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Volumn 10, Issue 7, 2015, Pages

Distance-based configurational entropy of proteins from molecular dynamics simulations

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; ANTIPORTER; BETA 2 MICROGLOBULIN; BINDING PROTEIN; EXCHANGE PROTEIN DIRECTLY ACTIVATED BY CYCLIC AMP; GOLD NANOPARTICLE; PROTEIN; PROTEIN OPPA; UNCLASSIFIED DRUG; BACTERIAL PROTEIN; CARRIER PROTEIN; GUANINE NUCLEOTIDE EXCHANGE FACTOR; LIPOPROTEIN; OLIGOPEPTIDE-BINDING PROTEIN, BACTERIA; PROTEIN BINDING;

EID: 84941277320     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0132356     Document Type: Article
Times cited : (35)

References (81)
  • 1
    • 34447503697 scopus 로고    scopus 로고
    • Conformational entropy in molecular recognition by proteins
    • 17637663
    • Frederick KK, Marlow MS, Valentine KG, Wand AJ. Conformational entropy in molecular recognition by proteins. Nature. 2007;448:325-329. doi: 10.1038/nature05959 PMID: 17637663
    • (2007) Nature , vol.448 , pp. 325-329
    • Frederick, K.K.1    Marlow, M.S.2    Valentine, K.G.3    Wand, A.J.4
  • 2
    • 50349092827 scopus 로고    scopus 로고
    • Entropy-driven cAMPdependent allosteric control of inhibitory interactions in exchange proteins directly activated by cAMP
    • 18411261
    • Das R, Mazhab-Jafari MT, Chowdhury S, Sil Das S, Selvaratnam R, Melacini G. Entropy-driven cAMPdependent allosteric control of inhibitory interactions in exchange proteins directly activated by cAMP. J Biol Chem. 2008;283:19691-19703. doi: 10.1074/jbc. M802164200 PMID: 18411261
    • (2008) J Biol Chem. , vol.283 , pp. 19691-19703
    • Das, R.1    Mazhab-Jafari, M.T.2    Chowdhury, S.3    Sil Das, S.4    Selvaratnam, R.5    Melacini, G.6
  • 4
    • 84858228154 scopus 로고    scopus 로고
    • Determining the energy landscape of proteins by a fast isotope exchange NMR approach
    • 22380530
    • Rennella E, Corazza A, Codutti L, Bellotti V, Stoppini M, Viglino P, et al. Determining the energy landscape of proteins by a fast isotope exchange NMR approach. J Am Chem Soc. 2012;134:4457-4460. doi: 10.1021/ja209004q PMID: 22380530
    • (2012) J Am Chem Soc. , vol.134 , pp. 4457-4460
    • Rennella, E.1    Corazza, A.2    Codutti, L.3    Bellotti, V.4    Stoppini, M.5    Viglino, P.6
  • 5
    • 84855973736 scopus 로고    scopus 로고
    • Estimation of conformational entropy in protein-ligand interactions: A computational perspective
    • 22183546
    • Polyansky AA, Zubac R, Zagrovic B. Estimation of conformational entropy in protein-ligand interactions: a computational perspective. Methods Mol Biol. 2012;819:327-353. doi: 10.1007/978-1-61779-465-0-21 PMID: 22183546
    • (2012) Methods Mol Biol. , vol.819 , pp. 327-353
    • Polyansky, A.A.1    Zubac, R.2    Zagrovic, B.3
  • 6
    • 34347224684 scopus 로고    scopus 로고
    • Calculation of protein-ligand binding affinities
    • 17201676
    • Gilson MK, Zhou HX. Calculation of protein-ligand binding affinities. Annu Rev Biophys Biomol Struct. 2007;36:21-42. doi: 10.1146/annurev. biophys.36.040306.132550 PMID: 17201676
    • (2007) Annu Rev Biophys Biomol Struct , vol.36 , pp. 21-42
    • Gilson, M.K.1    Zhou, H.X.2
  • 7
    • 70349100806 scopus 로고    scopus 로고
    • Theory of free energy and entropy in noncovalent binding
    • 19588959
    • Zhou HX, Gilson MK. Theory of free energy and entropy in noncovalent binding. Chem Rev. 2009;109:4092-4107. doi: 10.1021/cr800551w PMID: 19588959
    • (2009) Chem Rev. , vol.109 , pp. 4092-4107
    • Zhou, H.X.1    Gilson, M.K.2
  • 8
    • 0031058541 scopus 로고    scopus 로고
    • The statistical-thermodynamic basis for computation of binding affinities: A critical review
    • 9138555
    • Gilson MK, Given JA, Bush BL, McCammon JA. The statistical-thermodynamic basis for computation of binding affinities: a critical review. Biophys J. 1997;72:1047-1069. doi: 10.1016/S0006-3495 (97) 78756-3 PMID: 9138555
    • (1997) Biophys J , vol.72 , pp. 1047-1069
    • Gilson, M.K.1    Given, J.A.2    Bush, B.L.3    McCammon, J.A.4
  • 9
    • 84857537331 scopus 로고    scopus 로고
    • Statistical mechanics and molecular dynamics in evaluating thermodynamic properties of biomolecular recognition
    • 22082669
    • Wereszczynski J, McCammon JA. Statistical mechanics and molecular dynamics in evaluating thermodynamic properties of biomolecular recognition. Q Rev Biophys. 2012;45:1-25. doi: 10.1017/S0033583511000096 PMID: 22082669
