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Volumn 80, Issue 11, 2012, Pages 2562-2572

Peptide binding to the PDZ3 domain by conformational selection

Author keywords

Free energy surface; Molecular dynamics; PDZ domain; Reaction coordinate optimization

Indexed keywords

PDZ PROTEIN; PROTEIN PDZ 3; UNCLASSIFIED DRUG;

EID: 84867206021     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.24137     Document Type: Article
Times cited : (13)

References (38)
  • 1
    • 5044224260 scopus 로고    scopus 로고
    • PDZ domain proteins of synapses
    • Kim E, Sheng M. PDZ domain proteins of synapses. Nat Rev Neurosci 2004; 5: 771-781.
    • (2004) Nat Rev Neurosci , vol.5 , pp. 771-781
    • Kim, E.1    Sheng, M.2
  • 2
    • 0036876382 scopus 로고    scopus 로고
    • Signaling complex organization by PDZ domain proteins
    • Fan J-S, Zhang M. Signaling complex organization by PDZ domain proteins. Neurosignals 2002; 11: 315-321.
    • (2002) Neurosignals , vol.11 , pp. 315-321
    • Fan, J.-S.1    Zhang, M.2
  • 3
    • 0030604722 scopus 로고    scopus 로고
    • Crystal structures of a complexed and peptide-free membrane protein-binding domain: molecular basis of peptide recognition by PDZ
    • Doyle DA, Lee A, Lewis J, Kim E, Sheng M, MacKinnon R. Crystal structures of a complexed and peptide-free membrane protein-binding domain: molecular basis of peptide recognition by PDZ. Cell 1996; 85: 1067-1076.
    • (1996) Cell , vol.85 , pp. 1067-1076
    • Doyle, D.A.1    Lee, A.2    Lewis, J.3    Kim, E.4    Sheng, M.5    MacKinnon, R.6
  • 5
    • 0036301446 scopus 로고    scopus 로고
    • Solution structure of the PDZ2 domain from cytosolic human phosphatase hPTP1E complexed with a peptide reveals contribution of the β2-β3 loop to PDZ domain-ligand interactions
    • Kozlov G, Banville D, Gehring K, Ekiel I. Solution structure of the PDZ2 domain from cytosolic human phosphatase hPTP1E complexed with a peptide reveals contribution of the β2-β3 loop to PDZ domain-ligand interactions. J Mol Biol 2002; 320: 813-820.
    • (2002) J Mol Biol , vol.320 , pp. 813-820
    • Kozlov, G.1    Banville, D.2    Gehring, K.3    Ekiel, I.4
  • 6
    • 78049307619 scopus 로고    scopus 로고
    • Crystallographic and nuclear magnetic resonance evaluation of the impact of peptide binding to the second PDZ domain of protein tyrosine phosphatase 1e
    • Zhang J, Sapienza PJ, Ke H, Chang A, Hengel SR, Wang H, Phillips GN, Lee AL. Crystallographic and nuclear magnetic resonance evaluation of the impact of peptide binding to the second PDZ domain of protein tyrosine phosphatase 1e. Biochemistry 2010; 49: 9280-9291.
    • (2010) Biochemistry , vol.49 , pp. 9280-9291
    • Zhang, J.1    Sapienza, P.J.2    Ke, H.3    Chang, A.4    Hengel, S.R.5    Wang, H.6    Phillips, G.N.7    Lee, A.L.8
  • 10
    • 44349160152 scopus 로고    scopus 로고
    • Conformational change upon ligand binding and dynamics of the PDZ domain from leukemia-associated Rho guanine nucleotide exchange factor
    • Liu J, Zhang J, Yang Y, Huang H, Shen W, Hu Q, Wang X, Wu J, Shi Y. Conformational change upon ligand binding and dynamics of the PDZ domain from leukemia-associated Rho guanine nucleotide exchange factor. Protein Sci 2008; 17: 1003-1014.
    • (2008) Protein Sci , vol.17 , pp. 1003-1014
    • Liu, J.1    Zhang, J.2    Yang, Y.3    Huang, H.4    Shen, W.5    Hu, Q.6    Wang, X.7    Wu, J.8    Shi, Y.9
  • 12
    • 36248996466 scopus 로고    scopus 로고
    • Scaffold proteins as dynamic switches
    • Zhang M. Scaffold proteins as dynamic switches. Nat Chem Biol 2007; 3: 756-757.
    • (2007) Nat Chem Biol , vol.3 , pp. 756-757
    • Zhang, M.1
  • 13
    • 77958563467 scopus 로고    scopus 로고
