Works by Yeates, Todd O.

Results: 67

Structural Analysis of CsoS1A and the Protein Shell of the Halothiobacillus neapolitanus Carboxysome.

Published in:

PLoS Biology, 2007, v. 5, n. 6, p. e144, doi. 10.1371/journal.pbio.0050144

By:

Tsai, Yingssu;
Sawaya, Michael R.;
Cannon, Gordon C.;
Cai, Fei;
Williams, Eric B.;
Heinhorst, Sabine;
Kerfeld, Cheryl A.;
Yeates, Todd O.

Publication type:

Article

The Genomics of Disulfide Bonding and Protein Stabilization in Thermophiles.

Published in:

PLoS Biology, 2005, v. 3, n. 9, p. 1549, doi. 10.1371/journal.pbio.0030309

By:

Beeby, Morgan;
O'Connor, Brian D.;
Ryttersgaard, Carsten;
Boutz, Daniel R.;
Perry, L. Jeanne;
Yeates, Todd O.

Publication type:

Article

The Genomics of Disulfide Bonding and Protein Stabilization in Thermophiles.

Published in:

PLoS Biology, 2005, v. 3, n. 8, p. 1, doi. 10.1371/journal.pbio.0030309

By:

Beeby, Morgan;
O'Connor, Brian D;
Ryttersgaard, Carsten;
Boutz, Daniel R;
Perry, L. Jeanne;
Yeates, Todd O

Publication type:

Article

GDAP: a web tool for genome-wide protein disulfide bond prediction.

Published in:

Nucleic Acids Research, 2004, v. 32, n. suppl 2, p. w360, doi. 10.1093/nar/gkh376

By:

O'Connor, Brian D.;
Yeates, Todd O.

Publication type:

Article

Visualization and interpretation of protein networks in Mycobacterium tuberculosis based on hierarchical clustering of genome‐wide functional linkage maps.

Published in:

Nucleic Acids Research, 2003, v. 31, n. 24, p. 7099, doi. 10.1093/nar/gkg924

By:

Strong, Michael;
Graeber, Thomas G.;
Beeby, Morgan;
Pellegrini, Matteo;
Thompson, Michael J.;
Yeates, Todd O.;
Eisenberg, David

Publication type:

Article

On the predictability of the orientation of protein domains joined by a spanning alpha-helical linker.

Published in:

PEDS: Protein Engineering, Design & Selection, 2015, v. 28, n. 11, p. 491, doi. 10.1093/protein/gzv035

By:

Yen-Ting Lai;
Lin Jiang;
Wuyang Chen;
Yeates, Todd O.

Publication type:

Article

Protein stabilization in a highly knotted protein polymer.

Published in:

PEDS: Protein Engineering, Design & Selection, 2011, v. 24, n. 8, p. 627, doi. 10.1093/protein/gzr024

By:

Sayre, Tobias C.;
Lee, Toni M.;
King, Neil P.;
Yeates, Todd O.

Publication type:

Article

Design of a symmetry‐broken tetrahedral protein cage by a method of internal steric occlusion.

Published in:

Protein Science: A Publication of the Protein Society, 2024, v. 33, n. 4, p. 1, doi. 10.1002/pro.4973

By:

Gladkov, Nika;
Scott, Elena A.;
Meador, Kyle;
Lee, Eric J.;
Laganowsky, Arthur D.;
Yeates, Todd O.;
Castells‐Graells, Roger

Publication type:

Article

AlphaFold predicts the most complex protein knot and composite protein knots.

Published in:

Protein Science: A Publication of the Protein Society, 2022, v. 31, n. 8, p. 1, doi. 10.1002/pro.4380

By:

Brems, Maarten A.;
Runkel, Robert;
Yeates, Todd O.;
Virnau, Peter

Publication type:

Article

Computational design of mixed chirality peptide macrocycles with internal symmetry.

