title: Loop folds in proteins and evolutionary conservation of folding nuclei.
abstract: 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.
authors.affiliation: Baker Center for Bioinformatics and Biological Statistics, Iowa State University, 123 Office and Lab Bldg., Ames 50011-3020, USA.
authors.forename: Andrzej
authors.initials: A
authors.lastname: Kloczkowski
authors.forename: Robert L
authors.initials: RL
authors.lastname: Jernigan
mesh_terms: 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
chemical_list: D003574:Cytochrome c Group; D009211:Myoglobin