Spelling protein structure.

Igor N Berezovsky; Alla Kirzhner; Valery M Kirzhner; Edward N Trifonov

doi:10.1080/07391102.2003.10506929

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PubMed · 14616029

Spelling protein structure.

Igor N Berezovsky·Alla Kirzhner·Valery M Kirzhner·Edward N Trifonov

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Abstract

Recent sequence analysis of complete prokaryotic proteomes suggests that in early evolutionary stages proteins were rather small, of the size 25-35 amino acids. Corroborating evidence comes from protein crystal data, which indicate this size for closed loops--universal structural units of globular proteins. In the latest development we were able to derive and structurally characterize several sequence/structure prototypes apparently representing early protein units. Structurally the prototypes appear as closed loops stabilized by end-to-end van der Waals interactions. While nearly standard in size the loops are highly diverse in terms of their secondary structure. A presentation of the protein as an assembly of descendants of the prototypes, the first of its kind, is described in detail here. The sequence and structure of the ATP-binding subunit of histidine permease of S. typhimurium is shown to contain several modified copies of different prototype elements, closed loops, and, thus, can be spelled as: x-PI-x-PIV-PVI-PII-PVII-x, where PI-PVII are the prototype elements. This study sets up the basic principles for the sequence/structure prototype spelling of globular proteins.

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ATP-Binding Cassette Transporters Adenosine Triphosphate Amino Acid Sequence Amino Acid Transport Systems, Basic Bacterial Proteins Crystallography, X-Ray Models, Molecular Models, Statistical Molecular Sequence Data Protein Conformation Protein Structure, Secondary Protein Structure, Tertiary Proteins Proteome Proteomics Salmonella typhimurium Journal Article Research Support, Non-U.S. Gov't

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Igor N Berezovsky, Alla Kirzhner, Valery M Kirzhner, Edward N Trifonov. 2003. Spelling protein structure.. https://doi.org/10.1080/07391102.2003.10506929

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