Regulation of the ordinal DNA translocation cycle in bacteriophage X29 through trans-subunit interactions

• 成果类型: Article
• 署名作者: Dargis, Rokas; Pajak, Joshua; Ariyawansa, Pavan; Morais, Marc C.; Jardine, PaulJ.; Arya, Gaurav
• 署名单位: Duke University; University of Massachusetts System; UMass Chan Medical School; University of Massachusetts Worcester; Indiana University System; Indiana University Bloomington; University of Minnesota System; University of Minnesota Twin Cities
• 刊物名称: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
• ISSN/ISSBN: 0027-13558
• DOI: 10.1073/pnas.2504780122
• 发表日期: 2025-07-03
• 关键词: force generation; COORDINATION; motor; division; provides; genome; rna; aaa

摘要

Certain viruses such as tailed bacteriophages and herpes simplex virus package double-stranded DNA into empty procapsids via powerful, ring-shaped molecular motors. High-resolution structures and force measurements on the DNA packaging motor of bacteriophage X29 revealed that its five ATPase subunits coordinate ATP hydrolysis with each other to maintain the proper cyclic sequence of DNA translocation steps about the ring. Here, we explore how the X29 motor regulates translocation by timing key events, namely ATP binding/hydrolysis and DNA gripping, through trans-subunit interactions. We used subunit dimers bound to DNA as our model system, a minimal system that still captures the conformation and trans-subunit interactions of the full pentameric motor complex. Molecular dynamics simulations of all-ATP and mixed ATP-ADP dimers revealed that the nucleotide occupancy of one subunit strongly affects the ability to hydrolyze ATP in the adjacent subunit by altering the free energy landscape of its catalytic glutamate approaching the gamma phosphate of ATP. Specifically, one ATP-bound subunit donates residues in trans that sterically block the neighboring subunit's catalytic glutamate. This steric hindrance is resolved when the first subunit hydrolyzes ATP and is ADP bound. This obstructive mechanism is supported by functional mutagenesis and appears to be conserved across several F29 relatives. Mutual information analysis of our simulations revealed intersubunit signaling pathways, via the trans-acting obstructive residues, that allow for sensing and communication between the binding pockets of adjacent subunits. This work reveals how the sequential order of DNA translocation events among subunits is preserved through trans-subunit interactions and pathways.