Keating Lab

Networks of bZIP protein-protein interactions diversified over a billion years of evolution

Aaron W. Reinke, Jiyeon Baek, Orr Ashenberg, Amy E. Keating

Science, 2013 [PMID: 23661758] [Full Text]

Multistate Protein Design Using CLEVER and CLASSY

Christopher Negron, and Amy E. Keating

Methods in Enzymology, 2013;523:171-90.[PMID: 23422430]

Peptide ligands for pro-survival protein Bfl-1 from computationally guided library screening

Sanjib Dutta, T. Scott Chen, and Amy E. Keating

ACS Chemical Biology, 2013 (In Press) [PMID: 23363053]

Helix Bundle Loops Determine Whether Histidine Kinases Autophosphorylate in Cis or in Trans

Orr Ashenberg, Amy E. Keating, and Michael T. Laub

Journal of Molecular Biology, 2013 (In Press) [PMID: 23333741]

bZIP transcription factors affecting secondary metabolism, sexual development and stress responses in Aspergillus nidulans

Wen-Bing Yin, Aaron W. Reinke, Melinda Szilágyi, Tamás Emri, Yi-Ming Chiang, Amy E. Keating, István Pócsi, Clay C. C. Wang and Nancy P. Keller

Microbiology, 2013 Jan;159(Pt 1):77-88 [PMID: 23154967]

Structure-based redesign of the binding specificity of anti-apoptotic Bcl-x(L)

T. Scott Chen, Hector Palacios, and Amy E. Keating

Journal of Molecular Biology, 2013 Jan 9;425(1):171-85 [PMID: 23154169]

In silico and in vitro elucidation of BH3 binding specificity toward Bcl-2

Nir London, Stefano Gullá, Amy E. Keating, and Ora Schueler-Furman

Biochemistry, 2012 Jul 24;51(29):5841-50 [PMID: 22702834]

Predictive Bcl-2 Family Binding Models Rooted in Experiment or Structure

Joe DeBartolo, Sanjib Dutta, Lothar Reich, and Amy E. Keating

Journal of Molecular Biology, 2012 Sep 7;422(1):124-44 [PMID: 22617328]

Designing specific protein-protein interactions using computation, experimental library screening, or integrated methods

T. Scott Chen, and Amy E. Keating

Protein Science, 2012 doi:10.1002/pro.2096. PMID: 22593041

The SYNZIP protein interaction toolbox: in vitro and in vivo specifications of heterospecific coiled-coil interaction domains

K. Evan Thompson, Caleb J. Bashor, Wendell A. Lim & Amy E. Keating

ACS Synthetic Biology, 2012 Apr 20;1(4):118-129. PMID: 22558529

Multicoil2: predicting coiled coils and their oligomerization states from sequence in the twilight zone

Jason Trigg, Karl Gutwin, Amy E. Keating & Bonnie Berger

PLoS One, 2011 6(8):e23519. PMID: 21901122

Determinants of homodimerization specificity in histidine kinases.

Orr Ashenberg, Kathryn Rozen-Gagnon, Michael T. Laub, Amy E. Keating

Journal of Molecular Biology, 2011 Oct;413(1):222-35. PMID: 21854787

Design of Peptide Inhibitors that Bind the bZIP Domain of Epstein-Barr Virus protein BZLF1

T. Scott Chen, Aaron W. Reinke and Amy E. Keating

Journal of Molecular Biology, 2011 Apr;408(2), 304–320 PMID: 21354428

Protein Binding Specificity versus Promiscuity

Gideon Schreiber & Amy E. Keating

Current Opinion in Structural Biology, 2011 Feb; 21(1):50-61 PMID: 21071205

Identifying and reducing error in cluster expansion approximations of protein energies

Seungsoo Hahn, Orr Asherberg, Gevorg Grigoryan, Amy E. Keating

Journal of Computational Chemistry, 2010 Dec;31(16):2900-14. PMID: 20602445

The MCL-1 BH3 Helix is an Exclusive MCL-1 inhibitor and Apoptosis Sensitizer

Michelle L. Stewart, Emiko Fire, Amy E. Keating, Loren D. Walensky

Nature Chemical Biology, 2010 Aug;6(8):595-601. PMID: 20562877

A synthetic coiled-coil interactome provides heterospecific modules for molecular engineering

Aaron W. Reinke, Robert A. Grant, Amy E. Keating.

J Am Chem Soc. 2010 May 5;132(17):6025-31.PMID: 20387835 

Determinants of BH3 Binding Specificity for Mcl-1 versus Bcl-x(L).

Sanjib Dutta, Stefano Gullá, T Scott Chen, Emiko Fire, Robert A. Grant, Amy E. Keating.

