John E Johnson

John E Johnson

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John E Johnson

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VIPERdb: A Tool for Virus Research.

Annu Rev Virol 2018 Sep;5(1):477-488

Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, USA; email:

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http://dx.doi.org/10.1146/annurev-virology-092917-043405DOI Listing
September 2018

Allosteric effects in bacteriophage HK97 procapsids revealed directly from covariance analysis of cryo EM data.

J Struct Biol 2018 May 10;202(2):129-141. Epub 2018 Jan 10.

Department of Integrative Structural and Computational Biology, The Scripps Research Institute, United States.

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http://dx.doi.org/10.1016/j.jsb.2017.12.013DOI Listing
May 2018

Cryo-EM Elucidation of the Structure of Bacteriophage P22 Virions after Genome Release.

Biophys J 2018 Mar;114(6):1295-1301

Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S00063495183018
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http://dx.doi.org/10.1016/j.bpj.2018.01.026DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5883611PMC
March 2018

Simulations indicate that scores of lionfish () colonized the Atlantic Ocean.

PeerJ 2017 19;5:e3996. Epub 2017 Dec 19.

HoBi Lab, Department of Life Sciences, Texas A&M University-Corpus Christi, Corpus Christi, TX, United States of America.

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http://dx.doi.org/10.7717/peerj.3996DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5740958PMC
December 2017

Enzymes and Enzyme Activity Encoded by Nonenveloped Viruses.

Annu Rev Virol 2017 09 21;4(1):221-240. Epub 2017 Jun 21.

Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037; email:

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http://dx.doi.org/10.1146/annurev-virology-101416-041944DOI Listing
September 2017

Intracellular Delivery of Luminescent Quantum Dots Mediated by a Virus-Derived Lytic Peptide.

Bioconjug Chem 2017 01 21;28(1):64-74. Epub 2016 Dec 21.

Florida State University , Department of Chemistry and Biochemistry, 95 Chieftan Way, Tallahassee, Florida 32306, United States.

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http://dx.doi.org/10.1021/acs.bioconjchem.6b00609DOI Listing
January 2017

Binding and entry of a non-enveloped T=4 insect RNA virus is triggered by alkaline pH.

Virology 2016 11 9;498:277-287. Epub 2016 Sep 9.

Department of Biochemistry and Microbiology, Rhodes University, Grahamstown 6140, South Africa. Electronic address:

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http://dx.doi.org/10.1016/j.virol.2016.08.028DOI Listing
November 2016

Virus particle dynamics derived from CryoEM studies.

Curr Opin Virol 2016 06 14;18:57-63. Epub 2016 Apr 14.

Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, United States. Electronic address:

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http://dx.doi.org/10.1016/j.coviro.2016.02.011DOI Listing
June 2016

Crystal Structure and Proteomics Analysis of Empty Virus-like Particles of Cowpea Mosaic Virus.

Structure 2016 Apr 24;24(4):567-575. Epub 2016 Mar 24.

Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA. Electronic address:

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http://dx.doi.org/10.1016/j.str.2016.02.011DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4828962PMC
April 2016

A virus-based nanoplasmonic structure as a surface-enhanced Raman biosensor.

Biosens Bioelectron 2016 Mar 21;77:306-14. Epub 2015 Sep 21.

Center for Bio/Molecular Science and Engineering, US Naval Research Laboratory, 4555 Overlook Avenue SW, Code 6900, Washington DC 20375, USA; Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom. Electronic address:

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http://dx.doi.org/10.1016/j.bios.2015.09.032DOI Listing
March 2016

Effect of the viral protease on the dynamics of bacteriophage HK97 maturation intermediates characterized by variance analysis of cryo EM particle ensembles.

J Struct Biol 2016 Mar 24;193(3):188-195. Epub 2015 Dec 24.

Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA. Electronic address:

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http://dx.doi.org/10.1016/j.jsb.2015.12.012DOI Listing
March 2016

CoVaMa: Co-Variation Mapper for disequilibrium analysis of mutant loci in viral populations using next-generation sequence data.

