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, DOE-Institute for Genomics and Proteomics (Director)

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.

Read More »

 

Biography

Professor Todd Yeates earned his PhD at UCLA developing X-ray crystallographic methods while working on early structures of membrane proteins, followed by postdoctoral research at the Scripps Research Institute elucidating the structures of viral capsids. Yeates joined the faculty at UCLA, where his research combines interests in molecular biology, biophysics and computational methods, applied to problems from molecular structure to genomic sequence analysis.

Current research in the lab focuses on large protein assemblies, including those found in nature and those that can be created in the laboratory by design. Research in the Yeates group laid out a structural understanding of protein-based metabolic organelles in bacteria, often called 'bacterial microcompartments'. On the design side, the Yeates group developed the first methods for designing highly symmetric self-assembling protein materials, such cubic cages, which are now finding applications in biomedicine, imaging, and biomaterials design.

Advances in computational genomics made by the group include the development of algorithms for inferring cellular functions for vast numbers of protein sequences using 'non‐homology' methods, which introduced a new paradigm for mining genomic data. Advances in theory and methods for structural biology include the development of universally used equations for analyzing diffraction data, a solution to the decades-old problem of why proteins crystallize in strongly favored symmetries, and development of protein-based scaffolds for cryo-EM imaging of small proteins. Yeates is the Director of the UCLA DOE-Institute for Genomics and Proteomics.

Research Interests

Molecular, Structural and Computational biology

Molecular Structure

 

Research in the Yeates laboratory covers the areas of molecular, structural and computational biology and design.

Much of the group’s current research focuses on a deep understanding of protein structures and large assemblies, with an emphasis on the underlying principles that guide their behavior and evolution, and which enable the atomic level design of novel self-assembling protein architectures.

Our studies of natural self-assembling protein architectures have focused on a remarkable but still not well-appreciated family of giant protein capsids inside many bacterial cells. Our structural studies on the carboxysome and related bacterial microcompartments laid out a mechanistic understanding for these extraordinary structures, showing that bacteria do possess true organelles.

In our frontier bioengineering studies, we are designing entirely novel protein architectures, including cubic cages and extended crystalline arrays in two and three dimensions. Various types of protein assemblies, natural and designed, are finding applications as active enzymatic materials, imaging scaffolds, and biotherapeutics.

Visit The Yeates Lab »

 

Honors & Awards

  • University of California Regents Scholarship
  • NSF Presidential Young Investigator
  • Sidhu Award - Pittsburgh Diffraction Society
  • McCoy Award for Excellence in Research – UCLA Chemistry
  • Plenary Lecture – German Crystallographic Society
  • Fellow of the American Association for the Advancement of Science
  • Hansen-Dow Award for Excellence in Teaching – UCLA Chemistry
  • Keynote Address – Foundations of Nanoscience
  • Program Chair – Annual Meeting of the Protein Society
  • American Society for Biochemistry and Molecular Biology - Delano Award in Computational Biosciences
  • Xinda Lecturer – Peking University

Publications

 

2020

Steyaert J, Yeates TO Editorial overview: Engineered proteins as tools in structural biology. Curr. Opin. Struct. Biol.. Feb 2020. 60:v-vi. 2020 PMID: 32228884
Yeates TO, Agdanowski MP, Liu Y Development of imaging scaffolds for cryo-electron microscopy. Curr. Opin. Struct. Biol.. Feb 2020. 60:142-149. 2020 PMID: 32066085
McConnell SA, Cannon KA, Morgan C, McAllister R, Amer BR, Clubb RT, Yeates TO Designed Protein Cages as Scaffolds for Building Multienzyme Materials. ACS Synth Biol. 02 2020. 9(2):381-391. 2020 PMID: 31922719

2019

Cannon KA, Park RU, Boyken SE, Nattermann U, Yi S, Baker D, King NP, Yeates TO Design and structure of two new protein cages illustrate successes and ongoing challenges in protein engineering. Protein Sci.. Dec 2019. :. 2019 PMID: 31840320
Yeates TO, McPherson A The structure of bovine β-lactoglobulin in crystals grown at pH 3.8 exhibiting novel threefold twinning. Acta Crystallogr F Struct Biol Commun. Oct 2019. 75(Pt 10):640-645. 2019 PMID: 31584012
Liu Y, Huynh DT, Yeates TO A 3.8 Å resolution cryo-EM structure of a small protein bound to an imaging scaffold. Nat Commun. 04 2019. 10(1):1864. 2019 PMID: 31015551
Cannon KA, Ochoa JM, Yeates TO High-symmetry protein assemblies: patterns and emerging applications. Curr. Opin. Struct. Biol.. Apr 2019. 55:77-84. 2019 PMID: 31005680
Yeates TO Protein assembles into Archimedean geometry. Nature. May 2019. 569(7756):340-342. 2019 PMID: 31076733

