Mura Lab

at the University of Virginia

Please note:
Publications (reverse chronological order)
The First Structure of a Second Hfq: A Paralog from the Ancient Aquificales Lineage by
Kimberly A. Stanek & Cameron Mura*
(2019; in prep)

The RNA–associated Sm Superfamily: A Bioinformatic Note on Nomenclature by
Cameron Mura*, Kimberly A. Stanek, Stella Veretnik, & Philip E. Bourne
(2019; in prep)

The Oligomeric Plasticity of Cyclic Protein Assemblies: A Simulation-based Analysis of Sm Rings by
Charles E. McAnany, Berk Ekmekci, & Cameron Mura*
PLOS Computational Biology (2019; in prep)

A Stimuli-responsive, Pentapeptide, Nanofiber Hydrogel for Tissue Engineering by
James D. Tang, Cameron Mura, & Kyle J. Lampe*
(2019; submitted)

[arXiv link]
Ten Quick Tips for Using a Raspberry Pi by
Anthony C. Fletcher* & Cameron Mura
PLOS Computational Biology (2019; submitted)

[arXiv link]
The Small β–barrel Domain: A Survey-based Structural Analysis by
Philippe Youkharibache, Stella Veretnik*, Qingliang Li, Kimberly A. Stanek, Cameron Mura*, & Philip E. Bourne*
Structure (2019), in press, 1–27.
PMID 30393050
[DOI link] [bioRxiv link] (preprint bundled with Supplemental Material)
Structural Biology Meets Data Science: Does Anything Change? by
Cameron Mura, Eli J. Draizen, & Philip E. Bourne*
Current Opinion in Structural Biology (2018), 52, 95–102.
PMID 30267935
[DOI link] [arXiv link] (preprint bundled with Supplementary Material)
Producing Hfq/Sm Proteins and sRNAs for Structural and Biophysical Studies of Ribonucleoprotein Assembly by
Kimberly A. Stanek* & Cameron Mura*
Methods in Molecular Biology, volume on "Bacterial Regulatory RNA: Methods & Protocols"
Springer Protocols series (2018), 1737, 273–299
PMID 29484599
[PDF version] [DOI link] [bioRxiv link]
Popular scientific coverage:
Book Cover Illustration
thumbnail thumbnail
Crystal Structure and RNA-binding Properties of an Hfq Homolog from the Deep-branching Aquificae: Conservation of the Lateral RNA-binding Mode by
Kimberly A. Stanek, Jennifer Patterson-West, Peter S. Randolph, & Cameron Mura*
Acta Crystallographica Section D: Structural Biology (2017), 73, 294–315.
PMID 28375142
[PDF version] [DOI link] [bioRxiv link] PDB link to 5SZD PDB link to 5SZE
Popular scientific coverage:
Journal Cover Illustration (April 2017 Acta Cryst D)
thumbnail thumbnail
Toward a Designable Extracellular Matrix: Molecular Dynamics Simulations of an Engineered Laminin-mimetic, Elastin-like Fusion Protein by
James D. Tang, Charles E. McAnany, Cameron Mura, & Kyle J. Lampe*
Biomacromolecules (2016), 17(10), 3222–3233.
PMID 27627061
[PDF version] [DOI link] [arXiv link] (Supporting Website [text, trajectory animations])
Claws, Disorder, and Conformational Dynamics of the C-terminal Region of Human Desmoplakin by
Charles E. McAnany & Cameron Mura*
The Journal of Physical Chemistry B (2016), 120(33), 8654–8667.
PMID 27188911
[PDF version] [DOI link] [arXiv link] (Supporting Information; BUNDLE)
An Introduction to Programming for Bioscientists: A Python-based Primer by