    • Allostery is an intrinsic property of the protease domain of DegS: implications for enzyme function and evolution
    • Sohn J, Grant RA, Sauer RT. Allostery is an intrinsic property of the protease domain of DegS: implications for enzyme function and evolution. J Biol Chem 2010; 285: 34039-34047.
    • (2010) J Biol Chem , vol.285 , pp. 34039-34047
    • Sohn, J.1    Grant, R.A.2    Sauer, R.T.3
  • 15
    • 80055066238 scopus 로고    scopus 로고
    • Change in allosteric network affects binding affinities of PDZ domains: analysis through perturbation response scanning
    • Gerek ZN, Ozkan SB. Change in allosteric network affects binding affinities of PDZ domains: analysis through perturbation response scanning. PLoS Comput Biol 2011; 7: e1002154.
    • (2011) PLoS Comput Biol , vol.7
    • Gerek, Z.N.1    Ozkan, S.B.2
  • 16
    • 0033536602 scopus 로고    scopus 로고
    • Evolutionarily conserved pathways of energetic connectivity in protein families
    • Lockless SW, Ranganathan R. Evolutionarily conserved pathways of energetic connectivity in protein families. Science 1999; 286: 295-299.
    • (1999) Science , vol.286 , pp. 295-299
    • Lockless, S.W.1    Ranganathan, R.2
  • 17
    • 58949102247 scopus 로고    scopus 로고
    • Signaling pathways of PDZ2 domain: a molecular dynamics interaction correlation analysis
    • Kong Y, Karplus M. Signaling pathways of PDZ2 domain: a molecular dynamics interaction correlation analysis. Proteins 2009; 74: 145-154.
    • (2009) Proteins , vol.74 , pp. 145-154
    • Kong, Y.1    Karplus, M.2
  • 18
    • 77957231785 scopus 로고    scopus 로고
    • Induced fit, conformational selection and independent dynamic segments: an extended view of binding events
    • Csermely P, Palotai R, Nussinov R. Induced fit, conformational selection and independent dynamic segments: an extended view of binding events. Trends Biochem Sci 2010; 35: 539-546.
    • (2010) Trends Biochem Sci , vol.35 , pp. 539-546
    • Csermely, P.1    Palotai, R.2    Nussinov, R.3
  • 19
    • 79958136745 scopus 로고    scopus 로고
    • A role for both conformational selection and induced fit in ligand binding by the LAO protein
    • Silva D-A, Bowman GR, Sosa-Peinado A, Huang X. A role for both conformational selection and induced fit in ligand binding by the LAO protein. PLoS Comput Biol 2011; 7: e1002054.
    • (2011) PLoS Comput Biol , vol.7
    • Silva, D.-A.1    Bowman, G.R.2    Sosa-Peinado, A.3    Huang, X.4
  • 20
    • 68149177354 scopus 로고    scopus 로고
    • Activation of the West Nile virus NS3 protease: molecular dynamics evidence for a conformational selection mechanism
    • Ekonomiuk D, Caflisch A. Activation of the West Nile virus NS3 protease: molecular dynamics evidence for a conformational selection mechanism. Protein Sci 2009; 18: 1003-1011.
    • (2009) Protein Sci , vol.18 , pp. 1003-1011
    • Ekonomiuk, D.1    Caflisch, A.2
  • 21
    • 80052312953 scopus 로고    scopus 로고
    • Binding free energy landscape of domain-peptide interactions
    • Staneva I, Wallin S. Binding free energy landscape of domain-peptide interactions. PLoS Comput Biol 2011; 7: e1002131.
    • (2011) PLoS Comput Biol , vol.7
    • Staneva, I.1    Wallin, S.2
  • 26
    • 33846823909 scopus 로고
    • Particle mesh Ewald: an nlog(n) method for Ewald sums in large systems
    • Darden T, York D, Pedersen LG. Particle mesh Ewald: an nlog(n) method for Ewald sums in large systems. J Chem Phys 1993; 98: 10089.
    • (1993) J Chem Phys , vol.98 , pp. 10089
    • Darden, T.1    York, D.2    Pedersen, L.G.3
  • 28
    • 35748935079 scopus 로고    scopus 로고
    • Wordom: a program for efficient analysis of molecular dynamics simulations
    • Seeber M, Cecchini M, Rao F, Settanni G, Caflisch A. Wordom: a program for efficient analysis of molecular dynamics simulations. Bioinformatics 2007; 23: 2625-2627.