Published in:

Protein Science: A Publication of the Protein Society, 2020, v. 29, n. 12, p. 2433, doi. 10.1002/pro.3974

By:

Mulligan, Vikram Khipple;
Kang, Christine S.;
Sawaya, Michael R.;
Rettie, Stephen;
Li, Xinting;
Antselovich, Inna;
Craven, Timothy W.;
Watkins, Andrew M.;
Labonte, Jason W.;
DiMaio, Frank;
Yeates, Todd O.;
Baker, David

Publication type:

Article

Symmetry breaking and structural polymorphism in a bacterial microcompartment shell protein for choline utilization.

Published in:

Protein Science: A Publication of the Protein Society, 2020, v. 29, n. 11, p. 2201, doi. 10.1002/pro.3941

By:

Ochoa, Jessica M.;
Nguyen, Vy N.;
Nie, Mengxiao;
Sawaya, Michael R.;
Bobik, Thomas A.;
Yeates, Todd O.

Publication type:

Article

Design and structure of two new protein cages illustrate successes and ongoing challenges in protein engineering.

Published in:

Protein Science: A Publication of the Protein Society, 2020, v. 29, n. 4, p. 919, doi. 10.1002/pro.3802

By:

Cannon, Kevin A.;
Park, Rachel U.;
Boyken, Scott E.;
Nattermann, Una;
Yi, Sue;
Baker, David;
King, Neil P.;
Yeates, Todd O.

Publication type:

Article

Searching for frameshift evolutionary relationships between protein sequence families.

Published in:

Proteins, 1999, v. 37, n. 2, p. 278, doi. 10.1002/(SICI)1097-0134(19991101)37:2<278::AID-PROT12>3.0.CO;2-X

By:

Pellegrini, Matteo;
Yeates, Todd O.

Publication type:

Article

A fast algorithm for genome-wide analysis of proteins with repeated sequences.

Published in:

Proteins, 1999, v. 35, n. 4, p. 440, doi. 10.1002/(SICI)1097-0134(19990601)35:4<440::AID-PROT7>3.0.CO;2-Y

By:

Pellegrini, Matteo;
Marcotte, Edward M.;
Yeates, Todd O.

Publication type:

Article

Highly Constrained Multiple-Copy Refinement of Protein Crystal Structures

Published in:

Proteins, 1997, v. 29, n. 4, p. 426

By:

Pellegrini, Matco;
Gronbech-Jensen, Niels;
Kelly, Jennifer A.;
Pfluegl, Gaston M.L.;
Yeates, Todd O

Publication type:

Article

Simulation of protein crystal nucleation.

Published in:

Proteins, 1997, v. 28, n. 4, p. 515, doi. 10.1002/(SICI)1097-0134(199708)28:4<515::AID-PROT5>3.0.CO;2-8

By:

Pellegrini, Matteo;
Wukovitz, Stephanie W.;
Yeates, Todd O.

Publication type:

Article

Exploring Bacterial Organelle Interactomes: A Model of the Protein-Protein Interaction Network in the Pdu Microcompartment.

Published in:

PLoS Computational Biology, 2015, v. 11, n. 2, p. 1, doi. 10.1371/journal.pcbi.1004067

By:

Jorda, Julien;
Liu, Yu;
Bobik, Thomas A.;
Yeates, Todd O.

Publication type:

Article

Design and Construction of a Designed Ankyrin Repeat Protein (DARPin) Display Library.

Published in:

Current Protocols, 2024, v. 4, n. 1, p. 1, doi. 10.1002/cpz1.960

By:

Morselli, Marco;
Holton, Thomas R.;
Pellegrini, Matteo;
Yeates, Todd O.;
Arbing, Mark A.

Publication type:

Article

Facile methods for heterologous production of bacterial microcompartments in diverse host species.

Published in:

Microbial Biotechnology, 2018, v. 11, n. 1, p. 160, doi. 10.1111/1751-7915.12869

By:

Yeates, Todd O.;
Bobik, Thomas A.

Publication type:

Article

(Quasi-)Racemic X-ray Structures of Glycosylated and Non-Glycosylated Forms of the Chemokine Ser-CCL1 Prepared by Total Chemical Synthesis.

Published in:

Angewandte Chemie International Edition, 2014, v. 53, n. 20, p. 5194, doi. 10.1002/anie.201400679

By:

Okamoto, Ryo;
Mandal, Kalyaneswar;
Sawaya, Michael R.;
Kajihara, Yasuhiro;
Yeates, Todd O.;
Kent, Stephen B. H.

