Figure 6a Projections of the topo I MD motions along the first eigenvector. The two extreme projections and the average protein structure are represented from two different viewpoints. Core subdomains I, II and III are represented in yellow, blue and red, respectively; the C terminal domain in cyan; the intact DNA and scissile strands in purple and gold, respectively. (A) The rotation of core subdomain I and II in the directions shown by the yellow and blue arrows, respectively. The two residues with the largest displacement along this eigenvector, Glu232 and Lys320, are labelled and represented with yellow spheres. (B) The concerted motion of the 12 13 14 sheet, permitted by the high flexibility of the loop centred on Gly520 (red sphere). Such a motion is coupled with that of helix 13, containing Asp533 (red sphere)..
Protein concerted motions in the DNA human topoisomerase I complex
Nucleic Acids Res. 2003 Mar 1; 31(5):1525-1535
The collective motions of the core and C terminal domains of human topoisomerase I (topo I) have been analysed by molecular dynamics simulation of the.....
The collective motions of the core and C terminal domains of human topoisomerase I (topo I) have been analysed by molecular dynamics simulation of the protein in covalent complex with a 22 bp DNA duplex. The analysis evidenced a great number of correlated movements of core subdomain I and II residues, and a central role for helix 5 in the protein DNA communication, in particular with the scissile strand downstream of the cleavage site. The flow of information between these core subdomains and DNA suggests that subdomains I and II play an essential role in the DNA relaxation process. In core subdomain III the majority of DNA contacting residues do not communicate with protein regions far from DNA, suggesting that they have a structural role. However, selected core subdomain III residues, involved in the orientation of the active site region, show correlated movements with residues distant from DNA, indicating that the information concerning the catalytic event is also transmitted. The flexibility of two loops formed by residues 519 520 and 580 584 seems indispensable to the dynamic participation of core subdomain III to the DNA cleavage and religation steps. The motion of specific residues has also been found to explain the effect of single point mutations that make topo I resistant to the anticancer drug camptothecin.
Copyright 2003 Oxford University Press