Methods 2015 Dec 25;91:40-47. Epub 2015 Sep 25.

Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ymeth.2015.09.021DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4684750PMC
December 2015

Architecture of the Complex Formed by Large and Small Terminase Subunits from Bacteriophage P22.

J Mol Biol 2015 Oct 21;427(20):3285-3299. Epub 2015 Aug 21.

Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 233 South 10th Street Philadelphia, PA 19107, USA. Electronic address:

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http://dx.doi.org/10.1016/j.jmb.2015.08.013DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4587339PMC
October 2015

ClickSeq: Fragmentation-Free Next-Generation Sequencing via Click Ligation of Adaptors to Stochastically Terminated 3'-Azido cDNAs.

J Mol Biol 2015 Aug 24;427(16):2610-6. Epub 2015 Jun 24.

Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.

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http://dx.doi.org/10.1016/j.jmb.2015.06.011DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4523409PMC
August 2015

Data to knowledge: how to get meaning from your result.

IUCrJ 2015 Jan 1;2(Pt 1):45-58. Epub 2015 Jan 1.

Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA.

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http://dx.doi.org/10.1107/S2052252514023306DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4285880PMC
January 2015

Virus-templated plasmonic nanoclusters with icosahedral symmetry via directed self-assembly.

Small 2014 Aug 15;10(15):3058-63. Epub 2014 Apr 15.

Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, 4555 Overlook Ave., SW, Code 6900, Washington, DC, 20375, USA.

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http://dx.doi.org/10.1002/smll.201400470DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4283761PMC
August 2014

Assembly and maturation of a T = 4 quasi-equivalent virus is guided by electrostatic and mechanical forces.

Viruses 2014 Aug 22;6(8):3348-62. Epub 2014 Aug 22.

Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.

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http://dx.doi.org/10.3390/v6083348DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4147699PMC
August 2014

Single-particle EM reveals plasticity of interactions between the adenovirus penton base and integrin αVβ3.

Proc Natl Acad Sci U S A 2014 Jun 2;111(24):8815-9. Epub 2014 Jun 2.

Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037;

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http://dx.doi.org/10.1073/pnas.1404575111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4066496PMC
June 2014

Dynamic and geometric analyses of Nudaurelia capensis ω virus maturation reveal the energy landscape of particle transitions.

J Mol Recognit 2014 Apr;27(4):230-7

Department of Chemistry and Biochemistry, and Division of Biological Sciences, University of California, San Diego, La Jolla, CA, 92093-0378, USA.

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http://dx.doi.org/10.1002/jmr.2354DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3987702PMC
April 2014

Architecture of a dsDNA viral capsid in complex with its maturation protease.

Structure 2014 Feb 19;22(2):230-7. Epub 2013 Dec 19.

Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA. Electronic address:

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http://dx.doi.org/10.1016/j.str.2013.11.007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3939775PMC
February 2014

Discovery of functional genomic motifs in viruses with ViReMa-a Virus Recombination Mapper-for analysis of next-generation sequencing data.

Nucleic Acids Res 2014 Jan 16;42(2):e11. Epub 2013 Oct 16.

Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.

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http://dx.doi.org/10.1093/nar/gkt916DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3902915PMC
January 2014

Maximizing the potential of electron cryomicroscopy data collected using direct detectors.

J Struct Biol 2013 Nov 12;184(2):193-202. Epub 2013 Sep 12.

Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037.

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http://dx.doi.org/10.1016/j.jsb.2013.09.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3832241PMC
November 2013

Diffraction structural biology - a new horizon.

J Synchrotron Radiat 2013 Nov 11;20(Pt 6):819. Epub 2013 Oct 11.

Nagoya Industrial Science Research Institute, 1-13 Yotsuya-dori, Chikusa-ku, Nagoya 464-0819, Japan.

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http://dx.doi.org/10.1107/S0909049513025478DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3795535PMC
November 2013

Cystovirus maturation at atomic resolution.

Structure 2013 Aug;21(8):1266-8

Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.

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http://dx.doi.org/10.1016/j.str.2013.07.009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3779430PMC
August 2013

Virus assembly and maturation: auto-regulation through allosteric molecular switches.

