메뉴 건너뛰기




Volumn 55, Issue 12, 2016, Pages 1784-1800

Role of Electrostatic Interactions in Binding of Peptides and Intrinsically Disordered Proteins to Their Folded Targets: 2. the Model of Encounter Complex Involving the Double Mutant of the c-Crk N-SH3 Domain and Peptide Sos

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACIDS; ARGININE; BIOCHEMISTRY; ELECTROSTATICS; MOLECULAR DYNAMICS; NUCLEAR MAGNETIC RESONANCE; SYSTEMS ENGINEERING;

EID: 84962433266     PISSN: 00062960     EISSN: 15204995     Source Type: Journal    
DOI: 10.1021/acs.biochem.5b01283     Document Type: Article
Times cited : (16)

References (72)
  • 2
    • 78650863624 scopus 로고    scopus 로고
    • Atomic-level characterization of the ensemble of the Aβ1-42 monomer in water using unbiased Molecular Dynamics simulations and spectral algorithms
    • Sgourakis, N. G., Merced-Serrano, M., Boutsidis, C., Drineas, P., Du, Z. M., Wang, C. Y., and Garcia, A. E. (2011) Atomic-level characterization of the ensemble of the Aβ1-42 monomer in water using unbiased Molecular Dynamics simulations and spectral algorithms J. Mol. Biol. 405, 570-583 10.1016/j.jmb.2010.10.015
    • (2011) J. Mol. Biol. , vol.405 , pp. 570-583
    • Sgourakis, N.G.1    Merced-Serrano, M.2    Boutsidis, C.3    Drineas, P.4    Du, Z.M.5    Wang, C.Y.6    Garcia, A.E.7
  • 4
    • 84864581257 scopus 로고    scopus 로고
    • A preformed binding interface in the unbound ensemble of an intrinsically disordered protein: Evidence from molecular simulations
    • Knott, M. and Best, R. B. (2012) A preformed binding interface in the unbound ensemble of an intrinsically disordered protein: evidence from molecular simulations PLoS Comput. Biol. 8, e1002605 10.1371/journal.pcbi.1002605
    • (2012) PLoS Comput. Biol. , vol.8
    • Knott, M.1    Best, R.B.2
  • 5
    • 84913530471 scopus 로고    scopus 로고
    • A relationship between the transient structure in the monomeric state and the aggregation propensities of α-synuclein and β-synuclein
    • Allison, J. R., Rivers, R. C., Christodoulou, J. C., Vendruscolo, M., and Dobson, C. M. (2014) A relationship between the transient structure in the monomeric state and the aggregation propensities of α-synuclein and β-synuclein Biochemistry 53, 7170-7183 10.1021/bi5009326
    • (2014) Biochemistry , vol.53 , pp. 7170-7183
    • Allison, J.R.1    Rivers, R.C.2    Christodoulou, J.C.3    Vendruscolo, M.4    Dobson, C.M.5
  • 6
    • 84922102867 scopus 로고    scopus 로고
    • Correlation of chemical shifts predicted by molecular dynamics simulations for partially disordered proteins
    • Karp, J. M., Erylimaz, E., and Cowburn, D. (2015) Correlation of chemical shifts predicted by molecular dynamics simulations for partially disordered proteins J. Biomol. NMR 61, 35-45 10.1007/s10858-014-9879-2
    • (2015) J. Biomol. NMR , vol.61 , pp. 35-45
    • Karp, J.M.1    Erylimaz, E.2    Cowburn, D.3
  • 7
    • 80052231359 scopus 로고    scopus 로고
    • Homogeneous and heterogeneous tertiary structure ensembles of amyloid-β peptides
    • Ball, K. A., Phillips, A. H., Nerenberg, P. S., Fawzi, N. L., Wemmer, D. E., and Head-Gordon, T. (2011) Homogeneous and heterogeneous tertiary structure ensembles of amyloid-β peptides Biochemistry 50, 7612-7628 10.1021/bi200732x
    • (2011) Biochemistry , vol.50 , pp. 7612-7628
    • Ball, K.A.1    Phillips, A.H.2    Nerenberg, P.S.3    Fawzi, N.L.4    Wemmer, D.E.5    Head-Gordon, T.6
  • 8
    • 80052820089 scopus 로고    scopus 로고
    • 15N relaxation, and Molecular Dynamics simulations: How fast is segmental diffusion in denatured ubiquitin?
