Weak points of antiparallel {beta}-sheets. How are they filled up in globular proteins? |
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Authors: | Finkelstein, Alexei V. Nakamura, Haruki |
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Affiliation: | Institute of Protein Research, Russian Academy of Sciences 142292, Pushchino, Moscow Region, Russian Federation 1Protein Engineering Research Institute 6-2-3, Furuedai, Suita, Osaka, 565, Japan |
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Abstract: | A lack of knowledge about the construction of tight packingis now the main obstacle for a successful design of artificialproteins. In this paper we examine a way of close packing antiparallelß-sandwihes. We show that there are some weakpoints at the surfaces of ß-sheets, which cannotbe filled by the surrounding aliphatic side chains that arethe most abundant. Theoretically, these weak pointscan be filled either by aromatic side chains of the same sheetor by the residues of the other parts of the protein molecule.The analysis of protein structures shows that both possibilitiesare used by nature and that there are many cases when theseweak points are not filled by any atom. They remainfree and form a majority of the defects of close packing inprotein globules. |
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Keywords: | antiparallel ß -sheet/ aromatic side chains/ close packing/ de novo design/ packing defects |
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