2018

Thompson MC, Cascio D, Yeates TO Microfocus diffraction from different regions of a protein crystal: structural variations and unit-cell polymorphism. Acta Crystallogr D Struct Biol. May 2018. 74(Pt 5):411-421. 2018 PMID: 29717712
Liu Y, Gonen S, Gonen T, Yeates TO Near-atomic cryo-EM imaging of a small protein displayed on a designed scaffolding system. Proc. Natl. Acad. Sci. U.S.A.. Mar 2018. :. 2018 PMID: 29507202
Yeates TO, Bobik TA Facile methods for heterologous production of bacterial microcompartments in diverse host species. Microb Biotechnol. Jan 2018. 11(1):160-162. 2018 PMID: 29205936

2017

Park J, Chun S, Bobik TA, Houk KN, Yeates TO Molecular Dynamics Simulations of Selective Metabolite Transport across the Propanediol Bacterial Microcompartment Shell. J Phys Chem B. Aug 2017. 121(34):8149-8154. 2017 PMID: 28829618
Yeates TO, Wheatley NM Putting the RuBisCO pieces together. Science. 12 2017. 358(6368):1253-1254. 2017 PMID: 29217555

2016

Lai YT, Hura GL, Dyer KN, Tang HY, Tainer JA, Yeates TO Designing and defining dynamic protein cage nanoassemblies in solution. Sci Adv. Dec 2016. 2(12):e1501855. 2016 PMID: 27990489
Chowdhury C, Chun S, Sawaya MR, Yeates TO, Bobik TA The function of the PduJ microcompartment shell protein is determined by the genomic position of its encoding gene. Mol. Microbiol.. Sep 2016. 101(5):770-83. 2016 PMID: 27561553
Bale JB, Gonen S, Liu Y, Sheffler W, Ellis D, Thomas C, Cascio D, Yeates TO, Gonen T, King NP, Baker D Accurate design of megadalton-scale two-component icosahedral protein complexes. Science. Jul 2016. 353(6297):389-94. 2016 PMID: 27463675
Wheatley NM, Eden KD, Ngo J, Rosinski JS, Sawaya MR, Cascio D, Collazo M, Hoveida H, Hubbell WL, Yeates TO A PII-like protein regulated by bicarbonate: Structural and biochemical studies of the carboxysome-associated CPII protein. J. Mol. Biol.. Jul 2016. :. 2016 PMID: 27464895
Yeates TO, Liu Y, Laniado J The design of symmetric protein nanomaterials comes of age in theory and practice. Curr. Opin. Struct. Biol.. Jul 2016. 39:134-143. 2016 PMID: 27476148
Jorda J, Leibly DJ, Thompson MC, Yeates TO Structure of a novel 13 nm dodecahedral nanocage assembled from a redesigned bacterial microcompartment shell protein. Chem. Commun. (Camb.). Apr 2016. 52(28):5041-4. 2016 PMID: 26988700
Jorda J, Sawaya MR, Yeates TO Progress in low-resolution ab initio phasing with CrowdPhase. Acta Crystallogr D Struct Biol. Mar 2016. 72(Pt 3):446-53. 2016 PMID: 26960132

2015

Lai YT, Jiang L, Chen W, Yeates TO On the predictability of the orientation of protein domains joined by a spanning alpha-helical linker. Protein Eng. Des. Sel.. Nov 2015. 28(11):491-9. 2015 PMID: 26243886
Tsai Y, Holton T, Yeates TO Diffusion accessibility as a method for visualizing macromolecular surface geometry. Protein Sci.. Oct 2015. 24(10):1702-5. 2015 PMID: 26189444
Bale JB, Park RU, Liu Y, Gonen S, Gonen T, Cascio D, King NP, Yeates TO, Baker D Structure of a designed tetrahedral protein assembly variant engineered to have improved soluble expression. Protein Sci.. Oct 2015. 24(10):1695-701. 2015 PMID: 26174163
Leibly DJ, Arbing MA, Pashkov I, DeVore N, Waldo GS, Terwilliger TC, Yeates TO A Suite of Engineered GFP Molecules for Oligomeric Scaffolding. Structure. Sep 2015. 23(9):1754-68. 2015 PMID: 26278175
McNamara DE, Senese S, Yeates TO, Torres JZ Structures of potent anticancer compounds bound to tubulin. Protein Sci.. Jul 2015. 24(7):1164-72. 2015 PMID: 25970265
Liu Y, Jorda J, Yeates TO, Bobik TA The PduL Phosphotransacylase Is Used To Recycle Coenzyme A within the Pdu Microcompartment. J. Bacteriol.. Jul 2015. 197(14):2392-9. 2015 PMID: 25962918
Ort DR, Merchant SS, Alric J, Barkan A, Blankenship RE, Bock R, Croce R, Hanson MR, Hibberd JM, Long SP, Moore TA, Moroney J, Niyogi KK, Parry MA, Peralta-Yahya PP, Prince RC, Redding KE, Spalding MH, van Wijk KJ, Vermaas WF, von Caemmerer S, Weber AP, Yeates TO, Yuan JS, Zhu XG Redesigning photosynthesis to sustainably meet global food and bioenergy demand. Proc. Natl. Acad. Sci. U.S.A.. Jun 2015. :. 2015 PMID: 26124102
Thompson MC, Cascio D, Leibly DJ, Yeates TO An allosteric model for control of pore opening by substrate binding in the EutL microcompartment shell protein. Protein Sci.. Jun 2015. 24(6):956-75. 2015 PMID: 25752492
Chowdhury C, Chun S, Pang A, Sawaya MR, Sinha S, Yeates TO, Bobik TA Selective molecular transport through the protein shell of a bacterial microcompartment organelle. Proc. Natl. Acad. Sci. U.S.A.. Mar 2015. 112(10):2990-5. 2015 PMID: 25713376
Jorda J, Liu Y, Bobik TA, Yeates TO Exploring bacterial organelle interactomes: a model of the protein-protein interaction network in the Pdu microcompartment. PLoS Comput. Biol.. Feb 2015. 11(2):e1004067. 2015 PMID: 25646976