    • 15N relaxation, and Molecular Dynamics simulations: how fast is segmental diffusion in denatured ubiquitin? J. Am. Chem. Soc. 133, 14614-14628 10.1021/ja201605c
    • (2011) J. Am. Chem. Soc. , vol.133 , pp. 14614-14628
    • Xue, Y.1    Skrynnikov, N.R.2
  • 9
    • 84857774493 scopus 로고    scopus 로고
    • Structure and dynamics of an unfolded protein examined by Molecular Dynamics simulation
    • Lindorff-Larsen, K., Trbovic, N., Maragakis, P., Piana, S., and Shaw, D. E. (2012) Structure and dynamics of an unfolded protein examined by Molecular Dynamics simulation J. Am. Chem. Soc. 134, 3787-3791 10.1021/ja209931w
    • (2012) J. Am. Chem. Soc. , vol.134 , pp. 3787-3791
    • Lindorff-Larsen, K.1    Trbovic, N.2    Maragakis, P.3    Piana, S.4    Shaw, D.E.5
  • 10
    • 84887831600 scopus 로고    scopus 로고
    • Conformational dynamics of the partially disordered yeast transcription factor GCN4
    • Robustelli, P., Trbovic, N., Friesner, R. A., and Palmer, A. G. (2013) Conformational dynamics of the partially disordered yeast transcription factor GCN4 J. Chem. Theory Comput. 9, 5190-5200 10.1021/ct400654r
    • (2013) J. Chem. Theory Comput. , vol.9 , pp. 5190-5200
    • Robustelli, P.1    Trbovic, N.2    Friesner, R.A.3    Palmer, A.G.4
  • 11
    • 84906850422 scopus 로고    scopus 로고
    • A maximum entropy approach to the study of residue-specific backbone angle distributions in alpha-synuclein, an intrinsically disordered protein
    • Mantsyzov, A. B., Maltsev, A. S., Ying, J. F., Shen, Y., Hummer, G., and Bax, A. (2014) A maximum entropy approach to the study of residue-specific backbone angle distributions in alpha-synuclein, an intrinsically disordered protein Protein Sci. 23, 1275-1290 10.1002/pro.2511
    • (2014) Protein Sci. , vol.23 , pp. 1275-1290
    • Mantsyzov, A.B.1    Maltsev, A.S.2    Ying, J.F.3    Shen, Y.4    Hummer, G.5    Bax, A.6
  • 12
    • 84908155664 scopus 로고    scopus 로고
    • Role of electrostatic interactions in binding of peptides and intrinsically disordered proteins to their folded targets. 1. NMR and MD characterization of the complex between the c-Crk N-SH3 domain and the peptide Sos
    • Xue, Y., Yuwen, T. R., Zhu, F. Q., and Skrynnikov, N. R. (2014) Role of electrostatic interactions in binding of peptides and intrinsically disordered proteins to their folded targets. 1. NMR and MD characterization of the complex between the c-Crk N-SH3 domain and the peptide Sos Biochemistry 53, 6473-6495 10.1021/bi500904f
    • (2014) Biochemistry , vol.53 , pp. 6473-6495
    • Xue, Y.1    Yuwen, T.R.2    Zhu, F.Q.3    Skrynnikov, N.R.4
  • 13
    • 33748518255 scopus 로고    scopus 로고
    • Comparison of multiple Amber force fields and development of improved protein backbone parameters
    • Hornak, V., Abel, R., Okur, A., Strockbine, B., Roitberg, A., and Simmerling, C. (2006) Comparison of multiple Amber force fields and development of improved protein backbone parameters Proteins: Struct., Funct., Genet. 65, 712-725 10.1002/prot.21123
    • (2006) Proteins: Struct., Funct., Genet. , vol.65 , pp. 712-725
    • Hornak, V.1    Abel, R.2    Okur, A.3    Strockbine, B.4    Roitberg, A.5    Simmerling, C.6
  • 14
    • 67649494492 scopus 로고    scopus 로고
    • Optimized Molecular Dynamics force fields applied to the helix-coil transition of polypeptides
    • Best, R. B. and Hummer, G. (2009) Optimized Molecular Dynamics force fields applied to the helix-coil transition of polypeptides J. Phys. Chem. B 113, 9004-9015 10.1021/jp901540t
    • (2009) J. Phys. Chem. B , vol.113 , pp. 9004-9015
    • Best, R.B.1    Hummer, G.2
  • 16
    • 0029643950 scopus 로고
    • Structural basis for the specific interaction of lysine-containing proline-rich peptides with the N-terminal SH3 domain of c-Crk
