Spelling Protein Structure

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 pr...

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Vydáno v:Journal of biomolecular structure & dynamics Ročník 21; číslo 3; s. 327 - 339
Hlavní autoři: Berezovsky, Igor N., Kirzhner, Alla, Kirzhner, Valery M., Trifonov, Edward N.
Médium: Journal Article
Jazyk:angličtina
Vydáno: England Taylor & Francis Group 01.12.2003
Témata:
Adenosine Triphosphate - chemistry
Amino Acid Sequence
Amino Acid Transport Systems, Basic - chemistry
ATP-Binding Cassette Transporters - chemistry
Bacterial Proteins - chemistry
Crystallography, X-Ray
Loop-n-lock elements
Models, Molecular
Models, Statistical
Molecular Sequence Data
Protein Conformation
Protein structure
Protein Structure, Secondary
Protein Structure, Tertiary
Proteins - chemistry
Proteome
Proteomic code
Proteomics - methods
Prototype units
Salmonella typhimurium - enzymology
Sequence/structure prototype
Spelling protein structure
ISSN:0739-1102, 1538-0254
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Popis
Shrnutí: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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ISSN:0739-1102
1538-0254
DOI:10.1080/07391102.2003.10506929