Molecular dynamics simulations of peptides

Hermans, J., Yun, R. H., Anderson, A. G. Precision of free-energies calculated by molecular dynamics simulations of peptides in solution. J. Comp. Chem. 13 (1992) 429-442... 

Smith, L.J., Mark, A. E., Dobson, C.M. and Gursten, W. F. (1998) Molecular dynamic simulation of peptide fragments from hen lysozyme insight into non-native protein conformation./. Mol. Biol. 280, 703-719. 

Fig. 3. Molecular dynamics simulations of peptide fragments corresponding to the predicted secondary structure in Fig. 2. H2.5 was discovered while trying to model the missing residues from the PrP prediction. All simulations began with the peptide in the a-helical conformation, and the average percentage of helix over the 2 ns simulation is given.

Zhang, Z., Shi, Y, Liu, H. Molecular dynamics simulations of peptides and proteins with amplified collective motions, Biophys. J. 2003, 84, 3583. 

Free Energies Calculated by Molecular Dynamics Simulations of Peptides in Solution. 

J. Hermans, R. H. Yun, and A. G. Anderson,/. Comput. Chem., 13, 429 (1992). Precision of Free Energies Calculated by Molecular Dynamics Simulations of Peptides in Solution. 

Y. Wang and K. Kuczera. Molecular dynamics simulations of cyclic and linear DPDPE Influence of the disulfide bond on peptide fiexibility. J. Phys. Chem., 100 2555-2563, 1996. 

Wilkes BC, Schiller PW. Molecular dynamics simulations of opioid peptide analogs containing multiple conformational restrictions. Int J Peptide Protein Res 1992 40 249-254. 

The unfolded states of eight different peptides, sampled in a corresponding number of molecular dynamics simulations of reversible peptide folding in solution under equilibrium conditions, are analyzed in this section (see Table I). 

Santiveri, C. M., Jimenez, M. A., Rico, M., van Gunsteren, W. F., and Daura, X. (2002). /3-Hairpin folding and stability Molecular dynamics simulations of designed peptides in aqueous solution. Submitted. 

Tirado-Rives ). and Jorgensen W. L. Molecular dynamics simulations of the unfolding of an alpha-helical analogue of ribonuclcase A S-peptide in water. Biochemistry (1991) 30(16) 3864-71. 

Yarovsky, L, Aguilar, M.I., and Hearn, M.T.W., High-performance liquid-chromatography of amino-acids, peptides and proteins. 125. Molecular-dynamics simulation of n-butyl chains chemically bonded to sihca-based reversed-phase high-performance liquid-chromatography sorbents, 7. Chromatogr. A, 660, 75, 1994. 

Nguyen HD, Hall CK (2004) Molecular dynamics simulations of spontaneous fibril formation by random-coil peptides. Proc. Natl. Acad. Sci. USA 101 16180-16185... 

Sung SS, Wu XW. Molecular dynamics simulation of synthetic peptide folding. Proteins Struct Funct Genet 1996 25 202-214. 

An important question regarding peptides and proteins is concerned with the equilibria among several conformational states. It has been suggested that enzyme function may be linked to the occurrence of particular conformations in solution.24 377 A mechanism recently proposed for the hydrolysis of oligosa-charides by the enzyme lysozyme, for example, is based on the observation of specific substrate and enzyme sidechain conformations in a molecular dynamics simulation of a lysozyme-substrate complex.378 Also, local conformational equilibria and the barriers between conformations are important in determining the rates and mechanisms of folding and rebinding processes. 

T Nonequilibrium Molecular Dynamics Simulation of Photoinduced Energy Flow in Peptides Theory Meets Experiment... 

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