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Volumn 392, Issue 3, 2009, Pages 823-836

Segmented Transition Pathway of the Signaling Protein Nitrogen Regulatory Protein C

Author keywords

conformational transition; nitrogen regulatory protein C; quasi harmonic analysis; simulation; targeted molecular dynamics

Indexed keywords

LIGAND; NITROGEN REGULATORY PROTEIN C; REGULATOR PROTEIN; UNCLASSIFIED DRUG;

EID: 69449087027     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2009.06.065     Document Type: Article
Times cited : (31)

References (74)
  • 1
    • 78651189765 scopus 로고
    • On the nature of allosteric transitions: a plausible model
    • Monod J., Wyman J., and Changeux J.P. On the nature of allosteric transitions: a plausible model. J. Mol. Biol. 12 (1965) 88-118
    • (1965) J. Mol. Biol. , vol.12 , pp. 88-118
    • Monod, J.1    Wyman, J.2    Changeux, J.P.3
  • 2
    • 37249032102 scopus 로고    scopus 로고
    • Dynamic personalities of proteins
    • Henzler-Wildman K., and Kern D. Dynamic personalities of proteins. Nature 450 (2007) 964-972
    • (2007) Nature , vol.450 , pp. 964-972
    • Henzler-Wildman, K.1    Kern, D.2
  • 3
    • 0346220393 scopus 로고    scopus 로고
    • The role of dynamics in allosteric regulation
    • Kern D., and Zuiderweg E.R.P. The role of dynamics in allosteric regulation. Curr. Opin. Struct. Biol. 13 (2003) 748-757
    • (2003) Curr. Opin. Struct. Biol. , vol.13 , pp. 748-757
    • Kern, D.1    Zuiderweg, E.R.P.2
  • 4
    • 0026320866 scopus 로고
    • The energy landscapes and motions of proteins
    • Frauenfelder H., Sligar S.G., and Wolynes P.G. The energy landscapes and motions of proteins. Science 254 (1991) 1598-1603
    • (1991) Science , vol.254 , pp. 1598-1603
    • Frauenfelder, H.1    Sligar, S.G.2    Wolynes, P.G.3
  • 5
    • 0033970020 scopus 로고    scopus 로고
    • Folding and binding cascades: dynamic landscapes and population shifts
    • Kumar S., Ma B., Tsai C.J., Sinha N., and Nussinov R. Folding and binding cascades: dynamic landscapes and population shifts. Protein Sci. 9 (2000) 10-19
    • (2000) Protein Sci. , vol.9 , pp. 10-19
    • Kumar, S.1    Ma, B.2    Tsai, C.J.3    Sinha, N.4    Nussinov, R.5
  • 6
    • 0036147568 scopus 로고    scopus 로고
    • Multiple diverse ligands binding at a single protein site: a matter of pre-existing populations
    • Ma B., Shatsky M., Wolfson H.J., and Nussinov R. Multiple diverse ligands binding at a single protein site: a matter of pre-existing populations. Protein Sci. 11 (2002) 184-197
    • (2002) Protein Sci. , vol.11 , pp. 184-197
    • Ma, B.1    Shatsky, M.2    Wolfson, H.J.3    Nussinov, R.4
  • 7
    • 48249141040 scopus 로고    scopus 로고
    • Allostery and cooperativity revisited
    • Cui Q., and Karplus M. Allostery and cooperativity revisited. Protein Sci. 17 (2008) 1295-1307
    • (2008) Protein Sci. , vol.17 , pp. 1295-1307
    • Cui, Q.1    Karplus, M.2
  • 8
    • 32344434479 scopus 로고    scopus 로고
    • The changing landscape of protein allostery
    • Swain J.F., and Gierasch L.M. The changing landscape of protein allostery. Curr. Opin. Struct. Biol. 16 (2006) 102-108
    • (2006) Curr. Opin. Struct. Biol. , vol.16 , pp. 102-108
    • Swain, J.F.1    Gierasch, L.M.2
  • 10
    • 25444469141 scopus 로고    scopus 로고
    • Out-of-plane motions in open sliding clamps: molecular dynamics simulations of eukaryotic and archaeal proliferating cell nuclear antigen
    • Kazmirski S.L., Zhao Y.X., Bowman G.D., O'Donnell M., and Kuriyan J. Out-of-plane motions in open sliding clamps: molecular dynamics simulations of eukaryotic and archaeal proliferating cell nuclear antigen. Proc. Natl Acad. Sci. USA 102 (2005) 13801-13806
