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Volumn 79, Issue 12, 2011, Pages 3511-3524

Factors determining electrostatic fields in molecular dynamics simulations of the ras/effector interface

Author keywords

Electrostatics calculations; Molecular dynamics simulation; P21Ras; Vibrational stark effect spectroscopy

Indexed keywords

GUANINE NUCLEOTIDE DISSOCIATION INHIBITOR; RAS PROTEIN;

EID: 81055156290     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.23095     Document Type: Article
Times cited : (21)

References (52)
  • 2
    • 1642553461 scopus 로고    scopus 로고
    • The dark side of Ras: regulation of apoptosis
    • Cox A, Der C. The dark side of Ras: regulation of apoptosis. Oncogene 2003; 22: 8999-9006.
    • (2003) Oncogene , vol.22 , pp. 8999-9006
    • Cox, A.1    Der, C.2
  • 3
    • 0037264633 scopus 로고    scopus 로고
    • Targeting ras signalling pathways in cancer therapy
    • Downward J. Targeting ras signalling pathways in cancer therapy. Nature Rev Cancer 2003; 3: 11-22.
    • (2003) Nature Rev Cancer , vol.3 , pp. 11-22
    • Downward, J.1
  • 4
    • 7444245100 scopus 로고    scopus 로고
    • Renewing the conspiracy theory debate: does Raf function alone to mediate Ras oncogenesis?
    • Repasky G, Chenette E, Der C. Renewing the conspiracy theory debate: does Raf function alone to mediate Ras oncogenesis? Trends Cell Bio 2004; 14: 639-647.
    • (2004) Trends Cell Bio , vol.14 , pp. 639-647
    • Repasky, G.1    Chenette, E.2    Der, C.3
  • 5
    • 0000953693 scopus 로고
    • An Unidentified Virus which causes the Rapid Production of Tumours in Mice
    • Harvey J. An Unidentified Virus which causes the Rapid Production of Tumours in Mice. Nature 1964; 204: 1104-1105.
    • (1964) Nature , vol.204 , pp. 1104-1105
    • Harvey, J.1
  • 6
    • 0024376173 scopus 로고
    • Ras oncogenes in human cancer: A review
    • Bos J. Ras oncogenes in human cancer: A review. Cancer Res 1989; 49: 4682-4689.
    • (1989) Cancer Res , vol.49 , pp. 4682-4689
    • Bos, J.1
  • 7
    • 0030920782 scopus 로고    scopus 로고
    • G protein mechanisms: Insights from structural analysis
    • Sprang S. G protein mechanisms: Insights from structural analysis. Annu Rev Biochem 1997; 66: 639-678.
    • (1997) Annu Rev Biochem , vol.66 , pp. 639-678
    • Sprang, S.1
  • 9
    • 78649568797 scopus 로고    scopus 로고
    • Vibrational stark effect spectroscopy at the interface of Ras and Rap1A bound to the Ras binding domain of RalGDS reveals an electrostatic mechanism for protein-protein interaction
    • Stafford AJ, Ensign DL, Webb LJ. Vibrational stark effect spectroscopy at the interface of Ras and Rap1A bound to the Ras binding domain of RalGDS reveals an electrostatic mechanism for protein-protein interaction. J Phys Chem B 2010; 114: 15331-15344.
    • (2010) J Phys Chem B , vol.114 , pp. 15331-15344
    • Stafford, A.J.1    Ensign, D.L.2    Webb, L.J.3
  • 10
    • 0034499168 scopus 로고    scopus 로고
    • Vibrational stark effects of nitriles I. Methods and experimental results
    • Andrews S, Boxer S. Vibrational stark effects of nitriles I. Methods and experimental results. J Phys Chem A 2000; 104: 11853-11863.
    • (2000) J Phys Chem A , vol.104 , pp. 11853-11863
    • Andrews, S.1    Boxer, S.2
  • 11
    • 0037165471 scopus 로고    scopus 로고
    • Vibrational stark effects of nitriles II. Physical origins of stark effects from experiment and perturbation models
    • Andrews S, Boxer S. Vibrational stark effects of nitriles II. Physical origins of stark effects from experiment and perturbation models. J Phys Chem A 2002; 106: 469-477.
