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IBM Journal of Research and Development  
Volume 45, Number 3/4, Page 499 (2001)
Deep computing for the life sciences
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Protein flexibility and electrostatic interactions

by S. Kumar, H. J. Wolfson, R. Nussinov
In this paper we address the interrelationship between electrostatic interactions and protein flexibility. Protein flexibility may imply small conformational changes due to the movement of backbone and of side-chain atoms, and/or large-scale molecular motions, in which parts of the protein move as rigid bodies with respect to one another. In particular, we focus on oppositely charged side chains interacting to form salt bridges. The paper has two parts: In the first, we illustrate that the majority of the salt bridges are formed within the independently folding, compact hydrophobic units (HFUs) of the proteins. On the other hand, salt bridges forming across the HFUs, where one amino acid resides in one HFU and its pairing “spouse” in a second, appear to be avoided. In the second part of the paper, we address electrostatic interactions in conformational isomers around the native state. We pick the protein Cyanovirin-N as an example. We show that salt bridges and ion pairs, with less optimal geome try, often interconvert between being stabilizing and destabilizing. We conclude that the stabilizing, or destabilizing, contribution of a salt bridge to protein structure is conformer-dependent.
Related Subjects: Biology and biomedical studies; Biotechnology; Protein folding