메뉴 건너뛰기




Volumn 375, Issue 2, 2008, Pages 460-470

Predicting the Effect of a Point Mutation on a Protein Fold: The Villin and Advillin Headpieces and Their Pro62Ala Mutants

Author keywords

advillin headpiece; metadynamics; molecular dynamics simulation; protein folding; villin headpiece

Indexed keywords

ADVILLIN; ALANINE; BINDING PROTEIN; MUTANT PROTEIN; PROLINE; UNCLASSIFIED DRUG; VILLIN;

EID: 36548999391     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2007.10.020     Document Type: Article
Times cited : (45)

References (44)
  • 1
    • 34347219018 scopus 로고    scopus 로고
    • Destruction of long range interactions by a single mutation in lysozyme
    • Zhou R., Eleftheriou M., Royyuru A.K., and Berne B.J. Destruction of long range interactions by a single mutation in lysozyme. Proc. Natl Acad. Sci. USA 104 (2007) 5824-5829
    • (2007) Proc. Natl Acad. Sci. USA , vol.104 , pp. 5824-5829
    • Zhou, R.1    Eleftheriou, M.2    Royyuru, A.K.3    Berne, B.J.4
  • 3
    • 33748248896 scopus 로고    scopus 로고
    • Using massively parallel simulation and Markovian models to study protein folding: examining the dynamics of the villin headpiece
    • Jayachandran G., Vishal V., and Pande V.S. Using massively parallel simulation and Markovian models to study protein folding: examining the dynamics of the villin headpiece. J. Chem. Phys. 124 (2006) 164902
    • (2006) J. Chem. Phys. , vol.124 , pp. 164902
    • Jayachandran, G.1    Vishal, V.2    Pande, V.S.3
  • 4
    • 1942505724 scopus 로고    scopus 로고
    • Solution structures of the C-terminal headpiece subdomains of human villin and advillin, evaluation of headpiece F-actin-binding requirements
    • Vermeulen W., Vanhaesebrouck P., Van Troys M., Verschueren M., Fant F., Goethals M., et al. Solution structures of the C-terminal headpiece subdomains of human villin and advillin, evaluation of headpiece F-actin-binding requirements. Protein Sci. 13 (2004) 1276-1287
    • (2004) Protein Sci. , vol.13 , pp. 1276-1287
    • Vermeulen, W.1    Vanhaesebrouck, P.2    Van Troys, M.3    Verschueren, M.4    Fant, F.5    Goethals, M.6
  • 5
    • 0031058410 scopus 로고    scopus 로고
    • NMR structure of the 35-residue villin headpiece subdomain
    • McKnight C.J., Matsudaira P.T., and Kim P.S. NMR structure of the 35-residue villin headpiece subdomain. Nat. Struct. Biol. 4 (1997) 180-184
    • (1997) Nat. Struct. Biol. , vol.4 , pp. 180-184
    • McKnight, C.J.1    Matsudaira, P.T.2    Kim, P.S.3
  • 6
    • 33745228454 scopus 로고    scopus 로고
    • Identification of the PXW sequence as a structural gatekeeper of the headpiece C-terminal subdomain fold
    • Vermeulen W., Van Troys M., Bourry D., Dewitte D., Rossenu S., Goethals M., et al. Identification of the PXW sequence as a structural gatekeeper of the headpiece C-terminal subdomain fold. J. Mol. Biol. 359 (2006) 1277-1292
    • (2006) J. Mol. Biol. , vol.359 , pp. 1277-1292
    • Vermeulen, W.1    Van Troys, M.2    Bourry, D.3    Dewitte, D.4    Rossenu, S.5    Goethals, M.6
  • 7
    • 0036180616 scopus 로고    scopus 로고
    • The role of aromatic residues in the hydrophobic core of the villin headpiece subdomain
    • Frank B.S., Vardar D., Buckley D.A., and McKnight C.J. The role of aromatic residues in the hydrophobic core of the villin headpiece subdomain. Protein Sci. 11 (2002) 680-687
    • (2002) Protein Sci. , vol.11 , pp. 680-687
    • Frank, B.S.1    Vardar, D.2    Buckley, D.A.3    McKnight, C.J.4