    • (2002) J Phys Chem A , vol.106 , pp. 469-477
    • Andrews, S.1    Boxer, S.2
  • 12
    • 0142072231 scopus 로고    scopus 로고
    • Vibrational stark effects calibrate the sensitivity of vibrational probes for electric fields in proteins
    • Suydam I, Boxer S. Vibrational stark effects calibrate the sensitivity of vibrational probes for electric fields in proteins. Biochemistry 2003; 42: 12050-12055.
    • (2003) Biochemistry , vol.42 , pp. 12050-12055
    • Suydam, I.1    Boxer, S.2
  • 13
    • 33750039654 scopus 로고    scopus 로고
    • Site-specific conversion of cysteine thiols into thiocyanate creates an IR probe for electric fields in proteins
    • Fafarman AT, Webb LJ, Chuang JI, Boxer SG. Site-specific conversion of cysteine thiols into thiocyanate creates an IR probe for electric fields in proteins. J Am Chem Soc 2006; 128: 13356-13357.
    • (2006) J Am Chem Soc , vol.128 , pp. 13356-13357
    • Fafarman, A.T.1    Webb, L.J.2    Chuang, J.I.3    Boxer, S.G.4
  • 14
    • 33746017658 scopus 로고    scopus 로고
    • Electric fields at the active site of an enzyme: direct comparison of experiment with theory
    • Suydam IT, Snow CD, Pande VS, Boxer SG. Electric fields at the active site of an enzyme: direct comparison of experiment with theory. Science 2006; 313: 200-204.
    • (2006) Science , vol.313 , pp. 200-204
    • Suydam, I.T.1    Snow, C.D.2    Pande, V.S.3    Boxer, S.G.4
  • 15
    • 38949205622 scopus 로고    scopus 로고
    • Electrostatic fields near the active site of human aldose reductase: 1. New inhibitors and vibrational stark effect measurements
    • Webb LJ, Boxer SG. Electrostatic fields near the active site of human aldose reductase: 1. New inhibitors and vibrational stark effect measurements. Biochemistry 2008; 47: 1588-1598.
    • (2008) Biochemistry , vol.47 , pp. 1588-1598
    • Webb, L.J.1    Boxer, S.G.2
  • 16
    • 77958474269 scopus 로고    scopus 로고
    • Nitrile bonds as infrared probes of electrostatics in ribonuclease S
    • Fafarman AT, Boxer SG. Nitrile bonds as infrared probes of electrostatics in ribonuclease S. J Phys Chem B 2010; 114: 13536-13544.
    • (2010) J Phys Chem B , vol.114 , pp. 13536-13544
    • Fafarman, A.T.1    Boxer, S.G.2
  • 17
    • 0017100947 scopus 로고
    • Theoretical studies of enzymic reactions: Dielectric, electrostatic, and steric stabilization of carbonium-ion in reaction of lysozyme
    • Warshel A, Levitt M. Theoretical studies of enzymic reactions: Dielectric, electrostatic, and steric stabilization of carbonium-ion in reaction of lysozyme. J Mol Biol 1976; 103: 227-249.
    • (1976) J Mol Biol , vol.103 , pp. 227-249
    • Warshel, A.1    Levitt, M.2
  • 18
    • 4243463817 scopus 로고
    • Electrostatics in biomolecular structure and dynamics
    • Davis M, McCammon J. Electrostatics in biomolecular structure and dynamics. Chem Rev 1990; 90: 509-521.
    • (1990) Chem Rev , vol.90 , pp. 509-521
    • Davis, M.1    McCammon, J.2
  • 19
    • 0029016182 scopus 로고
    • Classical electrostatics in biology and chemistry
    • Honig B, Nicholls A. Classical electrostatics in biology and chemistry. Science 1995; 268: 1144-1149.
    • (1995) Science , vol.268 , pp. 1144-1149
    • Honig, B.1    Nicholls, A.2
  • 20
    • 0035964342 scopus 로고    scopus 로고
    • Electrostatics of nanosystems: application to microtubules and the ribosome
    • Baker N, Sept D, Joseph S, Holst M, McCammon J. Electrostatics of nanosystems: application to microtubules and the ribosome. PNAS 2001; 98: 10037-10041.
    • (2001) PNAS , vol.98 , pp. 10037-10041
    • Baker, N.1    Sept, D.2    Joseph, S.3    Holst, M.4    McCammon, J.5