2014

Thompson MC, Crowley CS, Kopstein J, Bobik TA, Yeates TO Structure of a bacterial microcompartment shell protein bound to a cobalamin cofactor. Acta Crystallogr F Struct Biol Commun. Dec 2014. 70(Pt 12):1584-90. 2014 PMID: 25484204
Lai YT, Reading E, Hura GL, Tsai KL, Laganowsky A, Asturias FJ, Tainer JA, Robinson CV, Yeates TO Structure of a designed protein cage that self-assembles into a highly porous cube. Nat Chem. Dec 2014. 6(12):1065-71. 2014 PMID: 25411884
Bobik TA, Morales EJ, Shin A, Cascio D, Sawaya MR, Arbing M, Yeates TO, Rasche ME Structure of the methanofuran/methanopterin-biosynthetic enzyme MJ1099 from Methanocaldococcus jannaschii. Acta Crystallogr F Struct Biol Commun. Nov 2014. 70(Pt 11):1472-9. 2014 PMID: 25372812
Chowdhury C, Sinha S, Chun S, Yeates TO, Bobik TA Diverse bacterial microcompartment organelles. Microbiol. Mol. Biol. Rev.. Sep 2014. 78(3):438-68. 2014 PMID: 25184561
Thompson MC, Wheatley NM, Jorda J, Sawaya MR, Gidaniyan SD, Ahmed H, Yang Z, McCarty KN, Whitelegge JP, Yeates TO Identification of a unique Fe-S cluster binding site in a glycyl-radical type microcompartment shell protein. J. Mol. Biol.. Sep 2014. 426(19):3287-304. 2014 PMID: 25102080
Jorda J, Sawaya MR, Yeates TO CrowdPhase: crowdsourcing the phase problem. Acta Crystallogr. D Biol. Crystallogr.. Jun 2014. 70(Pt 6):1538-48. 2014 PMID: 24914965
King NP, Bale JB, Sheffler W, McNamara DE, Gonen S, Gonen T, Yeates TO, Baker D Accurate design of co-assembling multi-component protein nanomaterials. Nature. Jun 2014. 510(7503):103-8. 2014 PMID: 24870237
Sinha S, Cheng S, Sung YW, McNamara DE, Sawaya MR, Yeates TO, Bobik TA Alanine scanning mutagenesis identifies an asparagine-arginine-lysine triad essential to assembly of the shell of the Pdu microcompartment. J. Mol. Biol.. Jun 2014. 426(12):2328-45. 2014 PMID: 24747050
Jiménez-Osés G, Osuna S, Gao X, Sawaya MR, Gilson L, Collier SJ, Huisman GW, Yeates TO, Tang Y, Houk KN The role of distant mutations and allosteric regulation on LovD active site dynamics. Nat. Chem. Biol.. Jun 2014. 10(6):431-6. 2014 PMID: 24727900
Okamoto R, Mandal K, Sawaya MR, Kajihara Y, Yeates TO, Kent SB (Quasi-)racemic X-ray structures of glycosylated and non-glycosylated forms of the chemokine Ser-CCL1 prepared by total chemical synthesis. Angew. Chem. Int. Ed. Engl.. May 2014. 53(20):5194-8. 2014 PMID: 24692304
McNamara DE, Cascio D, Jorda J, Bustos C, Wang TC, Rasche ME, Yeates TO, Bobik TA Structure of dihydromethanopterin reductase, a cubic protein cage for redox transfer. J. Biol. Chem.. Mar 2014. 289(13):8852-64. 2014 PMID: 24523405
Wheatley NM, Sundberg CD, Gidaniyan SD, Cascio D, Yeates TO Structure and identification of a pterin dehydratase-like protein as a ribulose-bisphosphate carboxylase/oxygenase (RuBisCO) assembly factor in the α-carboxysome. J. Biol. Chem.. Mar 2014. 289(11):7973-81. 2014 PMID: 24459150
Thompson MC, Yeates TO A challenging interpretation of a hexagonally layered protein structure. Acta Crystallogr. D Biol. Crystallogr.. Jan 2014. 70(Pt 1):203-8. 2014 PMID: 24419393