    • (2005) Proc. Natl Acad. Sci. USA , vol.102 , pp. 13801-13806
    • Kazmirski, S.L.1    Zhao, Y.X.2    Bowman, G.D.3    O'Donnell, M.4    Kuriyan, J.5
  • 11
    • 0028455053 scopus 로고
    • Targeted molecular dynamics: a new approach for searching pathways of conformational transitions
    • Schlitter J., Engels M., and Kruger P. Targeted molecular dynamics: a new approach for searching pathways of conformational transitions. J. Mol. Graphics 12 (1994) 84-89
    • (1994) J. Mol. Graphics , vol.12 , pp. 84-89
    • Schlitter, J.1    Engels, M.2    Kruger, P.3
  • 12
    • 0000689085 scopus 로고
    • Predicting slow structural transitions in macromolecular systems: conformational flooding
    • Grubmüller H. Predicting slow structural transitions in macromolecular systems: conformational flooding. Phys. Rev. E 52 (1995) 2893-2906
    • (1995) Phys. Rev. E , vol.52 , pp. 2893-2906
    • Grubmüller, H.1
  • 13
    • 4344606960 scopus 로고    scopus 로고
    • Multidimensional adaptive umbrella sampling: applications to main chain and side chain peptide conformations
    • Bartels C., and Karplus M. Multidimensional adaptive umbrella sampling: applications to main chain and side chain peptide conformations. J. Comput. Chem. 18 (1997) 1450-1462
    • (1997) J. Comput. Chem. , vol.18 , pp. 1450-1462
    • Bartels, C.1    Karplus, M.2
  • 14
    • 0030711616 scopus 로고    scopus 로고
    • Molecular switch in signal transduction: reaction paths of the conformational changes in ras p21
    • Ma J., and Karplus M. Molecular switch in signal transduction: reaction paths of the conformational changes in ras p21. Proc. Natl Acad. Sci. USA 94 (1997) 11905
    • (1997) Proc. Natl Acad. Sci. USA , vol.94 , pp. 11905
    • Ma, J.1    Karplus, M.2
  • 15
    • 0036424048 scopus 로고    scopus 로고
    • Transition path sampling: throwing ropes over rough mountain passes, in the dark
    • Bolhuis P.G., Chandler D., Dellago C., and Geissler P.L. Transition path sampling: throwing ropes over rough mountain passes, in the dark. Annu. Rev. Phys. Chem. 53 (2002) 291-318
    • (2002) Annu. Rev. Phys. Chem. , vol.53 , pp. 291-318
    • Bolhuis, P.G.1    Chandler, D.2    Dellago, C.3    Geissler, P.L.4
  • 17
    • 14844286108 scopus 로고    scopus 로고
    • Usefulness and limitations of normal mode analysis in modeling dynamics of biomolecular complexes
    • Ma J. Usefulness and limitations of normal mode analysis in modeling dynamics of biomolecular complexes. Structure 13 (2005) 373-380
    • (2005) Structure , vol.13 , pp. 373-380
    • Ma, J.1
  • 18
    • 33747065536 scopus 로고    scopus 로고
    • Multiple-basin energy landscapes for large-amplitude conformational motions of proteins: structure-based molecular dynamics simulations
    • Okazaki K., Koga N., Takada S., Onuchic J.N., and Wolynes P.G. Multiple-basin energy landscapes for large-amplitude conformational motions of proteins: structure-based molecular dynamics simulations. Proc. Natl Acad. Sci. USA 103 (2006) 11844
    • (2006) Proc. Natl Acad. Sci. USA , vol.103 , pp. 11844
    • Okazaki, K.1    Koga, N.2    Takada, S.3    Onuchic, J.N.4    Wolynes, P.G.5
  • 19
    • 33748253737 scopus 로고    scopus 로고
    • Simulation of conformational transitions
    • van der Vaart A. Simulation of conformational transitions. Theor. Chem. Acc. 116 (2006) 183-193
    • (2006) Theor. Chem. Acc. , vol.116 , pp. 183-193
    • van der Vaart, A.1
  • 20
    • 37649014404 scopus 로고    scopus 로고
