Short-strong hydrogen bonds and a low barrier transition state for the proton transfer reaction in RNase A catalysis: a quantum chemical study

Vishveshwara, S and Madhusudhana, MS and Maizel Jr, Jacob V (2001) Short-strong hydrogen bonds and a low barrier transition state for the proton transfer reaction in RNase A catalysis: a quantum chemical study. In: Biophysical Chemistry, 89 (2-3). pp. 105-117.

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Abstract

There is growing evidence that some enzymes catalyze reactions through the formation of short–strong hydrogen bonds as first suggested by Gerlt and Gassman. Support comes from several experimental and quantum chemical studies that include correlation energies on model systems. In the present study, the process of proton transfer between hydroxyl and imidazole groups, a model of the crucial step in the hydrolysis of RNA by the enzymes of the RNase A family, is investigated at the quantum mechanical level of density functional theory and perturbation theory at the MP2 level. The model focuses on the nature of the formation of a complex between the important residues of the protein and the hydroxyl group of the substrate. We have also investigated different configurations of the ground state that are important in the proton transfer reaction. The nature of bonding between the catalytic unit of the enzyme and the substrate in the model is investigated by Bader's atoms in molecule theory. The contributions of solvation and vibrational energies corresponding to the reactant, the transition state and the product configurations are also evaluated. Furthermore, the effect of protein environment is investigated by considering the catalytic unit surrounded by complete proteins—RNase A and Angiogenin. The results, in general, indicate the formation of a short–strong hydrogen bond and the formation of a low barrier transition state for the proton transfer model of the enzyme.

Item Type:	Journal Article
Publication:	Biophysical Chemistry
Publisher:	Elsevier
Additional Information:	Copyright of this article belongs to Elsevier.
Keywords:	Hydrogen bond;Proton transfer;RNA hydrolysis;Rnase A
Department/Centre:	Division of Biological Sciences > Molecular Biophysics Unit
Date Deposited:	17 Oct 2007
Last Modified:	19 Sep 2010 04:40
URI:	http://eprints.iisc.ac.in/id/eprint/12297

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