    • Wu, X. D., Knudsen, B., Feller, S. M., Zheng, J., Sali, A., Cowburn, D., Hanafusa, H., and Kuriyan, J. (1995) Structural basis for the specific interaction of lysine-containing proline-rich peptides with the N-terminal SH3 domain of c-Crk Structure 3, 215-226 10.1016/S0969-2126(01)00151-4
    • (1995) Structure , vol.3 , pp. 215-226
    • Wu, X.D.1    Knudsen, B.2    Feller, S.M.3    Zheng, J.4    Sali, A.5    Cowburn, D.6    Hanafusa, H.7    Kuriyan, J.8
  • 17
    • 84885405882 scopus 로고    scopus 로고
    • Molecular Dynamics simulations of highly crowded amino acid solutions: Comparisons of eight different force field combinations with experiment and with each other
    • Andrews, C. T. and Elcock, A. H. (2013) Molecular Dynamics simulations of highly crowded amino acid solutions: comparisons of eight different force field combinations with experiment and with each other J. Chem. Theory Comput. 9, 4585-4602 10.1021/ct400371h
    • (2013) J. Chem. Theory Comput. , vol.9 , pp. 4585-4602
    • Andrews, C.T.1    Elcock, A.H.2
  • 18
    • 84902978469 scopus 로고    scopus 로고
    • Evaluating the strength of salt bridges: A comparison of current biomolecular force fields
    • Debiec, K. T., Gronenborn, A. M., and Chong, L. T. (2014) Evaluating the strength of salt bridges: a comparison of current biomolecular force fields J. Phys. Chem. B 118, 6561-6569 10.1021/jp500958r
    • (2014) J. Phys. Chem. B , vol.118 , pp. 6561-6569
    • Debiec, K.T.1    Gronenborn, A.M.2    Chong, L.T.3
  • 19
    • 84909598675 scopus 로고    scopus 로고
    • Balanced protein-water interactions improve properties of disordered proteins and non-specific protein association
    • Best, R. B., Zheng, W. W., and Mittal, J. (2014) Balanced protein-water interactions improve properties of disordered proteins and non-specific protein association J. Chem. Theory Comput. 10, 5113-5124 10.1021/ct500569b
    • (2014) J. Chem. Theory Comput. , vol.10 , pp. 5113-5124
    • Best, R.B.1    Zheng, W.W.2    Mittal, J.3
  • 20
    • 84898545475 scopus 로고    scopus 로고
    • Insights into the binding of intrinsically disordered proteins from molecular dynamics simulation
    • Baker, C. M. and Best, R. B. (2014) Insights into the binding of intrinsically disordered proteins from molecular dynamics simulation WIREs Comput. Mol. Sci. 4, 182-198 10.1002/wcms.1167
    • (2014) WIREs Comput. Mol. Sci. , vol.4 , pp. 182-198
    • Baker, C.M.1    Best, R.B.2
  • 21
    • 84881450365 scopus 로고    scopus 로고
    • NMR paves the way for atomic level descriptions of sparsely populated, transiently formed biomolecular conformers
    • Sekhar, A. and Kay, L. E. (2013) NMR paves the way for atomic level descriptions of sparsely populated, transiently formed biomolecular conformers Proc. Natl. Acad. Sci. U. S. A. 110, 12867-12874 10.1073/pnas.1305688110
    • (2013) Proc. Natl. Acad. Sci. U. S. A. , vol.110 , pp. 12867-12874
    • Sekhar, A.1    Kay, L.E.2
  • 22
    • 67849119942 scopus 로고    scopus 로고
    • Binding mechanism of an SH3 domain studied by NMR and ITC
    • Demers, J. P. and Mittermaier, A. (2009) Binding mechanism of an SH3 domain studied by NMR and ITC J. Am. Chem. Soc. 131, 4355-4367 10.1021/ja808255d
    • (2009) J. Am. Chem. Soc. , vol.131 , pp. 4355-4367
    • Demers, J.P.1    Mittermaier, A.2
  • 24
    • 0036291145 scopus 로고    scopus 로고
    • Predicting changes in the stability of proteins and protein complexes: A study of more than 1000 mutations
    • Guerois, R., Nielsen, J. E., and Serrano, L. (2002) Predicting changes in the stability of proteins and protein complexes: A study of more than 1000 mutations J. Mol. Biol. 320, 369-387 10.1016/S0022-2836(02)00442-4
    • (2002) J. Mol. Biol. , vol.320 , pp. 369-387
    • Guerois, R.1    Nielsen, J.E.2    Serrano, L.3
  • 26
    • 0001689741 scopus 로고
