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Volumn 101, Issue 7, 2011, Pages 1766-1771

Three force fields views of the 3 10 helix

Author keywords

[No Author keywords available]

Indexed keywords

PEPTIDE; PROTEIN;

EID: 80053373102     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1016/j.bpj.2011.08.044     Document Type: Article
Times cited : (46)

References (29)
  • 1
    • 0037174385 scopus 로고    scopus 로고
    • All-atom structure prediction and folding simulations of a stable protein
    • C. Simmerling, B. Strockbine, and A.E. Roitberg All-atom structure prediction and folding simulations of a stable protein J. Am. Chem. Soc. 124 2002 11258 11259
    • (2002) J. Am. Chem. Soc. , vol.124 , pp. 11258-11259
    • Simmerling, C.1    Strockbine, B.2    Roitberg, A.E.3
  • 2
    • 43849093505 scopus 로고    scopus 로고
    • Ten-microsecond molecular dynamics simulation of a fast-folding WW domain
    • P.L. Freddolino, and F. Liu K. Schulten Ten-microsecond molecular dynamics simulation of a fast-folding WW domain Biophys. J. 94 2008 L75 L77
    • (2008) Biophys. J. , vol.94
    • Freddolino, P.L.1    Liu, F.2    Schulten, K.3
  • 3
    • 67649412164 scopus 로고    scopus 로고
    • The Fip35 WW domain folds with structural and mechanistic heterogeneity in molecular dynamics simulations
    • D.L. Ensign, and V.S. Pande The Fip35 WW domain folds with structural and mechanistic heterogeneity in molecular dynamics simulations Biophys. J. 96 2009 L53 L55
    • (2009) Biophys. J. , vol.96
    • Ensign, D.L.1    Pande, V.S.2
  • 4
    • 77955606360 scopus 로고    scopus 로고
    • Tackling force-field bias in protein folding simulations: Folding of Villin HP35 and Pin WW domains in explicit water
    • J. Mittal, and R.B. Best Tackling force-field bias in protein folding simulations: folding of Villin HP35 and Pin WW domains in explicit water Biophys. J. 99 2010 L26 L28
    • (2010) Biophys. J. , vol.99
    • Mittal, J.1    Best, R.B.2
  • 5
    • 77957937199 scopus 로고    scopus 로고
    • Atomic-level characterization of the structural dynamics of proteins
    • D.E. Shaw, and P. Maragakis W. Wriggers Atomic-level characterization of the structural dynamics of proteins Science 330 2010 341 346
    • (2010) Science , vol.330 , pp. 341-346
    • Shaw, D.E.1    Maragakis, P.2    Wriggers, W.3
  • 6
    • 67650359927 scopus 로고    scopus 로고
    • Force field bias in protein folding simulations
    • P.L. Freddolino, and S. Park K. Schulten Force field bias in protein folding simulations Biophys. J. 96 2009 3772 3780
    • (2009) Biophys. J. , vol.96 , pp. 3772-3780
    • Freddolino, P.L.1    Park, S.2    Schulten, K.3
  • 7
    • 79952476196 scopus 로고    scopus 로고
    • Free-energy landscape of the GB1 hairpin in all-atom explicit solvent simulations with different force fields: Similarities and differences
    • R.B. Best, and J. Mittal Free-energy landscape of the GB1 hairpin in all-atom explicit solvent simulations with different force fields: similarities and differences Proteins 79 2011 1318 1328
    • (2011) Proteins , vol.79 , pp. 1318-1328
    • Best, R.B.1    Mittal, J.2
  • 8
    • 0033153245 scopus 로고    scopus 로고
    • Local interactions drive the formation of nonnative structure in the denatured state of human α-lactalbumin: A high resolution structural characterization of a peptide model in aqueous solution
    • S.J. Demarest, Y. Hua, and D.P. Raleigh Local interactions drive the formation of nonnative structure in the denatured state of human α-lactalbumin: a high resolution structural characterization of a peptide model in aqueous solution Biochemistry 38 1999 7380 7387
    • (1999) Biochemistry , vol.38 , pp. 7380-7387
    • Demarest, S.J.1    Hua, Y.2    Raleigh, D.P.3
  • 9
    • 33847072061 scopus 로고    scopus 로고
    • Transformation of an α-helix peptide into a β-hairpin induced by addition of a fragment results in creation of a coexisting state
    • M. Araki, and A. Tamura Transformation of an α-helix peptide into a β-hairpin induced by addition of a fragment results in creation of a coexisting state Proteins 66 2007 860 868
    • (2007) Proteins , vol.66 , pp. 860-868
    • Araki, M.1    Tamura, A.2
  • 11
    • 3142714765 scopus 로고    scopus 로고
    • Extending the treatment of backbone energetics in protein force fields: Limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations
    • A.D. MacKerell Jr., M. Feig, and C.L. Brooks 3rd Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations J. Comput. Chem. 25 2004 1400 1415
    • (2004) J. Comput. Chem. , vol.25 , pp. 1400-1415
    • Mackerell Jr., A.D.1    Feig, M.2    Brooks III, C.L.3
  • 12
    • 0029912748 scopus 로고    scopus 로고
    • Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids
    • DOI 10.1021/ja9621760, PII S0002786396021762
