Closed loops of TIM barrel protein fold.
The closed loops within the proteins of the TIM-barrel fold family are analyzed and compared sequence- and structure-wise. The size distribution of the closed loops of the TIM-barrels confirms universal preference to the standard size of 25-30 residues. 3D structural RMSD comparisons of the closed loops and presentation of their sequences in binary form suggest that the TIM-barrel proteins are built from descendants of several types of basic closed loop prototypes. Comparison of these prototypes points to a likely common ancestor--the alpha helix containing closed loops of 28 amino acids. The presumed ancestor is characterized by specific binary consensus sequence.
Frenkel
Zakhar M
ZM
Genome Diversity Center, Institute of Evolution, University of Haifa, Haifa 31905, Israel. zfrenkel@yahoo.com
Trifonov
Edward N
EN
D000595:Amino Acid Sequence; D017124:Conserved Sequence; D016208:Databases, Factual; D019143:Evolution, Molecular; D057927:Hydrophobic and Hydrophilic Interactions; D008958:Models, Molecular; D008969:Molecular Sequence Data; D011487:Protein Conformation; D017510:Protein Folding; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*; D017386:Sequence Homology, Amino Acid; D013329:Structure-Activity Relationship
D011506:Proteins