    • (2012) Q Rev Biophys. , vol.45 , pp. 1-25
    • Wereszczynski, J.1    McCammon, J.A.2
  • 10
    • 1842479952 scopus 로고    scopus 로고
    • Exploring protein native states and large-scale conformational change s with a modified generalized Born model
    • Onufriev A, Bashford D, Case DA. Exploring protein native states and large-scale conformational change s with a modified generalized Born model. Proteins: Struct, Func, Gen. 2004;55:383-394. doi: 10.1002/prot.20033
    • (2004) Proteins: Struct, Func, Gen , vol.55 , pp. 383-394
    • Onufriev, A.1    Bashford, D.2    Case, D.A.3
  • 11
    • 33646943202 scopus 로고    scopus 로고
    • Molecular dynamics: Survey of methods for simulating the activity of proteins
    • 16683746
    • Adcock SA, McCammon JA. Molecular dynamics: survey of methods for simulating the activity of proteins. Chem Rev. 2006;106:1589-1615. doi: 10.1021/cr040426m PMID: 16683746
    • (2006) Chem Rev. , vol.106 , pp. 1589-1615
    • Adcock, S.A.1    McCammon, J.A.2
  • 12
    • 0001616080 scopus 로고    scopus 로고
    • Replica-exchange molecular dynamics method for protein folding
    • Sugita Y, Okamoto Y. Replica-exchange molecular dynamics method for protein folding. Chem Phys Lett. 1999;314:141-151. doi: 10.1016/S0009-2614 (99) 01123-9
    • (1999) Chem Phys Lett. , vol.314 , pp. 141-151
    • Sugita, Y.1    Okamoto, Y.2
  • 14
    • 33847642496 scopus 로고    scopus 로고
    • Nearest-neighbor nonparametric method for estimating the configurational entropy of complex molecules
    • 17195154
    • Hnizdo V, Darian E, Fedorowicz A, Demchuk E, Li S, Singh H. Nearest-neighbor nonparametric method for estimating the configurational entropy of complex molecules. J Comput Chem. 2007;28:655-668. doi: 10.1002/jcc.20589 PMID: 17195154
    • (2007) J Comput Chem. , vol.28 , pp. 655-668
    • Hnizdo, V.1    Darian, E.2    Fedorowicz, A.3    Demchuk, E.4    Li, S.5    Singh, H.6
  • 15
    • 46449096350 scopus 로고    scopus 로고
    • Efficient calculation of configurational entropy from molecular simulations by combining the mutual-information expansion and nearest-neighbor methods
    • 18293293
    • Hnizdo V, Tan J, Killian BJ, Gilson MK. Efficient calculation of configurational entropy from molecular simulations by combining the mutual-information expansion and nearest-neighbor methods. J Comput Chem. 2008;29:1605-1614. doi: 10.1002/jcc.20919 PMID: 18293293
    • (2008) J Comput Chem. , vol.29 , pp. 1605-1614
    • Hnizdo, V.1    Tan, J.2    Killian, B.J.3    Gilson, M.K.4
  • 16
    • 84892863219 scopus 로고    scopus 로고
    • Comparing distance metrics for rotation using the k-nearest neighbors algorithm for entropy estimation
    • 24311273
    • Huggins DJ. Comparing distance metrics for rotation using the k-nearest neighbors algorithm for entropy estimation. J Comput Chem. 2014;35:377-385. doi: 10.1002/jcc.23504 PMID: 24311273
    • (2014) J Comput Chem. , vol.35 , pp. 377-385
    • Huggins, D.J.1
  • 17
    • 84857653095 scopus 로고    scopus 로고
    • Entropy balance in the intercalation process of an anti-cancer drug daunomycin
    • Mukherjee A. Entropy Balance in the Intercalation Process of an Anti-Cancer Drug Daunomycin. J Phys Chem Lett. 2011;2:3021-3026. doi: 10.1021/jz2013566
    • (2011) J Phys Chem Lett. , vol.2 , pp. 3021-3026
    • Mukherjee, A.1
  • 18
    • 48549083172 scopus 로고    scopus 로고
    • Conformational entropy of biomolecules: Beyond the quasi-harmonic approximation
    • 18546487
    • Numata J, Wan M, Knapp EW. Conformational entropy of biomolecules: beyond the quasi-harmonic approximation. Genome Inform. 2007;18:192-205. doi: 10.1142/9781860949920-0019 PMID: 18546487
    • (2007) Genome Inform , vol.18 , pp. 192-205
    • Numata, J.1    Wan, M.2    Knapp, E.W.3
  • 19
    • 67650047673 scopus 로고    scopus 로고
    • Thermodynamic properties of liquid water: An application of a nonparametric approach to computing the entropy of a neat fluid
    • 19851475
    • Wang L, Abel R, Friesner RA, Berne BJ. Thermodynamic properties of liquid water: an application of a nonparametric approach to computing the entropy of a neat fluid. J Chem Theory Comput. 2009;5:1462-1473. doi: 10.1021/ct900078k PMID: 19851475
    • (2009) J Chem Theory Comput. , vol.5 , pp. 1462-1473
    • Wang, L.1    Abel, R.2    Friesner, R.A.3    Berne, B.J.4
