Analyzing different parameters of steered molecular dynamics for small membrane interacting molecules

Journal of Molecular Graphics and Modelling

Volumn 24, Issue 1, 2005, Pages 59-71

  Lorenzo, Alicia C ^a   Bisch, Paulo M ^b  

^a INSTITUTO OSWALDO CRUZ   (Brazil)

^b FEDERAL UNIVERSITY OF RIO DE JANEIRO   (Brazil)

Author keywords

Membrane interacting systems; Non specific interaction forces; Simulation parameters; Steered molecular dynamics simulations

Indexed keywords

APPROXIMATION THEORY; COMPUTER SIMULATION; CORRELATION METHODS; ELECTROSTATICS; MATHEMATICAL MODELS; MEMBRANES; MOLECULES; PARAMETER ESTIMATION; POLARIZATION;

MEMBRANE-INTERACTING SYSTEMS; NON-SPECIFIC INTERACTION FORCES; SIMULATION PARAMETERS; STEERED MOLECULAR DYNAMICS SIMULATIONS;

MOLECULAR DYNAMICS;

PEPTIDE; TRYPTOPHAN;

ANALYTIC METHOD; ARTICLE; CORRELATION FUNCTION; DIELECTRIC CONSTANT; MEMBRANE; METHODOLOGY; MODEL; MOLECULAR DYNAMICS; PARAMETER; POLARIZATION; PRIORITY JOURNAL; REACTION ANALYSIS; SIMULATION;

EID: 24944490045     PISSN: 10933263     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmgm.2005.05.005     Document Type: Article

References (36)

