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

Authors:
; ; ; ; ;
Publication Date:
Research Org.:
Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)
Sponsoring Org.:
USDOE Office of Science (SC)
OSTI Identifier:
1282417
Alternate Identifier(s):
OSTI ID: 1250907; OSTI ID: 1565311
Grant/Contract Number:  
AC05-00OR22725
Resource Type:
Published Article
Journal Name:
Structure
Additional Journal Information:
Journal Name: Structure Journal Volume: 23 Journal Issue: 8; Journal ID: ISSN 0969-2126
Publisher:
Elsevier
Country of Publication:
United Kingdom
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Goh, Boon Chong, Perilla, Juan R., England, Matthew R., Heyrana, Katrina J., Craven, Rebecca C., and Schulten, Klaus. Atomic Modeling of an Immature Retroviral Lattice Using Molecular Dynamics and Mutagenesis. United Kingdom: N. p., 2015. Web. doi:10.1016/j.str.2015.05.017.
Goh, Boon Chong, Perilla, Juan R., England, Matthew R., Heyrana, Katrina J., Craven, Rebecca C., & Schulten, Klaus. Atomic Modeling of an Immature Retroviral Lattice Using Molecular Dynamics and Mutagenesis. United Kingdom. https://doi.org/10.1016/j.str.2015.05.017
Goh, Boon Chong, Perilla, Juan R., England, Matthew R., Heyrana, Katrina J., Craven, Rebecca C., and Schulten, Klaus. Sat . "Atomic Modeling of an Immature Retroviral Lattice Using Molecular Dynamics and Mutagenesis". United Kingdom. https://doi.org/10.1016/j.str.2015.05.017.
@article{osti_1282417,
title = {Atomic Modeling of an Immature Retroviral Lattice Using Molecular Dynamics and Mutagenesis},
author = {Goh, Boon Chong and Perilla, Juan R. and England, Matthew R. and Heyrana, Katrina J. and Craven, Rebecca C. and Schulten, Klaus},
abstractNote = {},
doi = {10.1016/j.str.2015.05.017},
journal = {Structure},
number = 8,
volume = 23,
place = {United Kingdom},
year = {Sat Aug 01 00:00:00 EDT 2015},
month = {Sat Aug 01 00:00:00 EDT 2015}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
https://doi.org/10.1016/j.str.2015.05.017

Citation Metrics:
Cited by: 30 works
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Works referenced in this record:

Visualization of a missing link in retrovirus capsid assembly
journal, February 2009

  • Cardone, Giovanni; Purdy, John G.; Cheng, Naiqian
  • Nature, Vol. 457, Issue 7230
  • DOI: 10.1038/nature07724

Overlapping Roles of the Rous Sarcoma Virus Gag p10 Domain in Nuclear Export and Virion Core Morphology
journal, July 2007

  • Scheifele, Lisa Z.; Kenney, Scott P.; Cairns, Tina M.
  • Journal of Virology, Vol. 81, Issue 19
  • DOI: 10.1128/JVI.01061-07

Characterization of Rous Sarcoma Virus Gag Particles Assembled In Vitro
journal, March 2001


HIV Gag polyprotein: processing and early viral particle assembly
journal, March 2013


Scalable molecular dynamics with NAMD
journal, January 2005

  • Phillips, James C.; Braun, Rosemary; Wang, Wei
  • Journal of Computational Chemistry, Vol. 26, Issue 16, p. 1781-1802
  • DOI: 10.1002/jcc.20289

Hierarchical coarse-graining strategy for protein-membrane systems to access mesoscopic scales
journal, January 2010

  • Ayton, Gary S.; Lyman, Edward; Voth, Gregory A.
  • Faraday Discuss., Vol. 144
  • DOI: 10.1039/B901996K

Mature HIV-1 capsid structure by cryo-electron microscopy and all-atom molecular dynamics
journal, May 2013

  • Zhao, Gongpu; Perilla, Juan R.; Yufenyuy, Ernest L.
  • Nature, Vol. 497, Issue 7451
  • DOI: 10.1038/nature12162

Electron cryotomography of immature HIV-1 virions reveals the structure of the CA and SP1 Gag shells
journal, March 2007

  • Wright, Elizabeth R.; Schooler, Jordan B.; Ding, H. Jane
  • The EMBO Journal, Vol. 26, Issue 8
  • DOI: 10.1038/sj.emboj.7601664

