Yeates, Todd O.


WebsiteHome URL
Division
Biochemistry
Title
Faculty
Professor
Specialties
Biochemistry
Biophysics
Structural and Computational Biology
Bioenergy and the Environment
Theory
Member
California NanoSystems Institute, JCCC Cancer and Stem Cell Biology Program Area

Contact Information

Email
Office
Boyer Hall 255A
(310) 206-4866
Lab
Boyer Hall 259
(310) 825-8901

Short Biography

Professor Yeates received his BS in 1983 and his PhD in 1988, both at UCLA. After working as a postdoctoral fellow at The Scripps Research Institute in La Jolla, he returned to UCLA as a member of the faulty in 1990

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.

Research Interest

Molecular, Structural and Computational biology

Molecular Structure

 

Our research covers the areas of molecular, structural and computational biology.

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.

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Honors & Awards

  • UCLA Hansen-Dow Award for Excellence in Teaching
  • UCLA McCoy Award for Excellence in Research
  • Pittsburgh Diffraction Society Sidhu Award
  • NSF Presidential Young Investigator
  • American Chemical Society
  • American Crystallographic Association
  • American Association for the Advancement of Science Fellow

Publications

2012

  • Yeates TO, Kent SB. (2012). Racemic protein crystallography. Annu Rev Biophys. 2012. 41:41-61. [Abstract]
  • Sawaya MR, Pentelute BL, Kent SB, Yeates TO. (2012). Single-wavelength phasing strategy for quasi-racemic protein crystal diffraction data. Acta Crystallogr. D Biol. Crystallogr.. Jan 2012. 68(Pt 1):62-8. [Abstract]
  • Johnson E, Nguyen PT, Yeates TO, Rees DC. (2012). Inward facing conformations of the MetNI methionine ABC transporter: Implications for the mechanism of transinhibition. Protein Sci.. Jan 2012. 21(1):84-96. [Abstract]
  • Jones EY, Yeates TO. (2012). Structure and function in complex macromolecular assemblies: some evolutionary themes. Curr. Opin. Struct. Biol.. Apr 2012. 22(2):197-9. [Abstract]
  • King NP, Sheffler W, Sawaya MR, Vollmar BS, Sumida JP, André I, Gonen T, Yeates TO, Baker D. (2012). Computational design of self-assembling protein nanomaterials with atomic level accuracy. Science. Jun 2012. 336(6085):1171-4. [Abstract]
  • Lai YT, Cascio D, Yeates TO. (2012). Structure of a 16-nm cage designed by using protein oligomers. Science. Jun 2012. 336(6085):1129. [Abstract]

2011

  • Tsai SJ, Yeates TO. (2011). Bacterial microcompartments insights into the structure, mechanism, and engineering applications. Prog Mol Biol Transl Sci. 2011. 103:1-20. [Abstract]
  • Jorda J, Yeates TO. (2011). Widespread disulfide bonding in proteins from thermophilic archaea. Archaea. 2011. 2011:409156. [Abstract]
  • Forse GJ, Ram N, Banatao DR, Cascio D, Sawaya MR, Klock HE, Lesley SA, Yeates TO. (2011). Synthetic symmetrization in the crystallization and structure determination of CelA from Thermotoga maritima. Protein Sci.. Jan 2011. 20(1):168-78. [Abstract]
  • Yeates TO, Thompson MC, Bobik TA. (2011). The protein shells of bacterial microcompartment organelles. Curr. Opin. Struct. Biol.. Apr 2011. 21(2):223-31. [Abstract]
  • Sayre TC, Lee TM, King NP, Yeates TO. (2011). Protein stabilization in a highly knotted protein polymer. Protein Eng. Des. Sel.. Aug 2011. 24(8):627-30. [Abstract]
  • Yeates TO. (2011). Nanobiotechnology: protein arrays made to order. Nat Nanotechnol. Sep 2011. 6(9):541-2. [Abstract]
  • Laganowsky A, Zhao M, Soriaga AB, Sawaya MR, Cascio D, Yeates TO. (2011). An approach to crystallizing proteins by metal-mediated synthetic symmetrization. Protein Sci.. Nov 2011. 20(11):1876-90. [Abstract]
  • Pickens LB, Sawaya MR, Rasool H, Pashkov I, Yeates TO, Tang Y. (2011). Structural and biochemical characterization of the salicylyl-acyltranferase SsfX3 from a tetracycline biosynthetic pathway. J. Biol. Chem.. Dec 2011. 286(48):41539-51. [Abstract]

