Thapar
Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095-1569, USA
J Biol Chem 277:1058-65. 2002.... - Generation of oxide nanopatterns by combining self-assembly of S-layer proteins and area-selective atomic layer depositionJiurong Liu
Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, California 90095, USA
J Am Chem Soc 130:16908-13. 2008..These nanopatterns of high-k materials are expected to facilitate further downscaling of logic and memory nanoelectronic devices... - Use of multiple anomalous dispersion to phase highly merohedrally twinned crystals of interleukin-1betaMarkus G Rudolph
Department of Molecular Biology and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
Acta Crystallogr D Biol Crystallogr 59:290-8. 2003..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... - Amyloid-like filaments and water-filled nanotubes formed by SOD1 mutant proteins linked to familial ALSJennifer Stine Elam
Department of Biochemistry and the Center for Biomolecular Structure Analysis, The University of Texas, Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, Texas 78229 3900, USA
Nat Struct Biol 10:461-7. 2003..Loss of this protection through conformational rearrangement in the metal-deficient enzyme could be a toxic property common to mutants of SOD1 linked to FALS... - Structure determination of a cocaine hydrolytic antibody from a pseudomerohedrally twinned crystalNicholas A Larsen
The Department of Molecular Biology and Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California, USA
Acta Crystallogr D Biol Crystallogr 58:2055-9. 2002..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...
Research Grants
- Elucidating Novel Topological Features in Protein StructuresTodd O Yeates; Fiscal Year: 2010..The proteins to be studied here possess unique features that make them valuable in efforts to achieve a fundamental understanding of protein structure and stability. ..
- Elucidating Novel Topological Features in Protein StructuresTODD YEATES; Fiscal Year: 2009..The proteins to be studied here possess unique features that make them valuable in efforts to achieve a fundamental understanding of protein structure and stability. ..