Protein Folding Pathways

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Liwo A, Khalili M, Scheraga HA (2005) Ab initio simulations of protein-folding pathways by molecular dynamics with the united-residue model of polypeptide chains. Proc. Natl. Acad. Sci. 

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Hilser, V. J. Freire, E. (1996a). Predicting the Equilibrium Protein Folding Pathway Structure-Based Analysis of Staphylococcal Nuclease. Proteins In Press. 

Sampling Kinetic Protein Folding Pathways using All-Atom Models... 

P.G. Bolhuis Sampling Kinetic Protein Folding Pathways using All-Atom Models, Lect. Notes Phys. 703, 393-433 (2006)... 

N. M. Amato, G. Song (2002) Using motion planning to study protein folding pathways. J. Comput. Biol. 9, pp. 149-168... 

An instructive parallel may be drawn between the identification and characterization of electron transfer pathways and the identification and characterization of protein folding pathways (199-202). In the simplest cases, both processes are intramolecular and involve a transition between an initial and final state. An advantage to understanding electron transfer pathways is that both states are structurally ordered, whereas protein folding converts a disordered initial state into a structurally ordered final state. In both situations, a number of mechanisms for this transition have been envisioned, ranging from a few dominant pathways to many, different pathways. The challenge in both cases is to develop experimental approaches that will define and enumerate the number of pathways. 

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