  • 20
    • 77953501154 scopus 로고    scopus 로고
    • Nearest neighbor estimates of entropy for multivariate circular distributions
    • Misra N, Singh H, Hnizdo V. Nearest neighbor estimates of entropy for multivariate circular distributions. Entropy (Basel). 2010;12:1125-1144. doi: 10.3390/e12051125
    • (2010) Entropy (Basel) , vol.12 , pp. 1125-1144
    • Misra, N.1    Singh, H.2    Hnizdo, V.3
  • 21
    • 84988603747 scopus 로고    scopus 로고
    • Grid inhomogeneous solvation theory: Hydration structure and thermodynamics of the miniature receptor cucurbit[7]uril
    • 22852591
    • Nguyen CN, Young TK, Gilson MK. Grid inhomogeneous solvation theory: hydration structure and thermodynamics of the miniature receptor cucurbit[7]uril. J Chem Phys. 2012;137:044101. doi: 10.1063/1. 4733951 PMID: 22852591
    • (2012) J Chem Phys. , vol.137 , pp. 044101
    • Nguyen, C.N.1    Young, T.K.2    Gilson, M.K.3
  • 22
    • 84902971173 scopus 로고    scopus 로고
    • Correlation as a determinant of configurational entropy in supramolecular and protein systems
    • 24702693
    • Fenley AT, Killian BJ, Hnizdo V, Fedorowicz A, Sharp DS, Gilson MK. Correlation as a Determinant of Configurational Entropy in Supramolecular and Protein Systems. J Phys Chem B. 2014;118:6447-6455. doi: 10.1021/jp411588b PMID: 24702693
    • (2014) J Phys Chem B , vol.118 , pp. 6447-6455
    • Fenley, A.T.1    Killian, B.J.2    Hnizdo, V.3    Fedorowicz, A.4    Sharp, D.S.5    Gilson, M.K.6
  • 23
    • 84904128550 scopus 로고    scopus 로고
    • Thermodynamics of water in an enzyme active site: Gridbased hydration analysis of coagulation factor Xa
    • 25018673
    • Nguyen CN, Cruz A, Gilson MK, Kurtzman T. Thermodynamics of water in an enzyme active site: gridbased hydration analysis of coagulation factor Xa. J Chem Theory Comput. 2014;10:2769-2780. doi: 10.1021/ct401110x PMID: 25018673
    • (2014) J Chem Theory Comput. , vol.10 , pp. 2769-2780
    • Nguyen, C.N.1    Cruz, A.2    Gilson, M.K.3    Kurtzman, T.4
  • 24
    • 0032971371 scopus 로고    scopus 로고
    • The CD1 system: Antigen-presenting molecules for T cell recognition of lipids and glycolipids
    • 10358761
    • Porcelli SA, Modlin RL. The CD1 system: antigen-presenting molecules for T cell recognition of lipids and glycolipids. Annu Rev Immunol. 1999;17:297-329. doi: 10.1146/annurev. immunol.17.1.297 PMID: 10358761
    • (1999) Annu Rev Immunol. , vol.17 , pp. 297-329
    • Porcelli, S.A.1    Modlin, R.L.2
  • 25
    • 0025831493 scopus 로고
    • Refined structure of the human histocompatibility antigen HLA-A2 at 2.6 Å A resolution
    • 2038058
    • Saper MA, Bjorkman PJ, Wiley DC. Refined structure of the human histocompatibility antigen HLA-A2 at 2.6 Å A resolution. J Mol Biol. 1991;219:277-319. doi: 10.1016/0022-2836 (91) 90567-P PMID: 2038058
    • (1991) J Mol Biol. , vol.219 , pp. 277-319
    • Saper, M.A.1    Bjorkman, P.J.2    Wiley, D.C.3
  • 26
    • 18244378561 scopus 로고    scopus 로고
    • The solution structure of human beta2-microglobulin reveals the prodromes of its amyloid transition
    • 11847272
    • Verdone G, Corazza A, Viglino P, Pettirossi F, Giorgetti S, Mangione P, et al. The solution structure of human beta2-microglobulin reveals the prodromes of its amyloid transition. Protein Sci. 2002;11:487-499. doi: 10.1110/ps.29002 PMID: 11847272
    • (2002) Protein Sci. , vol.11 , pp. 487-499
    • Verdone, G.1    Corazza, A.2    Viglino, P.3    Pettirossi, F.4    Giorgetti, S.5    Mangione, P.6
  • 27
    • 0032480888 scopus 로고    scopus 로고
    • Epac is a Rap1 guanine-nucleotide-exchange factor directly activated by cyclic AMP
    • 9853756
    • De Rooij J, Zwartkruis FJ, Verheijen MH, Cool RH, Nijman SM, Wittinghofer A, et al. Epac is a Rap1 guanine-nucleotide-exchange factor directly activated by cyclic AMP. Nature. 1998;396:474-477. doi: 10.1038/24884 PMID: 9853756
    • (1998) Nature , vol.396 , pp. 474-477
    • De Rooij, J.1    Zwartkruis, F.J.2    Verheijen, M.H.3    Cool, R.H.4    Nijman, S.M.5    Wittinghofer, A.6
  • 28
    • 82755171820 scopus 로고    scopus 로고
    • Role of dynamics in the autoinhibition and activation of the exchange protein directly activated by cyclic AMP (EPAC)
    • 21873431