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

  • Waheed, Abdul A.; Freed, Eric O.
  • AIDS Research and Human Retroviruses, Vol. 28, Issue 1
  • DOI: 10.1089/aid.2011.0230

Clustering Rules: A Comparison of Partitioning and Hierarchical Clustering Algorithms
journal, March 2006

  • Reynolds, A. P.; Richards, G.; de la Iglesia, B.
  • Journal of Mathematical Modelling and Algorithms, Vol. 5, Issue 4
  • DOI: 10.1007/s10852-005-9022-1

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

  • Sindhikara, Daniel J.; Emerson, Daniel J.; Roitberg, Adrian E.
  • Journal of Chemical Theory and Computation, Vol. 6, Issue 9
  • DOI: 10.1021/ct100281c

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

  • Bharat, T. A. M.; Castillo Menendez, L. R.; Hagen, W. J. H.
  • Proceedings of the National Academy of Sciences, Vol. 111, Issue 22
  • DOI: 10.1073/pnas.1401455111

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

  • Campos-Olivas, Ramón; Newman, John L.; Summers, Michael F.
  • Journal of Molecular Biology, Vol. 296, Issue 2
  • DOI: 10.1006/jmbi.1999.3475

Maturation of the HIV-1 core by a non-diffusional phase transition
journal, January 2015

  • Frank, Gabriel A.; Narayan, Kedar; Bess, Julian W.
  • Nature Communications, Vol. 6, Issue 1
  • DOI: 10.1038/ncomms6854

Higher-Order Structure of the Rous Sarcoma Virus SP Assembly Domain
journal, March 2014

  • Bush, D. L.; Monroe, E. B.; Bedwell, G. J.
  • Journal of Virology, Vol. 88, Issue 10
  • DOI: 10.1128/JVI.02659-13

The stoichiometry of Gag protein in HIV-1
journal, June 2004

  • Briggs, John A. G.; Simon, Martha N.; Gross, Ingolf
  • Nature Structural & Molecular Biology, Vol. 11, Issue 7
  • DOI: 10.1038/nsmb785

Direct measurement of Gag–Gag interaction during retrovirus assembly with FRET and fluorescence correlation spectroscopy
journal, September 2003

  • Larson, Daniel R.; Ma, Yu May; Vogt, Volker M.
  • Journal of Cell Biology, Vol. 162, Issue 7
  • DOI: 10.1083/jcb.200303200

Atomic-level modelling of the HIV capsid
journal, January 2011

  • Pornillos, Owen; Ganser-Pornillos, Barbie K.; Yeager, Mark
  • Nature, Vol. 469, Issue 7330
  • DOI: 10.1038/nature09640

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

  • Briggs, John A. G.; Johnson, Marc C.; Simon, Martha N.
  • Journal of Molecular Biology, Vol. 355, Issue 1
  • DOI: 10.1016/j.jmb.2005.10.025

Retroviral Capsid Assembly: A Role for the CA Dimer in Initiation
journal, June 2009

  • Purdy, John G.; Flanagan, John M.; Ropson, Ira J.
  • Journal of Molecular Biology, Vol. 389, Issue 2
  • DOI: 10.1016/j.jmb.2009.04.006

Comparative Protein Modelling by Satisfaction of Spatial Restraints
journal, December 1993


Potential Role for CA-SP in Nucleating Retroviral Capsid Maturation
journal, April 2014

  • England, M. R.; Purdy, J. G.; Ropson, I. J.
  • Journal of Virology, Vol. 88, Issue 13
  • DOI: 10.1128/JVI.00309-14

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

  • Datta, Siddhartha A. K.; Zhao, Zhuojun; Clark, Patrick K.
  • Journal of Molecular Biology, Vol. 365, Issue 3
  • DOI: 10.1016/j.jmb.2006.10.072

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

  • Bharat, Tanmay A. M.; Davey, Norman E.; Ulbrich, Pavel
  • Nature, Vol. 487, Issue 7407
  • DOI: 10.1038/nature11169

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

  • Best, Robert B.; Zhu, Xiao; Shim, Jihyun
  • Journal of Chemical Theory and Computation, Vol. 8, Issue 9
  • DOI: 10.1021/ct300400x

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

  • Han, Yun; Hou, Guangjin; Suiter, Christopher L.
  • Journal of the American Chemical Society, Vol. 135, Issue 47
  • DOI: 10.1021/ja406907h

RSV Capsid Polymorphism Correlates with Polymerization Efficiency and Envelope Glycoprotein Content: Implications that Nucleation Controls Morphogenesis
journal, February 2008

