title: Identification of kinetically hot residues in proteins.
abstract: A number of recent studies called attention to the presence of kinetically important residues underlying the formation and stabilization of folding nuclei in proteins, and to the possible existence of a correlation between conserved residues and those participating in the folding nuclei. Here, we use the Gaussian network model (GNM), which recently proved useful in describing the dynamic characteristics of proteins for identifying the kinetically hot residues in folded structures. These are the residues involved in the highest frequency fluctuations near the native state coordinates. Their high frequency is a manifestation of the steepness of the energy landscape near their native state positions. The theory is applied to a series of proteins whose kinetically important residues have been extensively explored: chymotrypsin inhibitor 2, cytochrome c, and related C2 proteins. Most of the residues previously pointed out to underlie the folding process of these proteins, and to be critically important for the stabilization of the tertiary fold, are correctly identified, indicating a correlation between the kinetic hot spots and the early forming structural elements in proteins. Additionally, a strong correlation between kinetically hot residues and loci of conserved residues is observed. Finally, residues that may be important for the stability of the tertiary structure of CheY are proposed.
authors.affiliation: Polymer Research Center, Bogazici University, and TUBITAK Advanced Polymeric Materials Research Center, Istanbul, Turkey.
authors.forename: M C
authors.initials: MC
authors.lastname: Demirel
authors.forename: A R
authors.initials: AR
authors.lastname: Atilgan
authors.forename: R L
authors.initials: RL
authors.lastname: Jernigan
authors.forename: B
authors.initials: B
authors.lastname: Erman
authors.forename: I
authors.initials: I
authors.lastname: Bahar
mesh_terms: D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000737:chemistry; D017124:Conserved Sequence; D003574:Cytochrome c Group / Q000737:chemistry*; D045362:Cytochromes c2; D007700:Kinetics; D008565:Membrane Proteins / Q000737:chemistry; D000072236:Methyl-Accepting Chemotaxis Proteins; D008958:Models, Molecular; D016011:Normal Distribution; D010455:Peptides / Q000737:chemistry*; D010940:Plant Proteins; D011487:Protein Conformation; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry*
chemical_list: D001426:Bacterial Proteins; D003574:Cytochrome c Group; D008565:Membrane Proteins; D000072236:Methyl-Accepting Chemotaxis Proteins; D010455:Peptides; D010940:Plant Proteins; D011506:Proteins; C093336:chymotrypsin inhibitor 2; D045362:Cytochromes c2