  • 23
    • 0008075262 scopus 로고    scopus 로고
    • Computational biochemistry and biophysics
    • In: Becker OM,Mackerell AD,Jr, editors. Atomistic models and force fields. New York: Marcel Dekker, Inc., pp -.
    • MacKerell AD, Jr. Computational biochemistry and biophysics. In: Becker OM, Mackerell AD, Jr, Roux B, Watanabe M, editors. Atomistic models and force fields. New York: Marcel Dekker, Inc., 2001; pp 7-38.
    • (2001) , pp. 7-38
    • MacKerell Jr., A.D.1    Roux, B.2    Watanabe, M.3
  • 24
    • 0242663237 scopus 로고    scopus 로고
    • Kollman P. A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations. J Comput Chem ; -.
    • Duan Y, Wu C, Chowdhury S, Lee M, Xiong G, Zhang W, Yang R, Cieplak P, Luo R, Lee T, Caldwell J, Wang J, Kollman P. A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations. J Comput Chem 2003; 24: 1999-2012.
    • (2003) , vol.24 , pp. 1999-2012
    • Duan, Y.1    Wu, C.2    Chowdhury, S.3    Lee, M.4    Xiong, G.5    Zhang, W.6    Yang, R.7    Cieplak, P.8    Luo, R.9    Lee, T.10    Caldwell, J.11    Wang, J.12
  • 27
    • 0001465616 scopus 로고
    • Chemical-shifts in proteins: A shielding trajectory analysis of the fluorine nuclear-magnetic- resonance spectrum of the Escherichia-coli galactose binding-protein using a multipole shielding polarizability local reaction field molecular-dynamics approach
    • Pearson J, Oldfield E, Lee F, Warshel A. Chemical-shifts in proteins: A shielding trajectory analysis of the fluorine nuclear-magnetic- resonance spectrum of the Escherichia-coli galactose binding-protein using a multipole shielding polarizability local reaction field molecular-dynamics approach. J Am Chem Soc 1993; 115: 6851-6862.
    • (1993) J Am Chem Soc , vol.115 , pp. 6851-6862
    • Pearson, J.1    Oldfield, E.2    Lee, F.3    Warshel, A.4
  • 28
    • 0029665619 scopus 로고    scopus 로고
    • Use of F-19 NMR to probe protein structure and conformational changes
    • Danielson M, Falke J. Use of F-19 NMR to probe protein structure and conformational changes. Ann Rev Biophys Biomol Struct 1996; 25: 163-195.
    • (1996) Ann Rev Biophys Biomol Struct , vol.25 , pp. 163-195
    • Danielson, M.1    Falke, J.2
  • 29
    • 0035451052 scopus 로고    scopus 로고
    • What axe the dielectric "constants" of proteins and how to validate electrostatic models?
    • Schutz C, Warshel A. What axe the dielectric "constants" of proteins and how to validate electrostatic models? Proteins Struct Funct Genet 2001; 44: 400-417.
    • (2001) Proteins Struct Funct Genet , vol.44 , pp. 400-417
    • Schutz, C.1    Warshel, A.2
  • 30
    • 0036681440 scopus 로고    scopus 로고
    • Empirical relationships between protein structure and carboxyl pK (a) values in proteins
    • Forsyth W, Antosiewiez J, Robertson A. Empirical relationships between protein structure and carboxyl pK (a) values in proteins. Proteins Struct Funct Genet 2002; 48: 388-403.
    • (2002) Proteins Struct Funct Genet , vol.48 , pp. 388-403
    • Forsyth, W.1    Antosiewiez, J.2    Robertson, A.3
  • 31
    • 33748106496 scopus 로고    scopus 로고
    • Hydrogen bonding markedly reduces the pK of buried carboxyl groups in proteins
    • Thurlkill RL, Grimsley GR, Scholtz M, Pace CN. Hydrogen bonding markedly reduces the pK of buried carboxyl groups in proteins. J Mol Biol 2006; 362: 594-604.
    • (2006) J Mol Biol , vol.362 , pp. 594-604
    • Thurlkill, R.L.1    Grimsley, G.R.2    Scholtz, M.3    Pace, C.N.4
  • 33
    • 44349142271 scopus 로고    scopus 로고
    • Electrostatic effects in a network of polar and ionizable groups in staphylococcal nuclease
