Michael Gryk's NMR group, University of Connecticut, USA

[markber]

Below is a copy of information about Gryk's lab from the website of University of Connecticut.

Michael R. Gryk Associate Professor of Molecular, Microbial and Structural Biology gryk@uchc.edu B.S., M.S., University of Connecticut Ph.D., Stanford University Molecular Biology and Biochemistry Graduate Program Accepting Lab Rotation Students: Summer '10, Fall '10, Spring '11

Areas of Interest 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 (http://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 (http://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 Publications Selected Publications Gryk M.R., Vyas J., & Maciejewski M.W. (2010) Biomolecular NMR data analysis. Prog Nucl Magn Reson Spectrosc., 56, 329-45. Fox-Erlich S., Schiller M.R., Gryk M.R. (2009) Structural Conservation of a short, functional, peptide sequence motif. Front. Biosci. 14, 1143-1151. Gryk, M.R. & Hoch, J.C. (2008) Local knowledge helps determine protein structures. PNAS, 105, 4533-4534. Mobli M., Maciejewski M.W., Gryk M.R. & Hoch J.C. (2007) An automated tool for maximum entropy reconstruction of biomolecular NMR spectra. Nat. Methods, 4, 467-8. Verdi, K.K., Ellis, H.J. & Gryk, M.R. (2007) Conceptual-level workflow modeling of scientific experiments using NMR as a case study. BMC Bioinformatics, 8:31. Balla S., Thapar V., Verma S., Luong T., Faghri T., Huang C.H., Rajasekaran S., del Campo J.J., Shinn J.H., Mohler W.A., Maciejewski M.W., Gryk M.R., Piccirillo B., Schiller S.R., & Schiller M.R. (2006) Minimotif Miner: a tool for investigating protein function. Nature Methods, 3, 175-177. Ellis, H.J.C., Fox-Erlich, S., Martyn, T.O., & Gryk, M.R. (2006) Development of an Integrated Framework for Protein Structure Determinations: A Logical Data Model for NMR Data Analysis. Third International Conference on Information Technology: New Generations, 613-618. Fox-Erlich, S., Martyn, T.O., Ellis, H.J.C, & Gryk, M.R. (2004) Delineation and Analysis of the Conceptual Data Model Implied by the ‘IUPAC Recommendations for Biochemical Nomenclature’, Prot. Science, 13, 2559-2558. Marintchev, A., Gryk, M.R., and Mullen, G.P. (2003) Site-Directed Mutagenesis Analysis of the Structural Interaction of the Single-Strand-Break Repair Protein, X-ray Cross-Complementing Group 1, with DNA Polymerase β Nucleic Acids Res., 31, 580-588. Gryk, M.R., Marintchev, A., Maciejewski, M.W., Robertson, A., Wilson, W.H., and Mullen, G.P. (2002) Mapping of the interaction interface of DNA Polymerase β with XRCC1. Structure, 10, 1709-1720. Maciejewski, M.W., Shin, R., Pan, B., Marintchev, A., Denninger, A., Mullen, M.A., Chen, K., Gryk, M.R., and Mullen, G.P. (2001). Solution structure of a viral DNA repair polymerase. Nature Struct. Biol. 8, 936-941. View more publications, see Pubmed listing.