    • Van Schouwen B, Selvaratnam R, Fogolari F, Melacini G. Role of dynamics in the autoinhibition and activation of the exchange protein directly activated by cyclic AMP (EPAC). J Biol Chem. 2011;286:42655-42669. doi: 10.1074/jbc. M111.277723 PMID: 21873431
    • (2011) J Biol Chem. , vol.286 , pp. 42655-42669
    • Van Schouwen, B.1    Selvaratnam, R.2    Fogolari, F.3    Melacini, G.4
  • 29
    • 0023038504 scopus 로고
    • Binding specificity of the periplasmic oligopeptide-binding protein from Escherichia coli
    • 3536860
    • Guyer CA, Morgan DG, Staros JV. Binding specificity of the periplasmic oligopeptide-binding protein from Escherichia coli. J Bacteriol. 1986;168:775-779. PMID: 3536860
    • (1986) J Bacteriol. , vol.168 , pp. 775-779
    • Guyer, C.A.1    Morgan, D.G.2    Staros, J.V.3
  • 30
    • 0037168045 scopus 로고    scopus 로고
    • Comparative binding energy (COMBINE) analysis of OppA-peptide complexes to relate structure to binding thermodynamics
    • 12383008
    • Wang T, Wade RC. Comparative binding energy (COMBINE) analysis of OppA-peptide complexes to relate structure to binding thermodynamics. J Med Chem. 2002;45:4828-4837. doi: 10.1021/jm020900l PMID: 12383008
    • (2002) J Med Chem. , vol.45 , pp. 4828-4837
    • Wang, T.1    Wade, R.C.2
  • 31
    • 0003527976 scopus 로고    scopus 로고
    • Sausalito, CA, USA: University Science Books
    • McQuarrie DA. Statistical Mechanics. Sausalito, CA, USA: University Science Books; 2000.
    • (2000) Statistical Mechanics
    • McQuarrie, D.A.1
  • 32
    • 0032968133 scopus 로고    scopus 로고
    • Implicit solvent models
    • 17030302
    • Roux B, Simonson T. Implicit solvent models. Biophys Chem. 1999;78:1-20. doi: 10.1016/S0301-4622 (98) 00226-9 PMID: 17030302
    • (1999) Biophys Chem. , vol.78 , pp. 1-20
    • Roux, B.1    Simonson, T.2
  • 33
    • 0028773889 scopus 로고
    • Volume changes on protein folding
    • 7922041
    • Harpaz Y, Gerstein M, Chothia C. Volume changes on protein folding. Structure. 1994;2:641-649. doi: 10.1016/S0969-2126 (00) 00065-4 PMID: 7922041
    • (1994) Structure , vol.2 , pp. 641-649
    • Harpaz, Y.1    Gerstein, M.2    Chothia, C.3
  • 34
    • 1542779656 scopus 로고    scopus 로고
    • Statistical thermodynamics of internal rotation in a hindering potential of mean force obtained from computer simulations
    • 12820124
    • Hnizdo V, Fedorowicz A, Singh H, Demchuk E. Statistical thermodynamics of internal rotation in a hindering potential of mean force obtained from computer simulations. J Comput Chem. 2003;24:1172-1183. doi: 10.1002/jcc.10289 PMID: 12820124
    • (2003) J Comput Chem. , vol.24 , pp. 1172-1183
    • Hnizdo, V.1    Fedorowicz, A.2    Singh, H.3    Demchuk, E.4
  • 35
    • 18744379773 scopus 로고    scopus 로고
    • Estimation of the absolute internal-rotation entropy of molecules with two torsional degrees of freedom from stochastic simulations
    • 15751106
    • Darian E, Hnizdo V, Fedorowicz A, Singh H, Demchuk E. Estimation of the absolute internal-rotation entropy of molecules with two torsional degrees of freedom from stochastic simulations. J Comput Chem. 2005;26:651-660. doi: 10.1002/jcc.20198 PMID: 15751106
    • (2005) J Comput Chem. , vol.26 , pp. 651-660
    • Darian, E.1    Hnizdo, V.2    Fedorowicz, A.3    Singh, H.4    Demchuk, E.5
  • 36
    • 0000127140 scopus 로고
    • Method for estimating the configurational entropy of native macromolecules
    • Karplus M, Kushick JN. Method for estimating the configurational entropy of native macromolecules. Macromolecules. 1981;14:325-332. doi: 10.1021/ma50003a019
    • (1981) Macromolecules , vol.14 , pp. 325-332
    • Karplus, M.1    Kushick, J.N.2
  • 37
    • 0000961995 scopus 로고
    • Evaluation of the configurational entropy for proteins: Application to molecular dynamics simulations of an alpha-helix
    • Levy RM, Karplus M, Kushick JN, Perahia D. Evaluation of the configurational entropy for proteins: application to molecular dynamics simulations of an alpha-helix. Macromolecules. 1984;17:1370-1374. doi: 10.1021/ma00137a013
    • (1984) Macromolecules , vol.17 , pp. 1370-1374
    • Levy, R.M.1    Karplus, M.2    Kushick, J.N.3    Perahia, D.4
  • 38
    • 0023475026 scopus 로고
    • Configurational entropy of native proteins
    • 3427197
    • Karplus M, Ichiye T, Pettitt BM. Configurational entropy of native proteins. Biophys J. 1987;52:1083-1085. doi: 10.1016/S0006-3495 (87) 83303-9 PMID: 3427197
    • (1987) Biophys J , vol.52 , pp. 1083-1085