2010

  • Yeates TO, Crowley CS, Tanaka S. (2010). Bacterial microcompartment organelles: protein shell structure and evolution. Annu Rev Biophys. 2010. 39:185-205. [Abstract]
  • Tanaka S, Sawaya MR, Yeates TO. (2010). Structure and mechanisms of a protein-based organelle in Escherichia coli. Science. Jan 2010. 327(5961):81-4. [Abstract]
  • Fan C, Cheng S, Liu Y, Escobar CM, Crowley CS, Jefferson RE, Yeates TO, Bobik TA. (2010). Short N-terminal sequences package proteins into bacterial microcompartments. Proc. Natl. Acad. Sci. U.S.A.. Apr 2010. 107(16):7509-14. [Abstract]
  • Han GW, Elsliger MA, Yeates TO, Xu Q, Murzin AG, Krishna SS, Jaroszewski L, Abdubek P, Astakhova T, Axelrod HL, Carlton D, Chen C, Chiu HJ, Clayton T, Das D, Deller MC, Duan L, Ernst D, Feuerhelm J, Grant JC, Grzechnik A, Jin KK, Johnson HA, Klock HE, Knuth MW, Kozbial P, Kumar A, Lam WW, Marciano D, McMullan D, Miller MD, Morse AT, Nigoghossian E, Okach L, Reyes R, Rife CL, Sefcovic N, Tien HJ, Trame CB, van den Bedem H, Weekes D, Hodgson KO, Wooley J, Deacon AM, Godzik A, Lesley SA, Wilson IA. (2010). Structure of a putative NTP pyrophosphohydrolase: YP_001813558.1 from Exiguobacterium sibiricum 255-15. Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun.. Oct 2010. 66(Pt 10):1237-44. [Abstract]
  • Banigan JR, Mandal K, Sawaya MR, Thammavongsa V, Hendrickx AP, Schneewind O, Yeates TO, Kent SB. (2010). Determination of the X-ray structure of the snake venom protein omwaprin by total chemical synthesis and racemic protein crystallography. Protein Sci.. Oct 2010. 19(10):1840-9. [Abstract]
  • King NP, Jacobitz AW, Sawaya MR, Goldschmidt L, Yeates TO. (2010). Structure and folding of a designed knotted protein. Proc. Natl. Acad. Sci. U.S.A.. Nov 2010. 107(48):20732-7. [Abstract]
  • Pentelute BL, Mandal K, Gates ZP, Sawaya MR, Yeates TO, Kent SB. (2010). Total chemical synthesis and X-ray structure of kaliotoxin by racemic protein crystallography. Chem. Commun. (Camb.). Nov 2010. 46(43):8174-6. [Abstract]
  • Crowley CS, Cascio D, Sawaya MR, Kopstein JS, Bobik TA, Yeates TO. (2010). Structural insight into the mechanisms of transport across the Salmonella enterica Pdu microcompartment shell. J. Biol. Chem.. Nov 2010. 285(48):37838-46. [Abstract]

2009

  • Sprinzak E, Cokus SJ, Yeates TO, Eisenberg D, Pellegrini M. (2009). Detecting coordinated regulation of multi-protein complexes using logic analysis of gene expression. BMC Syst Biol. 2009. 3:115. [Abstract]
  • Tanaka S, Sawaya MR, Phillips M, Yeates TO. (2009). Insights from multiple structures of the shell proteins from the beta-carboxysome. Protein Sci.. Jan 2009. 18(1):108-20. [Abstract]
  • Beeby M, Bobik TA, Yeates TO. (2009). Exploiting genomic patterns to discover new supramolecular protein assemblies. Protein Sci.. Jan 2009. 18(1):69-79. [Abstract]
  • Xie X, Pashkov I, Gao X, Guerrero JL, Yeates TO, Tang Y. (2009). Rational improvement of simvastatin synthase solubility in Escherichia coli leads to higher whole-cell biocatalytic activity. Biotechnol. Bioeng.. Jan 2009. 102(1):20-8. [Abstract]
  • Yu F, Song A, Xu C, Sun L, Li J, Tang L, Yu M, Yeates TO, Hu H, He J. (2009). Determining the DUF55-domain structure of human thymocyte nuclear protein 1 from crystals partially twinned by tetartohedry. Acta Crystallogr. D Biol. Crystallogr.. Mar 2009. 65(Pt 3):212-9. [Abstract]
  • Tsai Y, Sawaya MR, Yeates TO. (2009). Analysis of lattice-translocation disorder in the layered hexagonal structure of carboxysome shell protein CsoS1C. Acta Crystallogr. D Biol. Crystallogr.. Sep 2009. 65(Pt 9):980-8. [Abstract]
  • Gao X, Xie X, Pashkov I, Sawaya MR, Laidman J, Zhang W, Cacho R, Yeates TO, Tang Y. (2009). Directed evolution and structural characterization of a simvastatin synthase. Chem. Biol.. Oct 2009. 16(10):1064-74. [Abstract]
  • Dryden KA, Crowley CS, Tanaka S, Yeates TO, Yeager M. (2009). Two-dimensional crystals of carboxysome shell proteins recapitulate the hexagonal packing of three-dimensional crystals. Protein Sci.. Dec 2009. 18(12):2629-35. [Abstract]