2013

Nguyen HB, Hung LW, Yeates TO, Terwilliger TC, Waldo GS Split green fluorescent protein as a modular binding partner for protein crystallization. Acta Crystallogr. D Biol. Crystallogr.. Dec 2013. 69(Pt 12):2513-23. 2013 PMID: 24311592
Lai YT, Tsai KL, Sawaya MR, Asturias FJ, Yeates TO Structure and flexibility of nanoscale protein cages designed by symmetric self-assembly. J. Am. Chem. Soc.. May 2013. 135(20):7738-43. 2013 PMID: 23621606
Wheatley NM, Gidaniyan SD, Liu Y, Cascio D, Yeates TO Bacterial microcompartment shells of diverse functional types possess pentameric vertex proteins. Protein Sci.. May 2013. 22(5):660-5. 2013 PMID: 23456886
Jorda J, Lopez D, Wheatley NM, Yeates TO Using comparative genomics to uncover new kinds of protein-based metabolic organelles in bacteria. Protein Sci.. Feb 2013. 22(2):179-95. 2013 PMID: 23188745
Yeates TO, Jorda J, Bobik TA The shells of BMC-type microcompartment organelles in bacteria. J. Mol. Microbiol. Biotechnol.. 2013. 23(4-5):290-9. 2013 PMID: 23920492

2012

Lai YT, King NP, Yeates TO Principles for designing ordered protein assemblies. Trends Cell Biol.. Dec 2012. 22(12):653-61. 2012 PMID: 22975357
King NP, Sheffler W, Sawaya MR, Vollmar BS, Sumida JP, André I, Gonen T, Yeates TO, Baker D Computational design of self-assembling protein nanomaterials with atomic level accuracy. Science. Jun 2012. 336(6085):1171-4. 2012 PMID: 22654060
Lai YT, Cascio D, Yeates TO Structure of a 16-nm cage designed by using protein oligomers. Science. Jun 2012. 336(6085):1129. 2012 PMID: 22654051
Jones EY, Yeates TO Structure and function in complex macromolecular assemblies: some evolutionary themes. Curr. Opin. Struct. Biol.. Apr 2012. 22(2):197-9. 2012 PMID: 22444564
Sawaya MR, Pentelute BL, Kent SB, Yeates TO Single-wavelength phasing strategy for quasi-racemic protein crystal diffraction data. Acta Crystallogr. D Biol. Crystallogr.. Jan 2012. 68(Pt 1):62-8. 2012 PMID: 22194334
Johnson E, Nguyen PT, Yeates TO, Rees DC Inward facing conformations of the MetNI methionine ABC transporter: Implications for the mechanism of transinhibition. Protein Sci.. Jan 2012. 21(1):84-96. 2012 PMID: 22095702
Yeates TO, Kent SB Racemic protein crystallography. Annu Rev Biophys. 2012. 41:41-61. 2012 PMID: 22443988

2011

Pickens LB, Sawaya MR, Rasool H, Pashkov I, Yeates TO, Tang Y Structural and biochemical characterization of the salicylyl-acyltranferase SsfX3 from a tetracycline biosynthetic pathway. J. Biol. Chem.. Dec 2011. 286(48):41539-51. 2011 PMID: 21965680
Laganowsky A, Zhao M, Soriaga AB, Sawaya MR, Cascio D, Yeates TO An approach to crystallizing proteins by metal-mediated synthetic symmetrization. Protein Sci.. Nov 2011. 20(11):1876-90. 2011 PMID: 21898649
Yeates TO Nanobiotechnology: protein arrays made to order. Nat Nanotechnol. Sep 2011. 6(9):541-2. 2011 PMID: 21804551
Sayre TC, Lee TM, King NP, Yeates TO Protein stabilization in a highly knotted protein polymer. Protein Eng. Des. Sel.. Aug 2011. 24(8):627-30. 2011 PMID: 21669955
Yeates TO, Thompson MC, Bobik TA The protein shells of bacterial microcompartment organelles. Curr. Opin. Struct. Biol.. Apr 2011. 21(2):223-31. 2011 PMID: 21315581
Forse GJ, Ram N, Banatao DR, Cascio D, Sawaya MR, Klock HE, Lesley SA, Yeates TO Synthetic symmetrization in the crystallization and structure determination of CelA from Thermotoga maritima. Protein Sci.. Jan 2011. 20(1):168-78. 2011 PMID: 21082721
Tsai SJ, Yeates TO Bacterial microcompartments insights into the structure, mechanism, and engineering applications. Prog Mol Biol Transl Sci. 2011. 103:1-20. 2011 PMID: 21999993
Jorda J, Yeates TO Widespread disulfide bonding in proteins from thermophilic archaea. Archaea. 2011. 2011:409156. 2011 PMID: 21941460