  • 8
    • 0036428782 scopus 로고    scopus 로고
    • Simulation of folding of a small alpha-helical protein in atomistic detail using worldwide-distributed computing
    • Zagrovic B., Snow C.D., Shirts M.R., and Pande V.S. Simulation of folding of a small alpha-helical protein in atomistic detail using worldwide-distributed computing. J. Mol. Biol. 323 (2002) 927-937
    • (2002) J. Mol. Biol. , vol.323 , pp. 927-937
    • Zagrovic, B.1    Snow, C.D.2    Shirts, M.R.3    Pande, V.S.4
  • 9
    • 2542462060 scopus 로고    scopus 로고
    • Folding of the villin headpiece subdomain from random structures. Analysis of the charge distribution as a function of pH
    • Ripoll D.R., Vila J.A., and Scheraga H.A. Folding of the villin headpiece subdomain from random structures. Analysis of the charge distribution as a function of pH. J. Mol. Biol. 339 (2004) 915-925
    • (2004) J. Mol. Biol. , vol.339 , pp. 915-925
    • Ripoll, D.R.1    Vila, J.A.2    Scheraga, H.A.3
  • 10
    • 0345724787 scopus 로고    scopus 로고
    • Ab initio folding of helix bundle proteins using molecular dynamics simulations
    • Jang S.M., Kim E., Shin S., and Pak Y. Ab initio folding of helix bundle proteins using molecular dynamics simulations. J. Am. Chem. Soc. 125 (2003) 14841-14846
    • (2003) J. Am. Chem. Soc. , vol.125 , pp. 14841-14846
    • Jang, S.M.1    Kim, E.2    Shin, S.3    Pak, Y.4
  • 11
    • 27144440086 scopus 로고    scopus 로고
    • Efficient sampling of protein structures by model hopping
    • Kwak W., and Hansmann U.H.E. Efficient sampling of protein structures by model hopping. Phys. Rev. Lett. 95 (2005) 138102
    • (2005) Phys. Rev. Lett. , vol.95 , pp. 138102
    • Kwak, W.1    Hansmann, U.H.E.2
  • 12
    • 34249298006 scopus 로고    scopus 로고
    • Two-stage folding of HP-35 from ab initio simulations
    • Lei H., and Duan Y. Two-stage folding of HP-35 from ab initio simulations. J. Mol. Biol. 370 (2007) 196-206
    • (2007) J. Mol. Biol. , vol.370 , pp. 196-206
    • Lei, H.1    Duan, Y.2
  • 13
    • 11344285181 scopus 로고    scopus 로고
    • Study of the villin headpiece folding dynamics by combining coarse-grained Monte Carlo evolution and all-atom molecular dynamics
    • DeMori G.M., Colombo G., and Micheletti C. Study of the villin headpiece folding dynamics by combining coarse-grained Monte Carlo evolution and all-atom molecular dynamics. Proteins: Struct. Funct. Genet. 58 (2005) 459-471
    • (2005) Proteins: Struct. Funct. Genet. , vol.58 , pp. 459-471
    • DeMori, G.M.1    Colombo, G.2    Micheletti, C.3
  • 14
    • 1142279630 scopus 로고    scopus 로고
    • Contact pair dynamics during folding of two small proteins: chicken villin head piece and the Alzheimer protein beta-amyloid
    • Mukherjee A., and Bagchi B. Contact pair dynamics during folding of two small proteins: chicken villin head piece and the Alzheimer protein beta-amyloid. J. Chem. Phys. 120 (2004) 1602-1612
    • (2004) J. Chem. Phys. , vol.120 , pp. 1602-1612
    • Mukherjee, A.1    Bagchi, B.2
  • 15
    • 21644454399 scopus 로고    scopus 로고
    • Finding pathways between distant local minima
    • Carr J.M., Trygubenko S.A., and Wales D.J. Finding pathways between distant local minima. J. Chem. Phys. 122 (2005) 234903
    • (2005) J. Chem. Phys. , vol.122 , pp. 234903
    • Carr, J.M.1    Trygubenko, S.A.2    Wales, D.J.3
  • 16
    • 33645683978 scopus 로고    scopus 로고
