Illuminating an invisible state of the HIV-1 capsid protein CTD dimer using 19F NMR and weighted ensemble simulations

• 成果类型: Article
• 署名作者: Yang, Darian T.; Chong, Lillian T.; Gronenborn, Angela M.
• 署名单位: Pennsylvania Commonwealth System of Higher Education (PCSHE); University of Pittsburgh; Carnegie Mellon University; Pennsylvania Commonwealth System of Higher Education (PCSHE); University of Pittsburgh; Pennsylvania Commonwealth System of Higher Education (PCSHE); University of Pittsburgh
• 刊物名称: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
• ISSN/ISSBN: 0027-13605
• DOI: 10.1073/pnas.2420371122
• 发表日期: 2025-02-25
• 关键词: molecular-dynamics simulations; dimerization domain; amber; models; flexibility; software; reveals; SYSTEM

摘要

The HIV-1 capsid protein (CA) assembles into a conical shell during viral maturation, encasing and protecting the viral RNA genome. The C-terminal domain (CTD) the two-domain capsid protein dimerizes, and this dimer connects individual chains in the mature capsid lattice. Previous NMR studies have shown that different dimer arrangements can be formed by isolated capsid protein chains and in assembled capsid lattices; however, the dynamics and functional relevance of these alternate dimers are unknown. To explore the conformational landscape of the CA-CTD dimer, carried out atomistic molecular dynamics simulations using the weighted ensemble sampling strategy, generating an ensemble of conformations. Focusing on the two dimer forms previously observed via solution NMR, we refined the conformational ensemble to highlight two metastable states using a Markov state model. Experimentally, measured the interconversion rates between the two alternate dimers using 19F NMR, and these rates showed good agreement with the interconversion rates derived the simulations. After identifying the key interactions that distinguish the dimer states, the alternate dimer was further experimentally verified through disulfide crosslinking. Our results demonstrate the advantages of pairing weighted ensemble path sampling with 19F NMR to gain atomistic insights into the hidden dimer state of the HIV capsid protein.