2010

King NP, Jacobitz AW, Sawaya MR, Goldschmidt L, Yeates TO Structure and folding of a designed knotted protein. Proc. Natl. Acad. Sci. U.S.A.. Nov 2010. 107(48):20732-7. 2010 PMID: 21068371
Pentelute BL, Mandal K, Gates ZP, Sawaya MR, Yeates TO, Kent SB Total chemical synthesis and X-ray structure of kaliotoxin by racemic protein crystallography. Chem. Commun. (Camb.). Nov 2010. 46(43):8174-6. 2010 PMID: 20877851
Crowley CS, Cascio D, Sawaya MR, Kopstein JS, Bobik TA, Yeates TO Structural insight into the mechanisms of transport across the Salmonella enterica Pdu microcompartment shell. J. Biol. Chem.. Nov 2010. 285(48):37838-46. 2010 PMID: 20870711
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 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. 2010 PMID: 20944217
Banigan JR, Mandal K, Sawaya MR, Thammavongsa V, Hendrickx AP, Schneewind O, Yeates TO, Kent SB 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. 2010 PMID: 20669184
Fan C, Cheng S, Liu Y, Escobar CM, Crowley CS, Jefferson RE, Yeates TO, Bobik TA Short N-terminal sequences package proteins into bacterial microcompartments. Proc. Natl. Acad. Sci. U.S.A.. Apr 2010. 107(16):7509-14. 2010 PMID: 20308536
Tanaka S, Sawaya MR, Yeates TO Structure and mechanisms of a protein-based organelle in Escherichia coli. Science. Jan 2010. 327(5961):81-4. 2010 PMID: 20044574
Yeates TO, Crowley CS, Tanaka S Bacterial microcompartment organelles: protein shell structure and evolution. Annu Rev Biophys. 2010. 39:185-205. 2010 PMID: 20192762

2009

Dryden KA, Crowley CS, Tanaka S, Yeates TO, Yeager M Two-dimensional crystals of carboxysome shell proteins recapitulate the hexagonal packing of three-dimensional crystals. Protein Sci.. Dec 2009. 18(12):2629-35. 2009 PMID: 19844993
Gao X, Xie X, Pashkov I, Sawaya MR, Laidman J, Zhang W, Cacho R, Yeates TO, Tang Y Directed evolution and structural characterization of a simvastatin synthase. Chem. Biol.. Oct 2009. 16(10):1064-74. 2009 PMID: 19875080
Tsai Y, Sawaya MR, Yeates TO 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. 2009 PMID: 19690376
Yu F, Song A, Xu C, Sun L, Li J, Tang L, Yu M, Yeates TO, Hu H, He J 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. 2009 PMID: 19237743
Tanaka S, Sawaya MR, Phillips M, Yeates TO Insights from multiple structures of the shell proteins from the beta-carboxysome. Protein Sci.. Jan 2009. 18(1):108-20. 2009 PMID: 19177356
Beeby M, Bobik TA, Yeates TO Exploiting genomic patterns to discover new supramolecular protein assemblies. Protein Sci.. Jan 2009. 18(1):69-79. 2009 PMID: 19177352
Xie X, Pashkov I, Gao X, Guerrero JL, Yeates TO, Tang Y Rational improvement of simvastatin synthase solubility in Escherichia coli leads to higher whole-cell biocatalytic activity. Biotechnol. Bioeng.. Jan 2009. 102(1):20-8. 2009 PMID: 18988191
Sprinzak E, Cokus SJ, Yeates TO, Eisenberg D, Pellegrini M Detecting coordinated regulation of multi-protein complexes using logic analysis of gene expression. BMC Syst Biol. 2009. 3:115. 2009 PMID: 20003439

2008

Liu J, Mao Y, Lan E, Banatao DR, Forse GJ, Lu J, Blom HO, Yeates TO, Dunn B, Chang JP 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. 2008 PMID: 19053479
Yeates TO, Yu F Equations for determining tetartohedral twin fractions. Acta Crystallogr. D Biol. Crystallogr.. Nov 2008. 64(Pt 11):1158-64. 2008 PMID: 19020354
Kudryashov DS, Durer ZA, Ytterberg AJ, Sawaya MR, Pashkov I, Prochazkova K, Yeates TO, Loo RR, Loo JA, Satchell KJ, Reisler E 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. 2008 PMID: 19015515
Cheng S, Liu Y, Crowley CS, Yeates TO, Bobik TA Bacterial microcompartments: their properties and paradoxes. Bioessays. Nov 2008. 30(11-12):1084-95. 2008 PMID: 18937343
Crowley CS, Sawaya MR, Bobik TA, Yeates TO Structure of the PduU shell protein from the Pdu microcompartment of Salmonella. Structure. Sep 2008. 16(9):1324-32. 2008 PMID: 18786396
Yeates TO, Kerfeld CA, Heinhorst S, Cannon GC, Shively JM Protein-based organelles in bacteria: carboxysomes and related microcompartments. Nat. Rev. Microbiol.. Sep 2008. 6(9):681-91. 2008 PMID: 18679172
King NP, Lee TM, Sawaya MR, Cascio D, Yeates TO 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. 2008 PMID: 18513746
Sawaya MR, Kudryashov DS, Pashkov I, Adisetiyo H, Reisler E, Yeates TO 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. 2008 PMID: 18391412
Tanaka S, Kerfeld CA, Sawaya MR, Cai F, Heinhorst S, Cannon GC, Yeates TO Atomic-level models of the bacterial carboxysome shell. Science. Feb 2008. 319(5866):1083-6. 2008 PMID: 18292340

