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 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.
Berezovsky
Igor N
IN
Department of Structural Biology, The Weizmann Institute of Science, P.O.B. 26, Rehovot 76100, Israel. inberez@fas.harvard.edu
Kirzhner
Alla
A
Kirzhner
Valery M
VM
Trifonov
Edward N
EN
D018528:ATP-Binding Cassette Transporters / Q000737:chemistry; D000255:Adenosine Triphosphate / Q000737:chemistry; D000595:Amino Acid Sequence; D026923:Amino Acid Transport Systems, Basic / Q000737:chemistry; D001426:Bacterial Proteins / Q000737:chemistry; D018360:Crystallography, X-Ray; D008958:Models, Molecular; D015233:Models, Statistical; D008969:Molecular Sequence Data; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry*; D020543:Proteome; D040901:Proteomics / Q000379:methods*; D012486:Salmonella typhimurium / Q000201:enzymology
D018528:ATP-Binding Cassette Transporters; D026923:Amino Acid Transport Systems, Basic; D001426:Bacterial Proteins; D011506:Proteins; D020543:Proteome; C043828:histidine permease, Bacteria; D000255:Adenosine Triphosphate