2008

  • Tanaka S, Kerfeld CA, Sawaya MR, Cai F, Heinhorst S, Cannon GC, Yeates TO. (2008). Atomic-level models of the bacterial carboxysome shell. Science. Feb 2008. 319(5866):1083-6. [Abstract]
  • Sawaya MR, Kudryashov DS, Pashkov I, Adisetiyo H, Reisler E, Yeates TO. (2008). Multiple crystal structures of actin dimers and their implications for interactions in the actin filament. Acta Crystallogr. D Biol. Crystallogr.. Apr 2008. 64(Pt 4):454-65. [Abstract]
  • King NP, Lee TM, Sawaya MR, Cascio D, Yeates TO. (2008). Structures and functional implications of an AMP-binding cystathionine beta-synthase domain protein from a hyperthermophilic archaeon. J. Mol. Biol.. Jun 2008. 380(1):181-92. [Abstract]
  • Crowley CS, Sawaya MR, Bobik TA, Yeates TO. (2008). Structure of the PduU shell protein from the Pdu microcompartment of Salmonella. Structure. Sep 2008. 16(9):1324-32. [Abstract]
  • Yeates TO, Kerfeld CA, Heinhorst S, Cannon GC, Shively JM. (2008). Protein-based organelles in bacteria: carboxysomes and related microcompartments. Nat. Rev. Microbiol.. Sep 2008. 6(9):681-91. [Abstract]
  • Yeates TO, Yu F. (2008). Equations for determining tetartohedral twin fractions. Acta Crystallogr. D Biol. Crystallogr.. Nov 2008. 64(Pt 11):1158-64. [Abstract]
  • Kudryashov DS, Durer ZA, Ytterberg AJ, Sawaya MR, Pashkov I, Prochazkova K, Yeates TO, Loo RR, Loo JA, Satchell KJ, Reisler E. (2008). Connecting actin monomers by iso-peptide bond is a toxicity mechanism of the Vibrio cholerae MARTX toxin. Proc. Natl. Acad. Sci. U.S.A.. Nov 2008. 105(47):18537-42. [Abstract]
  • Cheng S, Liu Y, Crowley CS, Yeates TO, Bobik TA. (2008). Bacterial microcompartments: their properties and paradoxes. Bioessays. Nov 2008. 30(11-12):1084-95. [Abstract]
  • Liu J, Mao Y, Lan E, Banatao DR, Forse GJ, Lu J, Blom HO, Yeates TO, Dunn B, Chang JP. (2008). Generation of oxide nanopatterns by combining self-assembly of S-layer proteins and area-selective atomic layer deposition. J. Am. Chem. Soc.. Dec 2008. 130(50):16908-13. [Abstract]

2007

  • Yeates TO. (2007). Protein structure: evolutionary bridges to new folds. Curr. Biol.. Jan 2007. 17(2):R48-50. [Abstract]
  • Boutz DR, Cascio D, Whitelegge J, Perry LJ, Yeates TO. (2007). Discovery of a thermophilic protein complex stabilized by topologically interlinked chains. J. Mol. Biol.. May 2007. 368(5):1332-44. [Abstract]
  • Tsai Y, Sawaya MR, Cannon GC, Cai F, Williams EB, Heinhorst S, Kerfeld CA, Yeates TO. (2007). Structural analysis of CsoS1A and the protein shell of the Halothiobacillus neapolitanus carboxysome. PLoS Biol.. Jun 2007. 5(6):e144. [Abstract]
  • Yeates TO, Tsai Y, Tanaka S, Sawaya MR, Kerfeld CA. (2007). Self-assembly in the carboxysome: a viral capsid-like protein shell in bacterial cells. Biochem. Soc. Trans.. Jun 2007. 35(Pt 3):508-11. [Abstract]
  • Tanaka S, Sawaya MR, Kerfeld CA, Yeates TO. (2007). Structure of the RuBisCO chaperone RbcX from Synechocystis sp. PCC6803. Acta Crystallogr. D Biol. Crystallogr.. Oct 2007. 63(Pt 10):1109-12. [Abstract]
  • King NP, Yeates EO, Yeates TO. (2007). Identification of rare slipknots in proteins and their implications for stability and folding. J. Mol. Biol.. Oct 2007. 373(1):153-66. [Abstract]
  • Yeates TO, Clubb RT. (2007). Biochemistry. How some pili pull. Science. Dec 2007. 318(5856):1558-9. [Abstract]
  • Yeates TO, Norcross TS, King NP. (2007). Knotted and topologically complex proteins as models for studying folding and stability. Curr Opin Chem Biol. Dec 2007. 11(6):595-603. [Abstract]