Berk Ekmekci, Charles E. McAnany, & Cameron Mura*
PLOS Computational Biology (2016), 12(6): e1004867, 1–43.
PMID 27271528
[PDF version] [DOI link] [arXiv link] (Supporting Information; P4B Website [Python Chapters])
Known Structure, Unknown Function: An Inquiry-based Undergraduate Biochemistry Laboratory Course by
Cynthia Gray, Carol W. Price, Christopher T. Lee, Alison H. Dewald, Matthew A. Cline, Charles E. McAnany, Linda Columbus,* & Cameron Mura*
Biochemistry & Molecular Biology Education (2015), 43(4), 245–262.
PMID 26148241
[PDF version] [DOI link] [arXiv link] (Supplementary Information)
Interplay of the Bacterial Ribosomal A-site, S12 Protein Mutations and Paromomycin Binding: A Molecular Dynamics Study by
Joanna Panecka, Cameron Mura, & Joanna Trylska*
PLOS ONE (2014), 9(11): e111811, 1–17.
PMID 25379961
[PDF version] [DOI link] (Supporting Information)
An Introduction to Biomolecular Simulations and Docking by
Cameron Mura* & Charles E. McAnany
Molecular Simulation (2014), 40(10-11), 732–764.
PMID n/a
[PDF version] [DOI link] [arXiv link]
Popular scientific coverage:
arXiv blog (local copy)
Archaeal and Eukaryotic Homologs of Hfq: A Structural and Evolutionary Perspective on Sm Function by
Cameron Mura*, Peter S. Randolph, Jennifer Patterson, & Aaron E. Cozen
RNA Biology (2013), 10(4), 636–651.
PMID 23579284
[PDF version] [DOI link]
Rapid Colorimetric Assays to Qualitatively Distinguish RNA and DNA in Biomolecular Samples by
Jennifer Patterson & Cameron Mura*
Journal of Visualized Experiments (2013), 72: e50225, 1–10.
PMID 23407542
[PDF version] [DOI link] (Materials sheet; Video)
video snapshot thumbnail
Abstractions, Algorithms and Data Structures for Structural Bioinformatics in PyCogent by
Marcin Cieślik, Zygmunt S. Derewenda, & Cameron Mura*
Journal of Applied Crystallography (2011), 44(2), 424–428.
PMID 22479120
[PDF version] [DOI link] [arXiv link] (Supplementary Materials: text, use-case 1 Python code, use-case 2 Python code)
A Lightweight, Flow-based Toolkit for Parallel and Distributed Bioinformatics Pipelines by
Marcin Cieślik & Cameron Mura*
BMC Bioinformatics (2011), 12(61), 1–11.
[highly accessed]PMID 21352538
[PDF version] [DOI link] (Less erroneous version [fewer typos]; Additional File 1)
thumbnail thumbnail
Molecular Dynamics of Potential rRNA Binders: Single-Stranded Nucleic Acids and Some Analogues by
Joanna Panecka, Cameron Mura, & Joanna Trylska*
The Journal of Physical Chemistry B (2011), 115(3), 532–546.
PMID 21192664
[PDF version] [DOI link]
An Introduction to Biomolecular Graphics by
Cameron Mura*, Colin M. McCrimmon, Jason Vertrees, & Michael R. Sawaya
PLoS Computational Biology (2010), 6(8): e1000918, 1–11.
PMID 20865174
[PDF version] [DOI link] (Supplementary Materials)
thumbnail thumbnail
PaPy: Parallel and Distributed Data-processing Pipelines in Python by
Marcin Cieślik & Cameron Mura*
Proceedings of SciPy2009: The 8th Annual Conference on Python for Scientific Computing (2009), 41–47.

