Curriculum vitae

Matthew D. Zimmerman, Ph.D.

Home 4100 Cypress Pointe Dr.
Charlottesville, VA 22901
Work Dept. of Molecular Physiology and Biological Physics
University of Virginia
1340 Jefferson Park Ave
Charlottesville, VA 22908
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Ph.D. in Biophysics, University of Virginia, Charlottesville, VA
The crystallization expert system Xtaldb and its application to the structure of the 5’-nucleotidase YfbR and other proteins.
Advisor: Prof. Wladek Minor
B.S. in Biochemistry cum laude, Juniata College, Huntingdon, PA 1998

Research Experience

Instructor of Research 2012–
Research AssociateUniversity of Virginia, Dept. Mol. Physio. and Biol. Physics (Prof. Wladek Minor) 2007–2012
  • Designed and implemented LabDB, a comprehensive laboratory information management system (LIMS) for structural biology and in vitro bioinformatics analyses.
  • Developed modules of LabDB to import data from diverse laboratory equipment.
  • Helped supervise experimental data management pipelines of four large-scale (NIH U54) consortia, including two PSI:Biology high-throughput centers.
  • Built the PSI:Biology Knowledgebase Publications Portal.
  • Determined 20+ PDB structures by X-ray diffraction.
  • Conducted and published several bioinformatics studies of properties of protein structure, including crystallographic space group, solvent content and temperatures of crystallization.
Research Assistant University of Virginia, Interdisciplinary Prog. in Biophys. (Prof. Wladek Minor) 2002–2007
  • Determined the structure and mechanism of substrate specificity of an HD domain phosphohydrolase by X-ray diffraction, enzymatic assays and docking studies.
  • Developed Xtaldb, an expert system for quantitative analysis of macromolecular crystallization experiments, including implementation of a novel algorithm for balanced screen design.
Research AssistantUniversity of Virginia, Interdisciplinary Prog. in Biophys. (Prof. Michael Wiener) 1999–2002
  • Conducted structural studies of bacterial homologues of the peripheral benzodiazepine receptor.
NSF Research Assistant Carnegie Mellon University, Pittsburgh, PA (Prof. Gordon Rule)

  • Co-crystallized an N-terminal fragment of the r termination protein in complex with oligonucleotide
Jun–Aug 1997
Research Assistant Juniata College, Huntingdon, PA (Prof. Jeffrey Demarest)

  • Partially isolated a specific chloride channel inhibitor from an aquatic plant (Acorus calamus) by preparative TLC
  • Tested for activity in an Ussing chamber using isolated gastric mucosa of the mudpuppy (Necturus maculosus)
Jun–Aug 1996

Teaching, Writing and Service Experience

Research associate search committee 2013
Referee for Journal of Applied Crystallography 2011
Technical consultant and reviewer of the official HKL-2000 manual 2011
Reviewer and editor of 30+ manuscripts for peer-reviewed journals 2008–2015
Invited seminar at Longwood University, “Bioinformatics in structural genomics: How computer science is saving modern structural biology” 2005

Honors and Awards

First Place Student Poster Contest at Mid-Atlantic Protein Crystallography Meeting 2007
ISGO Young Scientist Travel Award for ICSG Meeting in Beijing, China 2006
US National Committee for Crystallography Travel Award for IUCr Congress XX in Florence, Italy 2005


