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A rational route to probing membrane proteins

Amy E Keating
2007 Genome Biology  
A recent report describes the design of short peptides that bind specifically to transmembrane regions of integrins, providing an exciting tool for probing the biology of membrane proteins.
doi:10.1186/gb-2007-8-5-214 pmid:17540048 pmcid:PMC1929131 fatcat:flp6uikacbhfbm357mpbaweuai

Protein binding specificity versus promiscuity

Gideon Schreiber, Amy E Keating
2011 Current Opinion in Structural Biology  
Acknowledgments We thank members of the Schreiber and Keating laboratories for their thoughtful contributions to our studies of specificity.  ...  Dutta S, Gulla S, Chen TS, Fire E, Grant RA, Keating AE. Determinants of BH3 binding specificity for Mcl-1 versus Bcl-xL. J Mol Biol 2010;398:747-762.  ...  Newman JR, Keating AE. Comprehensive identification of human bZIP interactions with coiledcoil arrays. Science 2003;300:2097-2101. [PubMed: 12805554] 40. Reinke AW, Grigoryan G, Keating AE.  ... 
doi:10.1016/j.sbi.2010.10.002 pmid:21071205 pmcid:PMC3053118 fatcat:amem3aj7n5h3disvw2vsbhtrp4

Predicting specificity in bZIP coiled-coil protein interactions

Jessica H Fong, Amy E Keating, Mona Singh
2004 Genome Biology  
Genome Biology 2004, 5:R11 Genome Biology 2004, 5:R11 w (g,e),E,+ = w (g,e),+,E = 1.0; w (g,e),D,+ = w (g,e),+,D = w (g,e),Q,+ = w (g,e),+,Q = 0.5; w (g,e),-,-= w (g,e),+,+ = -1.0; w (a,a),N,N = 1.0  ...  For example, we require w (g,e),K,E > 0, w (g,e),E,E < 0. (5) These types of constraints are used to capture some of the features of the simple electrostatic weights.  ... 
doi:10.1186/gb-2004-5-2-r11 pmid:14759261 pmcid:PMC395749 fatcat:ydx2gvhlmbcthayqkbxqskxh74

AVID: an integrative framework for discovering functional relationships among proteins

Taijiao Jiang, Amy E Keating
2005 BMC Bioinformatics  
All of the data are available as downloadable files as well as through an interactive website at http://web.mit.edu/biology/keating/AVID.  ...  Sia and members of the Keating lab for comments on the manuscript. The AVID web site was developed by K. Weston.  ... 
doi:10.1186/1471-2105-6-136 pmid:15929793 pmcid:PMC1177925 fatcat:whcfjnx2nvfnbghgyfrynbbyxa

Designing helical peptide inhibitors of protein–protein interactions

Raheleh Rezaei Araghi, Amy E Keating
2016 Current Opinion in Structural Biology  
Acknowledgments Work in the Keating lab on peptide inhibitors of bZIP transcription factors and Bcl-2 proteins has been supported by awards GM067681, GM110048 and GM084181 from the National Institute of  ...  We thank members of the Keating and Walensky labs for discussions about helical peptide inhibitor design, and the Letai and Walensky labs for collaborating with us to test designed helical inhibitors of  ...  Towards this end, we recently developed one-bead-one-compound library methods that can be used to optimize stapled peptides (Rezaei Araghi and Keating, submitted).  ... 
doi:10.1016/j.sbi.2016.04.001 pmid:27123812 pmcid:PMC5282971 fatcat:dbt5iztp2rcdzkyajifvahcamu

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

Christina M. Taylor, Amy E. Keating
2005 Biochemistry  
Lee, E. Oakes, G. Grigoryan and D. Mujumdar for experimental and computational assistance and/or helpful discussions. We thank members of the Keating Lab, G. Hersch, T. Keating, and T.  ...  Parallel and antiparallel coiled coils also have different interactions on the surface, with g to e' interactions in parallel versus e to e' and g to g' in antiparallel structures (Figure 2A and B)  ...  In the parallel orientation, salt bridges typically occur between the g position of one helix and the next e position of a partner helix (e' + ).  ... 
doi:10.1021/bi051493t pmid:16331985 pmcid:PMC2526250 fatcat:gzj4x3xyuzaardwoogaqxorsfi

TERMinator: A Neural Framework for Structure-Based Protein Design using Tertiary Repeating Motifs [article]

Alex J. Li, Vikram Sundar, Gevorg Grigoryan, Amy E. Keating
2022 arXiv   pre-print
as: E cp (R i = m, R j = n, {R u = r u }) = E s (R i = m) + E s (R j = n) + E p (R i = m, R j = n) + u =m,n (E p (R i = m, R u = r u ) + E p (R u = r u , R j = n)) From this energy, we can compute the  ...  In our Potts model, the singleton term takes the form h i (s i ) = E s (R i = m) , where E s is a lookup table of energies for placing residue m at position i.  ... 
arXiv:2204.13048v1 fatcat:f3xyg2jvmnb6ppry4me6gyfwye

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

Gevorg Grigoryan, Aaron W. Reinke, Amy E. Keating
2009 Nature  
Keating: keating@mit.edu. Supplementary Information is linked to the online version of the paper at www.nature.com/nature. Author Contributions GG, AWR and AEK conceived the project.  ...  The following 10 amino acids were allowed: V, L, N, I, K, A, R, T, S, and E for a positions; L, V, I, M, H, Y, T, A, K, and F for d positions; E, K, R, Q, L, S, T, A, V, and I for e positions; E, K, Q,  ...  Given this sequence, energy gaps between the design•target dimer and al design•competitor dimers, including design•design, are calculated as gap=E design:competitor − E design:t arg et .  ... 
doi:10.1038/nature07885 pmid:19370028 pmcid:PMC2748673 fatcat:fvuxwmcdtrdgvac4pv77zxcnvm

