Michael R. Gryk, Ph.D.
Associate Professor of Molecular, Microbial and Structural Biology|
Academic Office Location: Molecular, Microbial and Structural Biology University of Connecticut Health Center 263 Farmington Avenue Farmington, CT 06030-3305 |
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| Phone: | 860-679-4785 |
| Fax: | 860-679-3408 |
| Email: | gryk@neuron.uchc.edu |
| Website(s): |
Molecular Biology & Biochemistry Graduate Program |
Education
Post-Graduate Training
Awards
| Degree | Institution | Major |
|---|---|---|
| Ph.D. | Stanford University | Biophysics |
| B.S. | University of Connecticut | Biophysics |
| M.S. | University of Connecticut | Chemistry |
Post-Graduate Training
| Training | Institution | Specialty |
|---|---|---|
| Post Doctoral | European Molecular Biology Laboratory | Postdoctoral Research Assistant in the Laboratory of Dr. Hartmut Oschkinat. |
| Post Doctoral | University of Connecticut Health Center | Postdoctoral Research Assistant in the Laboratory of Dr. Gregory P. Mullen |
Awards
| Name of Award/Honor | Awarding Organization |
|---|---|
| DAAD post-doctoral fellowship (declined) | Deutscher Akademischer Austausch Dienst |
| Training Grant 1990-1994 | NIH |
| Member | Golden Key National Honor Society |
| Biophysics Award for Distinguished Undergraduate Research Honors Scholar | Phi Beta Kappa Honor Society |
| Who's Who Among Students in American Universities | Who's Who Among Students in American Universities |
| University Scholar | UCONN Phi Kappa Phi Honor Society |
| Member | Alpha Lambda Delta Honor Society |
| Bruce Mahon Scholarship 1986-1990 |
The focus of our laboratory is structural bioinformatics. We are currently involved in several projects on this topic, mainly the use of NMR spectroscopy as a tool for macromolecular characterization and molecular structure as an aid to bioinformatics.
Particular projects include the development of CONNJUR (connjur.uchc.edu) – an open source integration platform for biomolecular NMR data processing; utilizing non-uniform sampling techniques and the use of maximum entropy methods for spectral reconstruction; and the development of a database of short linear motifs which confer specific functions to proteins (mnm.engr.uconn.edu). NMR studies involve DNA repair proteins of relatively large molecular weight for NMR spectroscopy (20-70 kDa). Current methods to overcome the difficulties inherent in studying these large systems include extensive labeling using stable isotopes and the use of TROSY-based pulse sequences. A critical mission of the lab is the facility approach to NMR, such that as advancements are made, they are tailored for ease-of-use both internally and externally when possible.
--CONNJUR NMR Software Integration
--MiniMotif Miner
--Structural Biology Facility
--Structural Biology Tools
Particular projects include the development of CONNJUR (connjur.uchc.edu) – an open source integration platform for biomolecular NMR data processing; utilizing non-uniform sampling techniques and the use of maximum entropy methods for spectral reconstruction; and the development of a database of short linear motifs which confer specific functions to proteins (mnm.engr.uconn.edu). NMR studies involve DNA repair proteins of relatively large molecular weight for NMR spectroscopy (20-70 kDa). Current methods to overcome the difficulties inherent in studying these large systems include extensive labeling using stable isotopes and the use of TROSY-based pulse sequences. A critical mission of the lab is the facility approach to NMR, such that as advancements are made, they are tailored for ease-of-use both internally and externally when possible.