2006

  • Sawaya MR, Cannon GC, Heinhorst S, Tanaka S, Williams EB, Yeates TO, Kerfeld CA. (2006). 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.. Mar 2006. 281(11):7546-55. [Abstract]
  • Laidman J, Forse GJ, Yeates TO. (2006). Conformational change and assembly through edge beta strands in transthyretin and other amyloid proteins. Acc. Chem. Res.. Sep 2006. 39(9):576-83. [Abstract]
  • Norcross TS, Yeates TO. (2006). A framework for describing topological frustration in models of protein folding. J. Mol. Biol.. Sep 2006. 362(3):605-21. [Abstract]
  • Banatao DR, Cascio D, Crowley CS, Fleissner MR, Tienson HL, Yeates TO. (2006). An approach to crystallizing proteins by synthetic symmetrization. Proc. Natl. Acad. Sci. U.S.A.. Oct 2006. 103(44):16230-5. [Abstract]
  • Yeates TO, Beeby M. (2006). Biochemistry. Proteins in a small world. Science. Dec 2006. 314(5807):1882-3. [Abstract]

2005

  • Chaudhuri BN, Yeates TO. (2005). A computational method to predict genetically encoded rare amino acids in proteins. Genome Biol.. 2005. 6(9):R79. [Abstract]
  • Kerfeld CA, Sawaya MR, Tanaka S, Nguyen CV, Phillips M, Beeby M, Yeates TO. (2005). Protein structures forming the shell of primitive bacterial organelles. Science. Aug 2005. 309(5736):936-8. [Abstract]
  • Kudryashov DS, Sawaya MR, Adisetiyo H, Norcross T, Hegyi G, Reisler E, Yeates TO. (2005). The crystal structure of a cross-linked actin dimer suggests a detailed molecular interface in F-actin. Proc. Natl. Acad. Sci. U.S.A.. Sep 2005. 102(37):13105-10. [Abstract]
  • Beeby M, O'Connor BD, Ryttersgaard C, Boutz DR, Perry LJ, Yeates TO. (2005). The genomics of disulfide bonding and protein stabilization in thermophiles. PLoS Biol.. Sep 2005. 3(9):e309. [Abstract]
  • Bowers PM, O'Connor BD, Cokus SJ, Sprinzak E, Yeates TO, Eisenberg D. (2005). Utilizing logical relationships in genomic data to decipher cellular processes. FEBS J.. Oct 2005. 272(20):5110-8. [Abstract]

2004

  • Bowers PM, Pellegrini M, Thompson MJ, Fierro J, Yeates TO, Eisenberg D. (2004). Prolinks: a database of protein functional linkages derived from coevolution. Genome Biol.. 2004. 5(5):R35. [Abstract]
  • Chaudhuri BN, Chan S, Perry LJ, Yeates TO. (2004). 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.. Jun 2004. 279(23):24585-91. [Abstract]
  • O'Connor BD, Yeates TO. (2004). GDAP: a web tool for genome-wide protein disulfide bond prediction. Nucleic Acids Res.. Jul 2004. 32(Web Server issue):W360-4. [Abstract]
  • Bowers PM, Cokus SJ, Eisenberg D, Yeates TO. (2004). Use of logic relationships to decipher protein network organization. Science. Dec 2004. 306(5705):2246-9. [Abstract]

