Influence of the local amino acid sequence upon the zones of the torsional angles phi and psi adopted by residues in proteins.
A set of parameters is derived to express the influence of the local amino acid sequence on the torsional angles phi and psi adopted by each residue in a protein. The formalism used, which is based on information theory, evaluates the probability for a given residue to be in a particular zone of the Ramachandran map. Comparisons with crystallographic structures suggest that the method can extract almost all of the available information from the local sequence and show that the local sequence carries only, on average, about 65% of the information necessary for specifying the conformation of a given residue in a protein. The rest is specified by long-range interactions that are specific for each protein fold. The parameters derived here provide a more detailed description of the prediction than other methods in allowing the allocation of the torsional angles for residues having an aperiodic structure and are intended to be used for directing the conformational search in a subsequent simulation of the three-dimensional structure. This method should also predict segments of the polypeptide chain that are the most stable and thus less sensitive to long-range interactions.
Gibrat
J F
JF
Unité d'Ingénierie des Protéines, Bâtiment des Biotechnologies, INRA, Jouy-en-Josas, France.
Robson
B
B
Garnier
J
J
D000595:Amino Acid Sequence; D000818:Animals; D016208:Databases, Factual; D006801:Humans; D008433:Mathematics; D008962:Models, Theoretical; D008969:Molecular Sequence Data; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D012689:Sequence Homology, Nucleic Acid; D014361:Trypsin Inhibitors / Q000737:chemistry
D011506:Proteins; D014361:Trypsin Inhibitors