    • On searching in, sampling of, and dynamically moving through conformational space of biomolecular systems: a review
    • Christen M., and van Gunsteren W.F. On searching in, sampling of, and dynamically moving through conformational space of biomolecular systems: a review. J. Comput. Chem. 29 (2008) 157-166
    • (2008) J. Comput. Chem. , vol.29 , pp. 157-166
    • Christen, M.1    van Gunsteren, W.F.2
  • 21
    • 41949100049 scopus 로고    scopus 로고
    • Recent advances in implicit solvent-based methods for biomolecular simulations
    • Chen J., Brooks C.L., and Khandogin J. Recent advances in implicit solvent-based methods for biomolecular simulations. Curr. Opin. Struct. Biol. 18 (2008) 140-148
    • (2008) Curr. Opin. Struct. Biol. , vol.18 , pp. 140-148
    • Chen, J.1    Brooks, C.L.2    Khandogin, J.3
  • 22
    • 0027794972 scopus 로고
    • Targeted molecular dynamics simulation of conformational change-application to the T ↔ R transition in insulin
    • Schlitter J., Engels M., Krüger P., Jacoby E., and Wollmer A. Targeted molecular dynamics simulation of conformational change-application to the T ↔ R transition in insulin. Mol. Simul. 10 (1993) 291-308
    • (1993) Mol. Simul. , vol.10 , pp. 291-308
    • Schlitter, J.1    Engels, M.2    Krüger, P.3    Jacoby, E.4    Wollmer, A.5
  • 23
    • 0000127140 scopus 로고
    • Method for estimating the configurational entropy of macromolecules
    • Karplus M., and Kushick J.N. Method for estimating the configurational entropy of macromolecules. Macromolecules 14 (1981) 325-332
    • (1981) Macromolecules , vol.14 , pp. 325-332
    • Karplus, M.1    Kushick, J.N.2
  • 24
    • 0026076090 scopus 로고
    • Collective motions in proteins: a covariance analysis of atomic fluctuations in molecular dynamics and normal mode simulations
    • Ichiye T., and Karplus M. Collective motions in proteins: a covariance analysis of atomic fluctuations in molecular dynamics and normal mode simulations. Proteins Struct. Funct. Genet. 11 (1991) 205-217
    • (1991) Proteins Struct. Funct. Genet. , vol.11 , pp. 205-217
    • Ichiye, T.1    Karplus, M.2
  • 26
    • 0020698476 scopus 로고
    • Dynamics of proteins: elements and function
    • Karplus M., and McCammon J.A. Dynamics of proteins: elements and function. Annu. Rev. Biochem. 52 (1983) 263-300
    • (1983) Annu. Rev. Biochem. , vol.52 , pp. 263-300
    • Karplus, M.1    McCammon, J.A.2
  • 27
    • 0001295503 scopus 로고    scopus 로고
    • Principal component analysis and long time protein dynamics
    • Balsera M.A., Wriggers W., Oono Y., and Schulten K. Principal component analysis and long time protein dynamics. J. Phys. Chem. 100 (1996) 2567-2572
    • (1996) J. Phys. Chem. , vol.100 , pp. 2567-2572
    • Balsera, M.A.1    Wriggers, W.2    Oono, Y.3    Schulten, K.4
  • 28
    • 0000118827 scopus 로고
    • Harmonic and quasiharmonic descriptions of crambin
    • Teeter M.M., and Case D.A. Harmonic and quasiharmonic descriptions of crambin. J. Phys. Chem. 194 (1990) 8091-8097
    • (1990) J. Phys. Chem. , vol.194 , pp. 8091-8097
    • Teeter, M.M.1    Case, D.A.2
  • 29
    • 0242618314 scopus 로고    scopus 로고
    • Calculation of pathways for the conformational transition between the GTP- and GDP-bound states of the Ha-ras-p21 protein: calculations with explicit solvent simulations and comparison with calculations in vacuum
    • Díaz J.F., Wroblowski B., Schlitter J., and Engelborghs Y. Calculation of pathways for the conformational transition between the GTP- and GDP-bound states of the Ha-ras-p21 protein: calculations with explicit solvent simulations and comparison with calculations in vacuum. Proteins 28 (1997) 434-451
