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Volumn 5, Issue 4, 2010, Pages

Evaluating molecular mechanical potentials for helical peptides and proteins

Author keywords

[No Author keywords available]

Indexed keywords

ALANINE; APOLIPOPHORIN III; ARGININE; PEPTIDE DERIVATIVE; PROLINE DERIVATIVE; PROTEIN DERIVATIVE; UNCLASSIFIED DRUG; APOLIPOPROTEIN; PEPTIDE; PROTEIN; SOLVENT;

EID: 77956302920     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0010056     Document Type: Article
Times cited : (29)

References (38)
  • 1
    • 85047692291 scopus 로고    scopus 로고
    • Empirical Force Field Assessment: The Interplay Between Backbone Torsions and Non-covalent Term Scaling
    • Sorin EJ, Pande VS (2005) Empirical Force Field Assessment: the Interplay Between Backbone Torsions and Non-covalent Term Scaling. Journal of Computational Chemistry 26: 682-690.
    • (2005) Journal of Computational Chemistry , vol.26 , pp. 682-690
    • Sorin, E.J.1    Pande, V.S.2
  • 2
    • 33748518255 scopus 로고    scopus 로고
    • Comparison of Multiple Amber Force Fields and Development of Improved Protein Backbone Parameters. Proteins: Structure
    • Hornak V, Abel R, Okur A, Strockbine B, Roitberg A, et al. (2006) Comparison of Multiple Amber Force Fields and Development of Improved Protein Backbone Parameters. Proteins: Structure, Function, and Bioinformatics 65:712-725.
    • (2006) Function, and Bioinformatics , vol.65 , pp. 712-725
    • Hornak, V.1    Abel, R.2    Okur, A.3    Strockbine, B.4    Roitberg, A.5
  • 4
    • 2542564912 scopus 로고    scopus 로고
    • Advances and Continuing Challenges in Achieving Realistic and Predictive Simulations of the Properties of Organic and Biological Molecules
    • Kollman PA (1996) Advances and Continuing Challenges in Achieving Realistic and Predictive Simulations of the Properties of Organic and Biological Molecules. Accounts of Chemical Research 29: 461-469.
    • (1996) Accounts of Chemical Research , vol.29 , pp. 461-469
    • Kollman, P.A.1
  • 5
    • 0001398008 scopus 로고    scopus 로고
    • How Well Does a Restrained Electrostatic Potential (RESP) Model Perform in Calculating Conformational Energies of Organic and Biological Molecules?
    • Wang J, Cieplak P, Kollman PA (2000) How Well Does a Restrained Electrostatic Potential (RESP) Model Perform in Calculating Conformational Energies of Organic and Biological Molecules? Journal of Computational Chemistry 21: 1049-1074.
    • (2000) Journal of Computational Chemistry , vol.21 , pp. 1049-1074
    • Wang, J.1    Cieplak, P.2    Kollman, P.A.3
  • 7
    • 20544435097 scopus 로고    scopus 로고
    • Exploring the Helix-coil Transition via All-atom Equilibrium Ensemble Simulations
    • Sorin EJ, Pande VS (2005) Exploring the Helix-coil Transition via All-atom Equilibrium Ensemble Simulations. Biophysical Journal 88: 2472-2493.
    • (2005) Biophysical Journal , vol.88 , pp. 2472-2493
    • Sorin, E.J.1    Pande, V.S.2
  • 8
    • 30344484542 scopus 로고    scopus 로고
    • The solvation interface is a determining factor in peptide conformational preferences
    • Sorin EJ, Rhee YM, Shirts MR, Pande VS (2006) The solvation interface is a determining factor in peptide conformational preferences. Journal Of Molecular Biology 356: 248-256.
    • (2006) Journal of Molecular Biology , vol.356 , pp. 248-256
    • Sorin, E.J.1    Rhee, Y.M.2    Shirts, M.R.3    Pande, V.S.4
  • 9
    • 47149107224 scopus 로고    scopus 로고
    • Molecular Simulation of Multistate Peptide Dynamics: A Comparison Between Microsecond Timescale Sampling and Multiple Shorter Trajectories
    • Monticelli L, Sorin EJ, Tieleman DP, Pande VS, Colombo G (2008) Molecular Simulation of Multistate Peptide Dynamics: A Comparison Between Microsecond Timescale Sampling and Multiple Shorter Trajectories. Journal of Computational Chemistry 29: 1740-1752.
