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Title: Atomic Modeling of an Immature Retroviral Lattice Using Molecular Dynamics and Mutagenesis

Journal Article · · Structure

Research Organization:
Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)
Sponsoring Organization:
USDOE Office of Science (SC)
Grant/Contract Number:
AC05-00OR22725
OSTI ID:
1282417
Alternate ID(s):
OSTI ID: 1250907; OSTI ID: 1565311
Journal Information:
Structure, Journal Name: Structure Vol. 23 Journal Issue: 8; ISSN 0969-2126
Publisher:
ElsevierCopyright Statement
Country of Publication:
United Kingdom
Language:
English
Citation Metrics:
Cited by: 30 works
Citation information provided by
Web of Science

References (66)

Visualization of a missing link in retrovirus capsid assembly journal February 2009
Overlapping Roles of the Rous Sarcoma Virus Gag p10 Domain in Nuclear Export and Virion Core Morphology journal July 2007
Characterization of Rous Sarcoma Virus Gag Particles Assembled In Vitro journal March 2001
A Structurally Disordered Region at the C Terminus of Capsid Plays Essential Roles in Multimerization and Membrane Binding of the Gag Protein of Human Immunodeficiency Virus Type 1 journal February 2003
HIV Gag polyprotein: processing and early viral particle assembly journal March 2013
Scalable molecular dynamics with NAMD journal January 2005
Hierarchical coarse-graining strategy for protein-membrane systems to access mesoscopic scales journal January 2010
Mature HIV-1 capsid structure by cryo-electron microscopy and all-atom molecular dynamics journal May 2013
Electron cryotomography of immature HIV-1 virions reveals the structure of the CA and SP1 Gag shells journal March 2007
Three-Dimensional Analysis of Budding Sites and Released Virus Suggests a Revised Model for HIV-1 Morphogenesis journal December 2008
Multi-resolution contour-based fitting of macromolecular structures journal March 2002
HIV Type 1 Gag as a Target for Antiviral Therapy journal January 2012
Clustering Rules: A Comparison of Partitioning and Hierarchical Clustering Algorithms journal March 2006
Proteolytic refolding of the HIV-1 capsid protein amino-terminus facilitates viral core assembly journal March 1998
Exchange Often and Properly in Replica Exchange Molecular Dynamics journal July 2010
Charged Assembly Helix Motif in Murine Leukemia Virus Capsid: an Important Region for Virus Assembly and Particle Size Determination journal June 2003
GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit journal February 2013
Protease Cleavage Leads to Formation of Mature Trimer Interface in HIV-1 Capsid journal August 2012
Using Situs for the integration of multi-resolution structures journal January 2010
Cryo-electron microscopy of tubular arrays of HIV-1 Gag resolves structures essential for immature virus assembly journal May 2014
HIV-1 Assembly, Budding, and Maturation journal March 2012
Structure of the Carboxyl-Terminal Dimerization Domain of the HIV-1 Capsid Protein journal October 1997
Solution structure and dynamics of the Rous sarcoma virus capsid protein and comparison with capsid proteins of other retroviruses 1 1Edited by P. E. Wright journal February 2000
Maturation of the HIV-1 core by a non-diffusional phase transition journal January 2015
Higher-Order Structure of the Rous Sarcoma Virus SP Assembly Domain journal March 2014
The stoichiometry of Gag protein in HIV-1 journal June 2004
Direct measurement of Gag–Gag interaction during retrovirus assembly with FRET and fluorescence correlation spectroscopy journal September 2003
Atomic-level modelling of the HIV capsid journal January 2011
A Two-Pronged Structural Analysis of Retroviral Maturation Indicates that Core Formation Proceeds by a Disassembly-Reassembly Pathway Rather than a Displacive Transition journal October 2013
Cryo-electron Microscopy Reveals Conserved and Divergent Features of Gag Packing in Immature Particles of Rous Sarcoma Virus and Human Immunodeficiency Virus journal January 2006