Combinatorial bZIP dimers display complex DNA-binding specificity landscapes

José A Rodríguez-Martínez, Aaron W Reinke, Devesh Bhimsaria, Amy E Keating, Aseem Z Ansari
2017 eLife  
Sequences are in Supplementary file 1A. 727 Briefly, E. coli RP3098 cells transformed with bZIP clones were grown in 0.5 L LB 728 cultures at 37 °C to OD600 = 0.4-0.8.  ...  Genome Res 22, 1790-1797. 972 Campbell, Z.T., Bhimsaria, D., Valley, C.T., Rodriguez-Martinez, J.A., Menichelli, E., 973 Williamson, J.R., Ansari, A.Z., and Wickens, M. (2012).  ... 
doi:10.7554/elife.19272 pmid:28186491 pmcid:PMC5349851 fatcat:kq63rnf3mffwrojs7hhrhljsme

Healthcare-induced trauma in correctional facilities: a qualitative exploration

Johanna E. Elumn, Layne Keating, Amy B. Smoyer, Emily A. Wang
2021 Health & Justice  
Layne Keating was a member of the research team and participated in the data collection, analysis, and the writing of this manuscript. Dr.  ...  Amy Smoyer provided advice on the data analysis and reviewed and participated in the writing of this manuscript. Dr. Emily Wang provided guidance to Dr.  ... 
doi:10.1186/s40352-021-00139-5 pmid:34152487 pmcid:PMC8215321 fatcat:uxcbixxm3ffphopnxrruq3ydwm

Predicting helix orientation for coiled-coil dimers

James R. Apgar, Karl N. Gutwin, Amy E. Keating
2008 Proteins: Structure, Function, and Bioinformatics  
Model GK uses the physical energy function described by Grigoryan and Keating.18 Briefly, the energy function consists of three terms.  ...  Model ELEC assigns all occurrences of g-e' (parallel) or g-g' + e-e' (antiparallel) E-R, R-E, K-E or E-K pairs a weight of -1, while E-E, R-R, R-K, K-R, K-K, D-E, E-D and D-D pairs are given a weight of  ...  d-d' g-e' a-d' g-g' e-e' RISP CC a-a' d-d' g-e' g-a' d-e' a-d' g-g' e-e' a-e' d-g' RISP CC_all a-a' d-d' g-e' g-a' d-e' a-d' d-a' a-d' g-g' e-e' a-e' d-g' d-d' a-a' A prime (') designates a residue  ... 
doi:10.1002/prot.22118 pmid:18506779 pmcid:PMC2562949 fatcat:hnxrwrsmavdwzlh6q4dz3hasg4

A distributed residue network permits conformational binding specificity in a conserved family of actin remodelers [article]

Theresa Hwang, Robert A Grant, Amy E Keating
2021 bioRxiv   pre-print
., 2009; Schreiber and Keating, 2011) .  ...  We thank members of the Keating lab, Mouneimne lab, and F. Gertler for their thoughtful input on the manuscript.  ... 
doi:10.1101/2021.05.27.445944 fatcat:pb4bgwhspvdcbp4wwmfkxqyjxy

Determinants of Homodimerization Specificity in Histidine Kinases

Orr Ashenberg, Kathryn Rozen-Gagnon, Michael T. Laub, Amy E. Keating
2011 Journal of Molecular Biology  
Keating, a National Science Foundation CAREER Grant to M.T. Laub, and the National Science Foundation GRFP fellowship to O. Ashenberg.  ...  We thank members of the Keating laboratory (especially T.S. Chen, C. Negron, L. Reich, A. W. Reinke, and V. Potapov) and the Laub laboratory (especially E.J. Capra, B.S. Perchuk, and C.G.  ...  Discussion In this study we investigated the dimerization specificity of a pair of histidine-kinase paralogs from E. coli, EnvZ and RstB.  ... 
doi:10.1016/j.jmb.2011.08.011 pmid:21854787 pmcid:PMC3210482 fatcat:pu27hlzbjnfwzh4xsfsg22gxcu

AB-Bind: Antibody binding mutational database for computational affinity predictions

Sarah Sirin, James R. Apgar, Eric M. Bennett, Amy E. Keating
2015 Protein Science  
(3) , where E AB is the energy of the complex, and E A and E B are the energies of the interaction units in the unbound states.  ... 
doi:10.1002/pro.2829 pmid:26473627 pmcid:PMC4815335 fatcat:ebpb2plozfa4fnb2cwfjmaixca

Modular assembly of a protein nanotriangle using orthogonally interacting coiled coils

Won Min Park, Mostafa Bedewy, Karl K. Berggren, Amy E. Keating
2017 Scientific Reports  
Frappier for help with modeling, and members of the Keating lab for comments on the work and the manuscript. We thank J. Hopkins and R.  ...  Plasmids were separately transformed into E. coli strain BL21(DE3) cells (Agilent).  ...  (E) A two-step thermal annealing process for assembly of the linked-SYNZIP fusion proteins, and illustration of desired assemblies at each step.  ... 
doi:10.1038/s41598-017-10918-6 pmid:28874805 pmcid:PMC5585338 fatcat:rws4qacv7jdctc7xs34sql2nne
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