메뉴 건너뛰기




Volumn 108, Issue 10, 2015, Pages 2585-2590

Binding affinities controlled by shifting conformational equilibria: Opportunities and limitations

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN BINDING; UBIQUITIN;

EID: 84930011155     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1016/j.bpj.2015.04.012     Document Type: Article
Times cited : (10)

References (35)
  • 1
    • 0038148710 scopus 로고    scopus 로고
    • Conformational diversity and protein evolution - A 60-year-old hypothesis revisited
    • L.C. James, and D.S. Tawfik Conformational diversity and protein evolution - a 60-year-old hypothesis revisited Trends Biochem. Sci. 28 2003 361 368
    • (2003) Trends Biochem. Sci. , vol.28 , pp. 361-368
    • James, L.C.1    Tawfik, D.S.2
  • 2
    • 0037470496 scopus 로고    scopus 로고
    • Antibody multispecificity mediated by conformational diversity
    • L.C. James, P. Roversi, and D.S. Tawfik Antibody multispecificity mediated by conformational diversity Science 299 2003 1362 1367
    • (2003) Science , vol.299 , pp. 1362-1367
    • James, L.C.1    Roversi, P.2    Tawfik, D.S.3
  • 3
    • 0032580207 scopus 로고    scopus 로고
    • Allosteric effects of DNA on transcriptional regulators
    • J.A. Lefstin, and K.R. Yamamoto Allosteric effects of DNA on transcriptional regulators Nature 392 1998 885 888
    • (1998) Nature , vol.392 , pp. 885-888
    • Lefstin, J.A.1    Yamamoto, K.R.2
  • 4
    • 45849131354 scopus 로고    scopus 로고
    • Recognition dynamics up to microseconds revealed from an RDC-derived ubiquitin ensemble in solution
    • O.F. Lange, and N.A. Lakomek B.L. de Groot Recognition dynamics up to microseconds revealed from an RDC-derived ubiquitin ensemble in solution Science 320 2008 1471 1475
    • (2008) Science , vol.320 , pp. 1471-1475
    • Lange, O.F.1    Lakomek, N.A.2    De Groot, B.L.3
  • 5
    • 64849101493 scopus 로고    scopus 로고
    • Protein dynamism and evolvability
    • N. Tokuriki, and D.S. Tawfik Protein dynamism and evolvability Science 324 2009 203 207
    • (2009) Science , vol.324 , pp. 203-207
    • Tokuriki, N.1    Tawfik, D.S.2
  • 6
    • 70350340728 scopus 로고    scopus 로고
    • The role of dynamic conformational ensembles in biomolecular recognition
    • D.D. Boehr, R. Nussinov, and P.E. Wright The role of dynamic conformational ensembles in biomolecular recognition Nat. Chem. Biol. 5 2009 789 796
    • (2009) Nat. Chem. Biol. , vol.5 , pp. 789-796
    • Boehr, D.D.1    Nussinov, R.2    Wright, P.E.3
  • 7
    • 80053539881 scopus 로고    scopus 로고
    • Conformational selection or induced fit? 50 years of debate resolved
    • J.-P. Changeux, and S. Edelstein Conformational selection or induced fit? 50 years of debate resolved F1000 Biol. Rep. 3 2011 19
    • (2011) F1000 Biol. Rep. , vol.3 , pp. 19
    • Changeux, J.-P.1    Edelstein, S.2
  • 8
    • 0032824805 scopus 로고    scopus 로고
    • Folding funnels and binding mechanisms
    • B. Ma, and S. Kumar R. Nussinov Folding funnels and binding mechanisms Protein Eng. 12 1999 713 720
    • (1999) Protein Eng. , vol.12 , pp. 713-720
    • Ma, B.1    Kumar, S.2    Nussinov, R.3
  • 9
    • 0033621104 scopus 로고    scopus 로고
    • Folding and binding cascades: Shifts in energy landscapes
    • C.J. Tsai, B. Ma, and R. Nussinov Folding and binding cascades: shifts in energy landscapes Proc. Natl. Acad. Sci. USA 96 1999 9970 9972
    • (1999) Proc. Natl. Acad. Sci. USA , vol.96 , pp. 9970-9972
    • Tsai, C.J.1    Ma, B.2    Nussinov, R.3