    • (1997) Proteins , vol.28 , pp. 434-451
    • Díaz, J.F.1    Wroblowski, B.2    Schlitter, J.3    Engelborghs, Y.4
  • 30
    • 0037197932 scopus 로고    scopus 로고
    • Conformational pathways in the gating of Escherichia coli mechanosensitive channel
    • Kong Y., Shen Y., Warth T.E., and Ma J. Conformational pathways in the gating of Escherichia coli mechanosensitive channel. Proc. Natl Acad. Sci. USA 99 (2002) 5999
    • (2002) Proc. Natl Acad. Sci. USA , vol.99 , pp. 5999
    • Kong, Y.1    Shen, Y.2    Warth, T.E.3    Ma, J.4
  • 31
    • 0035815288 scopus 로고    scopus 로고
    • Dynamic coupling between the SH2 and SH3 domains of c-Src and Hck underlies their inactivation by C-terminal tyrosine phosphorylation
    • Young M.A., Gonfloni S., Superti-Furga G., Roux B., and Kuriyan J. Dynamic coupling between the SH2 and SH3 domains of c-Src and Hck underlies their inactivation by C-terminal tyrosine phosphorylation. Cell 105 (2001) 115-126
    • (2001) Cell , vol.105 , pp. 115-126
    • Young, M.A.1    Gonfloni, S.2    Superti-Furga, G.3    Roux, B.4    Kuriyan, J.5
  • 32
    • 0003438040 scopus 로고
    • Hoch J.A., and Silhavy T.J. (Eds), American Society for Microbiology Press, Washington, DC
    • In: Hoch J.A., and Silhavy T.J. (Eds). Two-Component Signal Transduction (1995), American Society for Microbiology Press, Washington, DC
    • (1995) Two-Component Signal Transduction
  • 33
    • 0033599026 scopus 로고    scopus 로고
    • Structure of a transiently phosphorylated switch in bacterial signal transduction
    • Kern D., Volkman B.F., Luginbuhl P., Nohaile M.J., Kustu S., and Wemmer D.E. Structure of a transiently phosphorylated switch in bacterial signal transduction. Nature 402 (1999) 894-898
    • (1999) Nature , vol.402 , pp. 894-898
    • Kern, D.1    Volkman, B.F.2    Luginbuhl, P.3    Nohaile, M.J.4    Kustu, S.5    Wemmer, D.E.6
  • 34
    • 0028927334 scopus 로고
    • Three- dimensional solution structure of the N-terminal receiver domain of NtrC
    • Volkman B.F., Nohaile M.J., Amy N.K., Kustu S., and Wemmer D.E. Three- dimensional solution structure of the N-terminal receiver domain of NtrC. Biochemistry 34 (1995) 1413-1424
    • (1995) Biochemistry , vol.34 , pp. 1413-1424
    • Volkman, B.F.1    Nohaile, M.J.2    Amy, N.K.3    Kustu, S.4    Wemmer, D.E.5
  • 35
    • 0035937443 scopus 로고    scopus 로고
    • Two-state allosteric behavior in a single-domain signaling protein
    • Volkman B.F., Lipson D., Wemmer D.E., and Kern D. Two-state allosteric behavior in a single-domain signaling protein. Science 291 (2001) 2429-2433
    • (2001) Science , vol.291 , pp. 2429-2433
    • Volkman, B.F.1    Lipson, D.2    Wemmer, D.E.3    Kern, D.4
  • 36
    • 0042165841 scopus 로고    scopus 로고
    • High-resolution solution structure of the beryllofluoride-activated NtrC receiver domain
    • Hastings C.A., Lee S.Y., Cho H.S., Yan D., Kustu S., and Wemmer D.E. High-resolution solution structure of the beryllofluoride-activated NtrC receiver domain. Biochemistry 42 (2003) 9081-9090
    • (2003) Biochemistry , vol.42 , pp. 9081-9090
    • Hastings, C.A.1    Lee, S.Y.2    Cho, H.S.3    Yan, D.4    Kustu, S.5    Wemmer, D.E.6
  • 37
    • 34250858152 scopus 로고    scopus 로고
    • Functional dynamics of response regulators using NMR relaxation techniques
    • Gardino A., and Kern D. Functional dynamics of response regulators using NMR relaxation techniques. Methods Enzymol. 423 (2007) 149-165
    • (2007) Methods Enzymol. , vol.423 , pp. 149-165
    • Gardino, A.1    Kern, D.2
  • 38