    • Gradient-enhanced triple-resonance three-dimensional NMR experiments with improved sensitivity
    • Muhandiram, D. R. and Kay, L. E. (1994) Gradient-enhanced triple-resonance three-dimensional NMR experiments with improved sensitivity J. Magn. Reson., Ser. B 103, 203-216 10.1006/jmrb.1994.1032
    • (1994) J. Magn. Reson., Ser. B , vol.103 , pp. 203-216
    • Muhandiram, D.R.1    Kay, L.E.2
  • 28
    • 0032511359 scopus 로고    scopus 로고
    • 15N chemical shift anisotropy relaxation interference: Unambiguous determination of rotational diffusion tensors and chemical exchange effects in biological macromolecules
    • 15N chemical shift anisotropy relaxation interference: Unambiguous determination of rotational diffusion tensors and chemical exchange effects in biological macromolecules J. Am. Chem. Soc. 120, 7905-7915 10.1021/ja980832l
    • (1998) J. Am. Chem. Soc. , vol.120 , pp. 7905-7915
    • Kroenke, C.D.1    Loria, J.P.2    Lee, L.K.3    Rance, M.4    Palmer, A.G.5
  • 32
    • 0029878720 scopus 로고    scopus 로고
    • VMD: Visual molecular dynamics
    • Humphrey, W., Dalke, A., and Schulten, K. (1996) VMD: visual molecular dynamics J. Mol. Graphics 14, 33-38 10.1016/0263-7855(96)00018-5
    • (1996) J. Mol. Graphics , vol.14 , pp. 33-38
    • Humphrey, W.1    Dalke, A.2    Schulten, K.3
  • 33
    • 0343614206 scopus 로고    scopus 로고
    • A systematic study of water models for molecular simulation: Derivation of water models optimized for use with a reaction field
    • van der Spoel, D., van Maaren, P. J., and Berendsen, H. J. C. (1998) A systematic study of water models for molecular simulation: derivation of water models optimized for use with a reaction field J. Chem. Phys. 108, 10220-10230 10.1063/1.476482
    • (1998) J. Chem. Phys. , vol.108 , pp. 10220-10230
    • Van Der Spoel, D.1    Van Maaren, P.J.2    Berendsen, H.J.C.3
  • 34
    • 77949395972 scopus 로고    scopus 로고
    • The shear viscosity of rigid water models
    • Gonzalez, M. A. and Abascal, J. L. F. (2010) The shear viscosity of rigid water models J. Chem. Phys. 132, 096101 10.1063/1.3330544
    • (2010) J. Chem. Phys. , vol.132 , pp. 096101
    • Gonzalez, M.A.1    Abascal, J.L.F.2
  • 35
    • 79954518426 scopus 로고    scopus 로고
    • Optimizing protein-solvent force fields to reproduce intrinsic conformational preferences of model peptides
    • Nerenberg, P. S. and Head-Gordon, T. (2011) Optimizing protein-solvent force fields to reproduce intrinsic conformational preferences of model peptides J. Chem. Theory Comput. 7, 1220-1230 10.1021/ct2000183
    • (2011) J. Chem. Theory Comput. , vol.7 , pp. 1220-1230
    • Nerenberg, P.S.1    Head-Gordon, T.2
  • 36
    • 84859950079 scopus 로고    scopus 로고
    • Optimizing solute-water van der Waals interactions to reproduce solvation free energies
    • Nerenberg, P. S., Jo, B., So, C., Tripathy, A., and Head-Gordon, T. (2012) Optimizing solute-water van der Waals interactions to reproduce solvation free energies J. Phys. Chem. B 116, 4524-4534 10.1021/jp2118373
    • (2012) J. Phys. Chem. B , vol.116 , pp. 4524-4534
    • Nerenberg, P.S.1    Jo, B.2    So, C.3    Tripathy, A.4    Head-Gordon, T.5
  • 37
    • 84939645682 scopus 로고    scopus 로고
    • Molecular Dynamics simulations of intrinsically disordered proteins: Force field evaluation and comparison with experiment
    • Henriques, J., Cragnell, C., and Skepo, M. (2015) Molecular Dynamics simulations of intrinsically disordered proteins: force field evaluation and comparison with experiment J. Chem. Theory Comput. 11, 3420-3431 10.1021/ct501178z
    • (2015) J. Chem. Theory Comput. , vol.11 , pp. 3420-3431
    • Henriques, J.1    Cragnell, C.2    Skepo, M.3
  • 38
    • 84872165531 scopus 로고    scopus 로고
    • Standard binding free energies from computer simulations: What is the best strategy?
