The three-dimensional structure of DNA packed within the capsid of bacteriophages is determined by the physical chemistry of DNA folding, certain features of the packaging process, and the characteristics of the capsid. In most cases, experiments only show averaged images of the DNA within the capsid, obscuring some details of the actual encapsidated DNA conformation. In this work, we have quantified the electrostatic character of the inner surface of the capsid for two phages, phi29 and lambda, finding different values of the superficial net charge. In the case of phage phi29, we found that the innermost capsid wall has an attractive character toward the confined nucleic acid, and we devised a capsid model capturing these features. We used this model to run molecular dynamics simulations aimed at unveiling how the interactions between the DNA and the capsid wall could affect the distribution and conformation of the packed genome. We found that DNA tends to be closer to the capsid wall, specially at early stages of the packaging process, as indicated by a more pronounced peak near the wall in the two-dimensional radial density profile. On the other hand, we quantified the orientation of the DNA strand across the capsid and found that our attractive model for the capsid doesn't trigger a different conformation of the packed genome compared with the non-attractive capsid wall.
Acknowledgements: The authors would like to thank the NSF-Access HPC Allocations team for giving us the opportunity to use the computational resources needed to run the simulations. This work used Purdue Anvil-GPU at Purdue University through allocation Discover: BIO220164 from the Advanced Cyberinfrastructure Coordination Ecosystem: Services & Support (ACCESS) program, which is supported by National Science Foundation grants #2138259, #2138286, #2138307, #2137603, and #2138296.