--CONNJUR NMR Software Integration
--MiniMotif Miner
--Structural Biology Facility
--Structural Biology Tools
Accepting Lab Rotation Students for FAll '13, Spring '14
Journal Articles
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Achieving high accuracy prediction of minimotifs
(2012) PLoS One 9 (7) e45589
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In support of the BMRB
(2012) Nat Struct Mol Biol (19) 854-60
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Minimotif Miner 3.0: database expansion and significantly improved reduction of false-positive predictions from consensus sequences
(2012) Nucleic Acids Res Database issue (40) D252-260
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CONNJUR spectrum translator: an open source application for reformatting NMR spectral data
(2011) J Biomol NMR 1 (50) 83-89
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Iterative Development of an Application to Support Nuclear Magnetic Resonance Data Analysis of Proteins
(2011) Proc Int Conf Inf Technol New Gener 1014-1020
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MimoSA: A system for minimotif annotation
(2010) BMC Bioinformatics (11) 328
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A proposed syntax for Minimotif Semantics, version 1
(2009) BMC Genomics (10)
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Minimotif miner 2nd release: A database and web system for motif search
(2009) Nucleic Acids Research SUPPL. 1 (37)
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VENN, a tool for titrating sequence conservation onto protein structures
(2009) Nucleic Acids Research 18 (37) e124
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Automatic maximum entropy spectral reconstruction in NMR
(2007) Journal of Biomolecular NMR 2 (39) 133-139
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Conceptual-level workflow modeling of scientific experiments using NMR as a case study
(2007) BMC Bioinformatics (8) 31
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High-performance exact algorithms for motif search
(2005) Journal of Clinical Monitoring and Computing 4-5 (19) 319-328
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Delineation and analysis of the conceptual data model implied by the "IUPAC Recommendations for Biochemical Nomenclature"
(2004) Protein Science 9 (13) 2559-2563
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Identification of small molecule synthetic inhibitors of DNA polymerase beta by NMR chemical shift mapping
(2004) Journal of Biological Chemistry 38 (279) 39736-39744
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Mapping of the interaction interface of DNA polymerase beta with XRCC1
(2002) Structure 12 (10) 1709-1720
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Solution structure of a viral DNA repair polymerase
(2001) Nature Structural Biology 11 (8) 936-941
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Solution structure of the single-strand break repair protein XRCC1 N- terminal domain
(1999) Nature Structural Biology 9 (6) 884-893
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Heteronuclear relaxation study of the PH domain of beta-spectrin: restriction of loop motions upon binding inositol trisphosphate
(1998) J Mol Biol 5 (280) 879-896
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AV77 hinge mutation stabilizes the helix-turn-helix domain of trp repressor
(1996) J Mol Biol 1 (255) 204-214
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Flexibility of DNA binding domain of trp repressor required for recognition of different operator sequences
(1996) Protein Sci 6 (5) 1195-1197
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Investigation of protein amide-proton exchange by 1H longitudinal spin relaxation
(1995) J Magn Reson B 3 (108) 220-234
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Solution dynamics of the trp repressor: a study of amide proton exchange by T1 relaxation
(1995) J Mol Biol 5 (246) 618-627
Conference Papers
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Development of an integrated framework for protein structure determinations: A logical data model for NMR data analysis
(2006) Proceedings - Third International Conference onInformation Technology: New Generations, ITNG 2006 (2006) 613-618
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Undergraduate research in bioinformatics - The CONNJUR project
(2006) Proceedings - Frontiers in Education Conference, FIE
Letters
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An automated tool for maximum entropy reconstruction of biomolecular NMR spectra [3]
(2007) Nature Methods 6 (4) 467-468
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1H, 13C and 15N resonance assignments for the perdeuterated 22kD palm-thumb domain of DNA polymerase β [9]
(2002) Journal of Biomolecular NMR 2 (22) 197-198
Notes
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Comment on "magnetic resonance spectroscopy identifies neural progenitor cells in the live human brain"
(2008) Science 5889 (321) 640; author reply 640
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Local knowledge helps determine protein structures
(2008) Proceedings of the National Academy of Sciences of the United States of America 12 (105) 4533-4534
Reviews
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Biomolecular NMR data analysis
(2010) Progress in Nuclear Magnetic Resonance Spectroscopy 4 (56) 329-345
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Structural conservation of a short, functional, peptide-sequence motif.
(2009) Frontiers in bioscience : a journal and virtual library (14) 1143-1151
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Site-directed mutagenesis analysis of the structural interaction of the single-strand-break repair protein, X-ray cross-complementing group 1, with DNA polymerase beta
(2003) Nucleic Acids Research 2 (31) 580-588