J Mol Biol 2013 May 26;425(9):1488-96. Epub 2013 Feb 26.

Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.

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http://dx.doi.org/10.1016/j.jmb.2013.02.021DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3664304PMC
May 2013

DNA bending-induced phase transition of encapsidated genome in phage λ.

Nucleic Acids Res 2013 Apr 28;41(8):4518-24. Epub 2013 Feb 28.

Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.

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http://dx.doi.org/10.1093/nar/gkt137DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3632124PMC
April 2013

Studying 18 MDa virus assemblies with native mass spectrometry.

Angew Chem Int Ed Engl 2013 Apr 28;52(14):4020-3. Epub 2013 Feb 28.

Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research, Utrecht Institute for Pharmaceutical Sciences and Netherlands Proteomics Centre, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands.

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http://dx.doi.org/10.1002/anie.201210197DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3949431PMC
April 2013

Virus maturation.

Annu Rev Biophys 2012 23;41:473-96. Epub 2012 Feb 23.

Department of Molecular Biology, The Scripps Research Institute, La Jolla, California 92037, USA.

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http://dx.doi.org/10.1146/annurev-biophys-042910-155407DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3607295PMC
March 2013

Dynamics in cryo EM reconstructions visualized with maximum-likelihood derived variance maps.

J Struct Biol 2013 Mar 12;181(3):195-206. Epub 2012 Dec 12.

Electrical and Computer Engineering, Cornell University, NY 14853, USA.

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http://dx.doi.org/10.1016/j.jsb.2012.11.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3870017PMC
March 2013

Confessions of an icosahedral virus crystallographer.

Authors:
John E Johnson

Microscopy (Oxf) 2013 Feb 4;62(1):69-79. Epub 2013 Jan 4.

Department of Molecular Biology, MB31, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA 92037, USA.

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http://dx.doi.org/10.1093/jmicro/dfs097DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3624677PMC
February 2013

Nucleotide-resolution profiling of RNA recombination in the encapsidated genome of a eukaryotic RNA virus by next-generation sequencing.

J Mol Biol 2012 Dec 13;424(5):257-69. Epub 2012 Oct 13.

Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.

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http://dx.doi.org/10.1016/j.jmb.2012.10.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3502730PMC
December 2012

Dissecting quasi-equivalence in nonenveloped viruses: membrane disruption is promoted by lytic peptides released from subunit pentamers, not hexamers.

J Virol 2012 Sep 3;86(18):9976-82. Epub 2012 Jul 3.

Department of Molecular Biology, The Scripps Research Institute, La Jolla California, USA.

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http://dx.doi.org/10.1128/JVI.01089-12DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3446560PMC
September 2012

Maturation in action: CryoEM study of a viral capsid caught during expansion.

Structure 2012 Aug 28;20(8):1384-90. Epub 2012 Jun 28.

Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.

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https://linkinghub.elsevier.com/retrieve/pii/S09692126120021
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http://dx.doi.org/10.1016/j.str.2012.05.011DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3418467PMC
August 2012

Bacteriophage HK97 capsid assembly and maturation.

Adv Exp Med Biol 2012 ;726:351-63

Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA.

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http://dx.doi.org/10.1007/978-1-4614-0980-9_15DOI Listing
April 2012

Capsomer dynamics and stabilization in the T = 12 marine bacteriophage SIO-2 and its procapsid studied by CryoEM.

Structure 2012 Mar;20(3):498-503

National Resource for Automated Molecular Microscopy, The Scripps Research Institute, La Jolla, CA 92037, USA.

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http://dx.doi.org/10.1016/j.str.2012.01.007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3302160PMC
March 2012

Nucleic acid packaging in viruses.

Curr Opin Struct Biol 2012 Feb 23;22(1):65-71. Epub 2012 Jan 23.

Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, United States.

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http://dx.doi.org/10.1016/j.sbi.2011.11.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3288730PMC
February 2012

Mechanics of bacteriophage maturation.

