Specificity in molecular design: a physical framework for probing the determinants of binding specificity and promiscuity in a biological environment

Article Abstract:

Molecular binding in analyzed with an emphasis on understanding the determinants of specificity from a physical framework. The molecule's size and the ionic strength of the solution have affected binding specificity and the results have provided physical insights into the general determinants of binding specificity and promiscuity in a biological environment.

Research and Development in the Physical, Engineering, and Life Sciences, Molecular Biology, Ligands (Biochemistry), Van der Waals forces

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Electrostatic complementary at ligand binding sites: Application to chorismate mutase

Article Abstract:

Charge optimization was applied to the chorismate mutase from Bacillus subtilis binding an endo-oxabicyclic transition-state analogue. The results suggest that hydrogen-bonded polar and charged groups, including the C11 carboxylate, the ether oxygen, and the hydroxyl, are all extremely complementary to the site.

Bacillus subtilis, Ligands, Ligands (Chemistry), Chemical properties

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Evaluation of ab initio charge determination methods for use in continuum solvation calculations

Article Abstract:

A comprehensive evaluation of the performance of many methods for the ab initio determination of partial atomic charges in continuum electrostatic calculations is given. The potential of the various methods are compared with each other.

Nuclear energy, Structure, Methods engineering

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