The influence of different treatments of electrostatic interactions on the thermodynamics of folding of peptides

Article Abstract:

Replica exchange molecular dynamics simulations were performed to investigate the effects of different electrostatic treatments on the structure and thermodynamics of a small beta-hairpin forming peptide. Simulations on the beta-hairpin forming peptide and on additional control peptides indicate that generalized reaction field treatment of electrostatics offers a satisfactory compromise between accuracy and computational speed for the identification of low-energy conformations.

Peptides, Mechanical properties

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Folding of the 25 residue A[beta](12-36) peptide in TFE/Water: Temperature-dependent transition from a funneled free-energy landscape to a rugged one

Article Abstract:

The multicanonical molecular dynamics simulations were used to determine the free-energy landscape of the Alzheimer [beta]-amyloid peptide A[beta](12-36) in a 2,2,2-trifluoroethanol (TFE)/water solution. The analysis has shown that hydrogen bond formation between TFE and A[beta] was increased with decreasing temperature, while that between water and A[beta] was depressed.

Observations, Amyloid beta-protein, Hydrogen bonding, Hydrogen bonds, Chemical properties

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Ultrafast folding of a computationally designed Trp-cage mutant: Trp2-cage

Article Abstract:

Miniproteins provide useful model systems for understanding the principles of protein folding and design and these proteins also serve as useful test cases for theories of protein folding. A computationally designed mutant of the 20-residue Trp-cage miniprotein, Trp2-cage, is presented.

Monte Carlo method, Monte Carlo methods, Circular dichroism

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