2007

Yeates TO, Clubb RT Biochemistry. How some pili pull. Science. Dec 2007. 318(5856):1558-9. 2007 PMID: 18063774
Yeates TO, Norcross TS, King NP Knotted and topologically complex proteins as models for studying folding and stability. Curr Opin Chem Biol. Dec 2007. 11(6):595-603. 2007 PMID: 17967433
Tanaka S, Sawaya MR, Kerfeld CA, Yeates TO Structure of the RuBisCO chaperone RbcX from Synechocystis sp. PCC6803. Acta Crystallogr. D Biol. Crystallogr.. Oct 2007. 63(Pt 10):1109-12. 2007 PMID: 17881829
King NP, Yeates EO, Yeates TO Identification of rare slipknots in proteins and their implications for stability and folding. J. Mol. Biol.. Oct 2007. 373(1):153-66. 2007 PMID: 17764691
Tsai Y, Sawaya MR, Cannon GC, Cai F, Williams EB, Heinhorst S, Kerfeld CA, Yeates TO Structural analysis of CsoS1A and the protein shell of the Halothiobacillus neapolitanus carboxysome. PLoS Biol.. Jun 2007. 5(6):e144. 2007 PMID: 17518518
Yeates TO, Tsai Y, Tanaka S, Sawaya MR, Kerfeld CA Self-assembly in the carboxysome: a viral capsid-like protein shell in bacterial cells. Biochem. Soc. Trans.. Jun 2007. 35(Pt 3):508-11. 2007 PMID: 17511640
Boutz DR, Cascio D, Whitelegge J, Perry LJ, Yeates TO Discovery of a thermophilic protein complex stabilized by topologically interlinked chains. J. Mol. Biol.. May 2007. 368(5):1332-44. 2007 PMID: 17395198
Yeates TO Protein structure: evolutionary bridges to new folds. Curr. Biol.. Jan 2007. 17(2):R48-50. 2007 PMID: 17240325

2006

Yeates TO, Beeby M Biochemistry. Proteins in a small world. Science. Dec 2006. 314(5807):1882-3. 2006 PMID: 17185587
Banatao DR, Cascio D, Crowley CS, Fleissner MR, Tienson HL, Yeates TO An approach to crystallizing proteins by synthetic symmetrization. Proc. Natl. Acad. Sci. U.S.A.. Oct 2006. 103(44):16230-5. 2006 PMID: 17050682
Laidman J, Forse GJ, Yeates TO Conformational change and assembly through edge beta strands in transthyretin and other amyloid proteins. Acc. Chem. Res.. Sep 2006. 39(9):576-83. 2006 PMID: 16981673
Norcross TS, Yeates TO A framework for describing topological frustration in models of protein folding. J. Mol. Biol.. Sep 2006. 362(3):605-21. 2006 PMID: 16930616
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.. Mar 2006. 281(11):7546-55. 2006 PMID: 16407248

2005

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.. Oct 2005. 272(20):5110-8. 2005 PMID: 16218945
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.. Sep 2005. 102(37):13105-10. 2005 PMID: 16141336
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.. Sep 2005. 3(9):e309. 2005 PMID: 16111437
Kerfeld CA, Sawaya MR, Tanaka S, Nguyen CV, Phillips M, Beeby M, Yeates TO Protein structures forming the shell of primitive bacterial organelles. Science. Aug 2005. 309(5736):936-8. 2005 PMID: 16081736
Chaudhuri BN, Yeates TO A computational method to predict genetically encoded rare amino acids in proteins. Genome Biol.. 2005. 6(9):R79. 2005 PMID: 16168086

2004

Bowers PM, Cokus SJ, Eisenberg D, Yeates TO Use of logic relationships to decipher protein network organization. Science. Dec 2004. 306(5705):2246-9. 2004 PMID: 15618515
O'Connor BD, Yeates TO GDAP: a web tool for genome-wide protein disulfide bond prediction. Nucleic Acids Res.. Jul 2004. 32(Web Server issue):W360-4. 2004 PMID: 15215411
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. 2004 PMID: 15128449

2003

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.. Dec 2003. 31(24):7099-109. 2003 PMID: 14654685
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.. Sep 2003. 8(7):707-14. 2003 PMID: 12827458
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.. Jul 2003. 44(7):697-706. 2003 PMID: 12881497
Chaudhuri BN, Sawaya MR, Kim CY, Waldo GS, Park MS, Terwilliger TC, Yeates TO The crystal structure of the first enzyme in the pantothenate biosynthetic pathway, ketopantoate hydroxymethyltransferase, from M tuberculosis. Structure. Jul 2003. 11(7):753-64. 2003 PMID: 12842039
Padilla JE, Yeates TO 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. 2003 PMID: 12832754
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.. Jun 2003. 10(6):461-7. 2003 PMID: 12754496
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.. Feb 2003. 59(Pt 2):290-8. 2003 PMID: 12554939
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. Jan 2003. 11(1):55-65. 2003 PMID: 12517340

