Quantitative method for the assignment of hinge and shear mechanism in protein domain movements.
Bottom Line: A popular method for classification of protein domain movements apportions them into two main types: those with a 'hinge' mechanism and those with a 'shear' mechanism.This predictor was applied to give a 10-fold increase in the number of examples over the number previously available with a high degree of precision.The angle of rotation is also shown to be a good discriminator between the two mechanisms.
Affiliation: D'Arcy Thompson Centre for Computational Biology, School of Computing Sciences, University of East Anglia, Norwich, NR4 7TJ, UK.Show MeSH
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Mentions: Figure 4B shows the rotation angle plotted against the prediction value. One can discern a general trend for the rotation angle to increase with decreasing prediction value, i.e. the motions become more hinge-like. Large rotations occur below a prediction value of 0.45 in the hinge region. Most of the peaks there correspond to the peaks indicated in Figure 4A and also correspond to the ‘Pure new’ class. In fact, nearly 80% of those peaks in hinge are where Nnew is larger than Nmaint, Nexchpart, and Nexchpair. Figure 5 shows histograms for the rotation angles for the four categories. One can immediately see that for shear, rotations do not exceed 25°. For these cases, there is nearly always either predominance in the number of maintained, Nmaint, or the number of exchanged-partner contact changes, Nexchpart, indicating that for a preserved-interface movement the angle of rotation is limited to 25°.Fig. 5.
Affiliation: D'Arcy Thompson Centre for Computational Biology, School of Computing Sciences, University of East Anglia, Norwich, NR4 7TJ, UK.