    • W.L. Jorgensen, D.S. Maxwell, and J. Tirado-Rives Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids J. Am. Chem. Soc. 118 1996 11225 11236 (Pubitemid 26399746)
    • (1996) Journal of the American Chemical Society , vol.118 , Issue.45 , pp. 11225-11236
    • Jorgensen, W.L.1    Maxwell, D.S.2    Tirado-Rives, J.3
  • 14
    • 68949086461 scopus 로고    scopus 로고
    • Evaluating the performance of the ff99SB force field based on NMR scalar coupling data
    • L. Wickstrom, A. Okur, and C. Simmerling Evaluating the performance of the ff99SB force field based on NMR scalar coupling data Biophys. J. 97 2009 853 856
    • (2009) Biophys. J. , vol.97 , pp. 853-856
    • Wickstrom, L.1    Okur, A.2    Simmerling, C.3
  • 15
    • 78650880629 scopus 로고    scopus 로고
    • Order through disorder: Hyper-mobile C-terminal residues stabilize the folded state of a helical peptide. A molecular dynamics study
    • K.K. Patapati, and N.M. Glykos Order through disorder: hyper-mobile C-terminal residues stabilize the folded state of a helical peptide. A molecular dynamics study PLoS ONE 5 2010 e15290
    • (2010) PLoS ONE , vol.5 , pp. 15290
    • Patapati, K.K.1    Glykos, N.M.2
  • 16
    • 0042415783 scopus 로고    scopus 로고
    • NAMD2: Greater scalability for parallel molecular dynamics
    • L. Kale, and R. Skeel K. Schulten NAMD2: greater scalability for parallel molecular dynamics J. Comput. Phys. 151 1999 283 312
    • (1999) J. Comput. Phys. , vol.151 , pp. 283-312
    • Kale, L.1    Skeel, R.2    Schulten, K.3
  • 19
    • 33749172039 scopus 로고    scopus 로고
    • Software news and updates carma: A molecular dynamics analysis program
    • DOI 10.1002/jcc.20482
    • N.M. Glykos Software news and updates. CARMA: a molecular dynamics analysis program J. Comput. Chem. 27 2006 1765 1768 (Pubitemid 44476671)
    • (2006) Journal of Computational Chemistry , vol.27 , Issue.14 , pp. 1765-1768
    • Glykos, N.M.1
  • 20
    • 0026076090 scopus 로고
    • Collective motions in proteins: A covariance analysis of atomic fluctuations in molecular dynamics and normal mode simulations
    • T. Ichiye, and M. Karplus Collective motions in proteins: a covariance analysis of atomic fluctuations in molecular dynamics and normal mode simulations Proteins 11 1991 205 217
    • (1991) Proteins , vol.11 , pp. 205-217
    • Ichiye, T.1    Karplus, M.2
  • 22
    • 10844292652 scopus 로고    scopus 로고
    • Energy landscape of a small peptide revealed by dihedral angle principal component analysis
    • DOI 10.1002/prot.20310
    • Y. Mu, P.H. Nguyen, and G. Stock Energy landscape of a small peptide revealed by dihedral angle principal component analysis Proteins 58 2005 45 52 (Pubitemid 39665615)
    • (2005) Proteins: Structure, Function and Genetics , vol.58 , Issue.1 , pp. 45-52
    • Mu, Y.1    Nguyen, P.H.2    Stock, G.3
  • 23
    • 34547297406 scopus 로고    scopus 로고
    • Dihedral angle principal component analysis of molecular dynamics simulations
    • A. Altis, and P.H. Nguyen G. Stock Dihedral angle principal component analysis of molecular dynamics simulations J. Chem. Phys. 126 2007 244111
    • (2007) J. Chem. Phys. , vol.126 , pp. 244111
    • Altis, A.1    Nguyen, P.H.2    Stock, G.3
  • 24
    • 0029619259 scopus 로고
    • Knowledge-based protein secondary structure assignment
    • DOI 10.1002/prot.340230412
    • D. Frishman, and P. Argos Knowledge-based protein secondary structure assignment Proteins 23 1995 566 579 (Pubitemid 26009520)
    • (1995) Proteins: Structure, Function and Genetics , vol.23 , Issue.4 , pp. 566-579
    • Frishman, D.1    Argos, P.2
  • 25
    • 0020997912 scopus 로고
    • Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features
    • W. Kabsch, and C. Sander Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features Biopolymers 22 1983 2577 2637
    • (1983) Biopolymers , vol.22 , pp. 2577-2637
    • Kabsch, W.1    Sander, C.2
  • 28
    • 33645033314 scopus 로고    scopus 로고
    • Comparing atomistic simulation data with the NMR experiment: How much can NOEs actually tell us?
    • B. Zagrovic, and W.F. van Gunsteren Comparing atomistic simulation data with the NMR experiment: how much can NOEs actually tell us? Proteins 63 2006 210 218
    • (2006) Proteins , vol.63 , pp. 210-218
    • Zagrovic, B.1    Van Gunsteren, W.F.2
  • 29
    • 68949107624 scopus 로고    scopus 로고
    • Secondary structure propensities in peptide folding simulations: A systematic comparison of molecular mechanics interaction schemes
    • D. Matthes, and B.L. de Groot Secondary structure propensities in peptide folding simulations: a systematic comparison of molecular mechanics interaction schemes Biophys. J. 97 2009 599 608
    • (2009) Biophys. J. , vol.97 , pp. 599-608
    • Matthes, D.1    De Groot, B.L.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.