Crystallography and Computational Biosciences

The Crystallography and Computational Biosciences Shared Resource serves as a portal for access to state-of-the-art X-ray crystallographic equipment, technical support, high-performance computing, and scientific consultation for Cancer Center researchers. The Shared Resource exists to meet the growing needs for structure determination and computational analysis of protein and DNA/RNA structure, function and dynamics for a diverse array of projects ranging from basic science questions to drug design.

About X-ray Crystallography

Macromolecular X-ray crystallography is an experimental scientific method to determine the three-dimensional structure of proteins, DNA/RNA, their complexes, and the complexes of a variety of ligands including cofactors, substrates, lead drug candidates, etc. We use this information to develop novel therapies, as it is essential for assessing and exploiting the biological function of the target protein.

About Our X-ray Technology

The X-ray facility houses two state-of-the-art diffractometers (Rigaku Saturn 92/007 and RaxisIV/RUH) and all the necessary ancillary equipment (e.g. microscopes, crystallization cabinets, and cryo-cooling devices). The Wake Forest School of Medicine and Department of Biochemistry fully supports this facility through service contracts and a full-time computer system manager. Consultation about protein expression and purification is available through the Hollis and Lowther laboratories. On the computational side, the Shared Resource provides access to a 1064-core Linux cluster that is shared among the users at WFU and WFSM. This cluster is maintained by and the infrastructure is provided by the University.

A few recent collaborations include:

Development of PI3K-kinase inhibitors
Development of fatty acid synthase inhibitors
Dissection of the molecular basis for peroxiredoxin inactivation and repair by sulfiredoxin
Structure and function of the mammalian TREX1 3' exonuclease and RNase H2 enzymes

Services We Provide

Consulting on feasibility of structure determination
Identification of possible other existing structures
Access to our X-ray defraction facility
Determination of the molecular structure

About Computational Biosciences

The Computational Bioscience portion of the Crystallography and Computational Biosciences Shared Resource provides access to cutting-edge modeling and simulation methods through consultation and collaboration with the director, Fred Salsbury, PhD.

Our main expertise lies in structure-based classical modeling, docking and analysis, but additional expertise exists in computational biology/bioinformatics, and in quantum mechanical calculations. A few recent collaborations include:

Molecular simulations of mismatch repair proteins
Molecular simulations of redox proteins
Analysis of communication within proteins based on molecular simulations
Computational modification and docking of drug leads into active sites
Quantum mechanical calculations of model systems of novel DNA-Zn interactions

Services We Provide

Due to the complexity of the problems and solutions involved, our first service is consultation:

Determine if the problem is amenable to computation.
Decide what sort of computations need to be performed.
Determine if the scale of the computations involved are worth the time.

Calculations that we can readily perform include:

Molecular dynamics
Protein-protein docking
Protein-ligand docking
Various bioinformatic analyses

Reaction-diffusion modeling, quantum mechanical calculations and other mathematical modeling may be possible.

Directors

Freddie R. Salsbury Jr., PhD, Associate Professor, Department of Physics
W. Todd Lowther, PhD, Associate Professor, Department of Biochemistry
Thomas Hollis, PhD, Associate Professor, Department of Biochemistry

Published Research

Selected illustrative publications with member of the Cancer Center include:

Shaban, N.M., Harvey, S., Perrino, F.W., & Hollis, T. (2010) The structure of the mammalian RNase H2 complex provides insight into RNA:DNA hybrid processing to prevent immune dysfunction. J. Biol. Chem., 285, 3617-24.
de Silva, U., Perrino, F.W., & Hollis, T. (2009) DNA binding induces active site conformational change in the human TREX2 3' exonuclease. Nuc. Acids Res. 37, 2411-7. PMC2673414
Perrino, F.W., Harvey, S, Shaban, N.M., & Hollis, T. (2009) RNaseH2 mutants that cause Aicardi-Goutieres syndrome are active nucleases. J. Mol Med, 87, 25-30.
Lowther, W.T. and Haynes, A.C. (2010) Reduction of cysteine sulfinic acid in eukaryotic, typical 2-Cys peroxiredoxins by sulfiredoxin. Antioxid. Redox. Signal., in press. (PMID 20712415)
Jönsson, T.J., Murray, M.S., Johnson, L.C., Poole, L.B., and Lowther, W.T. (2005). Structural basis for the retroreduction of inactivated peroxiredoxins by human sulfiredoxin. Biochemistry 44, 8634-8642.
Y. Yuan, M. H. Knaggs, L. B. Poole, J. S. Fetrow and F. R. Salsbury Jr.,"Conformational and oligomeric effects on the cysteine pKa of typaredoxin peroxidase", Journal of Biomolecular Structure and Dynamics, in press
Vasilyeva, J. E. Clodfelter, B. Rector, T. Hollis, K. D. Scarpinato, F. R. Salsbury Jr. Small molecule induction of MSH2-dependent cell death suggests a vital role of mismatch repair proteins in cell death, DNA Repair 8, 103-112 (2009)
F. R. Salsbury Jr., S. T. Knutson, L. B. Poole, and J. S. Fetrow, Functional Site Profiling and Electrostatic Analysis of Cysteines Modifiable to Cysteines Sulfenic Acid, Protein Science 17:299-312 (2008)
M. H. Knaggs, F. R. Salsbury, M. H. Edgell, J. S. Fetrow. Insights into CheY relaxation and relaxation derived from molecular dynamics simulations. Biophys J. 2006 Dec 15
F. R. Salsbury, Jr, Clodfelter, J. E., Gentry, M. B., Hollis, T., Drotschmann, K., The molecular mechanism of DNA damage recognition by MutS homologs and its distinction from mismatch binding , Nucleic Acids Research, 34 (8) 2173-2185 (2006)