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Use of MM-PB/SA in estimating the free energies of proteins: Application to native, intermediates, and unfolded villin headpiece by Matthew R. Lee; Yong Duan; Peter A. Kollman is a Biochemistry, Genetics and Molecular Biology article available to read on EtoBox.

What is Use of MM-PB/SA in estimating the free energies of proteins: Application to native, intermediates, and unfolded villin headpiece about?

We investigated the stability of three different ensembles of the 36-mer villin headpiece subdomain, the native, a compact folding intermediate, and the random coil. Structures were taken from a 1-s molecular dynamics folding simulation and a 100-ns control simulation on the native structure. Our approach for each conformation is to first determine the solute internal energy from the molecular mechanics potential and then to add the change resulting from solvation (⌬G solv ). Explicit water was used to run the simulation, and a continuum model was used to estimate ⌬G solv with the finite difference Poisson-Boltzmann model accounting for the polarization part and a linearly surface area-dependent term for the non-polar part. We leave out the solute vibrational entropy from these values but demonstrate that there is no statistical difference among the native, folding intermediate, and random coil ensembles. We find the native ensemble to be Ϸ26 kcal/mol more stable than the folding intermediate and Ϸ39 kcal/mol more stable than the random coil ensemble. With an experimental estimate for the free energy of denaturation equal to 3 kcal/mol, we approximate the non-native degeneracy to l

Who reads Use of MM-PB/SA in estimating the free energies of proteins: Application to native, intermediates, and unfolded villin headpiece?

Author

Matthew R. Lee; Yong Duan; Peter A. Kollman

Publisher

John Wiley and Sons; Wiley (John Wiley & Sons); Wiley-Liss Inc; Wiley (ISSN 0887-3585)

Published

2000

Language

EN

Field

Biochemistry, Genetics and Molecular Biology (Life Sciences)