Dynamic Nuclear Polarization Magic-Angle Spinning Nuclear Magnetic Resonance Combined with Molecular Dynamics Simulations Permits Detection of Order and Disorder in Viral Assemblies

doi:10.1021/acs.jpcb.9b02293

	Dynamic Nuclear Polarization Magic-Angle Spinning Nuclear Magnetic Resonance Combined with Molecular Dynamics Simulations Permits Detection of Order and Disorder in Viral Assemblies
	Gupta, Rupal 1,3,9; Zhang, Huilan 1,3; Lu, Manman 1,3; Hou, Guangjin 1,3,10; Caporini, Marc 2,8; Rosay, Melanie 2; Maas, Werner 2; Struppe, Jochem 2; Ahn, Jinwoo 3,4; Byeon, In-Ja L.3,4
刊名	JOURNAL OF PHYSICAL CHEMISTRY B
	2019-06-20
卷号	123 期号:24 页码:5048-5058
ISSN号	1520-6106
DOI	10.1021/acs.jpcb.9b02293
通讯作者	Pintacuda, Guido(guido.pintacuda@ens-Iyon.fr) ; Lesage, Anne(Anne.Lesage@ens-lyon.fr) ; Gronenborn, Angela M.(amg100@pitt.edu) ; Polenova, Tatyana(tpolenov@udel.edu)
英文摘要	We report dynamic nuclear polarization (DNP)-enhanced magic-angle spinning (MAS) NMR spectroscopy in viral capsids from HIV-1 and bacteriophage AP205. Viruses regulate their life cycles and infectivity through modulation of their structures and dynamics. While static structures of capsids from several viruses are now accessible with near-atomic-level resolution, atomic-level understanding of functionally important motions in assembled capsids is lacking. We observed up to 64-fold signal enhancements by DNP, which permitted in-depth analysis of these assemblies. For the HIV-1 CA assemblies, a remarkably high spectral resolution in the 3D and 2D heteronuclear data sets permitted the assignment of a significant fraction of backbone and side-chain resonances. Using an integrated DNP MAS NMR and molecular dynamics (MD) simulation approach, the conformational space sampled by the assembled capsid at cryogenic temperatures was mapped. Qualitatively, a remarkable agreement was observed for the experimental C-13/N-15 chemical shift distributions and those calculated from substructures along the MD trajectory. Residues that are mobile at physiological temperatures are frozen out in multiple conformers at cryogenic conditions, resulting in broad experimental and calculated chemical shift distributions. Overall, our results suggest that DNP MAS NMR measurements in combination with MD simulations facilitate a thorough understanding of the dynamic signatures of viral capsids.
资助项目	National Institutes of Health (NIH)[P50A1150481] ; GRAL[ANR-10-LABX-49-01] ; Finovi (Fondation Innovations en Infectiologie) ; NSF[CHE0959496] ; NIGMS[P30GM110758] ; FRISBI[ANR-10-INSB-05-02] ; FRISBI[UMS 3518 CNRS-CEA-UJA-EMBL] ; GRAL within the Grenoble Partnership for Structural Biology (PSB)[ANR-10-LABX-49-01] ; GRAL within the Grenoble Partnership for Structural Biology (PSB)[UMS 3518 CNRS-CEA-UJA-EMBL] ; Rhone-Alpes Region ; Fondation Recherche Medicale (FRM) ; Fonds FEDER ; Centre National de la Recherche Scientifique (CNRS) ; CEA ; University of Grenoble ; EMBL ; GIS-Infrastructures en Biologie Sante et Agronomie (IBISA) ; Electron Microscopy platform of the Integrated Structural Biology of Grenoble (ISBG)[UMS 3518]
