Advanced search

Filter By:

Journal Check one or more journals to show results from those journals only.

Choose more journals

Article type Check one or more article types to show results from those article types only.
Subject Check one or more subjects to show results from those subjects only.
Date Choose a date option to show results from those dates only.

Custom date range

Clear all filters
Sort by:
Showing 1–18 of 18 results
Advanced filters: Author: Juan R. Perilla Clear advanced filters

  • The HTLV-1 capsid (CA) domain of Gag was resolved to 3.4 Å resolution and reveals insights into immature lattice stabilization, the varying lattice curvatures and distances from the membrane, and the dispensable nature of inositol hexakisphosphate (IP6) for immature particle assembly.

    • William G. Arndt
    • Alireza Ramezani
    • Louis M. Mansky
    ResearchOpen Access
    Nature Communications
    Volume: 17, P: 1-12

  • Rubisco is a central enzyme in the global CO2 fixation during photosynthesis. Using cryo-ET on cryo-FIB milled alga cells, the authors reveal the native structures, interactions, and spatial organization of Rubisco within the pyrenoid of green algae.

    • Nadav Elad
    • Zhen Hou
    • Peijun Zhang
    ResearchOpen Access
    Nature Communications
    Volume: 16, P: 1-13

  • IP6 is a critical host cofactor for HIV-1 assembly and infectivity. In this study, the authors uncover the structural basis by which HIV-1 adapts to a deficiency in IP6 packaging through a G225R mutation at the C-terminus of the capsid protein.

    • Yanan Zhu
    • Alex B. Kleinpeter
    • Peijun Zhang
    ResearchOpen Access
    Nature Communications
    Volume: 16, P: 1-16

  • The large and complex HIV-1 capsid modulates several molecular events during HIV-1’s infective cycle. Here the authors use all-atom molecular dynamic simulations to probe the biophysical properties of the genome-free HIV-1 capsid.

    • Juan R. Perilla
    • Klaus Schulten
    ResearchOpen Access
    Nature Communications
    Volume: 8, P: 1-10

  • Here the authors report SBCG2 an update to the neural network based, Shape-Based Coarse Graining (SBCG) approach for creating coarse grained molecular topologies with atomistic detail. They show how SBCG2 can reduce the computational costs of simulating very large assemblies like the HIV-1 capsid allowing simulation on commodity hardware.

    • Alexander J. Bryer
    • Juan S. Rey
    • Juan R. Perilla
    ResearchOpen Access
    Nature Communications
    Volume: 14, P: 1-19

  • The hexagonal immature capsid lattice of human endogenous retrovirus K is determined at 3.2 Å resolution, which is an assembly of small molecule-stabilized hexamers via dimer and trimer interfaces, a highly conserved mechanism among retroviruses.

    • Anna-Sophia Krebs
    • Hsuan-Fu Liu
    • Peijun Zhang
    ResearchOpen Access
    Nature Communications
    Volume: 14, P: 1-11

  • The host cell factor cyclophilin A (CypA) interacts with the HIV-1 capsid and regulates infectivity. Here the authors combine cryo-EM, solid-state NMR and all-atom MD simulations, identifying an interaction interface between CypA and the HIV capsid that stabilizes the viral capsid and regulates infectivity.

    • Chuang Liu
    • Juan R. Perilla
    • Peijun Zhang
    ResearchOpen Access
    Nature Communications
    Volume: 7, P: 1-10

  • HIV maturation inhibitors such as bevirimat (BVM) interfering with Gag processing are emerging as alternative anti-retroviral drug candidates. Here, the authors report structures of assemblies of HIV-1 Gag fragments spanning the CA C-terminal domain and SP1 region bound to BVM.

    • Sucharita Sarkar
    • Kaneil K. Zadrozny
    • Tatyana Polenova
    ResearchOpen Access
    Nature Communications
    Volume: 14, P: 1-13

  • Chlamydia trachomatis forms membrane-bound inclusions inside the host cell that are decorated with IncA, a SNARE-like protein that promotes the fusion of inclusions. Here, Cingolani et al. show that the protein folds into a non-canonical four-helix bundle and identify an intramolecular clamp required for membrane fusion.

    • Gino Cingolani
    • Michael McCauley
    • Fabienne Paumet
    ResearchOpen Access
    Nature Communications
    Volume: 10, P: 1-12

  • The process of HIV particle maturation involves complex molecular transitions. Here the authors combine NMR spectroscopy, cryo-EM, and molecular dynamics simulations to provide insight into the conformational equilibria in CA-SP1 assemblies relevant to HIV-1 maturation intermediates formation.

    • Mingzhang Wang
    • Caitlin M. Quinn
    • Tatyana Polenova
    ResearchOpen Access
    Nature Communications
    Volume: 8, P: 1-12

  • Despite their relevance as regulators of actin severing and filament disassembly, few structural insights into the mechanism of cofilin-isoform-specific severing activity are reported. Here, the authors provide structural insights towards actin severing activity by human cofilin-2 obtained by MAS NMR and all-atom MD simulations. The results reveal an isoform-specific binding mode unique to CFL2 that may be related to its potent severing properties in-vivo.

    • Jodi Kraus
    • Ryan W. Russell
    • Tatyana Polenova
    ResearchOpen Access
    Nature Communications
    Volume: 13, P: 1-12

  • The status of the harlequin toads has not improved since 2004 despite species rediscoveries accompanied by increasing conservation efforts, and habitat destruction and degradation continue to threaten them today, according to an analysis of population status records over the period 2004–2022.

    • Stefan Lötters
    • Amadeus Plewnia
    • Enrique La Marca
    ResearchOpen Access
    Communications Earth & Environment
    Volume: 4, P: 1-8

  • Inositol hexakisphosphate, which is found in all mammalian cells, binds to two separate sites to promote the assembly and maturation of HIV-1 virus particles.

    • Robert A. Dick
    • Kaneil K. Zadrozny
    • Volker M. Vogt
    Research
    Nature
    Volume: 560, P: 509-512

  • In the Big Data era, a change of paradigm in the use of molecular dynamics is required. Trajectories should be stored under FAIR (findable, accessible, interoperable and reusable) requirements to favor its reuse by the community under an open science paradigm.

    • Rommie E. Amaro
    • Johan Åqvist
    • Modesto Orozco
    Comments & Opinion
    Nature Methods
    Volume: 22, P: 641-645