1. H. Grubmüller, B. Heymann, and P. Tavan Ligand binding: molecular mechanics calculation of streptavidin-biotin rupture force Science 271 1996 997 999
2. S. Izrailev, S. Stepaniants, M. Balsera, Y. Oono, and K. Schulten Molecular dynamics of unbinding of the avidin-biotin complex Biophys. J. 72 1997 1568 1581
3. B. Isralewitz, M. Gao, and K. Schulten Steered molecular dynamics and mechanical functions of proteins Curr. Opin. Struct. Biol. 11 2001 224 230
4. S-J. Marrink, O. Berger, P. Tieleman, and F. Jähnig Adhesion forces of lipids in a phospholipid membrane studied by molecular dynamics simulations Biophys. J. 74 1998 931 943
5. S. Izrailev, A.R. Crofts, E.A. Berry, and K. Schulten Steered molecular dynamics simulation of the rieske subunit motion in the cytochrome bc1 complex Biophys. J. 77 1999 1753 1768
6. B. Heymann, and H. Grubmüller ANO2/DNP-happen unbinding forces studied by molecular dynamics atomic force microscopy simulations Chem. Phys. Lett. 303 1999 1 9
7. H. Lu, B. Isralewitz, A. Krammer, V. Vogel, and K. Schulten Unfolding of titin immunoglobulin domains by steered molecular dynamics simulation Biophys. J. 75 1998 662 671
8. M.V. Bayas, K. Schulten, and D. Leckband Forced detachment of the CD2-CD58 complex Biophys. J. 84 2003 2223 2233
9. A.C. Lorenzo, and E.R. Caffarena Elastic properties-Young's modulus determination and structural stability of the tropocollagen molecule: a computational study by Steered Molecular Dynamics J. Biomech. 65/7 2005 1527 1533
10. H. Jäckle, and P.L. Luisi Conformational study of histidine- and tryptophan-containing peptides in solution based upon the combination of nuclear magnetic resonance, circular dichroism, and fluorescence measurements J. Phys. Chem. 88 1984 1767 1777
11. 2] oxytocin Biochemistry 31 1992 1585 1594
12. J.W. Ponder, and F.M. Richards Tertiary templates for proteins. Use of packing criteria in the enumeration of allowed sequences for different structural classes J. Med. Biol. 193 1987 775 791
13. R.A. Engh, L.X.Q. Chen, and G.R. Fleming Conformational dynamics of tryptophan: a proposal for the origin of the non-exponential florescence decay Chem. Phys. Lett. 126 3/4 1986 365 372
14. H.L. Gordon, H.C. Jarrell, A.G. Szabo, K.J. Willis, and R.L. Somorjai Molecular dynamics simulations of the conformational dynamics of tryptophan J. Phys. Chem. 96 4 1992 1915 1921
15. P.G. Pascutti, E.P.G. Areas, A.S. Ito, K.C. Mundin, and P.M. Bisch Molecular dynamics of peptides at membrane-water interfaces Progress Biophys. Mol. Biol. 65 Suppl. 1 1996 49
16. W.C. Wimley, K. Gawrisch, T.P. Creamer, and S.H. White Direct measurements of salt-bridge energies using a peptide model system: Implications for protein stability Proc. Natl. Acad. 93 1996 2985 2990
17. W.C. Wimley, T.P. Creamer, and S.H. White Solvation energies of amino acid side chains and backbone in a family of host-guest pentapeptides Biochemistry 35 1996 5109 5124
18. W.C. Wimley, and S.H. White Experimentally determined hydrophobicity scale for proteins at membrane interfaces Nat. Struct. Biol. 3 1996 842 848
19. E.P.G. Arêas, P.G. Pascutti, S. Schreier, K.C. Mundim, and P.M. Bisch Molecular dynamics simulations of signal sequence at a membrane/water interface J. Phys. Chem. 99 1995 14882
20. P.G. Pascutti, K.C. Mundim, A.S. Ito, and P.M. Bisch Polarization effects on peptide conformations at water-membrane interface by molecular dynamics simulation J. Comp. Chem. 20 9 1999 971 982
21. A.C. Lorenzo, P.G. Pascutti, and P.M. Bisch Non-specific interaction forces at water-membrane interface by forced molecular dynamics simulations J. Comp. Chem. 24 2003 328 339
22. W.F. van Gunsteren, and H.J.C. Berendsen Groningen Molecular Simulation (GROMOS) Library Manual 1987 Biomos Groningen
23. W.R.P. Scott, P.H. Hunenberger, I.G. Tironi, A.E. Mark, S.R. Billeter, J. Fennen, A.E. Torda, T. Huber, P. Kruger, and W.F. van Gunsteren The GROMOS biomolecular simulation program package J. Phys. Chem. 103 1999 3596 3607
24. J.N. Israelachvilli Intermolecular and Surface Forces 2nd ed. 1991 Academic Press
25. M. Uematsu, and E.U. Franck J. Phys. Chem. 9 1980 1291 1306
26. C. Tandford The Hydrophobic Effect 1973/1980 Wiley New York
27. J.R. Reizt, F.J. Milford, and R.W. Christy Foundations of Electromagnetic Theory 1967 Addison-Wesley Reading, MA
28. J.D. Jackson Classical Electrodynamics 1962 Wiley New York
29. P.G. Pascutti, M.M. Cassiano, A.S. Ito, K.C. Mundin, and P.M. Bisch Molecular dynamics simulations of peptides-membrane interactions Biophys. J. 72 2 1997 196
30. P.G. Pascutti, L.J. El-Jaik, K.C. Mundim, A.S. Ito, and P.M. Bisch Molecular dynamics simulation of α-melanocyte stimulating hormone in a water-membrane model interface Eur. Biophys. J. 28 1999 499 509
31. F.S. Leite, P.G. Pascutti, and C.B. Anteneodo Molecular modeling and dynamics of the sodium channel inactivation gate Biophys. J. 82 3 2002 1207 1215
32. K.B. Wiberg A scheme for strain energy minimization. Application to the cycloalkanes J. Am. Chem. Soc. 87 5 1965 1070 1078
33. H.J.C. Berendsen, J.P.M. Postma, W.F. van Gunstern, A. DiNola, and J.R. Haak Molecular dynamics with coupling to an external bath J. Chem. Phys. 81 1984 3684 3690
34. M. Balsera, S. Stepaniants, S. Izrailev, Y. Oono, and K. Schulten Reconstructing potential energy functions from simulated force-induced unbinding processes Biophys. J. 73 1997 1281 1287
35. E. Evans, and K. Ritchie Dynamic strength of molecular adhesion bonds Biophys. J. 72 1997 1541 1555
36. M.P. Aliste, J.L. MacCallum, and D.P. Tieleman Molecular dynamics simulations of pentapeptides at interfaces: salt bridge and cation-π interactions Biochemistry 42 2003 8976 8987