    • 33645317601 scopus 로고    scopus 로고
    • Molecular dynamic simulations of the N-terminal receiver domain of NtrC reveal intrinsic conformational flexibility in the inactive state
    • Hu X., and Wang Y. Molecular dynamic simulations of the N-terminal receiver domain of NtrC reveal intrinsic conformational flexibility in the inactive state. J. Biomol. Struct. Dyn. 23 (2006) 509-518
    • (2006) J. Biomol. Struct. Dyn. , vol.23 , pp. 509-518
    • Hu, X.1    Wang, Y.2
  • 39
    • 39649088661 scopus 로고    scopus 로고
    • Conformational switching upon phosphorylation: a predictive framework based on energy landscape principles
    • Lätzer J., Shen T., and Wolynes P.G. Conformational switching upon phosphorylation: a predictive framework based on energy landscape principles. Biochemistry 47 (2008) 2110-2122
    • (2008) Biochemistry , vol.47 , pp. 2110-2122
    • Lätzer, J.1    Shen, T.2    Wolynes, P.G.3
  • 40
    • 40549128343 scopus 로고    scopus 로고
    • Pathways for conformational change in nitrogen regulatory protein C from discrete path sampling
    • Khalili M., and Wales D.J. Pathways for conformational change in nitrogen regulatory protein C from discrete path sampling. J. Phys. Chem. B 112 (2008) 2456-2465
    • (2008) J. Phys. Chem. B , vol.112 , pp. 2456-2465
    • Khalili, M.1    Wales, D.J.2
  • 42
    • 0036219167 scopus 로고    scopus 로고
    • Improving the quality of protein structures derived by NMR spectroscopy
    • Spronk C.A.E.M., Linge J.P., Hilbers C.W., and Vuister G.W. Improving the quality of protein structures derived by NMR spectroscopy. J. Biomol. NMR 22 (2002) 281-289
    • (2002) J. Biomol. NMR , vol.22 , pp. 281-289
    • Spronk, C.A.E.M.1    Linge, J.P.2    Hilbers, C.W.3    Vuister, G.W.4
  • 43
    • 0036234027 scopus 로고    scopus 로고
    • Comparison of protein solution structures refined by molecular dynamics simulation in vacuum, with a generalized Born model, and with explicit water
    • Xia B., Tsui V., Case D.A., Dyson H.J., and Wright P.E. Comparison of protein solution structures refined by molecular dynamics simulation in vacuum, with a generalized Born model, and with explicit water. J. Biomol. NMR 22 (2002) 317-331
    • (2002) J. Biomol. NMR , vol.22 , pp. 317-331
    • Xia, B.1    Tsui, V.2    Case, D.A.3    Dyson, H.J.4    Wright, P.E.5
  • 46
    • 23044509110 scopus 로고    scopus 로고
    • NMR data collection and analysis protocol for high-throughput protein structure determination
    • Liu G., Shen Y., Atreya H.S., Parish D., Shao Y., Sukumaran D.K., et al. NMR data collection and analysis protocol for high-throughput protein structure determination. Proc. Natl Acad. Sci. USA 102 (2005) 10487-10492
    • (2005) Proc. Natl Acad. Sci. USA , vol.102 , pp. 10487-10492
    • Liu, G.1    Shen, Y.2    Atreya, H.S.3    Parish, D.4    Shao, Y.5    Sukumaran, D.K.6
  • 48
    • 0025398721 scopus 로고
    • WHAT IF: a molecular modeling and drug design program
    • Vriend G. WHAT IF: a molecular modeling and drug design program. J. Mol. Graphics 8 (1990) 52-56
    • (1990) J. Mol. Graphics , vol.8 , pp. 52-56
    • Vriend, G.1
  • 49
    • 34547179849 scopus 로고    scopus 로고
    • Protein backbone chemical shifts predicted from searching a database for torsion angle and sequence homology
    • Shen Y., and Bax A. Protein backbone chemical shifts predicted from searching a database for torsion angle and sequence homology. J. Biolmol. NMR 38 (2007) 289-302
    • (2007) J. Biolmol. NMR , vol.38 , pp. 289-302
    • Shen, Y.1    Bax, A.2
  • 50
    • 0020997912 scopus 로고
    • Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features