    • (2008) Journal of Computational Chemistry , vol.29 , pp. 1740-1752
    • Monticelli, L.1    Sorin, E.J.2    Tieleman, D.P.3    Pande, V.S.4    Colombo, G.5
  • 10
    • 0242663237 scopus 로고    scopus 로고
    • A Point-Charge Force Field for Molecular Mechanics Simulations of Proteins Based on Condensed-Phase Quantum Mechanical Calculations
    • Duan Y, Wu C, Chowdhury S, Lee MC, Xiong G, et al. (2003) A Point-Charge Force Field for Molecular Mechanics Simulations of Proteins Based on Condensed-Phase Quantum Mechanical Calculations. Journal of Computational Chemistry 24: 1999-2012.
    • (2003) Journal of Computational Chemistry , vol.24 , pp. 1999-2012
    • Duan, Y.1    Wu, C.2    Chowdhury, S.3    Lee, M.C.4    Xiong, G.5
  • 11
    • 0345862082 scopus 로고    scopus 로고
    • Characterization of non-alpha helical conformations in Ala peptides
    • Garcia AE (2004) Characterization of non-alpha helical conformations in Ala peptides. Polymer 45: 669-676.
    • (2004) Polymer , vol.45 , pp. 669-676
    • Garcia, A.E.1
  • 13
    • 0035789518 scopus 로고    scopus 로고
    • GROMACS 3.0: A package for molecular simulation and trajectory analysis
    • Lindahl E, Hess B, van der Spoel D (2001) GROMACS 3.0: a package for molecular simulation and trajectory analysis. Journal Of Molecular Modeling 7:306-317.
    • (2001) Journal of Molecular Modeling , vol.7 , pp. 306-317
    • Lindahl, E.1    Hess, B.2    van der Spoel, D.3
  • 14
    • 0035850758 scopus 로고    scopus 로고
    • β-hairpin folding simulations in atomistic detail using an implicit solvent model
    • Zagrovic B, Sorin EJ, Pande V (2001) β-hairpin folding simulations in atomistic detail using an implicit solvent model. Journal Of Molecular Biology 313: 151-169.
    • (2001) Journal of Molecular Biology , vol.313 , pp. 151-169
    • Zagrovic, B.1    Sorin, E.J.2    Pande, V.3
  • 17
    • 0027912723 scopus 로고
    • Electrostatic screening of charge and dipole interactions with the helix backbone
    • Lockhart DJ, Kim PS (1993) Electrostatic screening of charge and dipole interactions with the helix backbone. Science 260: 198-202.
    • (1993) Science , vol.260 , pp. 198-202
    • Lockhart, D.J.1    Kim, P.S.2
  • 20
    • 0030789351 scopus 로고    scopus 로고
    • Laser Temperature Jump Study of the Helix-Coil Kinetics of an Alanine Peptide Interpreted with a 'Kinetic Zipper' Model
    • Thompson PA, Eaton WA, Hofrichter J (1997) Laser Temperature Jump Study of the Helix-Coil Kinetics of an Alanine Peptide Interpreted with a 'Kinetic Zipper' Model. Biochemistry 36: 9200-9210.
    • (1997) Biochemistry , vol.36 , pp. 9200-9210
    • Thompson, P.A.1    Eaton, W.A.2    Hofrichter, J.3
  • 22
    • 0343005873 scopus 로고    scopus 로고
    • Molecular dynamics simulations of a polyalanine octapeptide under Ewald boundary conditions: Influence of artificial periodicity on peptide conformation
    • Weber W, Hunenberger PH, McCammon JA (2000) Molecular dynamics simulations of a polyalanine octapeptide under Ewald boundary conditions: Influence of artificial periodicity on peptide conformation. Journal of Physical Chemistry B 104: 3668-3675.
    • (2000) Journal of Physical Chemistry B , vol.104 , pp. 3668-3675
    • Weber, W.1    Hunenberger, P.H.2    McCammon, J.A.3
  • 26
    • 0038418381 scopus 로고    scopus 로고
    • NMR Solution Structure and Dynamics of an Exchangeable Apolipoprotein, Locusta migratoria Apolipophorin III
    • Fan D, Zheng Y, Yang D, Wang J (2003) NMR Solution Structure and Dynamics of an Exchangeable Apolipoprotein, Locusta migratoria Apolipophorin III. Journal Of Biological Chemistry 278: 21212-21220.
    • (2003) Journal of Biological Chemistry , vol.278 , pp. 21212-21220
    • Fan, D.1    Zheng, Y.2    Yang, D.3    Wang, J.4
  • 27
    • 0020997912 scopus 로고
    • Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features
    • Kabsch W, Sander C (1983) Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22: 2577-2637.
    • (1983) Biopolymers , vol.22 , pp. 2577-2637
    • Kabsch, W.1    Sander, C.2
  • 28
    • 4043162793 scopus 로고    scopus 로고
    • VEGA - An open platform to develop chemo-bio-informatics applications, using plug-in architecture and script programming
    • Pedretti A, Villa L, Vistoli G (2004) VEGA - An open platform to develop chemo-bio-informatics applications, using plug-in architecture and script programming. Journal of Computer-Aided Molecular Design 18: 167-173.
    • (2004) Journal of Computer-Aided Molecular Design , vol.18 , pp. 167-173
    • Pedretti, A.1    Villa, L.2    Vistoli, G.3
  • 29
    • 0000333671 scopus 로고
    • Theory of Helix-Coil Transition in Polypeptides
    • Lifson S, Roig A (1961) Theory of Helix-Coil Transition in Polypeptides. Journal Of Chemical Physics 34: 1963-1974.
    • (1961) Journal of Chemical Physics , vol.34 , pp. 1963-1974
    • Lifson, S.1    Roig, A.2
  • 32
    • 35948943745 scopus 로고    scopus 로고
    • Validation of Molecular Dynamics Simulations of Biomolecules Using NMR Spin Relaxation as Benchmarks: Application to the AMBER99SB Force Field
    • Showalter SA, Bruschweiler R (2007) Validation of Molecular Dynamics Simulations of Biomolecules Using NMR Spin Relaxation as Benchmarks: Application to the AMBER99SB Force Field. Journal of Chemical Theory and Computation 3: 961-975.
    • (2007) Journal of Chemical Theory and Computation , vol.3 , pp. 961-975
    • Showalter, S.A.1    Bruschweiler, R.2
  • 33
    • 46749127364 scopus 로고    scopus 로고
    • Are Current Molecular Dynamics Force Fields too Helical?
    • Best RB, Buchete N-V, Hummer G (2008) Are Current Molecular Dynamics Force Fields too Helical? Biophysical Journal 95: L07-L09.
    • (2008) Biophysical Journal , vol.95
    • Best, R.B.1    Buchete, N.-V.2    Hummer, G.3
  • 34
    • 67649494492 scopus 로고    scopus 로고
    • Optimized Molecular Dynamics Force Fields Applied to the Helix-Coil Transition of Polypeptides
    • Best RB, Hummer G (2009) Optimized Molecular Dynamics Force Fields Applied to the Helix-Coil Transition of Polypeptides. The Journal of Physical Chemistry B 113: 9004-9015.
    • (2009) The Journal of Physical Chemistry B , vol.113 , pp. 9004-9015
    • Best, R.B.1    Hummer, G.2
  • 35
    • 68949086461 scopus 로고    scopus 로고
    • Evaluating the Performance of the ff99SB Force Field Based on NMR Scalar Coupling Data
    • Wickstrom L, Okur A, Simmerling C (2009) Evaluating the Performance of the ff99SB Force Field Based on NMR Scalar Coupling Data. Biophysical Journal 97: 853-856.
    • (2009) Biophysical Journal , vol.97 , pp. 853-856
    • Wickstrom, L.1    Okur, A.2    Simmerling, C.3
  • 37
    • 20544455385 scopus 로고    scopus 로고
    • Role of Buried Polar Residues in Helix Bundle Stability and Lipid Binding of Apolipophorin III: Destabilization by Threonine 31
    • Weers PMM, Abdullahi WE, Cabrera JM, Hsu T-C (2005) Role of Buried Polar Residues in Helix Bundle Stability and Lipid Binding of Apolipophorin III: Destabilization by Threonine 31. Biochemistry 44: 8810-8816.
    • (2005) Biochemistry , vol.44 , pp. 8810-8816
    • Weers, P.M.M.1    Abdullahi, W.E.2    Cabrera, J.M.3    Hsu, T.-C.4
  • 38
    • 33645789374 scopus 로고    scopus 로고
    • A Novel Folding Intermediate State for Apolipoprotein A-I: Role of the Amino and Carboxy Termini
    • Gross E, Peng D-Q, Hazen SL, Smith JD (2006) A Novel Folding Intermediate State for Apolipoprotein A-I: Role of the Amino and Carboxy Termini. Biophysical Journal 90: 1362-1370.
    • (2006) Biophysical Journal , vol.90 , pp. 1362-1370
    • Gross, E.1    Peng, D.-Q.2    Hazen, S.L.3    Smith, J.D.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.