ArticleChemphyschem : a European journal of chemical physics and physical chemistry2016
Quantitative Characterization of Configurational Space Sampled by HIV-1 Nucleocapsid Using Solution NMR, X-ray Scattering and Protein Engineering.
Article in Chemphyschem : a European journal of chemical physics and physical chemistry, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- "It's Only a Model": When Protein Structure Predictions Need Experimental Validation, the Case of the HTLV-1 Tax Protein.Pathogens (Basel, Switzerland) · 2024Review
- Employing computational tools to design a multi-epitope vaccine targeting human immunodeficiency virus-1 (HIV-1).BMC genomics · 2023Article
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- Article
- Overview of the Nucleic-Acid Binding Properties of the HIV-1 Nucleocapsid Protein in Its Different Maturation States.Viruses · 2020Review
- Dynamic structure of the full-length scaffolding protein NHERF1 influences signaling complex assembly.The Journal of biological chemistry · 2019Article
- Retroviral nucleocapsid proteins and DNA strand transfers.Biochimie open · 2018Review
- Targeting a Dark Excited State of HIV-1 Nucleocapsid by Antiretroviral Thioesters Revealed by NMR Spectroscopy.Angewandte Chemie (International ed. in English) · 2018Article
- Article
- Dynamic intramolecular regulation of the histone chaperone nucleoplasmin controls histone binding and release.Nature communications · 2017Article
- Binding kinetics and substrate selectivity in HIV-1 protease-Gag interactions probed at atomic resolution by chemical exchange NMR.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- Transient HIV-1 Gag-protease interactions revealed by paramagnetic NMR suggest origins of compensatory drug resistance mutations.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
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Authors and funding
4 authors.
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Abstract
Nucleic-acid-related events in the HIV-1 replication cycle are mediated by nucleocapsid, a small protein comprising two zinc knuckles connected by a short flexible linker and flanked by disordered termini. Combining experimental NMR residual dipolar couplings, solution X-ray scattering and protein engineering with ensemble simulated annealing, we obtain a quantitative description of the configurational space sampled by the two zinc knuckles, the linker and disordered termini in the absence of nucleic acids. We first compute the conformational ensemble (with an optimal size of three members) of an engineered nucleocapsid construct lacking the N- and C-termini that satisfies the experimental restraints, and then validate this ensemble, as well as characterize the disordered termini, using the experimental data from the full-length nucleocapsid construct. The experimental and computational strategy is generally applicable to multidomain proteins. Differential flexibility within the linker results in asymmetric motion of the zinc knuckles which may explain their functionally distinct roles despite high sequence identity. One of the configurations (populated at a level of ≈40 %) closely resembles that observed in various ligand-bound forms, providing evidence for conformational selection and a mechanistic link between protein dynamics and function.
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