  • 10
    • 80052806086 scopus 로고    scopus 로고
    • Structure-based drug design of crizotinib (PF-02341066), a potent and selective dual inhibitor of mesenchymal-epithelial transition factor (c-MET) kinase and anaplastic lymphoma kinase (ALK)
    • J.J. Cui, and M. Tran-Dubé M.P. Edwards Structure-based drug design of crizotinib (PF-02341066), a potent and selective dual inhibitor of mesenchymal-epithelial transition factor (c-MET) kinase and anaplastic lymphoma kinase (ALK) J. Med. Chem. 54 2011 6342 6363
    • (2011) J. Med. Chem. , vol.54 , pp. 6342-6363
    • Cui, J.J.1    Tran-Dubé, M.2    Edwards, M.P.3
  • 11
    • 84858034356 scopus 로고    scopus 로고
    • Discovery of 1,2,4-triazine derivatives as adenosine A(2A) antagonists using structure based drug design
    • M. Congreve, and S.P. Andrews F.H. Marshall Discovery of 1,2,4-triazine derivatives as adenosine A(2A) antagonists using structure based drug design J. Med. Chem. 55 2012 1898 1903
    • (2012) J. Med. Chem. , vol.55 , pp. 1898-1903
    • Congreve, M.1    Andrews, S.P.2    Marshall, F.H.3
  • 12
  • 13
    • 79956017135 scopus 로고    scopus 로고
    • Computational design of proteins targeting the conserved stem region of influenza hemagglutinin
    • S.J. Fleishman, and T.A. Whitehead D. Baker Computational design of proteins targeting the conserved stem region of influenza hemagglutinin Science 332 2011 816 821
    • (2011) Science , vol.332 , pp. 816-821
    • Fleishman, S.J.1    Whitehead, T.A.2    Baker, D.3
  • 14
    • 79954633234 scopus 로고    scopus 로고
    • A de novo protein binding pair by computational design and directed evolution
    • J. Karanicolas, and J.E. Corn D. Baker A de novo protein binding pair by computational design and directed evolution Mol. Cell 42 2011 250 260
    • (2011) Mol. Cell , vol.42 , pp. 250-260
    • Karanicolas, J.1    Corn, J.E.2    Baker, D.3
  • 15
    • 84874032378 scopus 로고    scopus 로고
    • Computational design of novel protein binders and experimental affinity maturation
    • T.A. Whitehead, D. Baker, and S.J. Fleishman Computational design of novel protein binders and experimental affinity maturation Methods Enzymol. 523 2013 1 19
    • (2013) Methods Enzymol. , vol.523 , pp. 1-19
    • Whitehead, T.A.1    Baker, D.2    Fleishman, S.J.3
  • 16
    • 8844263008 scopus 로고    scopus 로고
    • Docking and scoring in virtual screening for drug discovery: Methods and applications
    • D.B. Kitchen, and H. Decornez J. Bajorath Docking and scoring in virtual screening for drug discovery: methods and applications Nat. Rev. Drug Discov. 3 2004 935 949
    • (2004) Nat. Rev. Drug Discov. , vol.3 , pp. 935-949
    • Kitchen, D.B.1    Decornez, H.2    Bajorath, J.3
  • 17
    • 78650800242 scopus 로고    scopus 로고
    • Accounting for conformational entropy in predicting binding free energies of protein-protein interactions
    • H. Kamisetty, and A. Ramanathan C.J. Langmead Accounting for conformational entropy in predicting binding free energies of protein-protein interactions Proteins 79 2011 444 462
    • (2011) Proteins , vol.79 , pp. 444-462
    • Kamisetty, H.1    Ramanathan, A.2    Langmead, C.J.3
  • 18
    • 84871298878 scopus 로고    scopus 로고
    • Conformational stabilization of ubiquitin yields potent and selective inhibitors of USP7
    • Y. Zhang, and L. Zhou J.E. Corn Conformational stabilization of ubiquitin yields potent and selective inhibitors of USP7 Nat. Chem. Biol. 9 2013 51 58