Proc Natl Acad Sci U S A 2012 Feb 30;109(7):2342-7. Epub 2012 Jan 30.

Natuur- en Sterrenkunde and LaserLab, VU University, 1081 HV Amsterdam, The Netherlands.

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http://dx.doi.org/10.1073/pnas.1109590109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3289345PMC
February 2012

Host RNAs, including transposons, are encapsidated by a eukaryotic single-stranded RNA virus.

Proc Natl Acad Sci U S A 2012 Feb 24;109(6):1907-12. Epub 2012 Jan 24.

Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.

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http://dx.doi.org/10.1073/pnas.1116168109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3277583PMC
February 2012

The 2.3-angstrom structure of porcine circovirus 2.

J Virol 2011 Aug 1;85(15):7856-62. Epub 2011 Jun 1.

Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.

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http://dx.doi.org/10.1128/JVI.00737-11DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3147897PMC
August 2011

Multiclass maximum-likelihood symmetry determination and motif reconstruction of 3-D helical objects from projection images for electron microscopy.

IEEE Trans Image Process 2011 Jul 17;20(7):1962-76. Epub 2011 Feb 17.

School of Electrical and Computer Engineering, Purdue University, West Lafayette, IN 47907, USA.

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http://dx.doi.org/10.1109/TIP.2011.2107329DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3142268PMC
July 2011

Pass the jelly rolls.

Structure 2011 Jul;19(7):904-6

Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA.

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http://dx.doi.org/10.1016/j.str.2011.06.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3242167PMC
July 2011

In vivo virus structures: simultaneous classification, resolution enhancement, and noise reduction in whole-cell electron tomography.

J Struct Biol 2011 Jun 15;174(3):425-33. Epub 2011 Mar 15.

Department of Biomedical Engineering, Cornell University, United States.

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http://dx.doi.org/10.1016/j.jsb.2011.03.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3091986PMC
June 2011

The Prohead-I structure of bacteriophage HK97: implications for scaffold-mediated control of particle assembly and maturation.

J Mol Biol 2011 May 27;408(3):541-54. Epub 2011 Jan 27.

Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.

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http://dx.doi.org/10.1016/j.jmb.2011.01.016DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3075369PMC
May 2011

Three-dimensional structure of a viral genome-delivery portal vertex.

Nat Struct Mol Biol 2011 May 17;18(5):597-603. Epub 2011 Apr 17.

Department of Biological Sciences, Purdue University, West Lafayette, Indiana, USA.

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http://dx.doi.org/10.1038/nsmb.2023DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3087855PMC
May 2011

Streptococcal M1 protein constructs a pathological host fibrinogen network.

Nature 2011 Apr;472(7341):64-8

Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, USA.

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http://dx.doi.org/10.1038/nature09967DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3268815PMC
April 2011

Flock house virus: a model system for understanding non-enveloped virus entry and membrane penetration.

Curr Top Microbiol Immunol 2010 ;343:1-22

Department of Chemistry, University of Puget Sound, Tacoma, WA, 98416, USA.

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http://dx.doi.org/10.1007/82_2010_35DOI Listing
January 2011

Cell entry by non-enveloped viruses.

Curr Top Microbiol Immunol 2010 ;343:v-vii

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January 2011

Transferrin-mediated targeting of bacteriophage HK97 nanoparticles into tumor cells.

Nanomedicine (Lond) 2011 Jan;6(1):55-68

Department of Molecular Biology & Center for Integrative Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.

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http://dx.doi.org/10.2217/nnm.10.99DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3091364PMC
January 2011

In vivo assembly of an archaeal virus studied with whole-cell electron cryotomography.

Structure 2010 Dec;18(12):1579-86

Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.

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http://dx.doi.org/10.1016/j.str.2010.10.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3042139PMC
December 2010

All-atom multiscale simulation of cowpea chlorotic mottle virus capsid swelling.

J Phys Chem B 2010 Sep;114(34):11181-95

Center for Cell and Virus Theory, Department of Chemistry, Indiana University, Bloomington, Indiana 47405, USA.

