Beta-turns and their distortions: a proposed new nomenclature.
Using the new version of a Protein Structural Database, BIPED, beta-turns have been extracted from 58 non-identical proteins (resolution less than or equal to 2 A) using the standard criteria that the distance between C alpha i and C alpha i + 3 is less than 7 A and that the central residues are not helical. It has been shown that 42% of these do not fit into the eight conventional turn types (I, I', II, II', VIa, VIb and VIII) as defined by phi, psi limits for residues i + 1 and i + 2. Most of the unclassified turns are 'distortions' of the standard turn types, lying just outside the specified limits. Eleven per cent of the turns are not related to the standard types, and have completely different phi, psi combinations. Therefore, the conformational space available to a trans tetrapeptide has been explored to find all two-residue phi, psi combinations which satisfy the criteria for beta-turn formation. The conformations generated by the search are the conformations observed in the data. On the basis of these observations a new nomenclature is suggested for beta-turns based on a shorthand descriptor of populated regions of the phi, psi plot. For example, it is proposed that a type I turn should now be described as an alpha alpha turn, the descriptor indicating the phi, psi regions of the i + 1 and i + 2 positions of the turn. The use of descriptors, which convey information about the turn type conformation, should aid protein structural workers in turn classification and visualization. The sequence preferences for the alpha beta turn have been elucidated: Pro, Asp and Ser at i + 1; Asn and His at i + 2; Pro at i + 3. These preferences have been explained in terms of specific interactions involving the side-chains. The beta-turn prediction program, BTURN 1.0, has been further developed by alterations to the calculation of parameters, the removal of incompatible multiple turn predictions and the inclusion of the distorted types alpha alpha and beta p gamma data in the respective sets of parameters, to yield BTURN 2.0. A variation of this beta-turn prediction program, called GORBTURN 1.0, has been developed, which uses the directional parameters produced from work by Garrett et al., to eliminate potential helix and strand-forming residues from the beta-turn prediction.(ABSTRACT TRUNCATED AT 400 WORDS)
Wilmot
C M
CM
Department of Crystallography, Birkbeck College, London, UK.
Thornton
J M
JM
D000595:Amino Acid Sequence; D007256:Information Systems; D008969:Molecular Sequence Data; D011487:Protein Conformation; D011506:Proteins / Q000145:classification; D015203:Reproducibility of Results; D012984:Software; D009626:Terminology as Topic
D011506:Proteins