    • Kabsch W., and Sander C. 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
  • 52
    • 0037671391 scopus 로고    scopus 로고
    • Interdomain dynamics and ligand binding: molecular dynamics simulations of glutamine binding protein
    • Pang A., Arinaminpathy Y., Sansom M.S.P., and Biggin P.C. Interdomain dynamics and ligand binding: molecular dynamics simulations of glutamine binding protein. FEBS Lett. 550 (2003) 168-174
    • (2003) FEBS Lett. , vol.550 , pp. 168-174
    • Pang, A.1    Arinaminpathy, Y.2    Sansom, M.S.P.3    Biggin, P.C.4
  • 54
    • 0029075795 scopus 로고
    • The essential dynamics of thermolysin: confirmation of the hinge-bending motion and comparison of simulations in vacuum and water
    • van Aalten D.M., Amadei A., Linssen A.B., Eijsink V.G., Vriend G., and Berendsen H.J. The essential dynamics of thermolysin: confirmation of the hinge-bending motion and comparison of simulations in vacuum and water. Proteins Struct. Funct. Genet. 22 (1995) 45-54
    • (1995) Proteins Struct. Funct. Genet. , vol.22 , pp. 45-54
    • van Aalten, D.M.1    Amadei, A.2    Linssen, A.B.3    Eijsink, V.G.4    Vriend, G.5    Berendsen, H.J.6
  • 55
    • 18144418170 scopus 로고    scopus 로고
    • Protein structural change upon ligand binding: linear response theory
    • Ikeguchi M., Ueno J., Sato M., and Kidera A. Protein structural change upon ligand binding: linear response theory. Phys. Rev. Lett. 94 (2005) 078102
    • (2005) Phys. Rev. Lett. , vol.94 , pp. 078102
    • Ikeguchi, M.1    Ueno, J.2    Sato, M.3    Kidera, A.4
  • 56
    • 34547666968 scopus 로고    scopus 로고
    • How well can we understand large-scale protein motions using normal modes of elastic network models?
    • Yang L., Song G., and Jernigan R.L. How well can we understand large-scale protein motions using normal modes of elastic network models?. Biophys. J. 93 (2007) 920-929
    • (2007) Biophys. J. , vol.93 , pp. 920-929
    • Yang, L.1    Song, G.2    Jernigan, R.L.3
  • 57
    • 36849039429 scopus 로고    scopus 로고
    • A hierarchy of timescales in protein dynamics is linked to enzyme catalysis
    • Henzler-Wildman K.A., Lei M., Thai V., Kerns S.J., Karplus M., and Kern D. A hierarchy of timescales in protein dynamics is linked to enzyme catalysis. Nature 450 (2007) 913-916
    • (2007) Nature , vol.450 , pp. 913-916
    • Henzler-Wildman, K.A.1    Lei, M.2    Thai, V.3    Kerns, S.J.4    Karplus, M.5    Kern, D.6
  • 58
    • 33846847773 scopus 로고    scopus 로고
    • Conformational transitions of adenylate kinase: switching by cracking
    • Whitford P.C., Miyashita O., Levy Y., and Onuchic J.N. Conformational transitions of adenylate kinase: switching by cracking. J. Mol. Biol. 366 (2007) 1661-1671
    • (2007) J. Mol. Biol. , vol.366 , pp. 1661-1671
    • Whitford, P.C.1    Miyashita, O.2    Levy, Y.3    Onuchic, J.N.4
  • 59
    • 17544365232 scopus 로고    scopus 로고
    • Finite temperature string method for the study of rare events
    • E W., Ren W., and Vanden-Eijnden E. Finite temperature string method for the study of rare events. J. Phys. Chem. B. 109 (2005) 6688
    • (2005) J. Phys. Chem. B. , vol.109 , pp. 6688
    • Weinan, E.1    Ren, W.2    Vanden-Eijnden, E.3
  • 60
    • 45949108535 scopus 로고    scopus 로고
    • Finding transition pathways using the string method with swarms of trajectories
    • Pan A.C., Sezer D., and Roux B. Finding transition pathways using the string method with swarms of trajectories. J. Phys. Chem. B. 112 (2008) 3432
    • (2008) J. Phys. Chem. B. , vol.112 , pp. 3432
