Research of conformational changes of complexes from protein VirE2-VirE1 the method of normal fashions

Before research by a method of normal fashions of complexes from protein VirE2, by means of package GROMOS96 of program Swiss-PdbViewer had been spent minimisation of energy of modelling complexes of protein VirE2.

The greatest conformational changes, as is known, are bound to low-frequency fashions. Models from two and four proteins VirE2 have been calculated 11 low-frequency normal fashions for structural models of complexes from proteins VirE2-VirE1. First six modes correspond to global locomotions of a molecula (alterations and turns with zero frequency), and will be ignored in following discussions. Following 5 modes - from the seventh on the eleventh - will be renumbered from the first on the fifth, accordingly.
Indicator of that, how many amino acids are involved in collective locomotions at normal fluctuations, degree kollektivnosti is.
The card of fluctuation of distances is a template which displays the maximum distances of fluctuations between all steams of atoms a C-alpha and between two maximum changes konformatsii. The distance augmentation is shown (fig. 3.21, 3.22, 3.24, 3.26) dark blue, reduction - red. Each cage corresponds to one residual. Grey lines are spent through each 10 residual, yellow lines - through each 100 residual (considering from the top left angle). Flexible and rigid regions, and also their relative locomotion, can be easily identified by means of such cards.
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