    • Gumbart, J. C., Roux, B., and Chipot, C. (2013) Standard binding free energies from computer simulations: what is the best strategy? J. Chem. Theory Comput. 9, 794-802 10.1021/ct3008099
    • (2013) J. Chem. Theory Comput. , vol.9 , pp. 794-802
    • Gumbart, J.C.1    Roux, B.2    Chipot, C.3
  • 39
    • 84882330872 scopus 로고    scopus 로고
    • Efficient determination of protein-protein standard binding free energies from first principles
    • Gumbart, J. C., Roux, B., and Chipot, C. (2013) Efficient determination of protein-protein standard binding free energies from first principles J. Chem. Theory Comput. 9, 3789-3798 10.1021/ct400273t
    • (2013) J. Chem. Theory Comput. , vol.9 , pp. 3789-3798
    • Gumbart, J.C.1    Roux, B.2    Chipot, C.3
  • 40
    • 80051673221 scopus 로고    scopus 로고
    • SHIFTX2: Significantly improved protein chemical shift prediction
    • Han, B., Liu, Y. F., Ginzinger, S. W., and Wishart, D. S. (2011) SHIFTX2: significantly improved protein chemical shift prediction J. Biomol. NMR 50, 43-57 10.1007/s10858-011-9478-4
    • (2011) J. Biomol. NMR , vol.50 , pp. 43-57
    • Han, B.1    Liu, Y.F.2    Ginzinger, S.W.3    Wishart, D.S.4
  • 41
    • 84928540182 scopus 로고    scopus 로고
    • High-resolution crystal structures of protein helices reconciled with three-centered hydrogen bonds and multipole electrostatics
    • Kuster, D. J., Liu, C., Fang, Z., Ponder, J. W., and Marshall, G. R. (2015) High-resolution crystal structures of protein helices reconciled with three-centered hydrogen bonds and multipole electrostatics PLoS One 10, e0123146 10.1371/journal.pone.0123146
    • (2015) PLoS One , vol.10
    • Kuster, D.J.1    Liu, C.2    Fang, Z.3    Ponder, J.W.4    Marshall, G.R.5
  • 42
    • 0026410969 scopus 로고
    • Relationship between Nuclear Magnetic Resonance chemical shift and protein secondary structure
    • Wishart, D. S., Sykes, B. D., and Richards, F. M. (1991) Relationship between Nuclear Magnetic Resonance chemical shift and protein secondary structure J. Mol. Biol. 222, 311-333 10.1016/0022-2836(91)90214-Q
    • (1991) J. Mol. Biol. , vol.222 , pp. 311-333
    • Wishart, D.S.1    Sykes, B.D.2    Richards, F.M.3
  • 43
    • 84855711579 scopus 로고    scopus 로고
    • Ensemble modeling of protein disordered states: Experimental restraint contributions and validation
    • Marsh, J. A. and Forman-Kay, J. D. (2012) Ensemble modeling of protein disordered states: Experimental restraint contributions and validation Proteins: Struct., Funct., Genet. 80, 556-572 10.1002/prot.23220
    • (2012) Proteins: Struct., Funct., Genet. , vol.80 , pp. 556-572
    • Marsh, J.A.1    Forman-Kay, J.D.2
  • 45
    • 84902953466 scopus 로고    scopus 로고
    • Comparison of structure determination methods for intrinsically disordered amyloid-β peptides
    • Ball, K. A., Wemmer, D. E., and Head-Gordon, T. (2014) Comparison of structure determination methods for intrinsically disordered amyloid-β peptides J. Phys. Chem. B 118, 6405-6416 10.1021/jp410275y
    • (2014) J. Phys. Chem. B , vol.118 , pp. 6405-6416
    • Ball, K.A.1    Wemmer, D.E.2    Head-Gordon, T.3
  • 46
    • 77952335311 scopus 로고    scopus 로고
    • Net charge per residue modulates conformational ensembles of intrinsically disordered proteins
    • Mao, A. H., Crick, S. L., Vitalis, A., Chicoine, C. L., and Pappu, R. V. (2010) Net charge per residue modulates conformational ensembles of intrinsically disordered proteins Proc. Natl. Acad. Sci. U. S. A. 107, 8183-8188 10.1073/pnas.0911107107
    • (2010) Proc. Natl. Acad. Sci. U. S. A. , vol.107 , pp. 8183-8188
    • Mao, A.H.1    Crick, S.L.2    Vitalis, A.3    Chicoine, C.L.4    Pappu, R.V.5
  • 47
