Inherent structure analysis of protein folding
Article Abstract:
An investigation by the inherent structures (IS) of the multidimensional potential energy landscape is applied to 46 bead [beta]-barrel forming version (BLN model) which folds into a four-stranded [beta]-barrel to determine 239 199 IS states. It is concluded that poor foldability corresponds to a large misfolding interval where the excited state is more than that of the native state.
Publication Name: Journal of Physical Chemistry B
Subject: Chemicals, plastics and rubber industries
ISSN: 1520-6106
Year: 2007
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Influence of Go-like interactions on global shapes of energy landscapes in [beta]-barrel forming model proteins: inherent structure analysis and statistical temperature molecular dynamics simulation
Article Abstract:
The properties of Go-like protein models are examined in terms of the potential energy landscape (PEL). The alteration of the PEL has induced a significant change in the folding mechanism and the appearance of multiple van der Waals loops in the statistical temperature of the Go-like model is associated with the development of the intermediate states.
Publication Name: Journal of Physical Chemistry B
Subject: Chemicals, plastics and rubber industries
ISSN: 1520-6106
Year: 2008
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Simulating temperature jumps for protein folding
Article Abstract:
The folding thermodynamics and kinetics of a polyalanine peptide is demonstrated by using newly developed computational method. The nonequilibrium relaxation of the populations of peptide is derived by using a mix of very efficient sampling techniques (REMD) to properly populate ensembles and conventional MD simulations.
Publication Name: Journal of Physical Chemistry B
Subject: Chemicals, plastics and rubber industries
ISSN: 1520-6106
Year: 2008
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