For citation purposes: Carugo O. Solvent accessible surface of globular proteins: how exposed and buried amino acid residues are divided. OA Biology 2013 Nov 01;1(1):1.

Review

 
Structural

Solvent accessible surface of globular proteins: how exposed and buried amino acid residues are divided

O Carugo
 

Authors affiliations

Chemistry Department, Pavia University, Viale Taramelli 12, I-27100 Pavia, Italy

* Corresponding author Email: olicar04@unipv.it

Abstract

Introduction

Globular protein structures are often divided into two regions, the surface, which is in contact with the surrounding molecules, and the interior, which is not accessible to the external molecules. Since most of the surrounding molecules, both in vitro and in vivo, are water molecules, it is clear that protein surface is essentially polar in order to make the protein molecule soluble and stable in an aqueous environment, whereas the protein interior tends to be formed by apolar and hydrophobic amino acid residues. Despite this simple classification criterion, amino acids residues are usually identified, on the basis of the three-dimensional structures, according to a myriad of different criteria, some of which are briefly reviewed in the present article. A simple and ecumenical criterion can be based on the fact that the best separation of the two regions (surface and interior) must be reflected by the maximisation of the difference in hydrophobicity between the two regions. In this article, this simple criterion is examined on the basis of a statistical survey of an ensemble of carefully selected protein crystal structures.

Conclusion

In this article, it is shown that with the use of information published in scientific journals and disseminated in databases, it is easy to give a sound and quantitative framework to a fundamental concept like that of the amino acid polarity/apolarity antinomy.

Licensee OA Publishing London 2013. Creative Commons Attribution License (CC-BY)
Keywords