    • 84865358451 scopus 로고    scopus 로고
    • Identification of minimally interacting modules in an intrinsically disordered protein
    • Sethi, A., Tian, J. H., Vu, D. M., and Gnanakaran, S. (2012) Identification of minimally interacting modules in an intrinsically disordered protein Biophys. J. 103, 748-757 10.1016/j.bpj.2012.06.052
    • (2012) Biophys. J. , vol.103 , pp. 748-757
    • Sethi, A.1    Tian, J.H.2    Vu, D.M.3    Gnanakaran, S.4
  • 48
    • 84923345528 scopus 로고    scopus 로고
    • Kinetic modulation of a disordered protein domain by phosphorylation
    • Stanley, N., Esteban-Martin, S., and De Fabritiis, G. (2014) Kinetic modulation of a disordered protein domain by phosphorylation Nat. Commun. 5, 5272 10.1038/ncomms6272
    • (2014) Nat. Commun. , vol.5 , pp. 5272
    • Stanley, N.1    Esteban-Martin, S.2    De Fabritiis, G.3
  • 50
    • 84921481627 scopus 로고    scopus 로고
    • Disordered structural ensembles of vasopressin and oxytocin and their mutants
    • Yedvabny, E., Nerenberg, P. S., So, C., and Head-Gordon, T. (2015) Disordered structural ensembles of vasopressin and oxytocin and their mutants J. Phys. Chem. B 119, 896-905 10.1021/jp505902m
    • (2015) J. Phys. Chem. B , vol.119 , pp. 896-905
    • Yedvabny, E.1    Nerenberg, P.S.2    So, C.3    Head-Gordon, T.4
  • 51
    • 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
    • Best, R. B. and Mittal, J. (2011) Free-energy landscape of the GB1 hairpin in all-atom explicit solvent simulations with different force fields: Similarities and differences Proteins: Struct., Funct., Genet. 79, 1318-1328 10.1002/prot.22972
    • (2011) Proteins: Struct., Funct., Genet. , vol.79 , pp. 1318-1328
    • Best, R.B.1    Mittal, J.2
  • 52
    • 84870015758 scopus 로고    scopus 로고
    • Effects of molecular crowding on the dynamics of intrinsically disordered proteins
    • Cino, E. A., Karttunen, M., and Choy, W. Y. (2012) Effects of molecular crowding on the dynamics of intrinsically disordered proteins PLoS One 7, e49876 10.1371/journal.pone.0049876
    • (2012) PLoS One , vol.7
    • Cino, E.A.1    Karttunen, M.2    Choy, W.Y.3
  • 53
    • 84872167078 scopus 로고    scopus 로고
    • Critical assessment of current force fields. Short peptide test case
    • Vymetal, J. and Vondrasek, J. (2013) Critical assessment of current force fields. Short peptide test case J. Chem. Theory Comput. 9, 441-451 10.1021/ct300794a
    • (2013) J. Chem. Theory Comput. , vol.9 , pp. 441-451
    • Vymetal, J.1    Vondrasek, J.2
  • 54
    • 84905701176 scopus 로고    scopus 로고
    • Comparing atomistic molecular mechanics force fields for a difficult target: A case study on the Alzheimer's amyloid β-peptide
    • Gerben, S. R., Lemkul, J. A., Brown, A. M., and Bevan, D. R. (2014) Comparing atomistic molecular mechanics force fields for a difficult target: a case study on the Alzheimer's amyloid β-peptide J. Biomol. Struct. Dyn. 32, 1817-1832 10.1080/07391102.2013.838518
    • (2014) J. Biomol. Struct. Dyn. , vol.32 , pp. 1817-1832
    • Gerben, S.R.1    Lemkul, J.A.2    Brown, A.M.3    Bevan, D.R.4
  • 55
    • 84892963298 scopus 로고    scopus 로고
    • Assessing the accuracy of physical models used in protein-folding simulations: Quantitative evidence from long molecular dynamics simulations
    • Piana, S., Klepeis, J. L., and Shaw, D. E. (2014) Assessing the accuracy of physical models used in protein-folding simulations: quantitative evidence from long molecular dynamics simulations Curr. Opin. Struct. Biol. 24, 98-105 10.1016/j.sbi.2013.12.006
    • (2014) Curr. Opin. Struct. Biol. , vol.24 , pp. 98-105
    • Piana, S.1    Klepeis, J.L.2    Shaw, D.E.3
  • 57
    • 84940688641 scopus 로고    scopus 로고