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http://pubs.acs.org/doi/abs/10.1021/jp102314e
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http://dx.doi.org/10.1021/jp102314eDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2996875PMC
September 2010

Critical salt bridges guide capsid assembly, stability, and maturation behavior in bacteriophage HK97.

Mol Cell Proteomics 2010 Aug 22;9(8):1752-63. Epub 2010 Mar 22.

Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.

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http://dx.doi.org/10.1074/mcp.M000039-MCP201DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2938056PMC
August 2010

Subunits fold at position-dependent rates during maturation of a eukaryotic RNA virus.

Proc Natl Acad Sci U S A 2010 Aug 26;107(32):14111-5. Epub 2010 Jul 26.

Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.

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http://dx.doi.org/10.1073/pnas.1004221107DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2922577PMC
August 2010

An automated procedure for detecting protein folds from sub-nanometer resolution electron density.

J Struct Biol 2010 Jun 22;170(3):513-21. Epub 2009 Dec 22.

Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.

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http://dx.doi.org/10.1016/j.jsb.2009.12.014DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2866771PMC
June 2010

Structure and function of a genetically engineered mimic of a nonenveloped virus entry intermediate.

J Virol 2010 May 17;84(9):4737-46. Epub 2010 Feb 17.

Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.

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http://dx.doi.org/10.1128/JVI.02670-09DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2863772PMC
May 2010

Virus particle maturation: insights into elegantly programmed nanomachines.

Authors:
John E Johnson

Curr Opin Struct Biol 2010 Apr 9;20(2):210-6. Epub 2010 Feb 9.

Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.

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http://dx.doi.org/10.1016/j.sbi.2010.01.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2854226PMC
April 2010

Balanced electrostatic and structural forces guide the large conformational change associated with maturation of T = 4 virus.

Biophys J 2010 Apr;98(7):1337-43

Department of Molecular Biology, The Scripps Research Institute, La Jolla, California, USA.

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http://dx.doi.org/10.1016/j.bpj.2009.12.4283DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2849064PMC
April 2010

HK97 maturation studied by crystallography and H/2H exchange reveals the structural basis for exothermic particle transitions.

J Mol Biol 2010 Mar 20;397(2):560-74. Epub 2010 Jan 20.

Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.

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http://dx.doi.org/10.1016/j.jmb.2010.01.016DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2855905PMC
March 2010

Crystal structure of the DNA-recognition component of the bacterial virus Sf6 genome-packaging machine.

Proc Natl Acad Sci U S A 2010 Feb 19;107(5):1971-6. Epub 2010 Jan 19.

Department of Molecular Biosciences, University of Kansas, 1200 Sunnyside Avenue, Lawrence, KS 66045, USA.

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http://www.pnas.org/cgi/doi/10.1073/pnas.0908569107
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http://dx.doi.org/10.1073/pnas.0908569107DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2836615PMC
February 2010

Potato virus X as a novel platform for potential biomedical applications.

Nano Lett 2010 Jan;10(1):305-12

Department of Cell Biology, Center for Integrative Molecular Biosciences, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA.

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http://dx.doi.org/10.1021/nl9035753DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2958517PMC
January 2010

Dynamics and stability in maturation of a T=4 virus.

J Mol Biol 2009 Sep 20;392(3):803-12. Epub 2009 Jul 20.

Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.

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http://dx.doi.org/10.1016/j.jmb.2009.07.038DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2766526PMC
September 2009

Dissecting the functional domains of a nonenveloped virus membrane penetration peptide.

J Virol 2009 Jul 15;83(13):6929-33. Epub 2009 Apr 15.

Department of Molecular Biology, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, CA 92037, USA.

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http://dx.doi.org/10.1128/JVI.02299-08DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2698515PMC
July 2009

Preliminary X-ray data analysis of crystalline hibiscus chlorotic ringspot virus.

Acta Crystallogr Sect F Struct Biol Cryst Commun 2009 Jun 22;65(Pt 6):589-93. Epub 2009 May 22.

Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Kent Ridge, Singapore 117543, Singapore.

