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A rational route to probing membrane proteins
2007
Genome Biology
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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
2011
Current Opinion in Structural Biology
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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
2004
Genome Biology
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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
2005
BMC Bioinformatics
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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
2016
Current Opinion in Structural Biology
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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†
2005
Biochemistry
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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]
2022
arXiv
pre-print
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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
2009
Nature
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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
2017
eLife
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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
2021
Health & Justice
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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
2008
Proteins: Structure, Function, and Bioinformatics
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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]
2021
bioRxiv
pre-print
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., 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
2011
Journal of Molecular Biology
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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
2015
Protein Science
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(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
2017
Scientific Reports
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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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