    • (2013) Nat. Chem. Biol. , vol.9 , pp. 51-58
    • Zhang, Y.1    Zhou, L.2    Corn, J.E.3
  • 19
    • 50349097986 scopus 로고    scopus 로고
    • Cofactor dependent conformational switching of GTPases
    • V. Hauryliuk, S. Hansson, and M. Ehrenberg Cofactor dependent conformational switching of GTPases Biophys. J. 95 2008 1704 1715
    • (2008) Biophys. J. , vol.95 , pp. 1704-1715
    • Hauryliuk, V.1    Hansson, S.2    Ehrenberg, M.3
  • 20
    • 76649086691 scopus 로고    scopus 로고
    • Alchemical free energy simulations for biological complexes: Powerful but temperamental
    • A. Aleksandrov, D. Thompson, and T. Simonson Alchemical free energy simulations for biological complexes: powerful but temperamental J. Mol. Recognit. 23 2010 117 127
    • (2010) J. Mol. Recognit. , vol.23 , pp. 117-127
    • Aleksandrov, A.1    Thompson, D.2    Simonson, T.3
  • 21
    • 80052401629 scopus 로고    scopus 로고
    • Solution structure of a minor and transiently formed state of a T4 lysozyme mutant
    • G. Bouvignies, and P. Vallurupalli L.E. Kay Solution structure of a minor and transiently formed state of a T4 lysozyme mutant Nature 477 2011 111 114
    • (2011) Nature , vol.477 , pp. 111-114
    • Bouvignies, G.1    Vallurupalli, P.2    Kay, L.E.3
  • 22
    • 84867375354 scopus 로고    scopus 로고
    • Modulation of a pre-existing conformational equilibrium tunes adenylate kinase activity
    • J. Ådén, and A. Verma M. Wolf-Watz Modulation of a pre-existing conformational equilibrium tunes adenylate kinase activity J. Am. Chem. Soc. 134 2012 16562 16570
    • (2012) J. Am. Chem. Soc. , vol.134 , pp. 16562-16570
    • Ådén, J.1    Verma, A.2    Wolf-Watz, M.3
  • 23
    • 37349046664 scopus 로고    scopus 로고
    • Mutations in the hydrophobic core of ubiquitin differentially affect its recognition by receptor proteins
    • A. Haririnia, and R. Verma D. Fushman Mutations in the hydrophobic core of ubiquitin differentially affect its recognition by receptor proteins J. Mol. Biol. 375 2008 979 996
    • (2008) J. Mol. Biol. , vol.375 , pp. 979-996
    • Haririnia, A.1    Verma, R.2    Fushman, D.3
  • 24
    • 36049017659 scopus 로고    scopus 로고
    • The confine-and-release method: Obtaining correct binding free energies in the presence of protein conformational change
    • D.L. Mobley, J.D. Chodera, and K.A. Dill The confine-and-release method: obtaining correct binding free energies in the presence of protein conformational change J. Chem. Theory Comput. 3 2007 1231 1235
    • (2007) J. Chem. Theory Comput. , vol.3 , pp. 1231-1235
    • Mobley, D.L.1    Chodera, J.D.2    Dill, K.A.3
  • 25
    • 80052805301 scopus 로고    scopus 로고
    • Recent theoretical and computational advances for modeling protein-ligand binding affinities
    • C. Christov, Academic Press New York
    • E. Gallicchio, and R.M. Levy Recent theoretical and computational advances for modeling protein-ligand binding affinities C. Christov, Computational Chemistry Methods in Structural Biology Vol. 85 2011 Academic Press New York
    • (2011) Computational Chemistry Methods in Structural Biology , vol.85
    • Gallicchio, E.1    Levy, R.M.2
  • 26
    • 0023380976 scopus 로고
    • Thermodynamic cycle integration by computer simulation as a tool for obtaining free energy differences in molecular chemistry
    • W.F. van Gunsteren, and H.J. Berendsen Thermodynamic cycle integration by computer simulation as a tool for obtaining free energy differences in molecular chemistry J. Comput. Aided Mol. Des. 1 1987 171 176