    • Pan, A.C.1    Sezer, D.2    Roux, B.3
  • 62
    • 0031576336 scopus 로고    scopus 로고
    • Torsion angle dynamics for NMR structure calculation with the new program Dyana
    • Güntert P., Mumenthaler C., and Wüthrich K. Torsion angle dynamics for NMR structure calculation with the new program Dyana. J. Mol. Biol. 273 (1997) 283-298
    • (1997) J. Mol. Biol. , vol.273 , pp. 283-298
    • Güntert, P.1    Mumenthaler, C.2    Wüthrich, K.3
  • 64
    • 10844247921 scopus 로고    scopus 로고
    • A modified TIP3P water potential for simulation with Ewald summation
    • Price D.J., and Brooks III C.L. A modified TIP3P water potential for simulation with Ewald summation. J. Chem. Phys. 121 (2004) 10096
    • (2004) J. Chem. Phys. , vol.121 , pp. 10096
    • Price, D.J.1    Brooks III, C.L.2
  • 65
    • 69449096502 scopus 로고    scopus 로고
    • Grubmüller, H. The Solvate Program Version 1.0. Web site
    • Grubmüller, H. The Solvate Program Version 1.0. Web site: http://www.mpibpc.mpg.de/groups/grubmueller/.
  • 66
    • 36749119973 scopus 로고
    • Deformable stochastic boundaries in molecular dynamics
    • Brooks III C.L., and Karplus M. Deformable stochastic boundaries in molecular dynamics. J. Chem. Phys. 79 (1983) 6312
    • (1983) J. Chem. Phys. , vol.79 , pp. 6312
    • Brooks III, C.L.1    Karplus, M.2
  • 67
    • 48749137581 scopus 로고
    • Stochastic boundary conditions for molecular dynamics simulations of ST2 water
    • Brünger A., Brooks III C.L., and Karplus M. Stochastic boundary conditions for molecular dynamics simulations of ST2 water. Chem. Phys. Lett. 105 (1984) 495-500
    • (1984) Chem. Phys. Lett. , vol.105 , pp. 495-500
    • Brünger, A.1    Brooks III, C.L.2    Karplus, M.3
  • 68
    • 0038792211 scopus 로고    scopus 로고
    • New analytic approximation to the standard molecular volume definition and its application to generalized Born calculations
    • Lee M.S., Feig M., Salsbury F.R., and Brooks III C.L. New analytic approximation to the standard molecular volume definition and its application to generalized Born calculations. J. Comput. Chem. 24 (2003) 1348-1356
    • (2003) J. Comput. Chem. , vol.24 , pp. 1348-1356
    • Lee, M.S.1    Feig, M.2    Salsbury, F.R.3    Brooks III, C.L.4
  • 69
    • 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
    • Mackerell A.D., Feig M., and Brooks III C.L. 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, A.D.1    Feig, M.2    Brooks III, C.L.3
  • 70
    • 33646940952 scopus 로고
    • Numerical integration of the Cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes
    • Ryckaert J.P., Ciccotti G., and Berendsen H.J. Numerical integration of the Cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J. Comput. Phys. 23 (1977) 327-341
    • (1977) J. Comput. Phys. , vol.23 , pp. 327-341
    • Ryckaert, J.P.1    Ciccotti, G.2    Berendsen, H.J.3
  • 71
    • 0030700726 scopus 로고    scopus 로고
    • Ligand-induced conformational changes in ras p21: a normal mode and energy minimization analysis
    • Ma J., and Karplus M. Ligand-induced conformational changes in ras p21: a normal mode and energy minimization analysis. J. Mol. Biol. 274 (1997) 114-131
    • (1997) J. Mol. Biol. , vol.274 , pp. 114-131
    • Ma, J.1    Karplus, M.2
  • 74
    • 69449102205 scopus 로고    scopus 로고
    • Sutanthavibul, S., Smith, B. V. & King, P. XFIG Drawing Program for the X Window System. Web site: http://www.xfig.org.
    • Sutanthavibul, S., Smith, B. V. & King, P. XFIG Drawing Program for the X Window System. Web site: http://www.xfig.org.


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.