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For: Harel M, Cohen M, Schreiber G. On the dynamic nature of the transition state for protein-protein association as determined by double-mutant cycle analysis and simulation. J Mol Biol 2007;371:180-96. [PMID: 17561113 DOI: 10.1016/j.jmb.2007.05.032] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2007] [Revised: 04/15/2007] [Accepted: 05/09/2007] [Indexed: 10/23/2022]
Number Cited by Other Article(s)
1
Henderson R, Anasti K, Manne K, Stalls V, Saunders C, Bililign Y, Williams A, Bubphamala P, Montani M, Kachhap S, Li J, Jaing C, Newman A, Cain DW, Lu X, Venkatayogi S, Berry M, Wagh K, Korber B, Saunders KO, Tian M, Alt F, Wiehe K, Acharya P, Alam SM, Haynes BF. Engineering immunogens that select for specific mutations in HIV broadly neutralizing antibodies. Nat Commun 2024;15:9503. [PMID: 39489734 PMCID: PMC11532496 DOI: 10.1038/s41467-024-53120-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 09/27/2024] [Indexed: 11/05/2024]  Open
2
Henderson R, Anasti K, Manne K, Stalls V, Saunders C, Bililign Y, Williams A, Bubphamala P, Montani M, Kachhap S, Li J, Jaing C, Newman A, Cain D, Lu X, Venkatayogi S, Berry M, Wagh K, Korber B, Saunders KO, Tian M, Alt F, Wiehe K, Acharya P, Alam SM, Haynes BF. Engineering immunogens that select for specific mutations in HIV broadly neutralizing antibodies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.15.571700. [PMID: 38168268 PMCID: PMC10760096 DOI: 10.1101/2023.12.15.571700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
3
Mishra RP, Goel G. Multiscale Model for Quantitative Prediction of Insulin Aggregation Nucleation Kinetics. J Chem Theory Comput 2021;17:7886-7898. [PMID: 34813303 DOI: 10.1021/acs.jctc.1c00499] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
4
Moldenhauer H, Díaz-Franulic I, Poblete H, Naranjo D. Trans-toxin ion-sensitivity of charybdotoxin-blocked potassium-channels reveals unbinding transitional states. eLife 2019;8:46170. [PMID: 31271355 PMCID: PMC6660193 DOI: 10.7554/elife.46170] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Accepted: 07/04/2019] [Indexed: 12/11/2022]  Open
5
Strickland M, Kale S, Strub MP, Schwieters CD, Liu J, Peterkofsky A, Tjandra N. Potential Regulatory Role of Competitive Encounter Complexes in Paralogous Phosphotransferase Systems. J Mol Biol 2019;431:2331-2342. [PMID: 31071328 DOI: 10.1016/j.jmb.2019.04.040] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 04/22/2019] [Accepted: 04/28/2019] [Indexed: 11/28/2022]
6
Gaffney KA, Hong H. The rhomboid protease GlpG has weak interaction energies in its active site hydrogen bond network. J Gen Physiol 2018;151:282-291. [PMID: 30420443 PMCID: PMC6400518 DOI: 10.1085/jgp.201812047] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 10/25/2018] [Indexed: 01/24/2023]  Open
7
Tackling the Antibiotic Resistance Caused by Class A β-Lactamases through the Use of β-Lactamase Inhibitory Protein. Int J Mol Sci 2018;19:ijms19082222. [PMID: 30061509 PMCID: PMC6121496 DOI: 10.3390/ijms19082222] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 07/23/2018] [Accepted: 07/25/2018] [Indexed: 12/27/2022]  Open
8
Complete protein-protein association kinetics in atomic detail revealed by molecular dynamics simulations and Markov modelling. Nat Chem 2017;9:1005-1011. [PMID: 28937668 DOI: 10.1038/nchem.2785] [Citation(s) in RCA: 237] [Impact Index Per Article: 33.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Accepted: 04/21/2017] [Indexed: 12/23/2022]
9
Moritsugu K, Terada T, Kidera A. Energy landscape of all-atom protein-protein interactions revealed by multiscale enhanced sampling. PLoS Comput Biol 2014;10:e1003901. [PMID: 25340714 PMCID: PMC4207830 DOI: 10.1371/journal.pcbi.1003901] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Accepted: 08/22/2014] [Indexed: 11/18/2022]  Open
10
Bashir Q, Meulenbroek EM, Pannu NS, Ubbink M. Engineering specificity in a dynamic protein complex with a single conserved mutation. FEBS J 2014;281:4892-905. [DOI: 10.1111/febs.13028] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2014] [Revised: 07/09/2014] [Accepted: 08/27/2014] [Indexed: 11/27/2022]
