dorsal/arxiv
View SchemaPhysical origins of protein superfamilies
| Authors | Konstantin B. Zeldovich, Igor N. Berezovsky, Eugene I. Sha |
|---|---|
| Categories | |
| ArXiv ID | q-bio/0508036 |
| URL | https://arxiv.org/abs/q-bio/0508036 |
Abstract
In this work, we discovered a fundamental connection between selection for protein stability and emergence of preferred structures of proteins. Using standard exact 3-dimensional lattice model we evolve sequences starting from random ones and determining exact native structure after each mutation. Acceptance of mutations is biased to select for stable proteins. We found that certain structures, wonderfold, are independently discovered numerous times as native states of stable proteins in many unrelated runs of selection. Diversity of sequences that fold into wonderfold structures gives rise to superfamilies, i.e. sets of dissimilar sequences that fold into the same or very similar structures. Wonderfolds appear to be the most designable structures out of complete set of compact lattice proteins. Furthermore, proteins having wondefolds as their native structure tend to be most thermostable among all evolved proteins. This effect is purely due to the favorable geometric properties of wonderfolds and, thus, dominates any dependence on sequences. The present work establishes a model of prebiotic structure selection, which identifies dominant structural patterns emerging upon optimization of proteins for survival in hot environment. Convergently discovered prebiotic initial superfamilies with wonderfold structures could have served as a seed for subsequent biological evolution involving gene duplications and divergence.
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"abstract": "In this work, we discovered a fundamental connection between selection for\nprotein stability and emergence of preferred structures of proteins. Using\nstandard exact 3-dimensional lattice model we evolve sequences starting from\nrandom ones and determining exact native structure after each mutation.\nAcceptance of mutations is biased to select for stable proteins. We found that\ncertain structures, wonderfold, are independently discovered numerous times as\nnative states of stable proteins in many unrelated runs of selection. Diversity\nof sequences that fold into wonderfold structures gives rise to superfamilies,\ni.e. sets of dissimilar sequences that fold into the same or very similar\nstructures. Wonderfolds appear to be the most designable structures out of\ncomplete set of compact lattice proteins. Furthermore, proteins having\nwondefolds as their native structure tend to be most thermostable among all\nevolved proteins. This effect is purely due to the favorable geometric\nproperties of wonderfolds and, thus, dominates any dependence on sequences. The\npresent work establishes a model of prebiotic structure selection, which\nidentifies dominant structural patterns emerging upon optimization of proteins\nfor survival in hot environment. Convergently discovered prebiotic initial\nsuperfamilies with wonderfold structures could have served as a seed for\nsubsequent biological evolution involving gene duplications and divergence.",
"arxiv_id": "q-bio/0508036",
"authors": [
"Konstantin B. Zeldovich",
"Igor N. Berezovsky",
"Eugene I. Sha"
],
"categories": [
"q-bio.GN",
"q-bio.BM",
"q-bio.PE"
],
"title": "Physical origins of protein superfamilies",
"url": "https://arxiv.org/abs/q-bio/0508036"
},
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