MicroED Structures of HIV-1 Gag CTD-SP1 Reveal Binding Interactions with the Maturation Inhibitor Bevirimat

Purdy, Michael D.; Shi, Dan; Chrustowicz, Jakub; Hattne, Johan; Gonen, Tamir; Yeager, Mark

doi:10.1101/241182

Cited by 5 publications

(14 citation statements)

References 38 publications

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“…Purdy et al additionally suggested that the side chain of K275 (K359 in their numbering scheme) interacts electrostatically with the carboxyl group of bound BVM (20). We do not detect differences in K275 side-chain signals in our 2D ssNMR spectra of VLPs with and without BVM.…”

Section: Discussioncontrasting

confidence: 48%

“…Thus, the immature protein lattice that exists within HIV-1 before the final cleavage step by PR is apparently a thermodynamically metastable state. To explain these observations, it was proposed (12)(13)(14)(15)(16) and subsequently demonstrated (17)(18)(19)(20) that a protein segment around the CA-SP1 junction forms α-helices in the immature Gag lattice, which in turn form six-helix bundles that act as an energetic or steric barrier to disassembly of the immature lattice and subsequent assembly of the mature lattice.…”

mentioning

confidence: 99%

“…The first maturation inhibitor to be investigated in detail was bevirimat (BVM), which was shown to prevent replication of infectious virions by interfering with CA-SP1 cleavage (8,9). Experimental data from cryogenic electron tomography (cryo-ET) of immature HIV-1 and virus-like particles (VLPs) (17) and from electron diffraction of crystals formed by the C-terminal domain of CA with SP1 (CA CTD -SP1) (20) show that BVM binds within six-helix bundles, but these data do not have sufficient resolution to reveal atomic-level details of the BVM binding site or to allow an atomic-level assessment of changes in CA-SP1 conformation, structural ordering, or dynamics that may arise from interactions with BVM.…”

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confidence: 99%

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Effects of an HIV-1 maturation inhibitor on the structure and dynamics of CA-SP1 junction helices in virus-like particles

Gupta

Louis

Tycko

2020

Proc. Natl. Acad. Sci. U.S.A.

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HIV-1 maturation involves conversion of the immature Gag polyprotein lattice, which lines the inner surface of the viral membrane, to the mature capsid protein (CA) lattice, which encloses the viral RNA. Maturation inhibitors such as bevirimat (BVM) bind within six-helix bundles, formed by a segment that spans the junction between the CA and spacer peptide 1 (SP1) subunits of Gag, and interfere with cleavage between CA and SP1 catalyzed by the HIV-1 protease (PR). We report solid-state NMR (ssNMR) measurements on spherical virus-like particles (VLPs), facilitated by segmental isotopic labeling, that provide information about effects of BVM on the structure and dynamics of CA–SP1 junction helices in the immature lattice. Although BVM strongly blocks PR-catalyzed CA–SP1 cleavage in VLPs and blocks conversion of VLPs to tubular CA assemblies, 15N and 13C ssNMR chemical shifts of segmentally labeled VLPs with and without BVM are very similar, indicating that interaction with BVM does not alter the six-helix bundle structure appreciably. Only the 15N chemical shift of A280 (the first residue of SP1) changes significantly, consistent with BVM binding to an internal ring of hydrophobic side chains of L279 residues. Measurements of transverse 15N spin relaxation rates reveal a reduction in the amplitudes and/or timescales of backbone N–H bond motions, corresponding to a rigidification of the six-helix bundles. Overall, our data show that inhibition of HIV-1 maturation by BVM involves changes in structure and dynamics that are surprisingly subtle, but still sufficient to produce a large effect on CA–SP1 cleavage.

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Section: Discussioncontrasting

confidence: 48%

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confidence: 99%

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confidence: 99%

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Effects of an HIV-1 maturation inhibitor on the structure and dynamics of CA-SP1 junction helices in virus-like particles

Gupta

Louis

Tycko

2020

Proc. Natl. Acad. Sci. U.S.A.

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“…This prevents maturation and triggers a morphological defect in virions produced by BVM-mediated replication [ 158 , 159 , 160 ]. Though putative, the binding site is suggested to be inside the six-helix bundle of the CA-SP1 region, therefore stabilising the complex and blocking PR-mediated cleavage [ 161 , 162 , 163 ]. This is also indicative that BVM binds to immature HIV-1 particles, as the binding site is absent following cleavage of CA in mature particles [ 164 ].…”

Section: Ca and Antiretroviral Drugsmentioning

confidence: 99%

The Role of Capsid in the Early Steps of HIV-1 Infection: New Insights into the Core of the Matter

AlBurtamani

Paul

Fassati

2021

Viruses

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In recent years, major advances in research and experimental approaches have significantly increased our knowledge on the role of the HIV-1 capsid in the virus life cycle, from reverse transcription to integration and gene expression. This makes the capsid protein a good pharmacological target to inhibit HIV-1 replication. This review covers our current understanding of the role of the viral capsid in the HIV-1 life cycle and its interaction with different host factors that enable reverse transcription, trafficking towards the nucleus, nuclear import and integration into host chromosomes. It also describes different promising small molecules, some of them in clinical trials, as potential targets for HIV-1 therapy.

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“…Data collection and refinement statistics of SaR2lox. References (42)(43)(44)(45)(46)(47)(48)(49)(50)(51)(52)(53)(54)(55)(56)(57)(58)(59)(60)(61)…”

Section: Supplementary Materialsmentioning

confidence: 99%

Solving a new R2lox protein structure by microcrystal electron diffraction

Lebrette

Clabbers

et al. 2019

Sci. Adv.

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Microcrystal electron diffraction (MicroED) has recently shown potential for structural biology. It enables the study of biomolecules from micrometer-sized 3D crystals that are too small to be studied by conventional x-ray crystallography. However, to date, MicroED has only been applied to redetermine protein structures that had already been solved previously by x-ray diffraction. Here, we present the first new protein structure—an R2lox enzyme—solved using MicroED. The structure was phased by molecular replacement using a search model of 35% sequence identity. The resulting electrostatic scattering potential map at 3.0-Å resolution was of sufficient quality to allow accurate model building and refinement. The dinuclear metal cofactor could be located in the map and was modeled as a heterodinuclear Mn/Fe center based on previous studies. Our results demonstrate that MicroED has the potential to become a widely applicable tool for revealing novel insights into protein structure and function.

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MicroED Structures of HIV-1 Gag CTD-SP1 Reveal Binding Interactions with the Maturation Inhibitor Bevirimat

Cited by 5 publications

References 38 publications

Effects of an HIV-1 maturation inhibitor on the structure and dynamics of CA-SP1 junction helices in virus-like particles

Effects of an HIV-1 maturation inhibitor on the structure and dynamics of CA-SP1 junction helices in virus-like particles

The Role of Capsid in the Early Steps of HIV-1 Infection: New Insights into the Core of the Matter

Solving a new R2lox protein structure by microcrystal electron diffraction

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