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.
Publication Name: Journal of Physical Chemistry B
Subject: Chemicals, plastics and rubber industries
ISSN: 1520-6106
Year: 2000
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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.
Publication Name: Journal of Physical Chemistry B
Subject: Chemicals, plastics and rubber industries
ISSN: 1520-6106
Year: 2000
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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.
Publication Name: Journal of Physical Chemistry B
Subject: Chemicals, plastics and rubber industries
ISSN: 1520-6106
Year: 2005
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