Research Papers

  1. Gront D, Grabowski M, Zimmerman MD, Raynor J, Tkaczuk KL, Minor W (2013) “Assessing the accuracy of template-based structure prediction metaservers by comparison with structural genomics structures.” J Struct Funct Genom. 13(4): 213-225.
  2. Majorek KA, Porebski PJ, Dayal A, Zimmerman MD, Jablonska K, Stewart AJ, Chruszcz M, Minor W. (2012). “Structural and immunological characterization of bovine, horse and rabbit serum allergens.” Mol Immunol. 52(3-4):174-182.
  3. Klimecka MM, Chruszcz M, Font J, Skarina T, Shumilin I, Onopryienko O, Porebski PJ, Cymborowski M, Zimmerman MD, Hasseman J, Glomski IJ, Lebioda L, Savchenko A, Edwards A, Minor W (2011) “Structural analysis of a putative aminoglycoside N-acetyltransferase from Bacilllus anthracis.” J Mol Biol. 410:411-423.
  4. Gabanyi MJ, Adams PD, Arnold K, Bordoli L, Carter LG, Flippen-Andersen J, Gifford L, Haas J, Kouranov A, McLaughlin WA, Micallef DI, Minor W, Shah R, Schwede T, Tao YP, Westbrook JD, Zimmerman M, Berman HM (2011) “The Structural Biology Knowledgebase: a portal to protein structures, sequences, functions, and methods.” J Struct Funct Genom. 12: 45-54.
  5. Sledz P, Kaminski R, Chruszcz M, Zimmerman MD, Minor W, Wozniak K (2010) ”An experimental charge density of HEPES.” Acta Cryst B. 66: 482-492
  6. Luo HB, Zheng H, Zimmerman MD, Chruszcz M, Skarina T, Egorova O, Savchenko A, Edwards AM, Minor W (2010) “Crystal structure and molecular modeling study of N-carbamoylsarcosine amidase Ta0454 from Thermoplasma acidophilum.” J Struct Biol. 169: 304-311
  7. Koclega KD, Chruszcz M, Zimmerman MD, Bujacz G, Minor W. (2010) “’Hot’ macromolecular crystals.” Cryst Growth Des. 10: 580-586
  8. Sledz P, Zheng H, Murzyn K, Chruszcz M, Zimmerman MD, Chordia MD, Joachimiak A, Minor W (2010) “New surface contacts formed upon reductive lysine methylation: improving the probability of protein crystallization.” Protein Sci. 19: 1395-404
  9. Wang S, Kirillova O, Chruszcz M, Gront D, Zimmerman MD, Cymborowski MT, Shumilin IA, Skarina T, Gorodichtchenskaia E, Savchenko A, Edwards AM, Minor W (2009) “The crystal structure of the AF2331 protein from Archaeoglobus fulgidus DSM 4304 forms an unusual interdigitated dimer with a new type of ? + ? fold.” Protein Sci. 18: 2410-2419
  10. Zimmerman MD, Proudfoot M, Yakunin A, Minor W (2008) “Structural insight into the mechanism of substrate specificity and catalytic activity of an HD domain phosphohydrolase: the 5′-deoxyribonucleotidase YfbR from Escherichia coli.” J Mol Biol. 378: 215-226
  11. Chruszcz M, Zimmerman MD, Wang S, Koclega KD, Zheng H, Evdokimova E, Kudritska M, Cymborowski M, Savchenko A, Edwards A, Minor W (2008) “Function-biased choice of additives for optimization of protein crystallization – the case of the putative thioesterase PA5185 from Pseudomonas aeruginosaCryst Growth Des. 8: 4054-4061
  12. Beloglazova N, Brown G, Zimmerman MD, Proudfoot M, Makarova KS, Kudritska M, Kochinyan S, Wang S, Chruszcz M, Minor W, Koonin EV, Edwards AM, Savchenko A, Yakunin AF (2008) “A novel family of sequence-specific endoribonucleases associated with the Clustered Regularly Interspaced Short Palindromic Repeats.” J Biol Chem 283: 20361-20371
  13. Chruszcz M, Potrzebowski W, Zimmerman, MD, Grabowski M, Zheng H, Lasota P, Minor W (2008) “Analysis of solvent content and oligomeric states in protein crystals—does symmetry matter?” Protein Sci 283: 20361-20371
  14. Petkowski JJ, Chruszcz M, Zimmerman MD, Zheng H, Skarina T, Onopriyenko O, Cymborowski MT, Koclega KD, Savchenko A, Edwards A, Minor W (2007) “Crystal structures of TM0549 and NE1324–two orthologs of coli AHAS isozyme III small regulatory subunit.” Protein Sci 16: 1360-1367
  15. Koclega KD, Chruszcz M, Zimmerman MD, Cymborowski M, Evdokimova E, Minor W (2007) “Crystal structure of a transcriptional regulator TM1030 from Thermotoga maritima solved by an unusual MAD experiment.” J Struct Biol 159: 424-432
  16. Zimmerman MD, Chruszcz M, Cymborowski M, Zheng H, Minor W (2006) “Disodium 4-nitrophenylphosphate hexahydrate.” Acta Cryst E 62: m884-m886
  17. Doyle CR, Zimmerman MD, Chruszcz M, Cymborowski M, Gawlicka-Chruszcz A, Minor W (2006) “Crystal structure of 6-(4-difluoromethoxy-3-methoxyphenyl)-3(2H)-pyridazinone, C12H10F2N2O3.” Z Kristallogr NCS 221: 359-360

