Paper Citing NAMD - Abstract
Xu, Xiaojun; Guardiani, Carlo; Yan, Chunli; Ivanov, Ivaylo
Opening pathways of the DNA clamps proliferating cell nuclear antigen and Rad9-Rad1-Hus1
NUCLEIC ACIDS RESEARCH, 41:10020-10031, DEC 2013
Proliferating cell nuclear antigen and the checkpoint clamp Rad9-Rad1-Hus1 topologically encircle DNA and act as mobile platforms in the recruitment of proteins involved in DNA damage response and cell cycle regulation. To fulfill these vital cellular functions, both clamps need to be opened and loaded onto DNA by a clamp loader complex-a process, which involves disruption of the DNA clamp's subunit interfaces. Herein, we compare the relative stabilities of the interfaces using the molecular mechanics Poisson-Boltzmann solvent accessible surface method. We identify the Rad9-Rad1 interface as the weakest and, therefore, most likely to open during clamp loading. We also delineate the dominant interface disruption pathways under external forces in multiple-trajectory steered molecular dynamics runs. We show that, similar to the case of protein folding, clamp opening may not proceed through a single interface breakdown mechanism. Instead, we identify an ensemble of opening pathways, some more prevalent than others, characterized by specific groups of contacts that differentially stabilize the regions of the interface and determine the spatial and temporal patterns of breakdown. In Rad9-Rad1-Hus1, the Rad9-Rad1 and Rad9-Hus1 interfaces share the same dominant unzipping pathway, whereas the Hus1-Rad1 interface is disrupted concertedly with no preferred directionality.
