Comparative study of the folding free energy landscape of a three-stranded beta-sheet protein with explicit and implicit solvent models

Article Abstract:

The PMF surface for the folding of a designed three-stranded beta-sheet protein Betanova by all-atom molecular dynamics (MD) simulations is investigated, applying two solvation models, explicit TIP3P water and implicit Generalized Born (GB) with a dielectric constant near that of water. Results indicate that the GB solvent model is sufficient for studying the folding thermodynamics of small polypeptides.

Polypeptides

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Are Many-Body effects Important in Protein Folding?

Article Abstract:

The importance of many-body and nonclassical effects, such as polarization and char ge transfer, on the folding of the beta nova protein is studied. The folding is accurately described by effective two-body potentials, despite the absence of explicit polarization and charge transfer in these models, is indicated.

Research and Development in the Physical, Engineering, and Life Sciences, Physical Sciences, Protein binding, Charge transfer

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A minimal model of three-state folding dynamics of helical proteins

Article Abstract:

A diffusion-collision-like model is described for helical proteins with three-folding dynamics. The model allows satisfactory calculation of the folding rate and reconstruction of the salient steps of the folding pathway of two proteins with three-state folding.

Collisional excitation

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