Publication type:

Article

The function of the PduJ microcompartment shell protein is determined by the genomic position of its encoding gene.

Published in:

Molecular Microbiology, 2016, v. 101, n. 5, p. 770, doi. 10.1111/mmi.13423

By:

Chowdhury, Chiranjit;
Chun, Sunny;
Sawaya, Michael R.;
Yeates, Todd O.;
Bobik, Thomas A

Publication type:

Article

Bacterial microcompartments: widespread prokaryotic organelles for isolation and optimization of metabolic pathways.

Published in:

Molecular Microbiology, 2015, v. 98, n. 2, p. 193, doi. 10.1111/mmi.13117

By:

Bobik, Thomas A.;
Lehman, Brent P.;
Yeates, Todd O.

Publication type:

Article

A 3.8 Å resolution cryo-EM structure of a small protein bound to an imaging scaffold.

Published in:

Nature Communications, 2019, v. 10, n. 1, p. N.PAG, doi. 10.1038/s41467-019-09836-0

By:

Liu, Yuxi;
Huynh, Duc T.;
Yeates, Todd O.

Publication type:

Article

Bacterial microcompartments: their properties and paradoxes.

Published in:

BioEssays, 2008, v. 30, n. 11/12, p. 1084, doi. 10.1002/bies.20830

By:

Shouqiang Cheng;
Yu Liu;
Crowley, Christopher S.;
Yeates, Todd O.;
Bobik, Thomas A.

Publication type:

Article

Structure of a designed protein cage that self-assembles into a highly porous cube.

Published in:

Nature Chemistry, 2014, v. 6, n. 12, p. 1065, doi. 10.1038/nchem.2107

By:

Lai, Yen-Ting;
Reading, Eamonn;
Hura, Greg L.;
Tsai, Kuang-Lei;
Laganowsky, Arthur;
Asturias, Francisco J.;
Tainer, John A.;
Robinson, Carol V.;
Yeates, Todd O.

Publication type:

Article

(Quasi-)Racemic X-ray Structures of Glycosylated and Non-Glycosylated Forms of the Chemokine Ser-CCL1 Prepared by Total Chemical Synthesis.

Published in:

Angewandte Chemie, 2014, v. 126, n. 20, p. 5294, doi. 10.1002/ange.201400679

By:

Okamoto, Ryo;
Mandal, Kalyaneswar;
Sawaya, Michael R.;
Kajihara, Yasuhiro;
Yeates, Todd O.;
Kent, Stephen B. H.

Publication type:

Article

Accurate design of co-assembling multi-component protein nanomaterials.

Published in:

Nature, 2014, v. 510, n. 7503, p. 103, doi. 10.1038/nature13404

By:

King, Neil P.;
Bale, Jacob B.;
Sheffler, William;
McNamara, Dan E.;
Gonen, Shane;
Gonen, Tamir;
Yeates, Todd O.;
Baker, David

Publication type:

Article

Widespread Disulfide Bonding in Proteins from Thermophilic Archaea.

Published in:

Archaea, 2011, p. 1, doi. 10.1155/2011/409156

By:

Jorda, Julien;
Yeates, Todd O.

Publication type:

Article

Rational improvement of simvastatin synthase solubility in Escherichia coli leads to higher whole-cell biocatalytic activity.

Published in:

Biotechnology & Bioengineering, 2009, v. 102, n. 1, p. 20, doi. 10.1002/bit.22028

By:

Xie, Xinkai;
Pashkov, Inna;
Gao, Xue;
Guerrero, Jennifer L.;
Yeates, Todd O.;
Tang, Yi

Publication type:

Article

X‐ray crystal structure of a designed rigidified imaging scaffold in the ligand‐free conformation.

Published in:

Acta Crystallographica: Section F, Structural Biology Communications, 2024, v. 80, n. 5, p. 107, doi. 10.1107/S2053230X2400414X

By:

Agdanowski, Matthew P.;
Castells-Graells, Roger;
Sawaya, Michael R.;
Cascio, Duilio;
Yeates, Todd O.;
Arbing, Mark A.

