Analysis of gammabeta, betagamma, gammagamma, betabeta continuous turns in proteins.
We report the observation of continuous turns in proteins which comprise individual gamma-turns or beta-turns or both that are situated immediately one after the other along the polypeptide chain. The continuous turns were identified from a representative data set of three-dimensional protein crystal structures. The gammabeta/betagamma, gammagamma and betabeta continuous turns represent peptides of varying amino acid residue lengths and conformations. The continuous turns frequently observed in proteins were: gammabeta, between a coil and a strand; betagamma, between a helix and a strand; gammagamma, between coils; and betabeta, either between a strand and a coil or between strands or coils. We determined the statistically significant amino acid residue preferences at individual positions in the turn, calculated amino acid positional potentials and analyzed main chain hydrogen bonds and side-chain interactions likely to stabilize the continuous turns. The data on continuous turns have been integrated in the database of structural motifs in proteins (DSMP) on our web server at (http://www.cdfd.org.in/dsmp.html). This is useful to make queries on sequences compatible with different continuous turns.
Guruprasad
K
K
Center for DNA Fingerprinting and Diagnostics (CDFD), Nacharam, Hyderabad - 500 076, India. guru@gvk.com
Prasad
M S
MS
Kumar
G R
GR
D016208:Databases, Factual; D006860:Hydrogen Bonding; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*
D011506:Proteins