    • Global optimization and folding pathways of selected alpha-helical proteins
    • Carr J.M., and Wales D.J. Global optimization and folding pathways of selected alpha-helical proteins. J. Chem. Phys. 123 (2005) 234901
    • (2005) J. Chem. Phys. , vol.123 , pp. 234901
    • Carr, J.M.1    Wales, D.J.2
  • 18
    • 34249071886 scopus 로고    scopus 로고
    • A bias-exchange approach to protein folding
    • Piana S., and Laio A. A bias-exchange approach to protein folding. J. Phys. Chem. B 111 (2007) 4553-4559
    • (2007) J. Phys. Chem. B , vol.111 , pp. 4553-4559
    • Piana, S.1    Laio, A.2
  • 19
    • 0001616080 scopus 로고    scopus 로고
    • Replica-exchange molecular dynamics method for protein folding
    • Sugita Y., and Okamoto Y. Replica-exchange molecular dynamics method for protein folding. Chem. Phys. Lett. 314 (1999) 141-151
    • (1999) Chem. Phys. Lett. , vol.314 , pp. 141-151
    • Sugita, Y.1    Okamoto, Y.2
  • 21
    • 34247639441 scopus 로고    scopus 로고
    • Folding free-energy landscape of villin headpiece subdomain from molecular dynamics simulations
    • Lei H., Wu C., Liu H., and Duan Y. Folding free-energy landscape of villin headpiece subdomain from molecular dynamics simulations. Proc. Natl Acad. Sci. USA 104 (2007) 4925-4930
    • (2007) Proc. Natl Acad. Sci. USA , vol.104 , pp. 4925-4930
    • Lei, H.1    Wu, C.2    Liu, H.3    Duan, Y.4
  • 22
    • 0027991081 scopus 로고
    • Estimation of changes in side chain configurational entropy in binding and folding: general methods and application to helix formation
    • Lee K.H., Xie D., Freire E., and Amzel L.M. Estimation of changes in side chain configurational entropy in binding and folding: general methods and application to helix formation. Proteins: Struct. Funct. Genet. 20 (1994) 68-84
    • (1994) Proteins: Struct. Funct. Genet. , vol.20 , pp. 68-84
    • Lee, K.H.1    Xie, D.2    Freire, E.3    Amzel, L.M.4
  • 24
    • 0029957505 scopus 로고    scopus 로고
    • The enthalpy change in protein folding and binding: refinement of parameters for structure-based calculations
    • Hilser V.J., Gomez J., and Freire E. The enthalpy change in protein folding and binding: refinement of parameters for structure-based calculations. Proteins: Struct. Funct. Genet. 26 (1996) 123-133
    • (1996) Proteins: Struct. Funct. Genet. , vol.26 , pp. 123-133
    • Hilser, V.J.1    Gomez, J.2    Freire, E.3
  • 25
    • 0029958659 scopus 로고    scopus 로고
    • Structure-based thermodynamic scale of alpha-helix propensities in amino acids
    • Luque I., Mayorga O.L., and Freire E. Structure-based thermodynamic scale of alpha-helix propensities in amino acids. Biochemistry 35 (1996) 13681-13688
    • (1996) Biochemistry , vol.35 , pp. 13681-13688
    • Luque, I.1    Mayorga, O.L.2    Freire, E.3
  • 26
    • 0030905238 scopus 로고    scopus 로고
    • Structure-based thermodynamic analysis of HIV-1 protease inhibitors
    • Bardi J.S., Luque I., and Freire E. Structure-based thermodynamic analysis of HIV-1 protease inhibitors. Biochemistry 36 (1997) 6588-6596
    • (1997) Biochemistry , vol.36 , pp. 6588-6596
    • Bardi, J.S.1    Luque, I.2    Freire, E.3
  • 27
    • 33750040264 scopus 로고    scopus 로고
    • Free-energy landscape for β hairpin folding from combined parallel tempering and metadynamics
    • Bussi G., Gervasio F., Laio A., and Parrinello M. Free-energy landscape for β hairpin folding from combined parallel tempering and metadynamics. J. Am. Chem. Soc. 128 (2006) 13435-13441
