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.

Potential energy

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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.

Molecular dynamics, Protein research, Van der Waals forces

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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.

Thermal properties, Alanine, Dynamics, Dynamics (Mechanics), Mechanical properties, Structure

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