    • (2007) Bioinformatics , vol.23 , pp. 2625-2627
    • Seeber, M.1    Cecchini, M.2    Rao, F.3    Settanni, G.4    Caflisch, A.5
  • 29
    • 79952498871 scopus 로고    scopus 로고
    • Wordom: a user-friendly program for the analysis of molecular structures, trajectories, and free energy surfaces
    • Seeber M, Felline A, Raimondi F, Muff S, Friedman R, Rao F, Caflisch A, Fanelli F. Wordom: a user-friendly program for the analysis of molecular structures, trajectories, and free energy surfaces. J Comput Chem 2011; 32: 1183-1194.
    • (2011) J Comput Chem , vol.32 , pp. 1183-1194
    • Seeber, M.1    Felline, A.2    Raimondi, F.3    Muff, S.4    Friedman, R.5    Rao, F.6    Caflisch, A.7    Fanelli, F.8
  • 30
    • 84858315783 scopus 로고    scopus 로고
    • Efficient construction of mesostate networks from molecular dynamics trajectories
    • Vitalis A, Caflisch A. Efficient construction of mesostate networks from molecular dynamics trajectories. J Chem Theor Comput 2012; 8: 1108-1120.
    • (2012) J Chem Theor Comput , vol.8 , pp. 1108-1120
    • Vitalis, A.1    Caflisch, A.2
  • 31
    • 33746567202 scopus 로고    scopus 로고
    • One-dimensional free-energy profiles of complex systems: progress variables that preserve the barriers
    • Krivov SV, Karplus M. One-dimensional free-energy profiles of complex systems: progress variables that preserve the barriers. J Phys Chem B 2006; 110: 12689-12698.
    • (2006) J Phys Chem B , vol.110 , pp. 12689-12698
    • Krivov, S.V.1    Karplus, M.2
  • 32
    • 52949137003 scopus 로고    scopus 로고
    • Diffusive reaction dynamics on invariant free energy profiles
    • Krivov SV, Karplus M. Diffusive reaction dynamics on invariant free energy profiles. Proc Natl Acad Sci USA 2008; 105: 13841-13846.
    • (2008) Proc Natl Acad Sci USA , vol.105 , pp. 13841-13846
    • Krivov, S.V.1    Karplus, M.2
  • 33
    • 49149121255 scopus 로고    scopus 로고
    • One-dimensional barrier preserving free-energy projections of a beta-sheet miniprotein: new insights into the folding process
    • Krivov SV, Muff S, Caflisch A, Karplus M. One-dimensional barrier preserving free-energy projections of a beta-sheet miniprotein: new insights into the folding process. J Phys Chem B 2008; 112: 8701-8714.
    • (2008) J Phys Chem B , vol.112 , pp. 8701-8714
    • Krivov, S.V.1    Muff, S.2    Caflisch, A.3    Karplus, M.4
  • 34
    • 4143090730 scopus 로고    scopus 로고
    • The protein folding network
    • Rao F, Caflisch A. The protein folding network. J Mol Biol 2004; 342: 299-306.
    • (2004) J Mol Biol , vol.342 , pp. 299-306
    • Rao, F.1    Caflisch, A.2
  • 35
    • 78049438869 scopus 로고    scopus 로고
    • Is protein folding sub-diffusive?
    • Krivov SV. Is protein folding sub-diffusive? PLoS Comput Biol 2010; 6: e1000921.
    • (2010) PLoS Comput Biol , vol.6
    • Krivov, S.V.1
  • 37
    • 12344311123 scopus 로고    scopus 로고
    • Detection of a hidden folding intermediate of the third domain of PDZ
    • Feng H, Vu N-D, Bai Y. Detection of a hidden folding intermediate of the third domain of PDZ. J Mol Biol 2005; 346: 345-353.
    • (2005) J Mol Biol , vol.346 , pp. 345-353
    • Feng, H.1    Vu, N.-D.2    Bai, Y.3
  • 38
    • 1642276423 scopus 로고    scopus 로고
    • Cdc42 regulates the Par-6 PDZ domain through an allosteric CRIB-PDZ transition
    • Peterson FC, Penkert RR, Volkman Brian F, Prehoda KE. Cdc42 regulates the Par-6 PDZ domain through an allosteric CRIB-PDZ transition. Mol Cell 2004; 13: 665-676.
    • (2004) Mol Cell , vol.13 , pp. 665-676
    • Peterson, F.C.1    Penkert, R.R.2    Volkman Brian, F.3    Prehoda, K.E.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.