C alpha-based torsion angles: a simple tool to analyze protein conformational changes.
A simple method is presented for the analysis of protein conformational changes based on the comparison of torsion angles defined by four consecutive C alpha atoms. The technique was applied successfully to proteins that undergo hinge motion and shear motion. In the case of both MBP and LAO, which represent examples of hinge motion, the plot of the differences in C alpha-torsion angles between the open and closed forms of the proteins helped us to formulate a more thorough description of the conformational change: a large displacement of one domain with respect to the other where one of the domains does not behave like a rigid body but exhibits some degree of flexibility. The analysis of citrate synthase, which is an example of shear motion, shows that the largest differences in C alpha-torsion angles between the open and closed conformations are clustered around residues that belong to segments connecting alpha-helices, whereas the helices themselves appear to be rigid; this is in agreement with previous results obtained by detailed least-squares superpositions (Lesk AM, Chothia C, 1984, J Mol Biol 174:175-191).
Department of Molecular Biology, Uppsala University, Sweden.
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D002135:Calcium-Binding Proteins; D002352:Carrier Proteins / Q000737:chemistry*; D018360:Crystallography, X-Ray / Q000379:methods; D016208:Databases, Factual; D058619:Maltose-Binding Proteins; D008433:Mathematics; D008962:Models, Theoretical; D009004:Monosaccharide Transport Proteins; D033902:Periplasmic Binding Proteins; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism; D012486:Salmonella typhimurium / Q000378:metabolism; D013314:Stress, Mechanical
D002135:Calcium-Binding Proteins; D002352:Carrier Proteins; D058619:Maltose-Binding Proteins; D009004:Monosaccharide Transport Proteins; D033902:Periplasmic Binding Proteins; D011506:Proteins; C023550:galactose-binding protein