2002

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.. Dec 2002. 58(Pt 12):2055-9. 2002 PMID: 12454464
Nitao LK, Yeates TO, Reisler E Conformational dynamics of the SH1-SH2 helix in the transition states of myosin subfragment-1. Biophys. J.. Nov 2002. 83(5):2733-41. 2002 PMID: 12414706
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.. Oct 2002. 9(10):734-9. 2002 PMID: 12219081
Yeates TO, Padilla JE Designing supramolecular protein assemblies. Curr. Opin. Struct. Biol.. Aug 2002. 12(4):464-70. 2002 PMID: 12163069
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.. Jul 2002. 99(15):9679-84. 2002 PMID: 12107280
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.. Jul 2002. 58(Pt 7):1104-10. 2002 PMID: 12077429
Ryttersgaard C, Griffith SC, Sawaya MR, MacLaren DC, Clarke S, Yeates TO Crystal structure of human L-isoaspartyl methyltransferase. J. Biol. Chem.. Mar 2002. 277(12):10642-6. 2002 PMID: 11792715

2001

Griffith SC, Sawaya MR, Boutz DR, Thapar N, Katz JE, Clarke S, Yeates TO 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. 2001 PMID: 11700066
Sawaya MR, Krogmann DW, Serag A, Ho KK, Yeates TO, Kerfeld CA Structures of cytochrome c-549 and cytochrome c6 from the cyanobacterium Arthrospira maxima. Biochemistry. Aug 2001. 40(31):9215-25. 2001 PMID: 11478889
Serag AA, Altenbach C, Gingery M, Hubbell WL, Yeates TO Identification of a subunit interface in transthyretin amyloid fibrils: evidence for self-assembly from oligomeric building blocks. Biochemistry. Aug 2001. 40(31):9089-96. 2001 PMID: 11478875
Padilla JE, Colovos C, Yeates TO 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. 2001 PMID: 11226219

2000

Colovos C, Toth EA, Yeates TO 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. 2000 PMID: 11053840
Toth EA, Worby C, Dixon JE, Goedken ER, Marqusee S, Yeates TO 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. 2000 PMID: 10926519
Eisenberg D, Marcotte EM, Xenarios I, Yeates TO Protein function in the post-genomic era. Nature. Jun 2000. 405(6788):823-6. 2000 PMID: 10866208

1999

Pellegrini M, Yeates TO Searching for frameshift evolutionary relationships between protein sequence families. Proteins. Nov 1999. 37(2):278-83. 1999 PMID: 10584072
Marcotte EM, Pellegrini M, Thompson MJ, Yeates TO, Eisenberg D A combined algorithm for genome-wide prediction of protein function. Nature. Nov 1999. 402(6757):83-6. 1999 PMID: 10573421
Marcotte EM, Pellegrini M, Yeates TO, Eisenberg D A census of protein repeats. J. Mol. Biol.. Oct 1999. 293(1):151-60. 1999 PMID: 10512723
Marcotte EM, Pellegrini M, Ng HL, Rice DW, Yeates TO, Eisenberg D Detecting protein function and protein-protein interactions from genome sequences. Science. Jul 1999. 285(5428):751-3. 1999 PMID: 10427000
Pellegrini M, Marcotte EM, Yeates TO A fast algorithm for genome-wide analysis of proteins with repeated sequences. Proteins. Jun 1999. 35(4):440-6. 1999 PMID: 10382671
Pellegrini M, Marcotte EM, Thompson MJ, Eisenberg D, Yeates TO Assigning protein functions by comparative genome analysis: protein phylogenetic profiles. Proc. Natl. Acad. Sci. U.S.A.. Apr 1999. 96(8):4285-8. 1999 PMID: 10200254
Yeates TO, Fam BC Protein crystals and their evil twins. Structure. Feb 1999. 7(2):R25-9. 1999 PMID: 10368291

1998

Kerfeld CA, Salmeen AE, Yeates TO Crystal structure and possible dimerization of the high-potential iron-sulfur protein from Chromatium purpuratum. Biochemistry. Oct 1998. 37(40):13911-7. 1998 PMID: 9760225

1997

Pellegrini M, Grønbech-Jensen N, Kelly JA, Pfluegl GM, Yeates TO Highly constrained multiple-copy refinement of protein crystal structures. Proteins. Dec 1997. 29(4):426-32. 1997 PMID: 9408940
Kerfeld CA, Wu YP, Chan C, Krogmann DW, Yeates TO 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. 1997 PMID: 15299860
Pellegrini M, Wukovitz SW, Yeates TO Simulation of protein crystal nucleation. Proteins. Aug 1997. 28(4):515-21. 1997 PMID: 9261867
Yeates TO Detecting and overcoming crystal twinning. Meth. Enzymol.. 1997. 276:344-58. 1997 PMID: 9048378
Yeates TO [22] Detecting and overcoming crystal twinning. Meth. Enzymol.. 1997. 276:344-358. 1997 PMID: 27799105

