The study of helical distortions due to environmental changes: choice of parameters.
Parameters like interhelical angles, helical parameters, levels of distortions, etc., have been analysed to test their sensitivity to environmental changes using a method developed in this laboratory. This analysis was done on protein structures solved under different environmental conditions like temperature and pH, and ligand binding. The study reveals that the helical parameters are not sensitive enough to study the effect of environmental changes on protein helices. On the other hand the helical distortions as well as changes in the interhelical angles are more sensitive to these changes. The study also provides with additional information like the origin of distortions in a helix when a ligand binds to a protein, bending in helical axis, identification and extent of domain movements, etc.
Sreekanth
R
R
Deparment of Crystallography and Biophysics, University of Madras, Chennai, India.
Rajan
S S
SS
D000465:Algorithms; D002147:Calmodulin / Q000737:chemistry; D018360:Crystallography, X-Ray; D006813:Humidity; D006863:Hydrogen-Ion Concentration; D008024:Ligands; D008958:Models, Molecular; D009211:Myoglobin / Q000737:chemistry; D009703:Nucleoside-Phosphate Kinase / Q000737:chemistry; D051026:Phosphoribosylglycinamide Formyltransferase / Q000737:chemistry; D011485:Protein Binding; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry*; D018168:Receptors, Retinoic Acid / Q000737:chemistry; D013696:Temperature; D019209:Troponin C / Q000737:chemistry; D000097768:Retinoic Acid Receptor gamma
D002147:Calmodulin; D008024:Ligands; D009211:Myoglobin; D009703:Nucleoside-Phosphate Kinase; D051026:Phosphoribosylglycinamide Formyltransferase; D011506:Proteins; D018168:Receptors, Retinoic Acid; D019209:Troponin C; D000097768:Retinoic Acid Receptor gamma; C019979:cytidylate kinase