    • An analysis of biomolecular force fields for simulations of polyglutamine in solution
    • Fluitt, A. M. and de Pablo, J. J. (2015) An analysis of biomolecular force fields for simulations of polyglutamine in solution Biophys. J. 109, 1009-1018 10.1016/j.bpj.2015.07.018
    • (2015) Biophys. J. , vol.109 , pp. 1009-1018
    • Fluitt, A.M.1    De Pablo, J.J.2
  • 58
    • 84941991978 scopus 로고    scopus 로고
    • Secondary structure of rat and human amylin across force fields
    • Hoffmann, K. Q., McGovern, M., Chiu, C.-C., and de Pablo, J. J. (2015) Secondary structure of rat and human amylin across force fields PLoS One 10, e0134091 10.1371/journal.pone.0134091
    • (2015) PLoS One , vol.10
    • Hoffmann, K.Q.1    McGovern, M.2    Chiu, C.-C.3    De Pablo, J.J.4
  • 59
    • 84921382154 scopus 로고    scopus 로고
    • Accuracy of current all-atom force-fields in modeling protein disordered states
    • Palazzesi, F., Prakash, M. K., Bonomi, M., and Barducci, A. (2015) Accuracy of current all-atom force-fields in modeling protein disordered states J. Chem. Theory Comput. 11, 2-7 10.1021/ct500718s
    • (2015) J. Chem. Theory Comput. , vol.11 , pp. 2-7
    • Palazzesi, F.1    Prakash, M.K.2    Bonomi, M.3    Barducci, A.4
  • 60
    • 84946898162 scopus 로고    scopus 로고
    • Structural ensembles of intrinsically disordered proteins depend strongly on force field: A comparison to experiment
    • Rauscher, S., Gapsys, V., Gajda, M. J., Zweckstetter, M., De Groot, B. L., and Grubmüller, H. (2015) Structural ensembles of intrinsically disordered proteins depend strongly on force field: a comparison to experiment J. Chem. Theory Comput. 11, 5513-5524 10.1021/acs.jctc.5b00736
    • (2015) J. Chem. Theory Comput. , vol.11 , pp. 5513-5524
    • Rauscher, S.1    Gapsys, V.2    Gajda, M.J.3    Zweckstetter, M.4    De Groot, B.L.5    Grubmüller, H.6
  • 61
    • 84905820860 scopus 로고    scopus 로고
    • New force field on modeling intrinsically disordered proteins
    • Wang, W., Ye, W., Jiang, C., Luo, R., and Chen, H. F. (2014) New force field on modeling intrinsically disordered proteins Chem. Biol. Drug Des. 84, 253-269 10.1111/cbdd.12314
    • (2014) Chem. Biol. Drug Des. , vol.84 , pp. 253-269
    • Wang, W.1    Ye, W.2    Jiang, C.3    Luo, R.4    Chen, H.F.5
  • 62
    • 84928503362 scopus 로고    scopus 로고
    • Water dispersion interactions strongly influence simulated structural properties of disordered protein states
    • Piana, S., Donchev, A. G., Robustelli, P., and Shaw, D. E. (2015) Water dispersion interactions strongly influence simulated structural properties of disordered protein states J. Phys. Chem. B 119, 5113-5123 10.1021/jp508971m
    • (2015) J. Phys. Chem. B , vol.119 , pp. 5113-5123
    • Piana, S.1    Donchev, A.G.2    Robustelli, P.3    Shaw, D.E.4
  • 63
    • 84933056911 scopus 로고    scopus 로고
    • Kirkwood-Buff approach rescues overcollapse of a disordered protein in canonical protein force fields
    • Mercadante, D., Milles, S., Fuertes, G., Svergun, D. I., Lemke, E. A., and Grater, F. (2015) Kirkwood-Buff approach rescues overcollapse of a disordered protein in canonical protein force fields J. Phys. Chem. B 119, 7975-7984 10.1021/acs.jpcb.5b03440
    • (2015) J. Phys. Chem. B , vol.119 , pp. 7975-7984
    • Mercadante, D.1    Milles, S.2    Fuertes, G.3    Svergun, D.I.4    Lemke, E.A.5    Grater, F.6
  • 64
    • 0036902235 scopus 로고    scopus 로고
    • Close-range electrostatic interactions in proteins
    • Kumar, S. and Nussinov, R. (2002) Close-range electrostatic interactions in proteins ChemBioChem 3, 604-617 10.1002/1439-7633(20020703)3:7<604::AID-CBIC604>3.0.CO;2-X
