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Protein Engineering vol. 16 no. 5 pp. 331-339, 2003
© 2003 Oxford University Press

Stranded in isolation: structural role of isolated extended strands in proteins

Narayanan Eswar1, C. Ramakrishnan and N. Srinivasan2

Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India 1Present address: Departments of Biopharmaceutical Sciences and Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94143-2240, USA

2 To whom correspondence should be addressed. e-mail: ns{at}mbu.iisc.ernet.in

Reasons for the formation of extended-strands (E-strands) in proteins are often associated with the formation of ß-sheets. However E-strands, not part of ß-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 Å) crystal structures of proteins, we have identified 518 isolated E-strands from 187 proteins. The two most distinguishing features of isolated E-strands from ß-strands in ß-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 ß-sheet forming ß-strands, among homologous protein structures. It is suggested that isolated ß-strands have many characteristics of loop segments but with repetitive ({phi},{psi}) values falling within the ß-region of the Ramachandran map.

Received April 8, 2002; revised March 31, 2003; accepted April 8, 2003.


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