Reviews and Book Chapters

  1. Berman HM, Gabayni MJ, Groom CR, Johnson JE, Murshudov GN, Nicholls RA, Reddy V, Schwede T, Zimmerman MD, Westbrook , Minor W (2015). “Data to knowledge: how to get meaning from your result.” IUCr J. 2:45-58.
  2. Zimmerman MD, Grabowski M, Domagalski MJ, MacLean EM, Chruszcz M, Minor W (2014) “Data management in the modern structural biology and biomedical research environment.” Meth Mol Biol. 1140:1-25.
  3. Domagalski, MJ, Zheng H, Zimmerman MD, Dauter Z, Wlodower A, Minor W (2014) “The quality and validation of structures from structural genomics.” Meth Mol Biol. 1091:297-314.
  4. Zheng H, Hou J, Zimmerman MD, Wlodower A, Minor W. (2014) “The future of crystallography in drug discovery.” Expert Opin Drug Discov. 9(2)
  5. Cymborowski M, Klimecka M, Chruszcz M, Zimmerman MD, Shumilin IA, Borek D, Lazarski K, Joachimiak A, Otwinowski Z, Anderson W, Minor W (2010) “To automate or not to automate: this is the question.” J Struct Funct Genomics. 11: 211-221
  6. Grabowski M, Chruszcz M, Zimmerman MD, Kirillova O, Minor W (2009) “Benefits of structural genomics for drug discovery research”. Infect Disord Drug Targets. 9: 459-474

Selected Conference Presentations

International Union of Crystallography Congress XXIII, Montreal, Canada
Transforming biomedical and structural data into information and knowledge (oral)
Aug 2014
American Crystallographic Association Meeting, New Orleans, LA
Enhancements to the LabDB crystallographic laboratory information management system (oral)
May 2011
Invited Seminar at Lodz University, Lodz, Poland
The LabDB crystallography LIMS, and its application to the structure of the 5’-nucleotidase YfbR (seminar)
Apr 2008
Keystone Symposia on Structural Genomics, Steamboat Springs, CO
Efficient experimental design and quantitative analysis of crystallization experiments with the Xtaldb expert system (oral)
Jan 2008
Mid-Atlantic Macromolecular Crystallography Meeting, Charlottesville, VA
Structural analysis of the mechanism of substrate specificity and catalytic activity of an HD-domain phosphohydrolase: the 5′-deoxyribonucleotidase YfbR (poster)
Jun 2007
International Conference on Structural Genomics, Beijing, China
A database-driven, component-based data management system for high- and low-throughput protein crystallography pipelines (poster)
Oct 2006
International Union of Crystallography Congress XX, Florence, Italy
The Xtaldb system for project salvaging in high-throughput crystallization (poster)
Aug 2005
Invited Seminar at Longwood University, Farmville, VA
Data Management in Structural Genomics, or How CS is Saving Modern Structural Biology (seminar)
Jan 2005
Mid-Atlantic Protein Crystallography Meeting, Baltimore, MD
A crystallization expert system: improved data collection and analysis through small-scale lab automation (oral)
Jun 2004
Biophysical Society Meeting, New Orleans, LA
Determination of Catalytic Rotation Rates of the Mutant Escherichia coli ATP Synthase by Phosphorescence Anisotropy (poster)
Feb 2000
National Conference on Undergraduate Research, Austin, TX
The isolation of a natural chloride channel blocker from an aquatic plant (poster)
Apr 1997