Genomic determinants of protein folding thermodynamics in prokaryotic organisms

被引:43
作者
Bastolla, U [1 ]
Moya, A
Viguera, E
van Ham, RCHJ
机构
[1] CSIC, INTA, Ctr Astrobiol, E-28850 Torrejon de Ardoz, Spain
[2] Univ Valencia, Inst Cavanilles Biodiversitat & Biol Evolut, E-46071 Valencia, Spain
[3] Univ Malaga, Dept Biol Celular & Genet, E-29071 Malaga, Spain
[4] Plant Res Int, NL-6700 AA Wageningen, Netherlands
关键词
protein folding; molecular evolution; orthologous proteins; intracellular bacteria; mutational bias;
D O I
10.1016/j.jmb.2004.08.086
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
Here we investigate how thermodynamic properties of orthologous proteins are influenced by the genomic environment in which they evolve. We performed a comparative computational study of 21 protein families in 73 prokaryotic species and obtained the following main results. (i) Protein stability with respect to the unfolded state and with respect to misfolding are anticorrelated. There appears to be a trade-off between these two properties, which cannot be optimized simultaneously. (ii) Folding thermodynamic parameters are strongly correlated with two genomic features, genome size and G + C composition. In particular, the normalized energy gap, an indicator of folding efficiency in statistical mechanical models of protein folding, is smaller in proteins of organisms with a small genome size and a compositional bias towards A + T. Such genomic features are characteristic for bacteria with an intracellular lifestyle. We interpret these correlations in light of mutation pressure and natural selection. A mutational bias toward A + T at the DNA level translates into a mutational bias toward more hydrophobic (and in general more interactive) proteins, a consequence of the structure of the genetic code. Increased hydrophobicity renders proteins more stable against unfolding but less stable against misfolding. Proteins with high hydrophobicity and low stability against misfolding occur in organisms with reduced genomes, like obligate intracellular bacteria. We argue that they are fixed because these organisms experience weaker purifying selection due to their small effective population sizes. This interpretation is supported by the observation of a high expression level of chaperones in these bacteria. Our results indicate that the mutational spectrum of a genome and the strength of selection significantly influence protein folding thermodynamics. (C) 2004 Elsevier Ltd. All rights reserved.
引用
收藏
页码:1451 / 1466
页数:16
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