Loop folds in proteins and evolutionary conservation of folding nuclei.
We show that loops of close contacts involving hydrophobic residues are important in protein folding. Contrary to Berezovsky Berezovsky and Trifonov (J Biomol Struct Dyn 20, 5-6, 2002) the loops important in protein folding usually are much larger in size than 23-31 residues, being instead comparable to the size of the protein for single domain proteins. Additionally what is important are not single loop contacts, but a highly interconnected network of such loop contacts, which provides extra stability to a protein fold and which leads to their conservation in evolution.
Kloczkowski
Andrzej
A
Baker Center for Bioinformatics and Biological Statistics, Iowa State University, 123 Office and Lab Bldg., Ames 50011-3020, USA.
Jernigan
Robert L
RL
D000595:Amino Acid Sequence; D000818:Animals; D017124:Conserved Sequence; D003574:Cytochrome c Group / Q000737:chemistry; D018397:Equidae; D019143:Evolution, Molecular; D057927:Hydrophobic and Hydrophilic Interactions; D008956:Models, Chemical; D009211:Myoglobin / Q000737:chemistry; D017510:Protein Folding; D017434:Protein Structure, Tertiary; D014907:Whales
D003574:Cytochrome c Group; D009211:Myoglobin