Publication type:

Article

Protein-based organelles in bacteria: carboxysomes and related microcompartments.

Published in:

Nature Reviews Microbiology, 2008, v. 6, n. 9, p. 681, doi. 10.1038/nrmicro1913

By:

Yeates, Todd O.;
Kerfeld, Cheryl A.;
Heinhorst, Sabine;
Cannon, Gordon C.;
Shively, Jessup M.

Publication type:

Article

Protein function in the post-genomic era.

Published in:

Nature, 2000, v. 405, n. 6788, p. 823, doi. 10.1038/35015694

By:

Eisenberg, David;
Marcotte, Edward M.;
Xenarios, Ioannis;
Yeates, Todd O.

Publication type:

Article

A combined algorithm for genome-wide prediction of protein function.

Published in:

Nature, 1999, v. 402, n. 6757, p. 83, doi. 10.1038/47048

By:

Marcotte, Edward M.;
Pellegrini, Matteo;
Thompson, Michael J.;
Yeates, Todd O.;
Eisenberg, David

Publication type:

Article

Making topological protein links using enzymatic reactions.

Published in:

National Science Review, 2024, v. 11, n. 3, p. 1, doi. 10.1093/nsr/nwae071

By:

Castells-Graells, Roger;
Yeates, Todd O

Publication type:

Article

MCPdb: The bacterial microcompartment database.

Published in:

PLoS ONE, 2021, v. 16, n. 3, p. 1, doi. 10.1371/journal.pone.0248269

By:

Ochoa, Jessica M.;
Bair, Kaylie;
Holton, Thomas;
Bobik, Thomas A.;
Yeates, Todd O.

Publication type:

Article

Amyloid-like filaments and water-filled nanotubes formed by SOD1 mutant proteins linked to familial ALS.

Published in:

Nature Structural Biology, 2003, v. 10, n. 6, p. 461, doi. 10.1038/nsb935

By:

Elam, Jennifer Stine;
Taylor, Alexander B;
Strange, Richard;
Antonyuk, Svetlana;
Doucette, Peter A;
Rodriguez, Jorge A;
Hasnain, S Samar;
Hayward, Lawrence J;
Valentine, Joan Selverstone;
Yeates, Todd O;
Hart, P John

Publication type:

Article

Erratum: Arrangement of subunits and ordering of β-strands in an amyloid sheet.

Published in:

2003

By:

Serag, Ahmed A.;
Altenbach, Christian;
Gingery, Mari;
Hubbell, Wayne L.;
Yeates, Todd O.

Publication type:

Erratum

Arrangement of subunits and ordering of β-strands in an amyloid sheet.

Published in:

Nature Structural Biology, 2002, v. 9, n. 10, p. 734, doi. 10.1038/nsb838

By:

Serag, Ahmed A.;
Altenbach, Christian;
Gingery, Mari;
Hubbell, Wayne L.;
Yeates, Todd O.

Publication type:

Article

The 1.6 Ä resolution structure of Fe-superoxide dismutase from the thermophilic cyanobacterium Thermosynechococcus elongatus.

Published in:

Journal of Biological Inorganic Chemistry (JBIC), 2003, v. 8, n. 7, p. 707, doi. 10.1007/s00775-003-0469-0

By:

Cheryl A. Kerfeld;
Stephanie Yoshida;
Kimberlee T. Tran;
Todd O. Yeates;
Duilio Cascio;
Hervé Bottin;
Catherine Berthomieu;
Miwa Sugiura;
Alain Boussac

Publication type:

Article

AlphaFold‐assisted structure determination of a bacterial protein of unknown function using X‐ray and electron crystallography.

Published in:

Acta Crystallographica: Section D, Structural Biology, 2024, v. 80, n. 4, p. 270, doi. 10.1107/S205979832400072X

By:

Miller, Justin E.;
Agdanowski, Matthew P.;
Dolinsky, Joshua L.;
Sawaya, Michael R.;
Cascio, Duilio;
Rodriguez, Jose A.;
Yeates, Todd O.

Publication type:

Article

Microfocus diffraction from different regions of a protein crystal: structural variations and unit‐cell polymorphism.