1996

Kerfeld CA, Chan C, Hirasawa M, Kleis-SanFrancisco S, Yeates TO, Knaff DB Isolation and characterization of soluble electron transfer proteins from Chromatium purpuratum. Biochemistry. Jun 1996. 35(24):7812-8. 1996 PMID: 8672482
Redinbo MR, Eide SM, Stone RL, Dixon JE, Yeates TO Crystallization and preliminary structural analysis of Bacillus subtilis adenylosuccinate lyase, an enzyme implicated in infantile autism. Protein Sci.. Apr 1996. 5(4):786-8. 1996 PMID: 8845770
Kelly JA, Feigon J, Yeates TO Reconciliation of the X-ray and NMR structures of the thrombin-binding aptamer d(GGTTGGTGTGGTTGG). J. Mol. Biol.. Mar 1996. 256(3):417-22. 1996 PMID: 8604127

1995

Wukovitz SW, Yeates TO Why protein crystals favour some space-groups over others. Nat. Struct. Biol.. Dec 1995. 2(12):1062-7. 1995 PMID: 8846217
Kerfeld CA, Anwar HP, Interrante R, Merchant S, Yeates TO The structure of chloroplast cytochrome c6 at 1.9 A resolution: evidence for functional oligomerization. J. Mol. Biol.. Jul 1995. 250(5):627-47. 1995 PMID: 7623381
Yeates TO Algorithms for evaluating the long-range accessibility of protein surfaces. J. Mol. Biol.. Jun 1995. 249(4):804-15. 1995 PMID: 7602592

1994

Kelly JA, Singer E, Osslund TD, Yeates TO Crystallization and preliminary structural studies of neurotrophin-3. Protein Sci.. Jun 1994. 3(6):982-3. 1994 PMID: 8069227
Redinbo MR, Yeates TO, Merchant S Plastocyanin: structural and functional analysis. J. Bioenerg. Biomembr.. Feb 1994. 26(1):49-66. 1994 PMID: 8027022

1993

Redinbo MR, Cascio D, Choukair MK, Rice D, Merchant S, Yeates TO The 1.5-A crystal structure of plastocyanin from the green alga Chlamydomonas reinhardtii. Biochemistry. Oct 1993. 32(40):10560-7. 1993 PMID: 8399201
Colovos C, Yeates TO Verification of protein structures: patterns of nonbonded atomic interactions. Protein Sci.. Sep 1993. 2(9):1511-9. 1993 PMID: 8401235
Redinbo MR, Yeates TO 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. 1993 PMID: 15299512
Yeates TO, Zhang KY Ambiguities in ab initio phasing. Science. Mar 1993. 259(5102):1771-2. 1993 PMID: 17816893
Yeates TO 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. 1993 PMID: 8442929

1991

Yeates TO, Jacobson DH, Martin A, Wychowski C, Girard M, Filman DJ, Hogle JM Three-dimensional structure of a mouse-adapted type 2/type 1 poliovirus chimera. EMBO J.. Sep 1991. 10(9):2331-41. 1991 PMID: 1651227

1990

Yeates TO Determination of the correct reference frame from an atomic coordinate list. Acta Crystallogr., A, Found. Crystallogr.. Jul 1990. 46 ( Pt 7):625-6. 1990 PMID: 2206485
Yeates TO, Rini JM Intensity-based domain refinement of oriented but unpositioned molecular replacement models. Acta Crystallogr., A, Found. Crystallogr.. May 1990. 46 ( Pt 5):352-9. 1990 PMID: 2198887

1989

Rees DC, Komiya H, Yeates TO, Allen JP, Feher G The bacterial photosynthetic reaction center as a model for membrane proteins. Annu. Rev. Biochem.. 1989. 58:607-33. 1989 PMID: 2673018

1988

Komiya H, Yeates TO, Rees DC, Allen JP, Feher G 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. 1988 PMID: 3057498
Yeates TO, Komiya H, Chirino A, Rees DC, Allen JP, Feher G 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. 1988 PMID: 3186702
Allen JP, Feher G, Yeates TO, Komiya H, Rees DC 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. 1988 PMID: 3054889
Yeates TO Simple statistics for intensity data from twinned specimens. Acta Crystallogr., A, Found. Crystallogr.. Mar 1988. 44 ( Pt 2):142-4. 1988 PMID: 3272147

1987

Yeates TO, Komiya H, Rees DC, Allen JP, Feher G 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. 1987 PMID: 3306679
Allen JP, Feher G, Yeates TO, Komiya H, Rees DC 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. 1987 PMID: 2819866
Allen JP, Feher G, Yeates TO, Komiya H, Rees DC 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. 1987 PMID: 3303032

1986

Allen JP, Feher G, Yeates TO, Rees DC, Deisenhofer J, Michel H, Huber R 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. 1986 PMID: 3022298