    • Karplus, M.1    Ichiye, T.2    Pettitt, B.M.3
  • 39
    • 0027390460 scopus 로고
    • The contribution of cross-links to protein stability: A normal mode analysis of the configurational entropy of the native state
    • 7680808
    • Tidor B, Karplus M. The contribution of cross-links to protein stability: a normal mode analysis of the configurational entropy of the native state. Proteins. 1993;15:71-79. doi: 10.1002/prot.340150109 PMID: 7680808
    • (1993) Proteins , vol.15 , pp. 71-79
    • Tidor, B.1    Karplus, M.2
  • 40
    • 0001351515 scopus 로고
    • Estimation of absolute and relative entropies of macromolecules using the covariance matrix
    • Schlitter J. Estimation of absolute and relative entropies of macromolecules using the covariance matrix. Chem Phys Lett. 1993;215:617-621. doi: 10.1016/0009-2614 (93) 89366-P
    • (1993) Chem Phys Lett. , vol.215 , pp. 617-621
    • Schlitter, J.1
  • 41
    • 0035828630 scopus 로고    scopus 로고
    • On the calculation of entropy from covariance matrices of the atomic fluctuations
    • Andricioaei I, Karplus M. On the calculation of entropy from covariance matrices of the atomic fluctuations. J Chem Phys. 2001;115:6289-6292. doi: 10.1063/1.1401821
    • (2001) J Chem Phys. , vol.115 , pp. 6289-6292
    • Andricioaei, I.1    Karplus, M.2
  • 42
    • 25844507555 scopus 로고    scopus 로고
    • The entropic cost of protein-protein association: A case study on acetylcholinesterase binding to fasciculin-2
    • 16100267
    • Minh DD, Bui JM, Chang CE, Jain T, Swanson JM, McCammon JA. The entropic cost of protein-protein association: a case study on acetylcholinesterase binding to fasciculin-2. Biophys J. 2005;89:L25-27. doi: 10.1529/biophysj.105.069336 PMID: 16100267
    • (2005) Biophys J , vol.89 , pp. L25-L27
    • Minh, D.D.1    Bui, J.M.2    Chang, C.E.3    Jain, T.4    Swanson, J.M.5    McCammon, J.A.6
  • 43
    • 38449097757 scopus 로고    scopus 로고
    • Accelerated entropy estimates with accelerated dynamics
    • 17949130
    • Minh DD, Hamelberg D, McCammon JA. Accelerated entropy estimates with accelerated dynamics. J Chem Phys. 2007;127:154105. doi: 10.1063/1.2794754 PMID: 17949130
    • (2007) J Chem Phys. , vol.127 , pp. 154105
    • Minh, D.D.1    Hamelberg, D.2    McCammon, J.A.3
  • 44
    • 33749172039 scopus 로고    scopus 로고
    • Carma: A molecular dynamics analysis program
    • 16917862
    • Glykos NM. Carma: a molecular dynamics analysis program. J Comput Chem. 2006;27:1765-1768. doi: 10.1002/jcc.20482 PMID: 16917862
    • (2006) J Comput Chem. , vol.27 , pp. 1765-1768
    • Glykos, N.M.1
  • 45
    • 77953512913 scopus 로고    scopus 로고
    • Thermodynamic and differential entropy under a change of variables
    • Hnizdo V, Gilson MK. Thermodynamic and Differential Entropy under a Change of Variables. Entropy (Basel). 2010;12:578-590. doi: 10.3390/e12030578
    • (2010) Entropy (Basel) , vol.12 , pp. 578-590
    • Hnizdo, V.1    Gilson, M.K.2
  • 46
    • 18344362394 scopus 로고
    • On the use of classical statistical mechanics in the treatment of polymer chain conformation
    • Go N, Scheraga HA. On the use of classical statistical mechanics in the treatment of polymer chain conformation. Macromolecules. 1976;9:535-542. doi: 10.1021/ma60052a001
    • (1976) Macromolecules , vol.9 , pp. 535-542
    • Go, N.1    Scheraga, H.A.2
  • 47
    • 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
    • 15185334
    • MacKerell AD, Feig M, Brooks CL. 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. 2004;25:1400-1415. doi: 10.1002/jcc.20065 PMID: 15185334
    • (2004) J Comput Chem. , vol.25 , pp. 1400-1415
    • MacKerell, A.D.1    Feig, M.2    Brooks, C.L.3
  • 48
    • 77953513118 scopus 로고    scopus 로고
    • Improved side-chain torsion potentials for the Amber ff99SB protein force field
    • 20408171
    • Lindorff-Larsen K, Piana S, Palmo K, Maragakis P, Klepeis JL, Dror RO, et al. Improved side-chain torsion potentials for the Amber ff99SB protein force field. Proteins. 2010;78:1950-1958. doi: 10.1002/prot.22711 PMID: 20408171
    • (2010) Proteins , vol.78 , pp. 1950-1958
    • Lindorff-Larsen, K.1    Piana, S.2    Palmo, K.3    Maragakis, P.4    Klepeis, J.L.5    Dror, R.O.6
  • 49
    • 79959720287 scopus 로고    scopus 로고
    • How robust are protein folding simulations with respect to force field parameterization?