Published in:

Acta Crystallographica: Section D, Structural Biology, 2018, v. 74, n. 5, p. 411, doi. 10.1107/S2059798318003479

By:

Thompson, Michael C.;
Cascio, Duilio;
Yeates, Todd O.

Publication type:

Article

Progress in low-resolution ab initio phasing with CrowdPhase.

Published in:

Acta Crystallographica: Section D, Structural Biology, 2016, v. 72, n. 3, p. 446, doi. 10.1107/S2059798316003405

By:

Jorda, Julien;
Sawaya, Michael R.;
Yeates, Todd O.

Publication type:

Article

Utilizing logical relationships in genomic data to decipher cellular processes.

Published in:

FEBS Journal, 2005, v. 272, n. 20, p. 5110, doi. 10.1111/j.1742-4658.2005.04946.x

By:

Bowers, Peter M.;
O'Connor, Brian D.;
Cokus, Shawn J.;
Sprinzak, Einat;
Yeates, Todd O.;
Eisenberg, David

Publication type:

Article

Crystal structure of MbnF: an NADPH‐dependent flavin monooxygenase from Methylocystis strain SB2.

Published in:

Acta Crystallographica: Section F, Structural Biology Communications, 2023, v. 79, n. 5, p. 111, doi. 10.1107/S2053230X23003035

By:

Stewart, Andrew;
Dershwitz, Philip;
Stewart, Charles;
Sawaya, Michael R.;
Yeates, Todd O.;
Semrau, Jeremy D.;
Zischka, Hans;
DiSpirito, Alan A.;
Bobik, Thomas A.

Publication type:

Article

Structural characterization of hexameric shell proteins from two types of choline‐utilization bacterial microcompartments.

Published in:

Acta Crystallographica: Section F, Structural Biology Communications, 2021, v. 77, n. 9, p. 275, doi. 10.1107/S2053230X21007470

By:

Ochoa, Jessica M.;
Mijares, Oscar;
Acosta, Andrea A.;
Escoto, Xavier;
Leon-Rivera, Nancy;
Marshall, Joanna D.;
Sawaya, Michael R.;
Yeates, Todd O.

Publication type:

Article

The structure of bovine β‐lactoglobulin in crystals grown at pH 3.8 exhibiting novel threefold twinning.

Published in:

Acta Crystallographica: Section F, Structural Biology Communications, 2019, v. 75, n. 10, p. 640, doi. 10.1107/S2053230X1901224X

By:

Yeates, Todd O.;
McPherson, Alexander

Publication type:

Article

Structure of a bacterial microcompartment shell protein bound to a cobalamin cofactor.

Published in:

Acta Crystallographica: Section F, Structural Biology Communications, 2014, v. 70, n. 12, p. 1584, doi. 10.1107/S2053230X1402158X

By:

Thompson, Michael C.;
Crowley, Christopher S.;
Kopstein, Jeffrey;
Bobik, Thomas A.;
Yeates, Todd O.

Publication type:

Article

Structure of the methanofuran/methanopterin-biosynthetic enzyme MJ1099 from Methanocaldococcus jannaschii.

Published in:

Acta Crystallographica: Section F, Structural Biology Communications, 2014, v. 70, n. 11, p. 1472, doi. 10.1107/S2053230X1402130X

By:

Bobik, Thomas A.;
Morales, Erick J.;
Shin, Annie;
Cascio, Duilio;
Sawaya, Michael R.;
Arbing, Mark;
Yeates, Todd O.;
Rasche, Madeline E.

Publication type:

Article

Nanobiotechnology: Protein arrays made to order.

Published in:

Nature Nanotechnology, 2011, v. 6, n. 9, p. 541, doi. 10.1038/nnano.2011.127

By:

Yeates, Todd O.

Publication type:

Article

fragment-based protein interface design algorithm for symmetric assemblies.

Published in:

PEDS: Protein Engineering, Design & Selection, 2021, v. 34, p. 1, doi. 10.1093/protein/gzab008

By:

Laniado, Joshua;
Meador, Kyle;
Yeates, Todd O

Publication type:

Article