Native state dynamics and mechanical properties of human topoisomerase I within a structure-based coarse-grained model.
A coarse grained molecular dynamics model with an implicit solvent is used to elucidate properties of the human topoisomerase I. The model is defined through the native structure and it allows covering significantly longer time scales than in all atom simulations. Single residue and double residue motional characteristics are studied. The results are consistent with all atom simulations reported in the literature indicating usefulness of the model in further studies of this protein. Novel findings include broadening of the description of the dynamic behavior of the lip and hinge regions and a characterization of the motional properties of the RRM binding site of the enzyme. We also consider mechanical stretching of the protein and identify sources of the force peaks. The elastic properties of topoisomerase I are predicted to be average in comparison to other proteins, yielding a maximum force of resistance to pulling which should be of order 120 pN. The contact unraveling pattern is consistent with the understanding of the structure and function of the protein. We find supporting evidence for the hypothesis that the C-terminal domain acquires an ordered structure upon binding with the core enzyme even though it forms a molten globule when in isolation.
Szklarczyk
Oliwia
O
Department of Computer Science, Institute of Theoretical Computer Science, ETH Zurich, Zurich, Switzerland.
Staroń
Krzysztof
K
Cieplak
Marek
M
D019295:Computational Biology; D003198:Computer Simulation; D004264:DNA Topoisomerases, Type I / Q000737:chemistry* / Q000378:metabolism; D006801:Humans; D008958:Models, Molecular; D011487:Protein Conformation; D017434:Protein Structure, Tertiary / Q000502:physiology
D004264:DNA Topoisomerases, Type I