    • Baran K, Chimenti M, Schlessman J, Fitch C, Herbst K, Garcia-Moreno B. Electrostatic effects in a network of polar and ionizable groups in staphylococcal nuclease. J Mol Biol 2008; 379: 1045-1062.
    • (2008) J Mol Biol , vol.379 , pp. 1045-1062
    • Baran, K.1    Chimenti, M.2    Schlessman, J.3    Fitch, C.4    Herbst, K.5    Garcia-Moreno, B.6
  • 35
    • 67349203635 scopus 로고    scopus 로고
    • The pK (a) values of acidic and basic residues buried at the same internal location in a protein are governed by different factors
    • Harms MJ, Castaneda CA, Schlessman JL, Sue GR, Isom DG, Cannon BR, Garcia-Moreno EB. The pK (a) values of acidic and basic residues buried at the same internal location in a protein are governed by different factors. J Mol Biol 2009; 389: 34-47.
    • (2009) J Mol Biol , vol.389 , pp. 34-47
    • Harms, M.J.1    Castaneda, C.A.2    Schlessman, J.L.3    Sue, G.R.4    Isom, D.G.5    Cannon, B.R.6    Garcia-Moreno, E.B.7
  • 37
    • 84986516411 scopus 로고
    • Application of the multimolecule and multiconformational RESP methodology to biopolymers: charge derivation for DNA, RNA, and proteins
    • Cieplak P, Cornell W, Bayly C, Kollman P. Application of the multimolecule and multiconformational RESP methodology to biopolymers: charge derivation for DNA, RNA, and proteins. J Comp Chem 1995; 16: 1357-1377.
    • (1995) J Comp Chem , vol.16 , pp. 1357-1377
    • Cieplak, P.1    Cornell, W.2    Bayly, C.3    Kollman, P.4
  • 41
    • 20544435097 scopus 로고    scopus 로고
    • Exploring the helix-coil transition via all-atom equilibrium ensemble simulations
    • Sorin E, Pande V. Exploring the helix-coil transition via all-atom equilibrium ensemble simulations. Biophys J 2005; 88: 2472-2493.
    • (2005) Biophys J , vol.88 , pp. 2472-2493
    • Sorin, E.1    Pande, V.2
  • 42
  • 43
    • 33748538349 scopus 로고    scopus 로고
    • Automatic atom type and bond type perception in molecular mechanical calculations
    • Wang J, Wang W, Kollman PA, Case DA. Automatic atom type and bond type perception in molecular mechanical calculations. J Mol Graph Model 2006; 25: 247-260.
    • (2006) J Mol Graph Model , vol.25 , pp. 247-260
    • Wang, J.1    Wang, W.2    Kollman, P.A.3    Case, D.A.4
  • 44
    • 84986524957 scopus 로고
    • Convergence acceleration of iterative sequences: the case of SCF iteration
    • Pulay P. Convergence acceleration of iterative sequences: the case of SCF iteration. Chem Phys Lett 1980; 73: 393-398.
    • (1980) Chem Phys Lett , vol.73 , pp. 393-398
    • Pulay, P.1
  • 46
    • 81055150540 scopus 로고    scopus 로고
    • Avogadro: an open-source molecular builder and visualization tool. Version 1.00
    • Avogadro: an open-source molecular builder and visualization tool. Version 1.00. .
  • 47
  • 48
    • 0029633155 scopus 로고
    • The calculation of the potential of mean force using computer simulations
    • Roux B. The calculation of the potential of mean force using computer simulations. Comput Phys Commun 1995; 91: 275-282.
    • (1995) Comput Phys Commun , vol.91 , pp. 275-282
    • Roux, B.1
  • 49
    • 17444366185 scopus 로고    scopus 로고
    • Temperature weighted histogram analysis method, replica exchange, and transition paths
    • Gallicchio E, Andrec M, Felts A, Levy R. Temperature weighted histogram analysis method, replica exchange, and transition paths. J Phys Chem B 2005; 109: 6722-6731.
    • (2005) J Phys Chem B , vol.109 , pp. 6722-6731
    • Gallicchio, E.1    Andrec, M.2    Felts, A.3    Levy, R.4


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