    • 21539772
    • Piana S, Lindorff-Larsen K, Shaw DE. How robust are protein folding simulations with respect to force field parameterization? Biophys J. 2011;100:L47-49. doi: 10.1016/j.bpj.2011.03.051 PMID: 21539772
    • (2011) Biophys J , vol.100 , pp. L47-L49
    • Piana, S.1    Lindorff-Larsen, K.2    Shaw, D.E.3
  • 50
    • 84857463877 scopus 로고    scopus 로고
    • Systematic validation of protein force fields against experimental data
    • 22384157
    • Lindorff-Larsen K, Maragakis P, Piana S, Eastwood MP, Dror RO, Shaw DE. Systematic validation of protein force fields against experimental data. PLoS ONE. 2012;7:e32131. doi: 10.1371/journal.pone. 0032131 PMID: 22384157
    • (2012) PLoS ONE , vol.7 , pp. e32131
    • Lindorff-Larsen, K.1    Maragakis, P.2    Piana, S.3    Eastwood, M.P.4    Dror, R.O.5    Shaw, D.E.6
  • 51
    • 0043180474 scopus 로고    scopus 로고
    • PISCES: A protein sequence culling server
    • 12912846
    • Wang G, Dunbrack RL. PISCES: a protein sequence culling server. Bioinformatics. 2003;19:1589-1591. doi: 10.1093/bioinformatics/btg224 PMID: 12912846
    • (2003) Bioinformatics , vol.19 , pp. 1589-1591
    • Wang, G.1    Dunbrack, R.L.2
  • 52
    • 0033614004 scopus 로고    scopus 로고
    • Asparagine and glutamine: Using hydrogen atom contacts in the choice of side-chain amide orientation
    • 9917408
    • Word JM, Lovell SC, Richardson JS, Richardson DC. Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation. J Mol Biol. 1999;285:1735-1747. doi: 10.1006/jmbi.1998.2401 PMID: 9917408
    • (1999) J Mol Biol. , vol.285 , pp. 1735-1747
    • Word, J.M.1    Lovell, S.C.2    Richardson, J.S.3    Richardson, D.C.4
  • 53
    • 0029881007 scopus 로고    scopus 로고
    • MOLMOL: A program for display and analysis of macromolecular structures
    • 8744573
    • Koradi R, Billeter M, Wuthrich K. MOLMOL: a program for display and analysis of macromolecular structures. J Mol Graph. 1996;14:51-55. doi: 10.1016/0263-7855 (96) 00009-4 PMID: 8744573
    • (1996) J Mol Graph , vol.14 , pp. 51-55
    • Koradi, R.1    Billeter, M.2    Wuthrich, K.3
  • 54
    • 79551496525 scopus 로고    scopus 로고
    • Molecular dynamics simulation of beta2-microglobulin in denaturing and stabilizing conditions
    • 21287627
    • Fogolari F, Corazza A, Varini N, Rotter M, Gumral D, Codutti L, et al. Molecular dynamics simulation of beta2-microglobulin in denaturing and stabilizing conditions. Proteins. 2011;79:986-1001. doi: 10. 1002/prot.22940 PMID: 21287627
    • (2011) Proteins , vol.79 , pp. 986-1001
    • Fogolari, F.1    Corazza, A.2    Varini, N.3    Rotter, M.4    Gumral, D.5    Codutti, L.6
  • 55
    • 67651236465 scopus 로고    scopus 로고
    • Metrics for 3D rotations: Comparison and analysis
    • Huyinh DQ. Metrics for 3D rotations: comparison and analysis. J Math Imaging Vis. 2009;35:155-164. doi: 10.1007/s10851-009-0161-2
    • (2009) J Math Imaging Vis. , vol.35 , pp. 155-164
    • Huyinh, D.Q.1
  • 56
    • 0000597752 scopus 로고
    • On random rotations in R3
    • Miles RE. On random rotations in R3. Biometrika. 1965;52:636-639. doi: 10.1093/biomet/52.3-4.636
    • (1965) Biometrika , vol.52 , pp. 636-639
    • Miles, R.E.1
  • 58
    • 0041784950 scopus 로고    scopus 로고
    • All-atom empirical potential for molecular modeling and dynamics Studies of proteins
    • 24889800
    • MacKerell ADJ, Bashford D, Bellott M, Dunbrack RLJ, Evanseck JD, Field MJ, et al. All-atom empirical potential for molecular modeling and dynamics Studies of proteins. J Phys Chem B. 1998;102:3586-3616. doi: 10.1021/jp973084f PMID: 24889800
    • (1998) J Phys Chem B , vol.102 , pp. 3586-3616
    • MacKerell, A.D.J.1    Bashford, D.2    Bellott, M.3    Dunbrack, R.L.J.4    Evanseck, J.D.5    Field, M.J.6
  • 61
    • 0029878720 scopus 로고    scopus 로고
    • VMD visual molecular dynamics
    • 8744570
