C-ALPHA-BASED TORSION ANGLES - A SIMPLE TOOL TO ANALYZE PROTEIN CONFORMATIONAL-CHANGES

A simple method is presented for the analysis of protein conformationa l changes based on the comparison of torsion angles defined by four co nsecutive C alpha atoms. The technique was applied successfully to pro teins 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 for ms 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 r igid body but exhibits some degree of flexibility. The analysis of cit rate synthase, which is an example of shear motion, shows that the lar gest differences in C alpha-torsion angles between the open and closed conformations are clustered around residues that belong to segments c onnecting or-helices, whereas the helices themselves appear to be rigi d; this is in agreement with previous results obtained by detailed lea st-squares superpositions (Lesk AM, Chothia C, 1984, J Mol Biol 174:17 5-191).