    • (1987) J. Comput. Aided Mol. Des. , vol.1 , pp. 171-176
    • Van Gunsteren, W.F.1    Berendsen, H.J.2
  • 27
    • 84908502680 scopus 로고    scopus 로고
    • A designed conformational shift to control protein binding specificity
    • S. Michielssens, and J.H. Peters B.L. de Groot A designed conformational shift to control protein binding specificity Angew. Chem. 53 2014 10367 10371
    • (2014) Angew. Chem. , vol.53 , pp. 10367-10371
    • Michielssens, S.1    Peters, J.H.2    De Groot, B.L.3
  • 28
    • 84868090870 scopus 로고    scopus 로고
    • Ubiquitin dynamics in complexes reveal molecular recognition mechanisms beyond induced fit and conformational selection
    • J.H. Peters, and B.L. de Groot Ubiquitin dynamics in complexes reveal molecular recognition mechanisms beyond induced fit and conformational selection PLOS Comput. Biol. 8 2012 e1002704
    • (2012) PLOS Comput. Biol. , vol.8 , pp. e1002704
    • Peters, J.H.1    De Groot, B.L.2
  • 29
    • 0017879183 scopus 로고
    • The Protein Data Bank: A computer-based archival file for macromolecular structures
    • F.C. Bernstein, and T.F. Koetzle M. Tasumi The Protein Data Bank: a computer-based archival file for macromolecular structures Arch. Biochem. Biophys. 185 1978 584 591
    • (1978) Arch. Biochem. Biophys. , vol.185 , pp. 584-591
    • Bernstein, F.C.1    Koetzle, T.F.2    Tasumi, M.3
  • 30
    • 46249092554 scopus 로고    scopus 로고
    • GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation
    • B. Hess, and C. Kutzner E. Lindahl GROMACS 4: algorithms for highly efficient, load-balanced, and scalable molecular simulation J. Chem. Theory Comput. 4 2008 435 447
    • (2008) J. Chem. Theory Comput. , vol.4 , pp. 435-447
    • Hess, B.1    Kutzner, C.2    Lindahl, E.3
  • 32
    • 0029985860 scopus 로고    scopus 로고
    • An efficient method for sampling the essential subspace of proteins
    • A. Amadei, and A.B.M. Linssen H.J.C. Berendsen An efficient method for sampling the essential subspace of proteins J. Biomol. Struct. Dyn. 13 1996 615 625
    • (1996) J. Biomol. Struct. Dyn. , vol.13 , pp. 615-625
    • Amadei, A.1    Linssen, A.B.M.2    Berendsen, H.J.C.3
  • 33
    • 0029811307 scopus 로고    scopus 로고
    • An extended sampling of the configurational space of HPr from E. Coli
    • B.L. de Groot, and A. Amadei H.J.C. Berendsen An extended sampling of the configurational space of HPr from E. coli Proteins 26 1996 314 322
    • (1996) Proteins , vol.26 , pp. 314-322
    • De Groot, B.L.1    Amadei, A.2    Berendsen, H.J.C.3
  • 34
    • 84986519238 scopus 로고
    • The weighted histogram analysis method for free-energy calculations on biomolecules. I. The method
    • S. Kumar, and J.M. Rosenberg P.A. Kollman The weighted histogram analysis method for free-energy calculations on biomolecules. I. The method J. Comput. Chem. 13 1992 1011 1021
    • (1992) J. Comput. Chem. , vol.13 , pp. 1011-1021
    • Kumar, S.1    Rosenberg, J.M.2    Kollman, P.A.3
  • 35
    • 78651282170 scopus 로고    scopus 로고
    • G-WHAM - A free weighted histogram analysis implementation including robust error and autocorrelation estimates
    • J.S. Hub, B.L. de Groot, and D. van der Spoel G-WHAM - a free weighted histogram analysis implementation including robust error and autocorrelation estimates JCTC 6 2010 3713 3720
    • (2010) JCTC , vol.6 , pp. 3713-3720
    • Hub, J.S.1    De Groot, B.L.2    Van Der Spoel, D.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.