11
Schilder J, Löhr F, Schwalbe H, Ubbink M. The cytochrome c peroxidase and cytochrome c encounter complex: the other side of the story. FEBS Lett 2014;588:1873-8. [PMID: 24726731 DOI: 10.1016/j.febslet.2014.03.055] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Revised: 03/18/2014] [Accepted: 03/26/2014] [Indexed: 11/18/2022]
12
Hiruma Y, Gupta A, Kloosterman A, Olijve C, Ölmez B, Hass MAS, Ubbink M. Hot-Spot Residues in the Cytochrome P450cam-Putidaredoxin Binding Interface. Chembiochem 2013;15:80-6. [DOI: 10.1002/cbic.201300582] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Indexed: 11/09/2022]
13
Schilder J, Ubbink M. Formation of transient protein complexes. Curr Opin Struct Biol 2013;23:911-8. [PMID: 23932200 DOI: 10.1016/j.sbi.2013.07.009] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Revised: 07/11/2013] [Accepted: 07/11/2013] [Indexed: 01/16/2023]
14
Clore GM, Venditti V. Structure, dynamics and biophysics of the cytoplasmic protein-protein complexes of the bacterial phosphoenolpyruvate: sugar phosphotransferase system. Trends Biochem Sci 2013;38:515-30. [PMID: 24055245 PMCID: PMC3831880 DOI: 10.1016/j.tibs.2013.08.003] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Revised: 08/07/2013] [Accepted: 08/09/2013] [Indexed: 10/26/2022]
15
Ahuja S, Jahr N, Im SC, Vivekanandan S, Popovych N, Le Clair SV, Huang R, Soong R, Xu J, Yamamoto K, Nanga RP, Bridges A, Waskell L, Ramamoorthy A. A model of the membrane-bound cytochrome b5-cytochrome P450 complex from NMR and mutagenesis data. J Biol Chem 2013;288:22080-95. [PMID: 23709268 DOI: 10.1074/jbc.m112.448225] [Citation(s) in RCA: 90] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]  Open
16
Scanu S, Foerster JM, Ullmann GM, Ubbink M. Role of Hydrophobic Interactions in the Encounter Complex Formation of the Plastocyanin and Cytochrome f Complex Revealed by Paramagnetic NMR Spectroscopy. J Am Chem Soc 2013;135:7681-92. [DOI: 10.1021/ja4015452] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
17
Contrasting factors on the kinetic path to protein complex formation diminish the effects of crowding agents. Biophys J 2013;103:1011-9. [PMID: 23009850 DOI: 10.1016/j.bpj.2012.08.009] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2012] [Revised: 07/29/2012] [Accepted: 08/02/2012] [Indexed: 01/30/2023]  Open
18
Kastritis PL, Bonvin AMJJ. On the binding affinity of macromolecular interactions: daring to ask why proteins interact. J R Soc Interface 2012;10:20120835. [PMID: 23235262 PMCID: PMC3565702 DOI: 10.1098/rsif.2012.0835] [Citation(s) in RCA: 276] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]  Open
19
Moal IH, Fernández-Recio J. SKEMPI: a Structural Kinetic and Energetic database of Mutant Protein Interactions and its use in empirical models. ACTA ACUST UNITED AC 2012;28:2600-7. [PMID: 22859501 DOI: 10.1093/bioinformatics/bts489] [Citation(s) in RCA: 179] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
20
Brown NG, Chow DC, Sankaran B, Zwart P, Prasad BVV, Palzkill T. Analysis of the binding forces driving the tight interactions between beta-lactamase inhibitory protein-II (BLIP-II) and class A beta-lactamases. J Biol Chem 2011;286:32723-35. [PMID: 21775426 PMCID: PMC3173220 DOI: 10.1074/jbc.m111.265058] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2011] [Revised: 06/25/2011] [Indexed: 12/19/2022]  Open
21
Marquer C, Fruchart-Gaillard C, Letellier G, Marcon E, Mourier G, Zinn-Justin S, Ménez A, Servent D, Gilquin B. Structural model of ligand-G protein-coupled receptor (GPCR) complex based on experimental double mutant cycle data: MT7 snake toxin bound to dimeric hM1 muscarinic receptor. J Biol Chem 2011;286:31661-75. [PMID: 21685390 DOI: 10.1074/jbc.m111.261404] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]  Open
22
Hanes MS, Reynolds KA, McNamara C, Ghosh P, Bonomo RA, Kirsch JF, Handel TM. Specificity and cooperativity at β-lactamase position 104 in TEM-1/BLIP and SHV-1/BLIP interactions. Proteins 2011;79:1267-76. [PMID: 21294157 PMCID: PMC3417816 DOI: 10.1002/prot.22961] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2010] [Revised: 11/30/2010] [Accepted: 12/02/2010] [Indexed: 01/07/2023]