2003

  • Kerfeld CA, Sawaya MR, Brahmandam V, Cascio D, Ho KK, Trevithick-Sutton CC, Krogmann DW, Yeates TO. (2003). The crystal structure of a cyanobacterial water-soluble carotenoid binding protein. Structure. Jan 2003. 11(1):55-65. [Abstract]
  • Rudolph MG, Kelker MS, Schneider TR, Yeates TO, Oseroff V, Heidary DK, Jennings PA, Wilson IA. (2003). Use of multiple anomalous dispersion to phase highly merohedrally twinned crystals of interleukin-1beta. Acta Crystallogr. D Biol. Crystallogr.. Feb 2003. 59(Pt 2):290-8. [Abstract]
  • Elam JS, Taylor AB, Strange R, Antonyuk S, Doucette PA, Rodriguez JA, Hasnain SS, Hayward LJ, Valentine JS, Yeates TO, Hart PJ. (2003). Amyloid-like filaments and water-filled nanotubes formed by SOD1 mutant proteins linked to familial ALS. Nat. Struct. Biol.. Jun 2003. 10(6):461-7. [Abstract]
  • Kerfeld CA, Sawaya MR, Bottin H, Tran KT, Sugiura M, Cascio D, Desbois A, Yeates TO, Kirilovsky D, Boussac A. (2003). 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.. Jul 2003. 44(7):697-706. [Abstract]
  • Chaudhuri BN, Sawaya MR, Kim CY, Waldo GS, Park MS, Terwilliger TC, Yeates TO. (2003). The crystal structure of the first enzyme in the pantothenate biosynthetic pathway, ketopantoate hydroxymethyltransferase, from M tuberculosis. Structure. Jul 2003. 11(7):753-64. [Abstract]
  • Padilla JE, Yeates TO. (2003). A statistic for local intensity differences: robustness to anisotropy and pseudo-centering and utility for detecting twinning. Acta Crystallogr. D Biol. Crystallogr.. Jul 2003. 59(Pt 7):1124-30. [Abstract]
  • Kerfeld CA, Yoshida S, Tran KT, Yeates TO, Cascio D, Bottin H, Berthomieu C, Sugiura M, Boussac A. (2003). The 1.6 A resolution structure of Fe-superoxide dismutase from the thermophilic cyanobacterium Thermosynechococcus elongatus. J. Biol. Inorg. Chem.. Sep 2003. 8(7):707-14. [Abstract]
  • Strong M, Graeber TG, Beeby M, Pellegrini M, Thompson MJ, Yeates TO, Eisenberg D. (2003). Visualization and interpretation of protein networks in Mycobacterium tuberculosis based on hierarchical clustering of genome-wide functional linkage maps. Nucleic Acids Res.. Dec 2003. 31(24):7099-109. [Abstract]

2002

  • Thapar N, Griffith SC, Yeates TO, Clarke S. (2002). Protein repair methyltransferase from the hyperthermophilic archaeon Pyrococcus furiosus. Unusual methyl-accepting affinity for D-aspartyl and N-succinyl-containing peptides. J. Biol. Chem.. Jan 2002. 277(2):1058-65. [Abstract]
  • Ryttersgaard C, Griffith SC, Sawaya MR, MacLaren DC, Clarke S, Yeates TO. (2002). Crystal structure of human L-isoaspartyl methyltransferase. J. Biol. Chem.. Mar 2002. 277(12):10642-6. [Abstract]
  • Mallick P, Boutz DR, Eisenberg D, Yeates TO. (2002). Genomic evidence that the intracellular proteins of archaeal microbes contain disulfide bonds. Proc. Natl. Acad. Sci. U.S.A.. Jul 2002. 99(15):9679-84. [Abstract]
  • Kerfeld CA, Sawaya MR, Krogmann DW, Yeates TO. (2002). Structure of cytochrome c6 from Arthrospira maxima: an assembly of 24 subunits in a nearly symmetric shell. Acta Crystallogr. D Biol. Crystallogr.. Jul 2002. 58(Pt 7):1104-10. [Abstract]
  • Yeates TO, Padilla JE. (2002). Designing supramolecular protein assemblies. Curr. Opin. Struct. Biol.. Aug 2002. 12(4):464-70. [Abstract]
  • Yeates TO. (2002). Structures of SET domain proteins: protein lysine methyltransferases make their mark. Cell. Oct 2002. 111(1):5-7. [Abstract]
  • Serag AA, Altenbach C, Gingery M, Hubbell WL, Yeates TO. (2002). Arrangement of subunits and ordering of beta-strands in an amyloid sheet. Nat. Struct. Biol.. Oct 2002. 9(10):734-9. [Abstract]
  • Nitao LK, Yeates TO, Reisler E. (2002). Conformational dynamics of the SH1-SH2 helix in the transition states of myosin subfragment-1. Biophys. J.. Nov 2002. 83(5):2733-41. [Abstract]
  • Larsen NA, Heine A, de Prada P, Redwan el-R, Yeates TO, Landry DW, Wilson IA. (2002). Structure determination of a cocaine hydrolytic antibody from a pseudomerohedrally twinned crystal. Acta Crystallogr. D Biol. Crystallogr.. Dec 2002. 58(Pt 12):2055-9. [Abstract]