    • (2002) ChemBioChem , vol.3 , pp. 604-617
    • Kumar, S.1    Nussinov, R.2
  • 65
    • 0037432563 scopus 로고    scopus 로고
    • Contribution of surface salt bridges to protein stability: Guidelines for protein engineering
    • Makhatadze, G. I., Loladze, V. V., Ermolenko, D. N., Chen, X. F., and Thomas, S. T. (2003) Contribution of surface salt bridges to protein stability: Guidelines for protein engineering J. Mol. Biol. 327, 1135-1148 10.1016/S0022-2836(03)00233-X
    • (2003) J. Mol. Biol. , vol.327 , pp. 1135-1148
    • Makhatadze, G.I.1    Loladze, V.V.2    Ermolenko, D.N.3    Chen, X.F.4    Thomas, S.T.5
  • 66
    • 84911471958 scopus 로고    scopus 로고
    • Protein thermal stability enhancement by designing salt bridges: A combined computational and experimental study
    • Lee, C. W., Wang, H. J., Hwang, J. K., and Tseng, C. P. (2014) Protein thermal stability enhancement by designing salt bridges: a combined computational and experimental study PLoS One 9, e112751 10.1371/journal.pone.0112751
    • (2014) PLoS One , vol.9
    • Lee, C.W.1    Wang, H.J.2    Hwang, J.K.3    Tseng, C.P.4
  • 67
    • 33745960026 scopus 로고    scopus 로고
    • Investigation of salt bridge stability in a Generalized Born solvent model
    • Geney, R., Layten, M., Gomperts, R., Hornak, V., and Simmerling, C. (2006) Investigation of salt bridge stability in a Generalized Born solvent model J. Chem. Theory Comput. 2, 115-127 10.1021/ct050183l
    • (2006) J. Chem. Theory Comput. , vol.2 , pp. 115-127
    • Geney, R.1    Layten, M.2    Gomperts, R.3    Hornak, V.4    Simmerling, C.5
  • 68
  • 69
    • 0037441481 scopus 로고    scopus 로고
    • Molecular dynamics simulation reveals a surface salt bridge forming a kinetic trap in unfolding of truncated Staphylococcal nuclease
    • Gruia, A. D., Fischer, S., and Smith, J. C. (2003) Molecular dynamics simulation reveals a surface salt bridge forming a kinetic trap in unfolding of truncated Staphylococcal nuclease Proteins: Struct., Funct., Genet. 50, 507-515 10.1002/prot.10312
    • (2003) Proteins: Struct., Funct., Genet. , vol.50 , pp. 507-515
    • Gruia, A.D.1    Fischer, S.2    Smith, J.C.3
  • 70
    • 84961978300 scopus 로고    scopus 로고
    • Electronic continuum model for molecular dynamics simulations of biological molecules
    • Leontyev, I. V. and Stuchebrukhov, A. A. (2010) Electronic continuum model for molecular dynamics simulations of biological molecules J. Chem. Theory Comput. 6, 1498-1508 10.1021/ct9005807
    • (2010) J. Chem. Theory Comput. , vol.6 , pp. 1498-1508
    • Leontyev, I.V.1    Stuchebrukhov, A.A.2
  • 71
    • 84907992125 scopus 로고    scopus 로고
    • Ff14ipq: A self-consistent force field for condensed-phase simulations of proteins
    • Cerutti, D. S., Swope, W. C., Rice, J. E., and Case, D. A. (2014) ff14ipq: a self-consistent force field for condensed-phase simulations of proteins J. Chem. Theory Comput. 10, 4515-4534 10.1021/ct500643c
    • (2014) J. Chem. Theory Comput. , vol.10 , pp. 4515-4534
    • Cerutti, D.S.1    Swope, W.C.2    Rice, J.E.3    Case, D.A.4
  • 72
    • 84990175702 scopus 로고    scopus 로고
    • Recent advances in polarizable force fields for macromolecules: Microsecond simulations of proteins using the classical Drude oscillator model
    • Huang, J., Lopes, P. E. M., Roux, B., and MacKerell, A. D. (2014) Recent advances in polarizable force fields for macromolecules: microsecond simulations of proteins using the classical Drude oscillator model J. Phys. Chem. Lett. 5, 3144-3150 10.1021/jz501315h
    • (2014) J. Phys. Chem. Lett. , vol.5 , pp. 3144-3150
    • Huang, J.1    Lopes, P.E.M.2    Roux, B.3    MacKerell, A.D.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.