Hydrophobic aided replica exchange: An efficient algorithm for protein folding in explicit solvent

Article Abstract:

The hydrophobic aided replica exchange method (HAREM) is introduced to accelerate the simulation of all-atom protein folding in explicit solvent. The method is applied to a small representative protein, the alpha-helix 3K(I), and it is found that the HAREM method successfully folds the protein with 4 ns, while the regular replicas exchange method does not fold the same protein within 5 ns, even with many more replicas.

Protein folding, Hydrophobic effect

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Exploring bovine pancreatic trypsin inhibitor phase transitions

Article Abstract:

An investigation of the phase diagram of bovine pancreatic trypsin inhibitor (BPT1)/350 mM KSCN at pH 4.9 by direct observation and numerical simulations is presented. It is found that the solubility of the chloride-like hexagonal polymorph is reverse with temperature and the monoclinic is direct, with solubility curves crossing at 12 degree Celsius.

Proteins, Protein structure, Monomers

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Structure and dynamics of the solvation of bovine pancreatic trypsin inhibitor in explicit water: A comparative study of the effects of solvent and protein polarizability

Article Abstract:

The results of molecular dynamics simulations of the bovine pancreatic trypsin inhibitor (BPTI) in water with force fields that explicitly include polarization for both the protein and the water are presented. The findings reveal that the solvating water's relaxation is most affected when both the protein and the water models are polarizable.

Science & research, Research, Molecular dynamics, Solvents

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