    • Humphrey W, Dalke A, Schulten K. VMD Visual Molecular Dynamics. J Mol Graph. 1996;14:33-38. doi: 10.1016/0263-7855 (96) 00018-5 PMID: 8744570
    • (1996) J Mol Graph , vol.14 , pp. 33-38
    • Humphrey, W.1    Dalke, A.2    Schulten, K.3
  • 62
    • 36449003554 scopus 로고
    • Constant pressure molecular dynamics algorithms
    • Martyna G, Tobias D, Klein M. Constant pressure molecular dynamics algorithms. J Chem Phys. 1994;101:4177-4189. doi: 10.1063/1.467468
    • (1994) J Chem Phys. , vol.101 , pp. 4177-4189
    • Martyna, G.1    Tobias, D.2    Klein, M.3
  • 63
    • 36449007836 scopus 로고
    • Constant pressure molecular dynamics simulation: The Langevin piston method
    • Feller S, Zhang Y, Pastor R, Brooks B. Constant pressure molecular dynamics simulation: The Langevin piston method. J Chem Phys. 1995;103:4613-4621. doi: 10.1063/1.470648
    • (1995) J Chem Phys. , vol.103 , pp. 4613-4621
    • Feller, S.1    Zhang, Y.2    Pastor, R.3    Brooks, B.4
  • 64
    • 0642340510 scopus 로고    scopus 로고
    • Amino acid empirical contact energy definition for fold recognition in the space of contact maps
    • 12689348
    • Berrera M, Molinari H, Fogolari F. Amino acid empirical contact energy definition for fold recognition in the space of contact maps. BMC Bioinformatics. 2003;4:8. doi: 10.1186/1471-2105-4-8 PMID: 12689348
    • (2003) BMC Bioinformatics , vol.4 , pp. 8
    • Berrera, M.1    Molinari, H.2    Fogolari, F.3
  • 65
    • 84864473993 scopus 로고    scopus 로고
    • H++ 3.0: Automating pK prediction and the preparation of biomolecular structures for atomistic molecular modeling and simulations
    • 22570416 Web Server issue
    • Anandakrishnan R, Aguilar B, Onufriev AV. H++ 3.0: automating pK prediction and the preparation of biomolecular structures for atomistic molecular modeling and simulations. Nucleic Acids Res. 2012;40(Web Server issue):W537-541. doi: 10.1093/nar/gks375 PMID: 22570416
    • (2012) Nucleic Acids Res , vol.40 , pp. W537-W541
    • Anandakrishnan, R.1    Aguilar, B.2    Onufriev, A.V.3
  • 66
    • 77952378812 scopus 로고    scopus 로고
    • ProMetCS: An atomistic force field for modeling protein-metal surface interactions in a continuum aquesous solvent
    • Kokh DB, Corni S, Winn PJ, Hoefling M, Gottschalk KE, C. WR. ProMetCS: An Atomistic Force Field for Modeling Protein-Metal Surface Interactions in a Continuum Aquesous Solvent. J Chem Theory Comput. 2010;6:1753-1768. doi: 10.1021/ct100086j
    • (2010) J Chem Theory Comput. , vol.6 , pp. 1753-1768
    • Kokh, D.B.1    Corni, S.2    Winn, P.J.3    Hoefling, M.4    Gottschalk, K.E.5    Wr, C.6
  • 67
    • 26444479778 scopus 로고
    • Optimization by simulated annealing
    • 17813860
    • Kirkpatrick S, D. GC, Vecchi MP. Optimization by Simulated Annealing. Science. 1983;220:671-680. doi: 10.1126/science.220.4598.671 PMID: 17813860
    • (1983) Science , vol.220 , pp. 671-680
    • Kirkpatrick, S.1    Gc, D.2    Vecchi, M.P.3
  • 68
    • 67650159736 scopus 로고    scopus 로고
    • GolP: An atomistic force-field to describe the interaction of proteins with Au (111) surfaces in water
    • Iori F, Di Felice R, Molinari E, Corni S. GolP: an atomistic force-field to describe the interaction of proteins with Au (111) surfaces in water. J Comp Chem. 2009;30:1465-1476. doi: 10.1002/jcc.21165
    • (2009) J Comp Chem. , vol.30 , pp. 1465-1476
    • Iori, F.1    Di Felice, R.2    Molinari, E.3    Corni, S.4
  • 70
    • 84925679910 scopus 로고    scopus 로고
    • Probing the influence of citrate-capped gold nanoparticles on an amyloidogenic protein
    • 25695203
    • Brancolini G, Corazza A, Vuano M, Fogolari F, Mimmi MC, Bellotti V, et al. Probing the Influence of Citrate-Capped Gold Nanoparticles on an Amyloidogenic Protein. ACS Nano. 2015;9:2600-2613. doi: 10.1021/nn506161j PMID: 25695203
    • (2015) ACS Nano , vol.9 , pp. 2600-2613