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http://dx.doi.org/10.1107/S1744309109015760DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2688417PMC
June 2009

The P22 tail machine at subnanometer resolution reveals the architecture of an infection conduit.

Structure 2009 Jun;17(6):789-99

National Resource for Automated Molecular Microscopy, The Scripps Institute, La Jolla, CA 92037, USA.

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http://dx.doi.org/10.1016/j.str.2009.04.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2714705PMC
June 2009

An unexpected twist in viral capsid maturation.

Nature 2009 Apr 8;458(7238):646-50. Epub 2009 Feb 8.

Department of Molecular Biology, The Scripps Research Institute, La Jolla, California 92037, USA.

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http://dx.doi.org/10.1038/nature07686DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2765791PMC
April 2009

Synergy of NMR, computation, and X-ray crystallography for structural biology.

Structure 2009 Apr;17(4):499-507

Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA.

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http://dx.doi.org/10.1016/j.str.2009.03.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2705668PMC
April 2009

Reciprocal space representations of helical objects and their projection images for helices constructed from motifs without spherical symmetry.

Ultramicroscopy 2009 Feb 8;109(3):253-63. Epub 2008 Nov 8.

Electrical and Computer Engineering, Purdue University, 465 Northwestern Avenue, West Lafayette, IN 47907-2035, USA.

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http://dx.doi.org/10.1016/j.ultramic.2008.10.014DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2713744PMC
February 2009

Genetics, biochemistry and structure of the archaeal virus STIV.

Biochem Soc Trans 2009 Feb;37(Pt 1):114-7

Department of Microbiology, Montana State University, Bozeman, MT 59715, USA.

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http://dx.doi.org/10.1042/BST0370114DOI Listing
February 2009

VIPERdb2: an enhanced and web API enabled relational database for structural virology.

Nucleic Acids Res 2009 Jan 3;37(Database issue):D436-42. Epub 2008 Nov 3.

Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.

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http://dx.doi.org/10.1093/nar/gkn840DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2686430PMC
January 2009

Characterization of large conformational changes and autoproteolysis in the maturation of a T=4 virus capsid.

J Virol 2009 Jan 5;83(2):1126-34. Epub 2008 Nov 5.

Department of Molecular Biology, The Scripps Research Institute, La Jolla, California 92037, USA.

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http://dx.doi.org/10.1128/JVI.01859-08DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2612371PMC
January 2009

Assembly architecture and DNA binding of the bacteriophage P22 terminase small subunit.

J Mol Biol 2008 Nov 27;383(3):494-501. Epub 2008 Aug 27.

School of Biological Sciences, University of Missouri-Kansas City, Kansas City, MO 64110-2499, USA.

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http://dx.doi.org/10.1016/j.jmb.2008.08.050DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2577774PMC
November 2008

Virus capsid expansion driven by the capture of mobile surface loops.

Structure 2008 Oct;16(10):1491-502

Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.

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http://dx.doi.org/10.1016/j.str.2008.06.014DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2586091PMC
October 2008

Multi-disciplinary studies of viruses: the role of structure in shaping the questions and answers.

Authors:
John E Johnson

J Struct Biol 2008 Sep 6;163(3):246-53. Epub 2008 Apr 6.

Department of Molecular Biology, The Scripps Research Institute, MB-31, 10550 N. Torrey Pines Road, La Jolla, CA 92037, USA.

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http://dx.doi.org/10.1016/j.jsb.2008.03.013DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2952275PMC
September 2008

Bacteriophage lambda stabilization by auxiliary protein gpD: timing, location, and mechanism of attachment determined by cryo-EM.

Structure 2008 Sep;16(9):1399-406

National Resource for Automated Molecular Microscopy, The Scripps Research Institute, La Jolla, CA 92037, USA.

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http://dx.doi.org/10.1016/j.str.2008.05.016DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2614288PMC
September 2008

An optimal exposure strategy for cryoprotected virus crystals with lattice constants greater than 1000 A.

J Synchrotron Radiat 2008 May 18;15(Pt 3):223-6. Epub 2008 Apr 18.

The Scripps Research Institute, USA.

