title: Twist-induced defects of the P-SSP7 genome revealed by modeling the cryo-EM density.
abstract: We consider the consequences of assuming that DNA inside of phages can be approximated as a strongly nonlinear persistence length polymer. Recent cryo-EM experiments find a hole in the density map of P-SSP7 phage, located in the DNA segment filling the portal channel of the phage. We use experimentally derived structural constraints with coarse-grained simulation techniques to consider contrasting model interpretations of reconstructed density in the portal channel. The coarse-grained DNA models used are designed to capture the effects of torsional strain and electrostatic environment. Our simulation results are consistent with the interpretation that the vacancy or hole in the experimental density map is due to DNA strain leading to strand separation. We further demonstrate that a moderate negative twisting strain is able to account for the strand separation. This effect of nonlinear persistence length may be important in other aspects of phage DNA packing.
authors: †Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas 77555-0304, United States.
authors: Qian
authors: Q
authors: Wang
authors: ‡Structural and Computational Biology and Molecular Biophysics Program, Baylor College of Medicine, Houston, Texas 77030, United States.
authors: Christopher G
authors: CG
authors: Myers
authors: †Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas 77555-0304, United States.|‡Structural and Computational Biology and Molecular Biophysics Program, Baylor College of Medicine, Houston, Texas 77030, United States.
authors: B Montgomery
authors: BM
authors: Pettitt
mesh_terms: D001435:Bacteriophages / Q000737:chemistry* / Q000235:genetics*; D003198:Computer Simulation; D004279:DNA, Viral / Q000737:chemistry*; D008854:Microscopy, Electron; D008956:Models, Chemical; D008957:Models, Genetic; D017711:Nonlinear Dynamics; D009690:Nucleic Acid Conformation; D055672:Static Electricity
chemical_list: D004279:DNA, Viral