A molecular dynamics study of the correlations between solvent-accessible surface, molecular volume, and folding state

Article Abstract:

A molecular dynamics study is conducted to analyze the correlations between the nuclear volume, solvent-accessible surface and the folding state of various unfolded conformers of a [alpha] or a [beta] protein with any helical peptide. The results prove that the unfolded conformations need not be necessarily extended, as the volume variation does not affect the folding state to a large extent and hence is ignored in the study of the interiors of the protein.

Protein folding, Molecular dynamics, Myoglobin, Structure, Report

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New protonation microequilibrium treatment in the case of some amino acid and peptide derivatives containing a bis(imidazolyl)methyl group

Article Abstract:

A microequilibrium analysis of a series of amino acid and peptide derivatives containing the chelating bis(imidazol-2-yl)methyl group is presented and measurement were performed in D(sub 2)O to follow the deprotonation steps. The main advantage of the method is that it does not require the synthesis and NMR microequilibrium analysis of substances modeling the individual parts of the target ligand, in contrast to the method used by others.

Nuclear magnetic resonance, Methyl groups, Methyl compounds

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Fidelity of phenylalanyl-tRNA synthetase in binding the natural amino acids

Article Abstract:

A study on phenylalanyl-tRNA synthetase (PheRS) globular protein has proved to be effective in predicting binding sites and binding affinities. Results show that Phe has the best binding energy as it binds site and energy of the 19 other natural amino acids to PheRs.

Transfer RNA, Globular proteins

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