  • Butan, Carmen; Winkler, Dennis C.; Heymann, J. Bernard
  • Journal of Molecular Biology, Vol. 376, Issue 4
  • DOI: 10.1016/j.jmb.2007.12.003

Dimeric Rous Sarcoma Virus Capsid Protein Structure Relevant to Immature Gag Assembly
journal, January 2004

  • Nandhagopal, Narayanasamy; Simpson, Alan A.; Johnson, Marc C.
  • Journal of Molecular Biology, Vol. 335, Issue 1
  • DOI: 10.1016/j.jmb.2003.10.034

Molecular dynamics simulations of large macromolecular complexes
journal, April 2015

  • Perilla, Juan R.; Goh, Boon Chong; Cassidy, C. Keith
  • Current Opinion in Structural Biology, Vol. 31
  • DOI: 10.1016/j.sbi.2015.03.007

A Structural Model for the Generation of Continuous Curvature on the Surface of a Retroviral Capsid
journal, March 2012

  • Bailey, Graham D.; Hyun, Jae-Kyung; Mitra, Alok K.
  • Journal of Molecular Biology, Vol. 417, Issue 3
  • DOI: 10.1016/j.jmb.2012.01.014

A de novo peptide hexamer with a mutable channel
journal, October 2011

  • Zaccai, Nathan R.; Chi, Bertie; Thomson, Andrew R.
  • Nature Chemical Biology, Vol. 7, Issue 12
  • DOI: 10.1038/nchembio.692

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

  • Datta, S. A. K.; Temeselew, L. G.; Crist, R. M.
  • Journal of Virology, Vol. 85, Issue 9
  • DOI: 10.1128/JVI.00006-11

Structure of the immature HIV-1 capsid in intact virus particles at 8.8 Å resolution
journal, November 2014

  • Schur, Florian K. M.; Hagen, Wim J. H.; Rumlová, Michaela
  • Nature, Vol. 517, Issue 7535
  • DOI: 10.1038/nature13838

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

  • Newman, John L.; Butcher, Eric W.; Patel, Dipti T.
  • Protein Science, Vol. 13, Issue 8
  • DOI: 10.1110/ps.04614804

Three-dimensional Structure of HIV-1 Virus-like Particles by Electron Cryotomography
journal, February 2005

  • Benjamin, Jordan; Ganser-Pornillos, Barbie K.; Tivol, William F.
  • Journal of Molecular Biology, Vol. 346, Issue 2
  • DOI: 10.1016/j.jmb.2004.11.064

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

  • Phillips, Judith M.; Murray, Paul S.; Murray, Diana
  • The EMBO Journal, Vol. 27, Issue 9
  • DOI: 10.1038/emboj.2008.71

Structure and assembly of immature HIV
journal, June 2009

  • Briggs, J. A. G.; Riches, J. D.; Glass, B.
  • Proceedings of the National Academy of Sciences, Vol. 106, Issue 27
  • DOI: 10.1073/pnas.0903535106

Peptide Folding: When Simulation Meets Experiment
journal, January 1999


An atomic-level mechanism for activation of the kinesin molecular motors
journal, February 2010

  • Sindelar, C. V.; Downing, K. H.
  • Proceedings of the National Academy of Sciences, Vol. 107, Issue 9
  • DOI: 10.1073/pnas.0911208107

Conserved and Variable Features of Gag Structure and Arrangement in Immature Retrovirus Particles
journal, September 2010

  • de Marco, A.; Davey, N. E.; Ulbrich, P.
  • Journal of Virology, Vol. 84, Issue 22
  • DOI: 10.1128/JVI.01423-10

Mutations in the Spacer Peptide and Adjoining Sequences in Rous Sarcoma Virus Gag Lead to Tubular Budding
journal, April 2008

  • Keller, P. W.; Johnson, M. C.; Vogt, V. M.
  • Journal of Virology, Vol. 82, Issue 14
  • DOI: 10.1128/JVI.00213-08

Virus maturation as a new HIV-1 therapeutic target
journal, June 2009

  • Adamson, Catherine S.; Salzwedel, Karl; Freed, Eric O.
  • Expert Opinion on Therapeutic Targets, Vol. 13, Issue 8
  • DOI: 10.1517/14728220903039714

Viral DNA Synthesis Defects in Assembly-Competent Rous Sarcoma Virus CA Mutants
journal, January 2001


VMD: Visual molecular dynamics
journal, February 1996