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http://dx.doi.org/10.1107/S0909049507064813DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2394789PMC
May 2008

The combination of chemical fixation procedures with high pressure freezing and freeze substitution preserves highly labile tissue ultrastructure for electron tomography applications.

J Struct Biol 2008 Mar 14;161(3):359-71. Epub 2007 Sep 14.

National Center for Microscopy and Imaging Research, Department of Neurosciences, University of California, San Diego, 1070 Basic Science Building MC 0608, 9500 Gilman Drive, La Jolla, CA 92093-0608, USA.

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http://dx.doi.org/10.1016/j.jsb.2007.09.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2459253PMC
March 2008

Visualizing flock house virus infection in Drosophila cells with correlated fluorescence and electron microscopy.

J Struct Biol 2008 Mar 19;161(3):439-46. Epub 2007 Sep 19.

Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.

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http://dx.doi.org/10.1016/j.jsb.2007.09.009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2408891PMC
March 2008

Development of bacteriophage p22 as a platform for molecular display: genetic and chemical modifications of the procapsid exterior surface.

Chembiochem 2008 Mar;9(4):514-8

Department of Microbiology, University of Alabama at Birmingham, BBRB 416 845 19th St South, Birmingham, AL 35294-2170, USA.

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http://dx.doi.org/10.1002/cbic.200700555DOI Listing
March 2008

Long term storage of virus templated fluorescent materials for sensing applications.

Nanotechnology 2008 Mar 13;19(10):105504. Epub 2008 Feb 13.

Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA.

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March 2008

Rescue of maturation-defective flock house virus infectivity with noninfectious, mature, viruslike particles.

J Virol 2008 Feb 12;82(4):2025-7. Epub 2007 Dec 12.

Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Rd. Mail MB-31, La Jolla, CA 92037, USA.

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http://dx.doi.org/10.1128/JVI.02278-07DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2258709PMC
February 2008

Activation, exposure and penetration of virally encoded, membrane-active polypeptides during non-enveloped virus entry.

Curr Protein Pept Sci 2008 Feb;9(1):16-27

Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA-92037, USA.

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February 2008

Exact reduced-complexity maximum likelihood reconstruction of multiple 3-D objects from unlabeled unoriented 2-D projections and electron microscopy of viruses.

IEEE Trans Image Process 2007 Dec;16(12):2865-78

School of Electrical and Computer Engineering, Purdue University, West Lafayette, IN 47907, USA.

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December 2007

Solution NMR studies of the maturation intermediates of a 13 MDa viral capsid.

J Am Chem Soc 2007 Jun 31;129(25):7867-76. Epub 2007 May 31.

Department of Molecular Biology, The Skaggs Institute for Chemical Biology and The Center for Integrative Molecular Biosciences, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA.

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http://dx.doi.org/10.1021/ja071118jDOI Listing
June 2007

DNA packaging and delivery machines in tailed bacteriophages.

Curr Opin Struct Biol 2007 Apr 28;17(2):237-43. Epub 2007 Mar 28.

Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.

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http://dx.doi.org/10.1016/j.sbi.2007.03.011DOI Listing
April 2007

Macromolecular mass spectrometry and electron microscopy as complementary tools for investigation of the heterogeneity of bacteriophage portal assemblies.

J Struct Biol 2007 Feb 19;157(2):371-83. Epub 2006 Sep 19.

Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA.

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http://dx.doi.org/10.1016/j.jsb.2006.09.003DOI Listing
February 2007

An engineered virus as a bright fluorescent tag and scaffold for cargo proteins--capture and transport by gliding microtubules.

J Nanosci Nanotechnol 2006 Aug;6(8):2451-60

Center for Bio/Molecular Science and Engineering, Code 6930, US Naval Research Laboratory, Washington, DC 20375, USA.

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August 2006

An engineered virus as a scaffold for three-dimensional self-assembly on the nanoscale.

Small 2005 Jul;1(7):702-6

Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, 4555 Overlook Avenue SW, Washington, DC 20375, USA.

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http://dx.doi.org/10.1002/smll.200500021DOI Listing
July 2005