Molecular dynamics study to investigate the effect of chemical substitutions of methionine 35 on the secondary structure of the amyloid [beta] (A[beta](1-42)) monomer in aqueous solution

Article Abstract:

Conformational changes in the electronic properties of the chemical group attached to the [C.sub.[gamma]]-methylene of methionine 35(Met35) are investigated by molecular dynamic simulation of amyloid [beta](A[beta](1-42)) monomer in aqueous solution. The oxidation of Met35 not only decreases the residue's hydrophobicity, but also its interaction with surrounding residues and water, resulting in changes in the structure of the C-terminus hydrophobic region.

Aqueous solution reactions, Atomic properties

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Ab initio and empirical model MD simulation studies of solvent effects on the properties of N-methylacetamide along the cis-trans isomerization pathway

Article Abstract:

The properties of N-methylacetamide along a cis-trans isomerization pathway reported by twisting about the C(O)-N bond are investigated at finite temperature both in vacuo and in explicit water solvent. The electronic structure of the NMA molecule predicted by the ab initio method along the reaction coordinate is analyzed to understand the changes in peptide 'partial-double' bond character [C(O)-N] as isomerization takes place.

Isomerization, Solvents

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Can proteins and crystals self-catalyze methyl rotations?

Article Abstract:

The chi(C(sub alpha)-C(sub beta) torsional barrier in the dipeptide alanine (N-methyl-L-alanyl-N-methylamide) crystal was investigated using ab initio calculations at various levels of theory, molecular mechanics, and molecular dynamics. It is suggested that environment-catalyzed rotation of methyl groups can occur both in the solid phase and in native biological structures, though the effect might be temperature-dependent.

Alanine

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