Retroviral Capsid Assembly: A Role for the CA Dimer in Initiation journal June 2009
Comparative Protein Modelling by Satisfaction of Spatial Restraints journal December 1993
Potential Role for CA-SP in Nucleating Retroviral Capsid Maturation journal April 2014
Human Immunodeficiency Virus Type 1 Assembly, Release, and Maturation book January 2007
Interactions between HIV-1 Gag Molecules in Solution: An Inositol Phosphate-mediated Switch journal January 2007
Structure and self-association of the Rous sarcoma virus capsid protein journal June 2000
Structure of the immature retroviral capsid at 8 Å resolution by cryo-electron microscopy journal June 2012
Roles of Matrix, p2, and N-Terminal Myristoylation in Human Immunodeficiency Virus Type 1 Gag Assembly journal January 2000
Functional Surfaces of the Human Immunodeficiency Virus Type 1 Capsid Protein journal May 2003
Optimization of the Additive CHARMM All-Atom Protein Force Field Targeting Improved Sampling of the Backbone ϕ, ψ and Side-Chain χ 1 and χ 2 Dihedral Angles journal August 2012
Genetic Determinants of Rous Sarcoma Virus Particle Size journal January 1998
Magic Angle Spinning NMR Reveals Sequence-Dependent Structural Plasticity, Dynamics, and the Spacer Peptide 1 Conformation in HIV-1 Capsid Protein Assemblies journal November 2013
RSV Capsid Polymorphism Correlates with Polymerization Efficiency and Envelope Glycoprotein Content: Implications that Nucleation Controls Morphogenesis journal February 2008
Dimeric Rous Sarcoma Virus Capsid Protein Structure Relevant to Immature Gag Assembly journal January 2004
Molecular dynamics simulations of large macromolecular complexes journal April 2015
Rous Sarcoma Virus Gag Protein-Oligonucleotide Interaction Suggests a Critical Role for Protein Dimer Formation in Assembly journal June 2002
A Structural Model for the Generation of Continuous Curvature on the Surface of a Retroviral Capsid journal March 2012
A de novo peptide hexamer with a mutable channel journal October 2011
Proton-Linked Dimerization of a Retroviral Capsid Protein Initiates Capsid Assembly journal May 2009
Nucleic Acid Binding-Induced Gag Dimerization in the Assembly of Rous Sarcoma Virus Particles In Vitro journal December 2003
On the Role of the SP1 Domain in HIV-1 Particle Assembly: a Molecular Switch? journal February 2011
Structure of the immature HIV-1 capsid in intact virus particles at 8.8 Å resolution journal November 2014
Myristoylation Is Required for Human Immunodeficiency Virus Type 1 Gag-Gag Multimerization in Mammalian Cells journal September 2007
Flexibility in the P2 domain of the HIV-1 Gag polyprotein journal August 2004
Three-dimensional Structure of HIV-1 Virus-like Particles by Electron Cryotomography journal February 2005
Elements in HIV-1 Gag contributing to virus particle assembly journal February 2013
A molecular switch required for retrovirus assembly participates in the hexagonal immature lattice journal April 2008
Structure and assembly of immature HIV journal June 2009
Peptide Folding: When Simulation Meets Experiment journal January 1999
An atomic-level mechanism for activation of the kinesin molecular motors journal February 2010
Conserved and Variable Features of Gag Structure and Arrangement in Immature Retrovirus Particles journal September 2010
Helical structure determined by NMR of the HIV-1 (345-392)Gag sequence, surrounding p2: Implications for particle assembly and RNA packaging journal February 2005
Mutations in the Spacer Peptide and Adjoining Sequences in Rous Sarcoma Virus Gag Lead to Tubular Budding journal April 2008
Virus maturation as a new HIV-1 therapeutic target journal June 2009
Viral DNA Synthesis Defects in Assembly-Competent Rous Sarcoma Virus CA Mutants journal January 2001
VMD: Visual molecular dynamics journal February 1996

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