
pmid: 14616029
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.
Models, Molecular, Proteomics, Salmonella typhimurium, Models, Statistical, Proteome, Protein Conformation, Molecular Sequence Data, Proteins, Crystallography, X-Ray, Protein Structure, Secondary, Protein Structure, Tertiary, Adenosine Triphosphate, Bacterial Proteins, Amino Acid Transport Systems, Basic, ATP-Binding Cassette Transporters, Amino Acid Sequence
Models, Molecular, Proteomics, Salmonella typhimurium, Models, Statistical, Proteome, Protein Conformation, Molecular Sequence Data, Proteins, Crystallography, X-Ray, Protein Structure, Secondary, Protein Structure, Tertiary, Adenosine Triphosphate, Bacterial Proteins, Amino Acid Transport Systems, Basic, ATP-Binding Cassette Transporters, Amino Acid Sequence
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