WOS关键词	HIV-1 CAPSID PROTEIN ; ENHANCED MAS NMR ; STRUCTURAL BIOLOGY ; COAT PROTEIN ; CONFORMATIONAL DISTRIBUTIONS ; VIRUS NUCLEOPROTEIN ; CHEMICAL-SHIFT ; INTACT VIRUS ; CRYO-EM ; BACTERIOPHAGE
WOS研究方向	Chemistry
语种	英语
出版者	AMER CHEMICAL SOC
WOS记录号	WOS:000472800700004
资助机构	National Institutes of Health (NIH) ; National Institutes of Health (NIH) ; GRAL ; GRAL ; Finovi (Fondation Innovations en Infectiologie) ; Finovi (Fondation Innovations en Infectiologie) ; NSF ; NSF ; NIGMS ; NIGMS ; FRISBI ; FRISBI ; GRAL within the Grenoble Partnership for Structural Biology (PSB) ; GRAL within the Grenoble Partnership for Structural Biology (PSB) ; Rhone-Alpes Region ; Rhone-Alpes Region ; Fondation Recherche Medicale (FRM) ; Fondation Recherche Medicale (FRM) ; Fonds FEDER ; Fonds FEDER ; Centre National de la Recherche Scientifique (CNRS) ; Centre National de la Recherche Scientifique (CNRS) ; CEA ; CEA ; University of Grenoble ; University of Grenoble ; EMBL ; EMBL ; GIS-Infrastructures en Biologie Sante et Agronomie (IBISA) ; GIS-Infrastructures en Biologie Sante et Agronomie (IBISA) ; Electron Microscopy platform of the Integrated Structural Biology of Grenoble (ISBG) ; Electron Microscopy platform of the Integrated Structural Biology of Grenoble (ISBG) ; National Institutes of Health (NIH) ; National Institutes of Health (NIH) ; GRAL ; GRAL ; Finovi (Fondation Innovations en Infectiologie) ; Finovi (Fondation Innovations en Infectiologie) ; NSF ; NSF ; NIGMS ; NIGMS ; FRISBI ; FRISBI ; GRAL within the Grenoble Partnership for Structural Biology (PSB) ; GRAL within the Grenoble Partnership for Structural Biology (PSB) ; Rhone-Alpes Region ; Rhone-Alpes Region ; Fondation Recherche Medicale (FRM) ; Fondation Recherche Medicale (FRM) ; Fonds FEDER ; Fonds FEDER ; Centre National de la Recherche Scientifique (CNRS) ; Centre National de la Recherche Scientifique (CNRS) ; CEA ; CEA ; University of Grenoble ; University of Grenoble ; EMBL ; EMBL ; GIS-Infrastructures en Biologie Sante et Agronomie (IBISA) ; GIS-Infrastructures en Biologie Sante et Agronomie (IBISA) ; Electron Microscopy platform of the Integrated Structural Biology of Grenoble (ISBG) ; Electron Microscopy platform of the Integrated Structural Biology of Grenoble (ISBG) ; National Institutes of Health (NIH) ; National Institutes of Health (NIH) ; GRAL ; GRAL ; Finovi (Fondation Innovations en Infectiologie) ; Finovi (Fondation Innovations en Infectiologie) ; NSF ; NSF ; NIGMS ; NIGMS ; FRISBI ; FRISBI ; GRAL within the Grenoble Partnership for Structural Biology (PSB) ; GRAL within the Grenoble Partnership for Structural Biology (PSB) ; Rhone-Alpes Region ; Rhone-Alpes Region ; Fondation Recherche Medicale (FRM) ; Fondation Recherche Medicale (FRM) ; Fonds FEDER ; Fonds FEDER ; Centre National de la Recherche Scientifique (CNRS) ; Centre National de la Recherche Scientifique (CNRS) ; CEA ; CEA ; University of Grenoble ; University of Grenoble ; EMBL ; EMBL ; GIS-Infrastructures en Biologie Sante et Agronomie (IBISA) ; GIS-Infrastructures en Biologie Sante et Agronomie (IBISA) ; Electron Microscopy platform of the Integrated Structural Biology of Grenoble (ISBG) ; Electron Microscopy platform of the Integrated Structural Biology of Grenoble (ISBG) ; National Institutes of Health (NIH) ; National Institutes of Health (NIH) ; GRAL ; GRAL ; Finovi (Fondation Innovations en Infectiologie) ; Finovi (Fondation Innovations en Infectiologie) ; NSF ; NSF ; NIGMS ; NIGMS ; FRISBI ; FRISBI ; GRAL within the Grenoble Partnership for Structural Biology (PSB) ; GRAL within the Grenoble Partnership for Structural Biology (PSB) ; Rhone-Alpes Region ; Rhone-Alpes Region ; Fondation Recherche Medicale (FRM) ; Fondation Recherche Medicale (FRM) ; Fonds FEDER ; Fonds FEDER ; Centre National de la Recherche Scientifique (CNRS) ; Centre National de la Recherche Scientifique (CNRS) ; CEA ; CEA ; University of Grenoble ; University of Grenoble ; EMBL ; EMBL ; GIS-Infrastructures en Biologie Sante et Agronomie (IBISA) ; GIS-Infrastructures en Biologie Sante et Agronomie (IBISA) ; Electron Microscopy platform of the Integrated Structural Biology of Grenoble (ISBG) ; Electron Microscopy platform of the Integrated Structural Biology of Grenoble (ISBG)
内容类型	期刊论文
源URL	[http://cas-ir.dicp.ac.cn/handle/321008/175066]
专题	大连化学物理研究所_中国科学院大连化学物理研究所
通讯作者	Pintacuda, Guido; Lesage, Anne; Gronenborn, Angela M.; Polenova, Tatyana
作者单位	1.Univ Delaware, Dept Chem & Biochem, Newark, DC 19716 USA 2.Bruker Biospin Corp, 15 Fortune Dr, Billerica, MA 01821 USA 3.Univ Pittsburgh, Sch Med, Pittsburgh Ctr HIV Prot Interact, 3501 Fifth Ave, Pittsburgh, PA 15213 USA 4.Univ Pittsburgh, Sch Med, Dept Biol Struct, 3501 Fifth Ave, Pittsburgh, PA 15213 USA 5.Leibniz Inst Mol Pharmacol, Robert Roessle Str 10, D-13125 Berlin, Germany 6.Ecole Normale Super Lyon, UMR CNRS 5280, Inst Sci Analyt, Ctr RMN Tres Hauts Champs, 5 Rue Doua, F-69100 Lyon, France 7.Ecole Polytech Fed Lausanne, Inst Sci & Ingn Chim, CH-1015 Lausanne, Switzerland 8.Amgen Inc, 360 Binney St, Cambridge, MA 02142 USA 9.CUNY Coll Staten Isl, Dept Chem, Bldg 6S,Room 214,2800 Victory Blvd, New York, NY 10314 USA 10.Chinese Acad Sci, Dalian Inst Chem Phys, State Key Lab Catalysis, Dalian 116023, Peoples R China
推荐引用方式 GB/T 7714	Gupta, Rupal,Zhang, Huilan,Lu, Manman,et al. Dynamic Nuclear Polarization Magic-Angle Spinning Nuclear Magnetic Resonance Combined with Molecular Dynamics Simulations Permits Detection of Order and Disorder in Viral Assemblies[J]. JOURNAL OF PHYSICAL CHEMISTRY B,2019,123(24):5048-5058.
APA	Gupta, Rupal.,Zhang, Huilan.,Lu, Manman.,Hou, Guangjin.,Caporini, Marc.,...&Polenova, Tatyana.(2019).Dynamic Nuclear Polarization Magic-Angle Spinning Nuclear Magnetic Resonance Combined with Molecular Dynamics Simulations Permits Detection of Order and Disorder in Viral Assemblies.JOURNAL OF PHYSICAL CHEMISTRY B,123(24),5048-5058.
MLA	Gupta, Rupal,et al."Dynamic Nuclear Polarization Magic-Angle Spinning Nuclear Magnetic Resonance Combined with Molecular Dynamics Simulations Permits Detection of Order and Disorder in Viral Assemblies".JOURNAL OF PHYSICAL CHEMISTRY B 123.24(2019):5048-5058.