Sobolev E.V., Danilkovich A.V., Tikhonov D.A.
RISM integral equation theory in study of thermodynamics of self-assembling ionic peptides
Mathematical Biology & Bioinformatics. 2012;7(2):493-507.
doi: 10.17537/2012.7.493.
References
- Honig B, Sharp K, Yang AS. Macroscopic models of aqueous solutions: biological and chemical applications. The Journal of Physical Chemistry. 1993;97:1101–1109. doi: 10.1021/j100108a002
- Still WC, Tempczyk A, Hawley RC, Hendrickson T. Semianalytical treatment of solvation for molecular mechanics and dynamics. Journal of the American Chemical Society. 1990;112:6127–6129. doi: 10.1021/ja00172a038
- Onufriev A, Bashford D, Case DA. Modification of the Generalized Born Model Suitable for Macromolecules. The Journal of Physical Chemistry B. 2000;104:3712–3720. doi: 10.1021/jp994072s
- Chandler D, Andersen HC. Optimized Cluster Expansions for Classical Fluids. II. Theory of Molecular Liquids. Journal of Chemical Physics. 1972;57:1930–1937.
- Kitao A, Hirata F, Go N. Effects of solvent on the conformation and the collective motions of a protein. 3. Free energy analysis by the extended RISM theory. The Journal of Physical Chemistry. 1993;97:10231–10235. doi: 10.1021/j100141a053
- Tikhonov DA, Polozov RV, Timoshenko EG, Kuznetsov YuA, Gorelov AV, Dawson KA. Hydration of a B–DNA fragment in the method of atom–atom correlation functions with the reference interaction site model approximation. Journal of Chemical Physics. 1998;109(4):1528-539. doi: 10.1063/1.476704
- Kinoshita M, Okamoto Y, Hirata F. Solvent effects on conformational stability of peptides: RISM analyses. Journal of Molecular Liquids. 2001;90:195–204. doi: 10.1016/S0167-7322(01)00122-2
- Sobolev EV, Tikhonov DA, Freedman H, Truong TN. Application of the RISM Method to Estimate the Relative Gibbs Free Energies of 4',6-Diamidino-2-phenylindole Binding Within the Minor Groove of a DNA Along Simulation Trajectory. Mathematical Biology and Bioinformatics. 2010;5:98–113 (in Russ.). doi: 10.17537/2010.5.98
- Tikhonov DA, Sobolev EV. Estimating the Gibbs energy of hydration from molecular dynamics trajectories obtained by integral equations of the theory of liquids in the RISM approximation. Russian Journal of Physical Chemistry A. 2011;85(4):654-659. doi: 10.1134/S0036024411030307
- Tikhonov DA, Sobolev EV. An Averaged Over Molecular Trajectories Method of Integral Equations of the Theory of Liquids in RISM Approximation. Mathematical Biology and Bioinformatics. 2010;5:188–201 (in Russ.). doi: 10.17537/2010.5.188
- Tikhonov DA, Sobolev EV. Method of Pseudoaveraged Functions in the RISM Theory. Temperature Dependence of Oxytocin Peptide Hydration. Mathematical Biology and Bioinformatics. 2010;5:202–214 (in Russ.). doi: 10.17537/2010.5.202
- Kovalenko A, Hirata F. Hydration free energy of hydrophobic solutes studied by a reference interaction site model with a repulsive bridge correction and a thermodynamic perturbation method. Journal of Chemical Physics. 2000;113:2793–2805. doi: 10.1063/1.1305885
- Danilkovich AV, Tikhonov DA, Sobolev EV, Shadrina TE, Udovichenko IP. Considering usage of different force-fields for molecular dynamic studies of the ionic peptides and their dimers. Mathematical Biology and Bioinformatics. 2011. 6(1):53–62 (in Russ.). doi: 10.17537/2011.6.53