    • Brancolini, G.1    Corazza, A.2    Vuano, M.3    Fogolari, F.4    Mimmi, M.C.5    Bellotti, V.6
  • 72
    • 0028871798 scopus 로고
    • Side-chain conformational entropy in protein folding
    • 8563620
    • Doig AJ, Sternberg MJ. Side-chain conformational entropy in protein folding. Protein Sci. 1995;4:2247-2251. doi: 10.1002/pro.5560041101 PMID: 8563620
    • (1995) Protein Sci. , vol.4 , pp. 2247-2251
    • Doig, A.J.1    Sternberg, M.J.2
  • 73
    • 0028343413 scopus 로고
    • Application of a self-consistent mean field theory to predict protein side-chains conformation and estimate their conformational entropy
    • 8196057
    • Koehl P, Delarue M. Application of a self-consistent mean field theory to predict protein side-chains conformation and estimate their conformational entropy. J Mol Biol. 1994;239:249-275. doi: 10.1006/jmbi.1994.1366 PMID: 8196057
    • (1994) J Mol Biol. , vol.239 , pp. 249-275
    • Koehl, P.1    Delarue, M.2
  • 74
    • 34547227692 scopus 로고    scopus 로고
    • Extraction of configurational entropy from molecular simulations via an expansion approximation
    • 17640119
    • Killian BJ, Yundenfreund Kravitz J, Gilson MK. Extraction of configurational entropy from molecular simulations via an expansion approximation. J Chem Phys. 2007;127:024107. doi: 10.1063/1. 2746329 PMID: 17640119
    • (2007) J Chem Phys. , vol.127 , pp. 024107
    • Killian, B.J.1    Yundenfreund Kravitz, J.2    Gilson, M.K.3
  • 75
    • 0023521842 scopus 로고
    • Analysis of the relationship between side-chain conformation and secondary structure in globular proteins
    • 3430610
    • McGregor MJ, Islam SA, Sternberg MJ. Analysis of the relationship between side-chain conformation and secondary structure in globular proteins. J Mol Biol. 1987;198:295-310. doi: 10.1016/0022-2836 (87) 90314-7 PMID: 3430610
    • (1987) J Mol Biol. , vol.198 , pp. 295-310
    • McGregor, M.J.1    Islam, S.A.2    Sternberg, M.J.3
  • 76
    • 0017157584 scopus 로고
    • A simplified representation of protein conformations for rapid simulation of protein folding
    • 957439
    • Levitt M. A simplified representation of protein conformations for rapid simulation of protein folding. J Mol Biol. 1976;104:59-107. doi: 10.1016/0022-2836 (76) 90004-8 PMID: 957439
    • (1976) J Mol Biol. , vol.104 , pp. 59-107
    • Levitt, M.1
  • 77
    • 0017776823 scopus 로고
    • Dynamics of folded proteins
    • 301613
    • McCammon JA, Gelin BR, Karplus M. Dynamics of folded proteins. Nature. 1977;267:585-590. doi: 10.1038/267585a0 PMID: 301613
    • (1977) Nature , vol.267 , pp. 585-590
    • McCammon, J.A.1    Gelin, B.R.2    Karplus, M.3
  • 78
    • 84936916896 scopus 로고
    • Robust locally weighted regression and smoothing scatterplots
    • Cleveland WS. Robust locally weighted regression and smoothing scatterplots. J Am Stat Assoc. 1979;74:829-836. doi: 10.1080/01621459.1979.10481038
    • (1979) J Am Stat Assoc. , vol.74 , pp. 829-836
    • Cleveland, W.S.1
  • 80
    • 0030473440 scopus 로고    scopus 로고
    • Insights into the local residual entropy of proteins provided by NMR relaxation
    • 8976574
    • Li Z, Raychaudhuri S, Wand AJ. Insights into the local residual entropy of proteins provided by NMR relaxation. Protein Sci. 1996;5:2647-2650. doi: 10.1002/pro.5560051228 PMID: 8976574
    • (1996) Protein Sci. , vol.5 , pp. 2647-2650
    • Li, Z.1    Raychaudhuri, S.2    Wand, A.J.3
  • 81
    • 0024745871 scopus 로고
    • The price of lost freedom: Entropy of bimolecular complex formation
    • 2813338
    • Finkelstein AV, Janin J. The price of lost freedom: entropy of bimolecular complex formation. Protein Eng. 1989;3:1-3. doi: 10.1093/protein/3.1.1 PMID: 2813338
    • (1989) Protein Eng , vol.3 , pp. 1-3
    • Finkelstein, A.V.1    Janin, J.2


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