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 (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.
Publications
Selected Publications
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.
rev. 4/09 |
