UCLA Chemistry and Biochemistry
Home Biochemistry  Inorganic    Organic     Physical  

Todd Yeates, Ph.D.

Website:

Todd Yeates's Home Page.

Work Email Address:

yeates@mbi.ucla.edu

Laboratory Address:

Laboratory
Paul Boyer Hall 259

Work Address:

Office
Paul Boyer Hall 255A

Lab Number:

1 (310) 825-8901

Work Phone Number:

1 (310) 206-4866
Professor
Biochemistry
Member
Biochemistry & Molecular Biology (BMB) Graduate Program, California NanoSystems Institute, JCCC Cancer Cell Biology Program Area

A 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

Prof. Yeates accepts graduate students through the Biochemistry and Molecular Biology (BMB) Graduate Program and the UCLA ACCESS Ph.D. Program.

Awards and Honors:

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

Research Interest:

Professor Yeates and his research group work in the areas of structural and computational biology. In the area of structural biology, a subject of special interest is the bacterial microcompartment, a virus-like structure that appears to serve as a primitive organelle inside certain bacterial cells. Strategies are also being developed for designing novel proteins that assemble into ordered nanometer scale structures. In the area of computational biology, the emphasis is on bioinformatics and comparative genomics. Recent work has led to the discovery of proteins that are able to maintain their stabilities at extreme temperatures through unusual mechanisms, for example by folding into knotted or interlinked conformations. In addition, new computational methods are being developed for deciphering protein function and protein interactions in the cell.


Detailed Biography:

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

Publications:

Chaudhuri BN, Yeates TO   A computational method to predict genetically encoded rare amino acids in proteins Genome Biol, 2005; 6(9): R79.
Beeby M, O'Connor BD, Ryttersgaard C, Boutz DR, Perry LJ, Yeates TO   The genomics of disulfide bonding and protein stabilization in thermophiles PLoS Biol, 2005; 3(9): e309.
Bowers PM, O'Connor BD, Cokus SJ, Sprinzak E, Yeates TO, Eisenberg D   Utilizing logical relationships in genomic data to decipher cellular processes Febs J, 2005; 272(20): 5110-8.
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.
Elam JS, Taylor AB, Strange R, Antonyuk S, Doucette PA, Rodriguez JA, Hasnain SS, Hayward LJ, Valentine JS, Yeates TO, Hart PJ   Amyloid-like filaments and water-filled nanotubes formed by SOD1 mutant proteins linked to familial ALS Nat Struct Biol, 2003; 10(6): 461-7.
Serag AA, Altenbach C, Gingery M, Hubbell WL, Yeates TO   Erratum: Arrangement of subunits and ordering of beta-strands in an amyloid sheet Nat Struct Biol, 2003; 10(1): 70.
Kerfeld CA, Sawaya MR, Bottin H, Tran KT, Sugiura M, Cascio D, Desbois A, Yeates TO, Kirilovsky D, Boussac A   Structural and EPR characterization of the soluble form of cytochrome c-550 and of the psbV2 gene product from the cyanobacterium Thermosynechococcus elongatus Plant Cell Physiol, 2003; 44(7): 697-706.
Kerfeld CA, Yoshida S, Tran KT, Yeates TO, Cascio D, Bottin H, Berthomieu C, Sugiura M, Boussac A   The 1.6 A resolution structure of Fe-superoxide dismutase from the thermophilic cyanobacterium Thermosynechococcus elongatus J Biol Inorg Chem, 2003; 8(7): 707-14.
Rudolph MG, Kelker MS, Schneider TR, Yeates TO, Oseroff V, Heidary DK, Jennings PA, Wilson IA   Use of multiple anomalous dispersion to phase highly merohedrally twinned crystals of interleukin-1beta Acta Crystallogr D Biol Crystallogr, 2003; 59(Pt 2): 290-8.
Serag AA, Altenbach C, Gingery M, Hubbell WL, Yeates TO   Arrangement of subunits and ordering of beta-strands in an amyloid sheet Nat Struct Biol, 2002; 9(10): 734-9.
Nitao LK, Yeates TO, Reisler E   Conformational dynamics of the SH1-SH2 helix in the transition states of myosin subfragment-1 Biophys J, 2002; 83(5): 2733-41.
Yeates TO, Padilla JE   Designing supramolecular protein assemblies Curr Opin Struct Biol, 2002; 12(4): 464-70.
Larsen NA, Heine A, de Prada P, Redwan el R, Yeates TO, Landry DW, Wilson IA   Structure determination of a cocaine hydrolytic antibody from a pseudomerohedrally twinned crystal Acta Crystallogr D Biol Crystallogr, 2002; 58(Pt 12): 2055-9.
Kerfeld CA, Sawaya MR, Krogmann DW, Yeates TO   Structure of cytochrome c6 from Arthrospira maxima: an assembly of 24 subunits in a nearly symmetric shell Acta Crystallogr D Biol Crystallogr, 2002; 58(Pt 7): 1104-10.
Sawaya MR, Cannon GC, Heinhorst S, Tanaka S, Williams EB, Yeates TO, Kerfeld CA   The Structure of beta-Carbonic Anhydrase from the Carboxysomal Shell Reveals a Distinct Subclass with One Active Site for the Price of Two J Biol Chem, 2006; 281(11): 7546-55.
Kudryashov DS, Sawaya MR, Adisetiyo H, Norcross T, Hegyi G, Reisler E, Yeates TO   The crystal structure of a cross-linked actin dimer suggests a detailed molecular interface in F-actin Proc Natl Acad Sci U S A, 2005; 102(37): 13105-10.
Bowers PM, Cokus SJ, Eisenberg D, Yeates TO   Use of logic relationships to decipher protein network organization Science, 2004; 306(5705): 2246-9.
O'Connor BD, Yeates TO   GDAP: a web tool for genome-wide protein disulfide bond prediction Nucleic Acids Res, 2004; 32(Web Server issue): W360-4.
Strong M, Graeber TG, Beeby M, Pellegrini M, Thompson MJ, Yeates TO, Eisenberg D   Visualization and interpretation of protein networks in Mycobacterium tuberculosis based on hierarchical clustering of genome-wide functional linkage maps Nucleic Acids Res, 2003; 31(24): 7099-109.
Padilla JE, Yeates TO   A statistic for local intensity differences: robustness to anisotropy and pseudo-centering and utility for detecting twinning. Acta crystallographica. Section D, Biological crystallography. , 2003; 59(Pt 7): 1124-30.
Kerfeld CA, Sawaya MR, Brahmandam V, Cascio D, Ho KK, Trevithick-Sutton CC, Krogmann DW, Yeates TO   The crystal structure of a cyanobacterial water-soluble carotenoid binding protein Structure (Cambridge, Mass. : 2001) , 2003; 11(1): 55-65.
Mallick P, Boutz DR, Eisenberg D, Yeates TO   Genomic evidence that the intracellular proteins of archaeal microbes contain disulfide bonds Proc Natl Acad Sci U S A, 2002; 99(15): 9679-84.
Ryttersgaard C, Griffith SC, Sawaya MR, MacLaren DC, Clarke S, Yeates TO   Crystal structure of human L-isoaspartyl methyltransferase J Biol Chem, 2002; 277(12): 10642-6.
UCLA Homepage  ·  UCLA Division of Physical Sciences  ·  © UC Regents  ·  General Information
Graduate Office  ·  Undergraduate Office  ·  Chair's Office