TY - JOUR
T1 - Protein flexibility and electrostatic interactions
AU - Kumar, S.
AU - Wolfson, H. J.
AU - Nussinov, R.
PY - 2001
Y1 - 2001
N2 - 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 geometry, 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.
AB - 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 geometry, 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.
UR - http://www.scopus.com/inward/record.url?scp=0035327168&partnerID=8YFLogxK
U2 - 10.1147/rd.453.0499
DO - 10.1147/rd.453.0499
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AN - SCOPUS:0035327168
SN - 0018-8646
VL - 45
SP - 499
EP - 512
JO - IBM Journal of Research and Development
JF - IBM Journal of Research and Development
IS - 3-4
ER -