[PDF version] [arXiv link]
RapA, the SWI/SNF Subunit of Escherichia coli RNA Polymerase, Promotes the Release of Nascent RNA from Transcription Complexes by
Brandon Yawn, Lin Zhang, Cameron Mura, & Maxim V. Sukhodolets*
Biochemistry (2009), 48, 7794–7806.
PMID 19580329
[PDF version] [DOI link]
Molecular Dynamics of a κB DNA Element: Base Flipping via Cross-strand Intercalative Stacking in a Microsecond-scale Simulation by
Cameron Mura* & J. Andrew McCammon
Nucleic Acids Research (2008), 36(15), 4941–4955.
PMID 18653524
Supplementary Website (animations, text, other info)
[PDF version] [DOI link] [arXiv link]
Sm-like Protein Hfq: Location of the ATP-binding Site and the Effect of ATP on Hfq•RNA Complexes by
Véronique Arluison, Shravan K. Mutyam, Cameron Mura, Sergio Marco, & Maxim V. Sukhodolets*
Protein Science (2007), 16, 1830–1841.
PMID 17660259
[PDF version] [DOI link]
7) Three-dimensional Structures of Fibrillar Sm Proteins: Hfq and Other Sm-like Proteins by
Véronique Arluison,†∗ Cameron Mura, Maria Romero-Guzmán, Jean Liquier, Olivier Pellegrini, Mari Gingery, Philippe Régnier, & Sergio Marco
Journal of Molecular Biology (2006), 356(1), 86–96.
PMID 16337963
[PDF version] [DOI link] (Supplementary Materials)
Popular scientific coverage:
2006 San Diego Supercomputer Center (SDSC) Wall Calendar
2006 SDSC multimedia gallery
2004 PDB Holiday Postcard (not from our work, but same Sm-like protein that was part of this study)
6) Structure and Assembly of an Augmented Sm-like Archaeal Protein 14-mer by
Cameron Mura, Martin Phillips, Anna Kozhukhovsky, & David Eisenberg*
Proceedings of the National Academy of Sciences USA (2003), 100(8), 4539–4544.
PMID 12668760
[PDF version] [DOI link] PDB link to 1M5Q
5) The Oligomerization and Ligand-binding Properties of Sm-like Archaeal Proteins (SmAPs) by
Cameron Mura, Anna Kozhukhovsky, Mari Gingery, Martin Phillips, & David Eisenberg*
Protein Science (2003), 12, 832–847.
PMID 12649441
[PDF version] [DOI link] PDB link to 1JBM PDB link to 1JRI PDB link to 1LOJ PDB link to 1LNX
Popular scientific coverage:
Book Cover Illustration (Lattman & Loll's Protein Crystallography)
Journal Cover Illustration (April 2003 Protein Science)
2003 PDB Holiday Postcard
2003 PDB Annual Report (see last page)
4) Structure and Function of an Archaeal Homolog of Survival Protein E (SurEα): An Acid Phosphatase with Purine Nucleotide Specificity by
Cameron Mura, Jonathan E. Katz, Steven G. Clarke, & David Eisenberg*
Journal of Molecular Biology (2003), 326(5), 1559–1575.
PMID 12595266
[PDF version] [DOI link] PDB link to 1L5X (Supplementary Materials; Erratum [HTML, PDF])
3) Structure of a Nudix Protein from Pyrobaculum aerophilum Reveals a Dimer with Two Intersubunit β–sheets by
Shuishu Wang, Cameron Mura, Michael R. Sawaya, & David Eisenberg*
Acta Crystallographica Section D: Biological Crystallography (2002), 58, 571–578.
PMID 11914479
[PDF version] [DOI link] PDB link to 1JRK PDB link to 1K26 PDB link to 1K2E
The Crystal Structure of a Heptameric Archaeal Sm Protein: Implications for the Eukaryotic SnRNP Core by
Cameron Mura, Duilio Cascio, Michael R. Sawaya, & David Eisenberg*
Proceedings of the National Academy of Sciences USA (2001), 98, 5532–5537.
PMID 11331747
[PDF version] [DOI link] PDB link to 1I8F
Oxyanion-Mediated Inhibition of Serine Proteases by
Steven R. Presnell, Girish S. Patil, Cameron Mura, Kevin M. Jude, Jennifer M. Conley, Jay A. Bertrand, Chih-Min Kam, James C. Powers, & Loren Dean Williams*
Biochemistry (1998), 37, 17068–17081.
PMID 9836602
[PDF version] [DOI link] PDB link to 1BJU PDB link to 1BJV
Dissertations, MS- and PhD-level (reverse chronological order)
Here, MS theses are denoted by one hourglass (⌛) and PhD dissertations by two (⌛⌛).
ml6) ⌛⌛ Structural and Functional Studies of the Hfq Family of Ancient Bacterial RNA-binding Proteins by
Kimberly A. Stanek (2018; PhD dissertation)
[PDF version] [DOI link]
ml5) ⌛⌛ Molecular Dynamics Simulations of Intrinsically Disordered Proteins and Biomolecular Assemblies by
Charles E. McAnany (2017; PhD dissertation)
[PDF version] [DOI link]
ml4) ⌛⌛ Structural and Functional Studies of Ancient RNA-binding Sm Proteins by
Peter S. Randolph (2016; PhD dissertation)
[PDF version] [DOI link]
ml3) ⌛⌛ Biochemical & Biophysical Studies of an Hfq Homolog from a Deep-branching Bacterium by
Jennifer Patterson West (2014; PhD dissertation)
[PDF version] [DOI link]
ml2) Broad Specificity of a Zinc-dependent Small Alcohol Dehydrogenase from Thermotoga maritima Involved in the Glycerol Dismutation Pathway by
Christopher T.-K. Lee (2013; MS thesis)
[PDF version]
ml1) Biophysical and RNA-binding Characterization of Hfq Proteins from Neisseria meningitidis, Vibrio cholerae and Escherichia coli by
