Proteins folding-unfolding dynamics

V Daggett, M Levitt. Protein folding <-> unfolding dynamics. Cuit Opm Stiaict Biol 4 291-295, 1994. 

Here we outline several issues that we feel are important to consider when designing or critically reviewing MD simulations of protein folding unfolding dynamics. This section lists the specific methods and rationales employed in our simulations and each is discussed in light of its importance to the accurate representation of protein dynamics. 

V. Daggett and M. Levitt, Curr. Opin. Struct. Biol., 4, 291 (1994). Protein Folding<. Unfolding Dynamics. 

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

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Qu KB, Vaughn JL, Sienkiewicz A, Scholes CP, Fetrow IS (1997) Kinetics and motional dynamics of spin-labeled yeast iso-1-cytochrome c.l. Stopped-flow electron paramagnetic resonance as a probe for protein folding/unfolding of the C-terminal helix spin-labeled at cysteine 102. Biochemistry 36 2884—2897... 

Apuy, J.L., Park, Z.-Y, Swartz, P.D., Dangott, L.J., Russell, D.H., Baldwin, TO. (2001) Pulsed-alkylation Mass Spectrometry for the Study of Protein Folding and Dynamics Development and Application to the Study of a Folding/Unfolding Intermediate of Bacterial Luciferase. Biochemistry 40 15153-15163. 

D. A. C. Beck and V. Daggett, Methods, 34,112 (2004). Methods for Molecular Dynamics Simulations of Protein Folding/Unfolding in Solution. 

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