    • (2006) J. Am. Chem. Soc. , vol.128 , pp. 13435-13441
    • Bussi, G.1    Gervasio, F.2    Laio, A.3    Parrinello, M.4
  • 28
    • 0028710015 scopus 로고
    • Local elevation: a method for improving the searching properties of molecular dynamics simulations
    • HÅber T., Torda A.E., and van Gunsteren W.F. Local elevation: a method for improving the searching properties of molecular dynamics simulations. J. Comput.-Aided Mol. Des. 8 (1994) 695-708
    • (1994) J. Comput.-Aided Mol. Des. , vol.8 , pp. 695-708
    • HÅber, T.1    Torda, A.E.2    van Gunsteren, W.F.3
  • 31
    • 4143145167 scopus 로고    scopus 로고
    • 10-residue folded peptide designed by segment statistics
    • Honda S., Yamasaki K., Sawada Y., and Morii H. 10-residue folded peptide designed by segment statistics. Structure 12 (2004) 1507-1518
    • (2004) Structure , vol.12 , pp. 1507-1518
    • Honda, S.1    Yamasaki, K.2    Sawada, Y.3    Morii, H.4
  • 34
    • 0242663237 scopus 로고    scopus 로고
    • A point-charge force field for molecular mechanics simulations of proteins
    • Duan Y., Wu C., Chowdhury S., Lee M.C., Xiong G., Zhang W., et al. A point-charge force field for molecular mechanics simulations of proteins. J. Comput. Chem. 24 (2003) 1999-2012
    • (2003) J. Comput. Chem. , vol.24 , pp. 1999-2012
    • Duan, Y.1    Wu, C.2    Chowdhury, S.3    Lee, M.C.4    Xiong, G.5    Zhang, W.6
  • 35
    • 0035425883 scopus 로고    scopus 로고
    • An improved GROMOS96 force field for aliphatic hydrocarbons in the condensed phase
    • Schuler L.D., Daura X., and van Gunsteren W.F. An improved GROMOS96 force field for aliphatic hydrocarbons in the condensed phase. J. Comput. Chem. 22 (2001) 1205-1218
    • (2001) J. Comput. Chem. , vol.22 , pp. 1205-1218
    • Schuler, L.D.1    Daura, X.2    van Gunsteren, W.F.3
  • 36
    • 0035913529 scopus 로고    scopus 로고
    • Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations
    • Kaminski G.A., Friesner R.A., Tirado-Rives J., and Jorgensen W.L. Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations. J. Phys. Chem. B 105 (2001) 6474-6487
    • (2001) J. Phys. Chem. B , vol.105 , pp. 6474-6487
    • Kaminski, G.A.1    Friesner, R.A.2    Tirado-Rives, J.3    Jorgensen, W.L.4
  • 38
    • 0035789518 scopus 로고    scopus 로고
    • GROMACS 3.0: a package for molecular simulation and trajectory analysis
    • Lindhal E., Hess B., and van der Spoel D. GROMACS 3.0: a package for molecular simulation and trajectory analysis. J. Mol. Model. 7 (2001) 306-317
    • (2001) J. Mol. Model. , vol.7 , pp. 306-317
    • Lindhal, E.1    Hess, B.2    van der Spoel, D.3
  • 41
    • 34547809547 scopus 로고
    • A unified formulation of the constant temperature molecular dynamics method
    • Nose S. A unified formulation of the constant temperature molecular dynamics method. J. Chem. Phys. 81 (1984) 511
    • (1984) J. Chem. Phys. , vol.81 , pp. 511
    • Nose, S.1
  • 43
    • 0004016501 scopus 로고
    • Transferable intermolecular potential functions for water, alcohols, and ethers. Application to liquid water
    • Jorgensen W.L., Chandrasekhar J., and Madura J.P. Transferable intermolecular potential functions for water, alcohols, and ethers. Application to liquid water. J. Chem. Phys. 79 (1983) 926-935
    • (1983) J. Chem. Phys. , vol.79 , pp. 926-935
    • Jorgensen, W.L.1    Chandrasekhar, J.2    Madura, J.P.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.