- Danilkovich AV, Sobolev EV, Tikhonov DA, Udovichenko IP, Lipkin VM. Distinctive H–(RLDL)4–OH Peptide Complexes Potentiate Nanostructure Self-Assembling in Water. Doklady Biochemistry and Biophysics. 2012;443:96–99. doi: 10.1134/S160767291202010X
- Zhang S. Fabrication of novel biomaterials through molecular self-assembly. Nature Biotechnology. 2003;21:1171–1178. doi: 10.1038/nbt874
- Hsieh PCH, Davis ME, Gannon J, MacGillivray C, Lee RT. Controlled delivery of PDGF-BB for myocardial protection using injectable self-assembling peptide nanofibers. Journal of Clinical Investigations. 2006;116:237–248. doi: 10.1172/JCI25878
- Ellis-Behnke RG, Liang Y-X, You S-W, Tay DKC, Zhang S, So K-F, Schneider GE. Nano neuro knitting: Peptide nanofiber scaffold for brain repair and axon regeneration with functional return of vision. Proceedings of National Academy of Sciences of the USA. 2006;103:5054–5059. doi: 10.1073/pnas.0600559103
- Hirata F, Rossky PJ, Pettitt BM. The interionic potential of mean force in a molecular polar solvent from an extended RISM equation. Journal of Chemical Physics. 1983;78:4133–4144. doi: 10.1063/1.445090
- Kovalenko A, Hirata F. Self-consistent description of a metal–water interface by the Kohn–Sham density functional theory and the three-dimensional reference interaction site model. Journal of Chemical Physics. 1999;110:10095–10112. doi: 10.1063/1.478883
- Lue L, Blankschtein D. Llquld-State Theory of Hydrocarbon-Water Systems: Application to Methane, Ethane, and Propane. The Journal of Physical Chemistry. 1992;96:8582–8594. doi: 10.1021/j100200a069
- Singer SJ, Chandler D. Free energy functions in the extended RISM approximation. Molecular Physics. 1985;55:621–625. doi: 10.1080/00268978500101591
- Chandler D, Singh Y, Richardson DM. Excess electrons in simple fluids. I. General equilibrium theory for classical hard sphere solvents. Journal of Chemical Physics. 1984;81:1975–1982. doi: 10.1063/1.447820
- Ten-no S, Iwata S. On the connection between the reference interaction site model integral equation theory and the partial wave expansion of the molecular Ornstein–Zernike equation. Journal of Chemical Physics. 1999;111:4865–4868. doi: 10.1063/1.479746
- Ten-no S. Free energy of solvation for the reference interaction site model: Critical comparison of expressions. Journal of Chemical Physics. 2001;115:3724–3731. doi: 10.1063/1.1389851
- HyperChem® Computational Chemistry. Practical Guide – Theory and Method, HC 70-00-04-00. Gainesville: Hypercube Inc, 2002. 350 p.
- Macindoe G, Mavridis L, Venkatraman V, Devignes M-D, Ritchie DW. HexServer: an FFT-based protein docking server powered by graphics processors. Nucleic Acids Research. 2010;38:445–449. doi: 10.1093/nar/gkq311
- Tovchigrechko A, Vakser IA. Development and testing of an automated approach to protein docking. Proteins. 2005;60:296–301. doi: 10.1002/prot.20573
- Case DA, Cheatham TE III, Darden T, Gohlke H, Luo R, Merz KM, Onufriev A, Simmerling C, Wang B, Woods RJ. The Amber biomolecular simulation programs. Journal of Computational Chemistry. 2005;26:1668–1688. doi: 10.1002/jcc.20290
- Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW, Klein ML. Comparison of simple potential functions for simulating liquid water. Journal of Chemical Physics. 1983;79:926–935. doi: 10.1063/1.445869
- Duan Y, Wu C, Chowdhury S, Lee MC, 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. Journal of Computational Chemistry. 2003;24:1999–2012. doi: 10.1002/jcc.10349
|
|
|