Werner Braun, PhD
Professor, Department of Biochemistry & Molecular Biology
Tel: (409) 747-6810
Fax: (409) 747-6000
E-mail: webraun@utmb.edu
Campus Location: 5.422, Research Bldg 6
Mail Route: 0304
Lab Webpage
Research
The challenge in the post genomic era is to make full use of the
vast genomic data in understanding the molecular mechanism of the
function of proteins. Funding from the Department of Energy has allowed
us to develop an expert system, MASIA, to quantitatively identify motifs
and patterns of diversity in protein sequences. MASIA, in combination
with homology modeling and molecular dynamics simulations, can be used
to characterize functional motifs in protein families. In collaboration
with Drs. T. Izumi and S. Mitra from the Sealy Center for Molecular
Science (SCMS) we are determining how apurinic/apyrimidinic
endonucleases respond to subtle differences in the structure and
dynamics of DNA sites damaged by low dose ionizing radiation. We are
relating motifs identified by MASIA to the function of DNA recognition,
catalysis and protein-protein interaction. Screening gene databases with
these novel motifs should reveal new candidates for APE related
proteins.
In a different avenue we are developing software tools for
determining protein structures by NMR in Structural Genomics Projects.
Manual analysis of the thousands of cross peaks in protein spectral data
is currently the most time consuming part of protein structure
determination by NMR. In a project funded primarily by the NSF, we are
developing new software tools to automate and integrate all individual
steps in the NMR structure determination process. Our NOAH-DIAMOD suite
can interpret NOE data in a fraction of the time that would be required
for manual assignment, with equivalent or better resolution. Using this
method we determined the 3D solution structure of water borne pheromones
from the marine mollusk Aplysia by NMR studies in a project with Drs.
G. Nagle and S. Painter (Department of Anatomy and Neurosciences). This
structure suggests potential receptor-binding sites of these pheromones
and we are examining common functional and structural characteristics of
pheromones of other species.
The self-correcting distance geometry based tools we developed
for NMR have also proven useful for modeling proteins, as demonstrated
by our performance CASP4 and CASP5 competition. We are using our methods
to model proteins of medical interest in several collaborative
projects. We are determining the structural characteristics of cedar
pollen allergens in collaboration Drs. E. Brooks, T. Midoro-Horiuti and
R. Goldblum (Department of Pediatrics). We have established 3D-database
of allergen structures, SDAP, which combines experimental results and
our models for other known allergens. In other projects, we have modeled
the structure of proteins involved in apoptosis and other forms of cell
lysis.
Publications