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An assessment of protein–ligand binding site polarizability

✍ Scribed by Akbar Nayeem; Stanley Krystek Jr.; Terry Stouch

Publisher
Wiley (John Wiley & Sons)
Year
2003
Tongue
English
Weight
865 KB
Volume
70
Category
Article
ISSN
0006-3525

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✦ Synopsis

Abstract

Electronic polarizability, an important physical property of biomolecules, is currently ignored in most biomolecular calculations. Yet, it is widely believed that polarization could account for a substantial fraction of the total nonbonded energy of a system. This belief is supported by studies of small complexes in vacuum. This perception is driving the development of a new class of polarizable force fields for biomolecular calculations. However, the quantification of this term for protein–ligand complexes has never been attempted. Here we explore the polarizable nature of protein–ligand complexes in order to evaluate the importance of this effect. We introduce two indexes describing the polarizability of protein binding sites. These we apply to a large range of pharmaceutically relevant complexes. We offer a recommendation of particular complexes as test systems with which to determine the effects of polarizability and as test cases with which to test the new generation of force fields. Additionally, we provide a tabulation of the amino acid composition of these binding sites and show that composition can be specific for certain classes of proteins. We also show that the relative abundance of some amino acids is different in binding sites than elsewhere in a protein's structure. © 2003 Wiley Periodicals, Inc. Biopolymers 70: 201–211, 2003

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