J Mol Biol. 2010 May 21;398(5):747-62. PMID: 20363230 

Specific coiled-coil interactions contribute to a global model of the structure of the spindle pole body

Nora Zizlsperger, Amy E. Keating

J Struct Biol. 170(2):246-56.(2010) Epub 2010 Feb 6. PMID: 20139001

Identification of bZIP interaction partners of viral proteins HBZ, MEQ, BZLF1, and K-bZIP using coiled-coil arrays

Aaron W. Reinke, Gevorg Grigoryan, Amy E. Keating

Biochemistry 49(9):1985-97. (2010) PMID: 20102225 

Mcl-1-Bim complexes accommodate surprising point mutations via minor structural changes

Emiko Fire, Stefano Gulla, Robert Grant, Amy E. Keating

Protein science 19(3):507-19. (2010) PMID: 20066663 

Design of protein-interaction specificity gives selective bZIP-binding peptides

Gevorg Grigoryan, Aaron W. Reinke, Amy E. Keating

Nature, 458, 859-864 (2009)

Cluster expansion models for flexible-backbone protein energetics

James R. Apgar, Seungsoo Hahn, Gevorg Grigoryan, Amy E. Keating

Journal of Computational Chemistry 30, 2402-13 (2009)

X-ray vs. NMR structures as templates for computational protein design

Michael Schneider, Xiaoran Fu, Amy E. Keating

Proteins 77, 97-110 (2009)

A computationally guided protein-interaction screen uncovers coiled-coil interactions involved in vesicle-mediated transport

Hong Zhang, Jinan Chen, Yongqiang Wang, Lin Peng, Xiaoxi Dong, Yi Lu, Amy E. Keating, Taijiao Jiang

Journal of  Molecular Biology 392, 228-241 (2009)

Analysis of coiled-coil interactions between core proteins of the spindle pole body

Nora Zizlsperger, Vladimir N. Malashkevich, Shirin Pillay, and Amy E. Keating

Biochemistry 47, 11858-68 (2008)

[HTML] [PDF] (MIT access only)

Structural specificity in coiled-coil interactions

Gevorg Grigoryan and Amy E Keating

Current Opinion in Structural Biology 18, 477-483 (2008)

[HTML] [PDF] (MIT access only)

Predicting helix orientation for coiled-coil dimers

James R. Apgar, Karl N. Gutwin, and Amy E. Keating

PROTEINS: Structure, Function, Bioinformatics 72, 1048-1065 (2008)

[Abstract] [PDF] (MIT access only)

Modeling backbone flexibility to achieve sequence diversity: the design of novel alpha-helical ligands for Bcl-xL.

Xiaoran Fu, James R. Apgar, Amy E. Keating

Journal of  Molecular Biology 371, 1099-117 (2007)


Computing van der Waals energies in the context of the rotamer approximation

Gevorg Grigoryan, Alejandro Ochoa, Amy E. Keating

PROTEINS: Structure, Function, Bioinformatics , 68(4): 863 - 878 (6 Jun 2007).

[Abstract] [PDF] (MIT access only)

Ultra-fast Evaluation of Protein Energies Directly from Sequence

Gevorg Grigoryan, Fei Zhou, Steve R Lustig, Gerbrand Ceder, Dane Morgan, Amy E. Keating

PLoS Computational Biology 2(6), e63 (June 2006)

[HTML] [PDF] (free access)

Structure-based prediction of bZIP partnering specificity

Gevorg Grigoryan and Amy E. Keating

J. Mol. Biol. 355, 1125-1142 (3 February, 2006)

[PDF] (MIT access only)  [Abstract] (free access)

Paircoil2: Improved Prediction of Coiled Coils from Sequence

Andrew V. McDonnell, Taijiao Jiang, Amy E. Keating and Bonnie Berger

Bioinformatics 22(3), 356-8 (2006)

paper (free access) click here for Paircoil2 web site

Orientation and Oligomerization Specificity of the Bcr Coiled-Coil Oligomerization Domain

Christina M. Taylor and Amy E. Keating

Biochemistry 44(49), 16246-56 (13 December, 2005)

[PDF] [HTML] (MIT access only)  [Abstract] (free access)

Coarse-Graining Protein Energetics in Sequence Variables

Fei Zhou, Gevorg Grigoryan, Steve R. Lustig, Amy E. Keating, Gerbrand Ceder, and Dane Morgan

Physical Review Letters 95, 148103 (September 30, 2005)

Abstract at PRL

AVID: An integrative framework for discovering functional relationships among proteins

Taijiao Jiang and Amy E Keating

BMC Bioinformatics 6, 136 (2005)

paper at BMC Bioinformatics (free access) AVID Server

Design of a Heterospecific, Tetrameric, 21-Residue Miniprotein with Mixed α/ß Structure

Mayssam H. Ali, Christina M. Taylor, Gevorg Grigoryan, Karen N. Allen, Barbara Imperiali, and Amy E. Keating

Structure 13(2), 225 - 234 (2005)

Predicting Specificity in bZIP Coiled-Coil Protein Interactions

Jessica H. Fong, Amy E. Keating and Mona Singh

Genome Biology 5, R11 (2004)
paper at Genome Biology (free access)

Comprehensive Identification of Human bZIP Interactions with Coiled-Coil Arrays

John R. S. Newman and Amy E. Keating

Science 300, 2097- 2101 (2003)

paper at Science (free access to this paper only)
Download raw bZIP
interaction data

The structure of VibH represents nonribosomal peptide synthetase condensation, cyclization and epimerization domains.

Thomas A. Keating, C. Gary Marshall, Christopher T. Walsh and Amy E. Keating

Nature Structure Biology 9, 22-526 (2002)

paper at NSB website (susbscription required for full-text access)

Side-chain repacking calculations for predicting structures and stabilities of heterodimeric coiled coils.

Amy E. Keating, Valdimir N. Malashkevich, Bruce Tidor and Peter S. Kim

Proceedings of the National Academy of Sciences, USA 98, 14825-14830 (2001)

paper at PNAS website (free access)