2001

  • Padilla JE, Colovos C, Yeates TO. (2001). Nanohedra: using symmetry to design self assembling protein cages, layers, crystals, and filaments. Proc. Natl. Acad. Sci. U.S.A.. Feb 2001. 98(5):2217-21. [Abstract]
  • Sawaya MR, Krogmann DW, Serag A, Ho KK, Yeates TO, Kerfeld CA. (2001). Structures of cytochrome c-549 and cytochrome c6 from the cyanobacterium Arthrospira maxima. Biochemistry. Aug 2001. 40(31):9215-25. [Abstract]
  • Serag AA, Altenbach C, Gingery M, Hubbell WL, Yeates TO. (2001). Identification of a subunit interface in transthyretin amyloid fibrils: evidence for self-assembly from oligomeric building blocks. Biochemistry. Aug 2001. 40(31):9089-96. [Abstract]
  • Griffith SC, Sawaya MR, Boutz DR, Thapar N, Katz JE, Clarke S, Yeates TO. (2001). Crystal structure of a protein repair methyltransferase from Pyrococcus furiosus with its L-isoaspartyl peptide substrate. J. Mol. Biol.. Nov 2001. 313(5):1103-16. [Abstract]

2000

  • Toth EA, Yeates TO. (2000). The structure of adenylosuccinate lyase, an enzyme with dual activity in the de novo purine biosynthetic pathway. Structure. Feb 2000. 8(2):163-74. [Abstract]
  • Eisenberg D, Marcotte EM, Xenarios I, Yeates TO. (2000). Protein function in the post-genomic era. Nature. Jun 2000. 405(6788):823-6. [Abstract]
  • Toth EA, Worby C, Dixon JE, Goedken ER, Marqusee S, Yeates TO. (2000). The crystal structure of adenylosuccinate lyase from Pyrobaculum aerophilum reveals an intracellular protein with three disulfide bonds. J. Mol. Biol.. Aug 2000. 301(2):433-50. [Abstract]
  • Colovos C, Toth EA, Yeates TO. (2000). Evaluation of phase accuracy via topological and geometrical analysis of electron-density maps. Acta Crystallogr. D Biol. Crystallogr.. Nov 2000. 56(Pt 11):1421-9. [Abstract]

1999

  • Yeates TO, Fam BC. (1999). Protein crystals and their evil twins. Structure. Feb 1999. 7(2):R25-9. [Abstract]
  • Pellegrini M, Marcotte EM, Thompson MJ, Eisenberg D, Yeates TO. (1999). Assigning protein functions by comparative genome analysis: protein phylogenetic profiles. Proc. Natl. Acad. Sci. U.S.A.. Apr 1999. 96(8):4285-8. [Abstract]
  • Pellegrini M, Marcotte EM, Yeates TO. (1999). A fast algorithm for genome-wide analysis of proteins with repeated sequences. Proteins. Jun 1999. 35(4):440-6. [Abstract]
  • Marcotte EM, Pellegrini M, Ng HL, Rice DW, Yeates TO, Eisenberg D. (1999). Detecting protein function and protein-protein interactions from genome sequences. Science. Jul 1999. 285(5428):751-3. [Abstract]
  • Marcotte EM, Pellegrini M, Yeates TO, Eisenberg D. (1999). A census of protein repeats. J. Mol. Biol.. Oct 1999. 293(1):151-60. [Abstract]
  • Pellegrini M, Yeates TO. (1999). Searching for frameshift evolutionary relationships between protein sequence families. Proteins. Nov 1999. 37(2):278-83. [Abstract]
  • Marcotte EM, Pellegrini M, Thompson MJ, Yeates TO, Eisenberg D. (1999). A combined algorithm for genome-wide prediction of protein function. Nature. Nov 1999. 402(6757):83-6. [Abstract]

