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, 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 Rigaku Saturn 92-Micromax007 and RaxisIV/RUH diffractometer with dual VariMx-HF Confocal Optic Systems and all the necessary ancillary equipment (e.g. microscopes, crystallization cabinets, and cryo-cooling devices). The facility was upgraded in 2012 with funds from the North Carolina Center for Biotechnology, as part its move to Wake Forest Biotech Place.
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 all aspects of protein expression, purification and feasibility of structure determination
- Identification ofcrystallization conditions and possible other existing structures
- Access to X-ray diffraction facility
- Determination of the molecular structure through collaboration
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
- 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.
- W. Todd Lowther, PhD, Associate Professor, Department of Biochemistry
- Thomas Hollis, PhD, Associate Professor, Department of Biochemistry
- Freddie R. Salsbury, Jr., PhD, Associate Professor, Department of Physics
Selected Published Research
Selected illustrative publications with member of the Cancer Center include:
- Powell RD, Holland PJ, Hollis T, Perrino FW. (2011) Aicardi-Goutieres syndrome gene and
HIV-1 restriction factor SAMHD1 is a dGTP-reg
- Lema Tome CM, Palma E, Ferluga S,
Lowther WT, Hantgan R, Wykosky J, and Debinski W (2012) Structural and
functional characterization of the monomeric Ephrin A1 binding site to the
EphA2 receptor. J Biol Chem 287:
- Riedel TJ, Knight J, Murray MS, Milliner
DS, Holmes RP, and Lowther WT (2012) 4-hydroxy-2-oxoglutarate
aldolase inactivity in primary hyperoxaluria type 3 and glyoxylate reductase
inhibition. Biochem Biophys Acta (Mol Basis for Disease) 1822: 1544-1552.
- