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Bioinformatics Advance Access originally published online on June 28, 2007
Bioinformatics 2007 23(17):2231-2238; doi:10.1093/bioinformatics/btm345
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© The Author 2007. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Different packing of external residues can explain differences in the thermostability of proteins from thermophilic and mesophilic organisms

Anna V. Glyakina 1, Sergiy O. Garbuzynskiy 2, Michail Yu. Lobanov 2 and Oxana V. Galzitskaya 2,*

1Institute of Mathematical Problems of Biology and 2Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia

*To whom correspondence should be addressed.


  Abstract

Motivation: Understanding the basis of protein stability in thermophilic organisms raises a general question: what structural properties of proteins are responsible for the higher thermostability of proteins from thermophilic organisms compared to proteins from mesophilic organisms?

Results: A unique database of 373 structurally well-aligned protein pairs from thermophilic and mesophilic organisms is constructed. Comparison of proteins from thermophilic and mesophilic organisms has shown that the external, water-accessible residues of the first group are more closely packed than those of the second. Packing of interior parts of proteins (residues inaccessible to water molecules) is the same in both cases. The analysis of amino acid composition of external residues of proteins from thermophilic organisms revealed an increased fraction of such amino acids as Lys, Arg and Glu, and a decreased fraction of Ala, Asp, Asn, Gln, Thr, Ser and His. Our theoretical investigation of folding/unfolding behavior confirms the experimental observations that the interactions that differ in thermophilic and mesophilic proteins form only after the passing of the transition state during folding. Thus, different packing of external residues can explain differences in thermostability of proteins from thermophilic and mesophilic organisms.

Availability: The database of 373 structurally well-aligned protein pairs is available at http://phys.protres.ru/resources/termo_meso_base.html

Contact: ogalzit{at}vega.protres.ru

Supplementary information: Supplementary data are available at Bioinformatics online.

Associate Editor: Burkhard Rost

Received on April 24, 2007; revised on June 25, 2007; accepted on June 25, 2007

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