Tomasz K. KabziƄski (2012; MS thesis)
[PDF version]
ml0) ⌛⌛ The Structures, Functions, & Evolution of Sm-like Archaeal Proteins (SmAPs) by
Cameron Mura (2002; PhD dissertation at UCLA)
See #cm2, below.
Technical notes, white papers, other writings (reverse chronological order)
Materials in this section are provided as is. Unless indicated otherwise, each item is copyrighted under the Creative Commons Attribution-ShareAlike license (by-sa CC-BY-SA icon); this means that one can freely use, distribute, and adapt the materials, subject to the restriction that one cite the original source of the material (i.e., this website).
cm26) In-Class Activity, II: Further Sequence and Structural Analysis of Nucleoside Kinases by
Cameron Mura*
[PDF version] (oct2017)
cm25) In-Class Activity, I: Molecular Visualization and Structural Analysis of Nucleoside Kinases by
Cameron Mura*
[PDF version] (oct2017)
cm24) Exploring Biomolecular Sequence ↔ Structure ↔ Function Relationships, II: A Primer on Comparative Sequence and Structure Analysis, and Molecular Visualization in PyMOL by
Cameron Mura*
[PDF version] (oct2017)
cm23) Exploring Biomolecular Sequence ↔ Structure ↔ Function Relationships, I: Focusing on Sequence and Taking a Putative Aminotransferase as a Case-study by
Cameron Mura*
[PDF version] (oct2013; last updated nov2017)
cm22) Understanding the Results of Electrostatics Calculations: Molecular and 'Isopotential' Surfaces by
Cameron Mura*
[PDF version] [arXiv link] (jul2014)
cm21) Cam's Unix Notes, 4 — Dropbox File Storage Quotas, from a Networked File-system Perspective by
Cameron Mura*
[PDF version] (03aug2013)
cm20) A Note on the Y–intercept in Ligand-binding Equations by
Cameron Mura*
[PDF version] (17dec2012)
cm19) Cam's Unix Notes, 3 — Structuring Your Directories by
Cameron Mura*
[PDF version] (02aug2012)
cm18) Cam's Unix Notes, 2 — Mixed Linux/Windows Computing Locales by
Cameron Mura*
[PDF version] (02aug2012)
cm17) Cam's Unix Notes, 1 — URI and Address Syntaxes by
Cameron Mura*
[PDF version] (02aug2012)
cm16) Ten Simple Rules for Creating Biomolecular Graphics by
Cameron Mura*
NB: See also "An Introduction to Biomolecular Graphics" (article #12, above) for a lengthier treatment of this subject.
[PDF version] [arXiv link] (2009)
cm15) Cam's Molecular Biology Notes, 4 — Detailed Pae SmAP3 purification protocols by
Cameron Mura*
[PDF version] (2009)
cm14) Cam's Molecular Biology Notes, 3 — The Award-winning "Pae Protocols", from Cloning → Expression → Purification by
Cameron Mura*
[PDF version] (2009)
cm13) Cam's Molecular Biology Notes, 2 — Running a DNA/Agarose Gel by
Cameron Mura*
[PDF version] (2009)
cm12) Cam's Molecular Biology Notes, 1 — Transforming E. coli with Plasmid DNA by
Cameron Mura*
[PDF version] (2009)
cm11) Final Configuration Steps in Preparing Your Own MediaWiki Instance by
Cameron Mura*
[PDF version] (feb2008)
cm10) PBCTools Plugin User's Guide — A tool for unwrapping MD trajectories computed under periodic boundary conditions on oblique lattices by
Jerome Henin, Olaf Lenz,* Cameron Mura, & Jan Saam
[PDF version] (2007; see also my VMD/Sandbox/WrappingStuff directory)
cm9) Solvation of DNA for molecular simulations: Adaptation of the Dowser software by
Cameron Mura*
[web page] (2006)
cm8) Cam's Linux software and operating system patches by
Cameron Mura*
[web page] (2005; CentOS 4, Fedora Core 4, Numeric Python, etc.)
cm7) Scaling Behavior of the NAMD Code at AMD's Developer Center by
Cameron Mura*, Justin Gullingsrud, & Robert Konecny
[PDF version] (sep2005)
cm6) Two new PyMOL tools: An 'average3d' Python module for computing & visualizing ensemble-averaged structures and 'makeCGOplates' for schematizing planar assemblies by
Cameron Mura*
[PDF version] (2005)
cm5) Development & Implementation of 'putty': A New PyMOL Cartoon Representation by
Cameron Mura*
[PDF version] [arXiv link] (dec2004)
cm4) The McCammon Group Document Server: Installation & Customization of the CERN Document Server Software (CDSware) by
Cameron Mura*
[PDF version] (2004; CDSware is the predecessor of the Invenio digital library software suite)
cm3) Cam's PyMOL Page: A Scientific & Educational Resource by
Cameron Mura*
[web page] (2003)
cm2) The Structures, Functions, & Evolution of Sm-like Archaeal Proteins (SmAPs) by
Cameron Mura*
[PDF version] [arXiv link] (2002; Mura PhD dissertation; higher-resolution version available upon request)
cm1) RaCC: A Rare Codon Calculator written in Perl/ by
Cameron Mura*
[web page] (2001)
cm0) Calculation of the Transition State and Design of a Catalyst for an RNA-catalyzed Inversion Reaction by
Cameron Mura* & K.N. Houk*
[PDF version] (aug1995)