Molecular dynamics protein folding

De Mori, G.M.S., Colombo, G., Micheletti, C. Study of the villin headpiece folding dynamics by combining coarse-grained Monte Carlo evolution and all-atom molecular dynamics. Protein. Struct. Funct. Genet. 2005, 58, 459-71. 

G. Ramachandran and T. Schlick. Beyond optimization Simulating the dynamics of supercoiled DNA by a macroscopic model. In P. M. Pardalos, D. Shal-loway, and G. Xue, editors. Global Minimization of Nonconvex Energy Functions Molecular Conformation and Protein Folding, volume 23 of DIM ACS Series in Discrete Mathematics and Theoretical Computer Science, pages 215-231, Providence, Rhode Island, 1996. American Mathematical Society. 

One drawback to a molecular dynamics simulation is that the trajectory length calculated in a reasonable time is several orders of magnitude shorter than any chemical process and most physical processes, which occur in nanoseconds or longer. This allows yon to study properties that change w ithin shorter time periods (such as energy finctnations and atomic positions), but not long-term processes like protein folding. 

Although the folding of short proteins has been simulated at the atomic level of detail [159,160], a simplified protein representation is often applied. Simplifications include using one or a few interaction centers per residue [161] as well as a lattice representation of a protein [162]. Some methods are hierarchical in that they begin with a simplified lattice representation and end up with an atomistic detailed molecular dynamics simulation [163]. 

M Levitt. Protein folding by constrained energy minimization and molecular dynamics. J Mol Biol 170 723-764, 1983. 

A Caflisch, M Karplus. Molecular dynamics studies of protein and peptide folding and unfolding. In K Merz Jr, S Le Grand, eds. The Protein Eoldmg Problem and Tertiary Structure Prediction. Boston Birkhauser, 1994, pp 193-230. 

Presently, only the molecular dynamics approach suffers from a computational bottleneck [58-60]. This stems from the inclusion of thousands of solvent molecules in simulation. By using implicit solvation potentials, in which solvent degrees of freedom are averaged out, the computational problem is eliminated. It is presently an open question whether a potential without explicit solvent can approximate the true potential sufficiently well to qualify as a sound protein folding theory [61]. A toy model study claims that it cannot [62], but like many other negative results, it is of relatively little use as it is based on numerous assumptions, none of which are true in all-atom representations. 

Dokholyan NV, Buldyrev SV, Stanley HE, Shakhnovich El. Discrete molecular dynamics studies of the folding of a protein-like model. Fold Des 1998 3 577-87. 

Gsponer J, Caflisch A. Molecular dynamics simulations of protein folding from the transition state. Proc Natl Acad Sci USA 2002 99 6719-24. 

Beck DAC, Daggett V. Methods for molecular dynamics simulations of protein folding/unfolding in solution. Methods 2004 34 112-20. 

Keywords Molecular dynamics, pAT. Protein folding, pH-dependent conformational change... 

Sugita Y, Okamoto Y (1999) Replica-exchange molecular dynamics method for protein folding. Chem Phys Lett 314 141—151. 

Three theory papers are also included. Determinants of the Polyproline II Helix from Modeling Studies by Creamer and Campbell reexamines and extends an earlier hypothesis about Pn and its determinants. Hydration Theory for Molecular Biophysics by Paulaitis and Pratt discusses the crucial role of water in both folded and unfolded proteins. Unfolded State of Peptides by Daura et al. focuses on the unfolded state of peptides studied primarily by molecular dynamics. 

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. 

Daggett, V. (2002). Molecular dynamics simulations of the protein unfolding/folding reaction. Acc. Chem. Res. 35, 422-429. Available at http //pubs.acs.org. 

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