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Mechanistic behavior and subtle key events during DNA clamp opening and closing in T4 bacteriophage

Journal Article


Abstract


  • Clamp loaders ensure processive DNA replication by loading the toroidal shaped sliding clamps onto the DNA. The sliding clamps serve as a platform for the attachment of polymerases and several other proteins associated with the regulation of various cellular processes. Clamp loaders are fascinating as nanomachines that engage in protein-protein and protein-DNA interactions. The loading mechanism of the clamp around dsDNA at the atomic level has not yet been fully explored. We performed microsecond timescale molecular dynamics simulations to reveal the dynamics of two different intermediate complexes involved in loading of the clamps around DNA. We conducted various time-dependent MD-driven analyses including the highly robust Molecular Mechanics Poisson-Boltzmann Surface Area (MMPBSA) calculations to observe changes in the structural elements of the clamp loader-clamp-DNA complexes in open and closed states. Our studies revealed the structural consequences of ATP hydrolysis events at different subunits of the clamp loader. This study would help in a better understanding of the clamp loading mechanism and would allow tackling various complications that might arise due to irregularities in this process.

Publication Date


  • 2022

Citation


  • Bhardwaj, V. K., Oakley, A., & Purohit, R. (2022). Mechanistic behavior and subtle key events during DNA clamp opening and closing in T4 bacteriophage. International Journal of Biological Macromolecules, 208, 11-19. doi:10.1016/j.ijbiomac.2022.03.021

Scopus Eid


  • 2-s2.0-85126270381

Web Of Science Accession Number


Start Page


  • 11

End Page


  • 19

Volume


  • 208

Abstract


  • Clamp loaders ensure processive DNA replication by loading the toroidal shaped sliding clamps onto the DNA. The sliding clamps serve as a platform for the attachment of polymerases and several other proteins associated with the regulation of various cellular processes. Clamp loaders are fascinating as nanomachines that engage in protein-protein and protein-DNA interactions. The loading mechanism of the clamp around dsDNA at the atomic level has not yet been fully explored. We performed microsecond timescale molecular dynamics simulations to reveal the dynamics of two different intermediate complexes involved in loading of the clamps around DNA. We conducted various time-dependent MD-driven analyses including the highly robust Molecular Mechanics Poisson-Boltzmann Surface Area (MMPBSA) calculations to observe changes in the structural elements of the clamp loader-clamp-DNA complexes in open and closed states. Our studies revealed the structural consequences of ATP hydrolysis events at different subunits of the clamp loader. This study would help in a better understanding of the clamp loading mechanism and would allow tackling various complications that might arise due to irregularities in this process.

Publication Date


  • 2022

Citation


  • Bhardwaj, V. K., Oakley, A., & Purohit, R. (2022). Mechanistic behavior and subtle key events during DNA clamp opening and closing in T4 bacteriophage. International Journal of Biological Macromolecules, 208, 11-19. doi:10.1016/j.ijbiomac.2022.03.021

Scopus Eid


  • 2-s2.0-85126270381

Web Of Science Accession Number


Start Page


  • 11

End Page


  • 19

Volume


  • 208