Stranded in isolation: structural role of isolated extended strands in proteins.
Reasons for the formation of extended-strands (E-strands) in proteins are often associated with the formation of beta-sheets. However E-strands, not part of beta-sheets, commonly occur in proteins. This raises questions about the structural role and stability of such isolated E-strands. Using a dataset of 250 largely non-homologous and high-resolution (<2 A) crystal structures of proteins, we have identified 518 isolated E-strands from 187 proteins. The two most distinguishing features of isolated E-strands from beta-strands in beta-sheets are the high preponderance of prolyl residues occuring in isolated E-strands and their high exposure to the surroundings. Removal of regions with polyproline conformation from the dataset did not significantly reduce the propensity of prolyl residues to occur in isolated E-strands. Isolated E-strands are often characterized by their main-chain amide and carbonyl groups involved in hydrogen bonding with polar side chains or water. They are often flanked by irregular loop structures and are less well conserved, than beta-sheet forming beta-strands, among homologous protein structures. It is suggested that isolated beta-strands have many characteristics of loop segments but with repetitive (phi,psi) values falling within the beta-region of the Ramachandran map.
Eswar
Narayanan
N
Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India.
Ramakrishnan
C
C
Srinivasan
N
N
D018360:Crystallography, X-Ray; D003627:Data Interpretation, Statistical; D030562:Databases, Protein; D005658:Fungi / Q000201:enzymology; D006860:Hydrogen Bonding; D009195:Peroxidase / Q000737:chemistry / Q000378:metabolism; D011392:Proline / Q000378:metabolism; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism
D011506:Proteins; D011392:Proline; D009195:Peroxidase