Modeling the interplay between geometrical and energetic effects in protein folding

Article Abstract:

A free-energy functional model is generalized by introducing cooperativity into the configurationally entropy and the internal energy based on polymer theory to make appropriate for comparison with protein folding simulations and experiments. Modifications to configurational entropy enable the model to account for loop-loop interactions, a contribution neglected in the original model.

Protein research, Entropy (Physics), Entropy (Thermodynamics)

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Effects of crowding and confinement on the structures of the transition state ensemble in proteins

Article Abstract:

The effect of macromolecular crowding and confinement on the changes in the transition state structures in comparison to bulk which was studied by using two variants of a coarse-grained model of the three-stranded [beta]-sheet WW domain and a fully automated progress variable clustering (PVC) algorithm is presented.

Analysis, Lipoproteins, Blood lipoproteins, Amino acid sequence, Amino acid sequencing, Structure, Chemical properties, Transition state (Chemistry), Proteolipids, Van der Waals forces

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Exploring the interplay between topology and secondary structural formation in the protein folding problem

Article Abstract:

Simple models with a single bead representation (C(sub alpha) models) helps in understanding the folding mechanism of small globular proteins. A minimalist representation of protein structures is used to investigate the competition between native side-chain contacts and nonspecific backbone hydrogen bonds.

Usage, Observations, Protein structure, Hydrogen bonding, Hydrogen bonds

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