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Optimal region of average side-chain entropy for fast protein folding

Published online by Cambridge University Press:  01 March 2000

OXANA V. GALZITSKAYA ,
ALEXEI K. SURIN  and
HARUKI NAKAMURA
OXANA V. GALZITSKAYA
Affiliation:
Biomolecular Engineering Research Institute, 6-2-3 Furuedai, Suita Osaka 565-0874, Japan Institute of Protein Research, Russian Academy of Sciences, 142292, Pushchino, Moscow Region, Russia
ALEXEI K. SURIN
Affiliation:
Institute of Protein Research, Russian Academy of Sciences, 142292, Pushchino, Moscow Region, Russia Kansai Medical University, 18-89 Uyamahigashi, Hirakata 573-1136, Japan
HARUKI NAKAMURA
Affiliation:
Biomolecular Engineering Research Institute, 6-2-3 Furuedai, Suita Osaka 565-0874, Japan Present address: Institute of Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan.
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Abstract

Search and study the general principles that govern kinetics and thermodynamics of protein folding generates new insight into the factors that control this process. Here, we demonstrate based on the known experimental data and using theoretical modeling of protein folding that side-chain entropy is one of the general determinants of protein folding. We show for proteins belonging to the same structural family that there exists an optimal relationship between the average side-chain entropy and the average number of contacts per residue for fast folding kinetics. Analysis of side-chain entropy for proteins that fold without additional agents demonstrates that there exists an optimal region of average side-chain entropy for fast folding. Deviation of the average side-chain entropy from the optimal region results in an anomalous protein folding process (prions, α-lytic protease, subtilisin, some DNA-binding proteins). Proteins with high or low side-chain entropy would have extended unfolded regions and would require some additional agents for complete folding. Such proteins are common in nature, and their structure properties have biological importance.

Keywords

Monte Carlo simulationsnative topologyoptimal balanceprotein stabilityside-chain packingunfolded regions
Type
Research Article
Information
Protein Science , Volume 9 , Issue 3 , March 2000 , pp. 580 - 586
Copyright
© 2000 The Protein Society

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