1998

  • Colovos C, Cascio D, Yeates TO. (1998). The 1.8 A crystal structure of the ycaC gene product from Escherichia coli reveals an octameric hydrolase of unknown specificity. Structure. Oct 1998. 6(10):1329-37. [Abstract]
  • Kerfeld CA, Salmeen AE, Yeates TO. (1998). Crystal structure and possible dimerization of the high-potential iron-sulfur protein from Chromatium purpuratum. Biochemistry. Oct 1998. 37(40):13911-7. [Abstract]

1997

  • Yeates TO. (1997). Detecting and overcoming crystal twinning. Meth. Enzymol.. 1997. 276:344-58. [Abstract]
  • Pellegrini M, Wukovitz SW, Yeates TO. (1997). Simulation of protein crystal nucleation. Proteins. Aug 1997. 28(4):515-21. [Abstract]
  • Bell CE, Yeates TO, Eisenberg D. (1997). Unusual conformation of nicotinamide adenine dinucleotide (NAD) bound to diphtheria toxin: a comparison with NAD bound to the oxidoreductase enzymes. Protein Sci.. Oct 1997. 6(10):2084-96. [Abstract]
  • Kerfeld CA, Wu YP, Chan C, Krogmann DW, Yeates TO. (1997). Crystals of the carotenoid protein from Arthrospira maxima containing uniformly oriented pigment molecules. Acta Crystallogr. D Biol. Crystallogr.. Nov 1997. 53(Pt 6):720-3. [Abstract]
  • Pellegrini M, Grønbech-Jensen N, Kelly JA, Pfluegl GM, Yeates TO. (1997). Highly constrained multiple-copy refinement of protein crystal structures. Proteins. Dec 1997. 29(4):426-32. [Abstract]

1996

  • Kelly JA, Feigon J, Yeates TO. (1996). Reconciliation of the X-ray and NMR structures of the thrombin-binding aptamer d(GGTTGGTGTGGTTGG). J. Mol. Biol.. Mar 1996. 256(3):417-22. [Abstract]
  • Redinbo MR, Eide SM, Stone RL, Dixon JE, Yeates TO. (1996). Crystallization and preliminary structural analysis of Bacillus subtilis adenylosuccinate lyase, an enzyme implicated in infantile autism. Protein Sci.. Apr 1996. 5(4):786-8. [Abstract]
  • Kerfeld CA, Chan C, Hirasawa M, Kleis-SanFrancisco S, Yeates TO, Knaff DB. (1996). Isolation and characterization of soluble electron transfer proteins from Chromatium purpuratum. Biochemistry. Jun 1996. 35(24):7812-8. [Abstract]

1995

  • Yeates TO. (1995). Algorithms for evaluating the long-range accessibility of protein surfaces. J. Mol. Biol.. Jun 1995. 249(4):804-15. [Abstract]
  • Kerfeld CA, Anwar HP, Interrante R, Merchant S, Yeates TO. (1995). The structure of chloroplast cytochrome c6 at 1.9 A resolution: evidence for functional oligomerization. J. Mol. Biol.. Jul 1995. 250(5):627-47. [Abstract]
  • Wukovitz SW, Yeates TO. (1995). Why protein crystals favour some space-groups over others. Nat. Struct. Biol.. Dec 1995. 2(12):1062-7. [Abstract]

1994

  • Redinbo MR, Yeates TO, Merchant S. (1994). Plastocyanin: structural and functional analysis. J. Bioenerg. Biomembr.. Feb 1994. 26(1):49-66. [Abstract]
  • Kerfeld CA, Yeates TO, Thornber JP. (1994). Purification and characterization of the peripheral antenna of the purple-sulfur bacterium Chromatium purpuratum: evidence of an unusual pigment-protein composition. Biochemistry. Mar 1994. 33(8):2178-84. [Abstract]
  • Kerfeld CA, Yeates TO, Thornber JP. (1994). Biochemical and spectroscopic characterization of the reaction center-LH1 complex and the carotenoid-containing B820 subunit of Chromatium purpuratum. Biochim. Biophys. Acta. Apr 1994. 1185(2):193-202. [Abstract]
  • Kelly JA, Singer E, Osslund TD, Yeates TO. (1994). Crystallization and preliminary structural studies of neurotrophin-3. Protein Sci.. Jun 1994. 3(6):982-3. [Abstract]

