Conversation 11: No. 1

category image Volume: Conversation 11
Issue Number 1
May 2000
ISBN 0-940030-80-2

How Do Hydrogen Bonds Contribute to Protein-DNA Recognition?

The average strength of hydrogen bonding interactions at the interface of 40 protein-DNA complexes comprising ~ 1500 potential hydrogen bonds and their free energies of formation have been estimated employing some recent advances in theoretical treatments of electrostatic interactions. The hydrogen bond spatial frequency distribution shows a maximum at a proton-acceptor distance of 2.1Å. The corresponding average interaction energy and the binding free energy are computed to be -1 kcal and +4 kcal/mol.H-bond respectively. Thus hydrogen bonds do not appear to provide the driving force for the formation of specific complexes from initially separated protein and DNA but serve to optimize the interactions in the specific complex once it is formed, via distance and angle requirements.

Surjit B. Dixit
Nidhi Arora1
B. Jayaram

Department of Chemistry
Indian Institute of Technology
Hauz Khas, New Delhi-110016, India
1Present address:
Department of Molecular Biology
The Scripps Research Institute
La Jolla, CA 92037, USA


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