23
Busby B, Oashi T, Willis CD, Ackermann MA, Kontrogianni-Konstantopoulos A, Mackerell AD, Bloch RJ. Electrostatic interactions mediate binding of obscurin to small ankyrin 1: biochemical and molecular modeling studies. J Mol Biol 2011;408:321-34. [PMID: 21333652 DOI: 10.1016/j.jmb.2011.01.053] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2010] [Revised: 01/25/2011] [Accepted: 01/28/2011] [Indexed: 10/18/2022]
24
Shifting the equilibrium between the encounter state and the specific form of a protein complex by interfacial point mutations. J Am Chem Soc 2010;132:11487-95. [PMID: 20672804 DOI: 10.1021/ja100867c] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
25
Pierce BG, Haidar JN, Yu Y, Weng Z. Combinations of affinity-enhancing mutations in a T cell receptor reveal highly nonadditive effects within and between complementarity determining regions and chains. Biochemistry 2010;49:7050-9. [PMID: 20681514 DOI: 10.1021/bi901969a] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
26
Schreiber G, Haran G, Zhou HX. Fundamental aspects of protein-protein association kinetics. Chem Rev 2010;109:839-60. [PMID: 19196002 DOI: 10.1021/cr800373w] [Citation(s) in RCA: 559] [Impact Index Per Article: 39.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
27
Fawzi NL, Doucleff M, Suh JY, Clore GM. Mechanistic details of a protein-protein association pathway revealed by paramagnetic relaxation enhancement titration measurements. Proc Natl Acad Sci U S A 2010;107:1379-84. [PMID: 20080627 PMCID: PMC2824347 DOI: 10.1073/pnas.0909370107] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
28
Gochin M, Cai L. The role of amphiphilicity and negative charge in glycoprotein 41 interactions in the hydrophobic pocket. J Med Chem 2009;52:4338-44. [PMID: 19534533 DOI: 10.1021/jm900190q] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
29
Harel M, Spaar A, Schreiber G. Fruitful and futile encounters along the association reaction between proteins. Biophys J 2009;96:4237-48. [PMID: 19450494 DOI: 10.1016/j.bpj.2009.02.054] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2008] [Revised: 02/02/2009] [Accepted: 02/20/2009] [Indexed: 10/20/2022]  Open
30
Insights into Positive and Negative Requirements for Protein–Protein Interactions by Crystallographic Analysis of the β-Lactamase Inhibitory Proteins BLIP, BLIP-I, and BLP. J Mol Biol 2009;389:289-305. [DOI: 10.1016/j.jmb.2009.03.058] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2008] [Revised: 03/15/2009] [Accepted: 03/20/2009] [Indexed: 11/24/2022]
31
The courtship of proteins: Understanding the encounter complex. FEBS Lett 2009;583:1060-6. [DOI: 10.1016/j.febslet.2009.02.046] [Citation(s) in RCA: 147] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2009] [Revised: 02/25/2009] [Accepted: 02/27/2009] [Indexed: 11/15/2022]
32
Principal determinants leading to transition state formation of a protein-protein complex, orientation trumps side-chain interactions. Proc Natl Acad Sci U S A 2009;106:2559-64. [PMID: 19196954 DOI: 10.1073/pnas.0809800106] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
33
Volkov AN, Bashir Q, Worrall JAR, Ubbink M. Binding hot spot in the weak protein complex of physiological redox partners yeast cytochrome C and cytochrome C peroxidase. J Mol Biol 2008;385:1003-13. [PMID: 19026661 DOI: 10.1016/j.jmb.2008.10.091] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2008] [Revised: 10/16/2008] [Accepted: 10/30/2008] [Indexed: 10/21/2022]
34
Sarewicz M, Borek A, Daldal F, Froncisz W, Osyczka A. Demonstration of short-lived complexes of cytochrome c with cytochrome bc1 by EPR spectroscopy: implications for the mechanism of interprotein electron transfer. J Biol Chem 2008;283:24826-36. [PMID: 18617515 PMCID: PMC2529009 DOI: 10.1074/jbc.m802174200] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2008] [Revised: 07/08/2008] [Indexed: 11/18/2022]  Open
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