1993

  • Yeates TO. (1993). The asymmetric regions of rotation functions between Patterson functions of arbitrarily high symmetry. Acta Crystallogr., A, Found. Crystallogr.. Jan 1993. 49 ( Pt 1):138-41. [Abstract]
  • Yeates TO, Zhang KY. (1993). Ambiguities in ab initio phasing. Science. Mar 1993. 259(5102):1771-2. [Abstract]
  • Redinbo MR, Yeates TO. (1993). Structure determination of plastocyanin from a specimen with a hemihedral twinning fraction of one-half. Acta Crystallogr. D Biol. Crystallogr.. Jul 1993. 49(Pt 4):375-80. [Abstract]
  • Kerfeld CA, Thornber JP, Yeates TO. (1993). Crystallization of two integral membrane pigment-protein complexes from the purple-sulfur bacterium Chromatium purpuratum. Protein Sci.. Aug 1993. 2(8):1352-5. [Abstract]
  • Colovos C, Yeates TO. (1993). Verification of protein structures: patterns of nonbonded atomic interactions. Protein Sci.. Sep 1993. 2(9):1511-9. [Abstract]
  • Redinbo MR, Cascio D, Choukair MK, Rice D, Merchant S, Yeates TO. (1993). The 1.5-A crystal structure of plastocyanin from the green alga Chlamydomonas reinhardtii. Biochemistry. Oct 1993. 32(40):10560-7. [Abstract]

1991

  • Yeates TO, Jacobson DH, Martin A, Wychowski C, Girard M, Filman DJ, Hogle JM. (1991). Three-dimensional structure of a mouse-adapted type 2/type 1 poliovirus chimera. EMBO J.. Sep 1991. 10(9):2331-41. [Abstract]

1990

  • Yeates TO, Rini JM. (1990). Intensity-based domain refinement of oriented but unpositioned molecular replacement models. Acta Crystallogr., A, Found. Crystallogr.. May 1990. 46 ( Pt 5):352-9. [Abstract]
  • Yeates TO. (1990). Determination of the correct reference frame from an atomic coordinate list. Acta Crystallogr., A, Found. Crystallogr.. Jul 1990. 46 ( Pt 7):625-6. [Abstract]

1989

1988

  • Yeates TO. (1988). Simple statistics for intensity data from twinned specimens. Acta Crystallogr., A, Found. Crystallogr.. Mar 1988. 44 ( Pt 2):142-4. [Abstract]
  • Yeates TO, Komiya H, Chirino A, Rees DC, Allen JP, Feher G. (1988). Structure of the reaction center from Rhodobacter sphaeroides R-26 and 2.4.1: protein-cofactor (bacteriochlorophyll, bacteriopheophytin, and carotenoid) interactions. Proc. Natl. Acad. Sci. U.S.A.. Nov 1988. 85(21):7993-7. [Abstract]
  • Allen JP, Feher G, Yeates TO, Komiya H, Rees DC. (1988). Structure of the reaction center from Rhodobacter sphaeroides R-26: protein-cofactor (quinones and Fe2+) interactions. Proc. Natl. Acad. Sci. U.S.A.. Nov 1988. 85(22):8487-91. [Abstract]
  • Komiya H, Yeates TO, Rees DC, Allen JP, Feher G. (1988). Structure of the reaction center from Rhodobacter sphaeroides R-26 and 2.4.1: symmetry relations and sequence comparisons between different species. Proc. Natl. Acad. Sci. U.S.A.. Dec 1988. 85(23):9012-6. [Abstract]

1987

  • Allen JP, Feher G, Yeates TO, Komiya H, Rees DC. (1987). Structure of the reaction center from Rhodobacter sphaeroides R-26: the cofactors. Proc. Natl. Acad. Sci. U.S.A.. Aug 1987. 84(16):5730-4. [Abstract]
  • Yeates TO, Komiya H, Rees DC, Allen JP, Feher G. (1987). Structure of the reaction center from Rhodobacter sphaeroides R-26: membrane-protein interactions. Proc. Natl. Acad. Sci. U.S.A.. Sep 1987. 84(18):6438-42. [Abstract]
  • Allen JP, Feher G, Yeates TO, Komiya H, Rees DC. (1987). Structure of the reaction center from Rhodobacter sphaeroides R-26: the protein subunits. Proc. Natl. Acad. Sci. U.S.A.. Sep 1987. 84(17):6162-6. [Abstract]

1986

  • Allen JP, Feher G, Yeates TO, Rees DC, Deisenhofer J, Michel H, Huber R. (1986). Structural homology of reaction centers from Rhodopseudomonas sphaeroides and Rhodopseudomonas viridis as determined by x-ray diffraction. Proc. Natl. Acad. Sci. U.S.A.. Nov 1986. 83(22):8589-93. [Abstract]