Mechanism of thioredoxin-catalyzed disulfide reduction. Activation of the buried thiol and role of the variable active-site residues

Article Abstract:

The reaction mechanism of the thioredoxins (Trx)-catalyzed reduction of disulfides is studied by using the generalized gradient approximation (GGA) of density functional theory (DFT) and classical molecular dynamics (MD). The MD simulations of CGPC, CGGC and the corresponding wild-type Trx and P34G Trx have shown that the activity of the thioredoxin active-site (CXYC) is determined by the structural rigidity associated with particular variable residues (XY) and the number of amide N-H groups.

Analysis, Usage, Molecular dynamics, Oxidation-reduction reaction, Oxidation-reduction reactions, Density functionals, Density functional theory, Catalysis, Amides, Chemical properties, Thioredoxin

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Hot spot occlusion from bulk water: A comprehensive study of the complex between the lysozyme HEL and the antibody FVD1.3

Article Abstract:

A computational alanine-scanning mutagenesis method is used for decomposing the binding free energy difference in its different energetic factors in order to obtain a microscopic level, atomistic picture of hot spot solvation to verify the O-ring hypothesis. It is inferred that within a flexible, dynamic protein model the warm/hot spot residues are kept sheltered from the bulk solvent during the whole simulation, and all the outcomes confirm the O-ring hypothesis.

Observations, Crystallography, Alanine, Mutagenesis, Structure, Protein-protein interactions

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Theoretical study of the unusual protonation properties of the active site cysteines in thioredoxin

Article Abstract:

The hypothesis of proton sharing between the active site thiols is studied by performing a linear transit scan for the transfer of the proton between the active site cysteines. The influence of the solvent and the enzymatic structure in the stabilization of the thiolates are analyzed.

All Other Basic Organic Chemical Manufacturing, Industrial Organic Chemicals, Mercaptans, Thiols, Cysteine

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