Simulating the electrostatic guidance of the vectorial translocations in hexameric helicases and translocases.
The molecular origin of the action of helicases is explored, starting with a model built based on the different X-ray structures of the large tumor antigen (LTag) hexameric helicase and a simplified model containing the ionized phosphate backbones of a single-strand DNA. The coupling between the protein structural changes and the translocation process is quantified using an effective electrostatic free-energy surface for the protein/DNA complex. This surface is then used in Langevin dynamics simulations of the time dependence of the translocation process. Remarkably, the simulated motion along the free-energy surface results in a vectorial translocation of the DNA, consistent with the biological process. The electrostatic energy of the system appears to reproduce the directionality of this process. Thus, we are able to provide a consistent structure-based molecular description of the energetic and dynamics of the translocation process. This analysis may have general implications for relating structural models to translocation directionality in helicases and other DNA translocases.
Liu
Hanbin
H
Departments of Chemistry, University of Southern California, Los Angeles, CA 90089, USA.
Shi
Yemin
Y
Chen
Xiaojiang S
XS
Warshel
Arieh
A
D000957:Antigens, Viral, Tumor / Q000737:chemistry* / Q000378:metabolism; D018360:Crystallography, X-Ray; D004265:DNA Helicases / Q000737:chemistry* / Q000378:metabolism; D004277:DNA, Single-Stranded / Q000737:chemistry* / Q000378:metabolism; D008954:Models, Biological; D008958:Models, Molecular; D011487:Protein Conformation; D055503:Protein Multimerization; D055672:Static Electricity
D000957:Antigens, Viral, Tumor; D004277:DNA, Single-Stranded; D004265:DNA Helicases