Relationships between amino acid sequence and backbone torsion angle preferences.
Statistical averages and correlations for backbone torsion angles of chymotrypsin inhibitor 2 are calculated by using the Rotational Isomeric States model of chain statistics. Statistical weights of torsional states of phipsi pairs, needed for the statistics of the full chain, are obtained in two different ways: 1) by using knowledge-based pairwise dependent phipsi energy maps from Protein Data Bank (PDB) and 2) by collecting torsion angle data from a large number of random coil configurations of an all-atom protein model with volume exclusion. Results obtained by using PDB data show strong correlations between adjacent torsion angle pairs belonging to both the same and different residues. These correlations favor the choice of the native-state torsion angles, and they are strongly context dependent, determined by the specific amino acid sequence of the protein. Excluded volume or steric clashes, only, do not introduce context-dependent phipsi correlations into the chain that would affect the choice of native-state torsional angles.
Keskin
O
O
College of Engineering and Center for Computational Biology and Bioinformatics, Koc University, Istanbul, Turkey.
Yuret
D
D
Gursoy
A
A
Turkay
M
M
Erman
B
B
D000409:Alanine / Q000737:chemistry; D003627:Data Interpretation, Statistical; D030562:Databases, Protein; D015233:Models, Statistical; D015394:Molecular Structure; D009010:Monte Carlo Method; D010455:Peptides / Q000737:chemistry; D010940:Plant Proteins; D011506:Proteins / Q000737:chemistry*; D020539:Sequence Analysis, Protein
D010455:Peptides; D010940:Plant Proteins; D011506:Proteins; C093336:chymotrypsin inhibitor 2; D000409:Alanine