Proteins simulation

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Zhou R and B J Berne 1995. A New Molecular Dynamics Method Combining the Reference Sys Propagator Algorithm with a Fast Multipole Method for Simulating Proteins and Ol Complex Systems. Journal of Chemical Physics 103 9444-9459. 

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Hansson T and J Aqvist 1995. Estimation of Binding Free Energies for HIV Proteinase Inhibitors b Molecular Dynamics Simulations. Protein Engineering 8 1137-1144. 

T Ichiye, M Karplus. Collective motions m proteins A covariance analysis of atomic fluctuations m molecular dynamics and normal mode simulations. Proteins Stiaict Eunct Genet 11 205-217, 1991. 

For 25 years, molecular dynamics simulations of proteins have provided detailed insights into the role of dynamics in biological activity and function [1-3]. The earliest simulations of proteins probed fast vibrational dynamics on a picosecond time scale. Fifteen years later, it proved possible to simulate protein dynamics on a nanosecond time scale. At present it is possible to simulate the dynamics of a solvated protein on the microsecond time scale [4]. These gains have been made through a combination of improved computer processing (Moore s law) and clever computational algorithms [5]. 

C Wilson, S Doniach. A computer model to dynamically simulate protein folding Studies with crambm. Proteins 6 193-209, 1989. 

AG Anderson, J Hermans. Microfoldmg Conformational probability map for the alanine dipeptide in water from molecular dynamics simulations. Proteins 3 262-265, 1988. 

Methylanaline could be transnitrosated with nitrite and S-nitrosocysteine and also by a simulated protein bound nitrite. In the latter case, an important factor was the local concentration of nitrosothiol groups on the matrix. The effects of S-nitrosocysteine as an inhibitor of lipid oxidation, as a color developer, and as an anticlostridial, have been reported recently in a turkey product (31). The Molar concentration of RSNO equating to 25 ppm nitrite gave similar results for color and inhibition of lipid oxidation but had less anti-clostridial activity. Transnitrosation between RSNO and heme protein was demonstrated. 

Biirgi R, Kollman PA, van Gunsteren WF (2002) Simulating proteins at constant pH An approach combining molecular dynamics and Monte Carlo simulation. Proteins 47 469-480. 

Colombo, G., Roccatano, D., and Mark, A. E. (2002). Folding and stability of the three-stranded beta-sheet peptide betanova Insights from molecular dynamics simulations. Proteins Strud. Fund. Genet. 46, 380—392. 

Oostenbrink, C. van Gunsteren, W.F., Free energies of binding of polychlorinated biphenyls to the estrogen receptor in a single simulation, Proteins 2004, 54, 237-246... 

Mangoni M, Roccatano D, Di Nola A. 1999. Docking of flexible ligands to flexible receptors in solution by molecular dynamics simulation. Proteins 35(2) 153-162. 

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Faraldo-Gomez, J.D., Forrest, L.R., Baaden, M., Bond, P.J., Domene, C., Patargias, G., Cuthbertson, J., Sansom, M.S.P. Conformational sampling and dynamics of membrane proteins from 10-nanosecond computer simulations. Proteins Struct. Funct. Bioinformatics 2004, 57, 783-91. 

In Figs. 7, we show the secondary structure of the simulated protein in solution and compare it against that obtained from the crystalline sample. We observed that the secondary structure of the simulated sample is essentially identical to the crystal structure, except for a marginal difference in the ft segment of the protein. 

Hamelberg D, Mongan J, McCammon JA (2004) Enhanced sampling of conformational transitions in proteins using full atomistic accelerated molecular dynamics simulations. Protein Sci 13 76-76... 

Li C, Shen J, Li W et al (2011) Possible ligand release pathway of dipeptidyl peptidase IV investigated by molecular dynamics simulations. Proteins 79(6) 1800-1809... 

Ponder JW, DA Case (2003) Force fields for protein simulations. Protein Sim. Adv. Protein Chem. 66 27... 

Ferrara P, J Apostolakis, A Caflisch (2002) Evaluation of a fast implicit solvent model for molecular dynamics simulations. Proteins Struct., Funct., Genet. 46 (1) 24—33... 

Wang W, Wang J, Kollman PA (1999) What determines the van der Waals coefficient 3 in die LIE (linear interaction energy) method to estimate binding free energies using molecular dynamic simulation, Proteins, 34 395 102... 

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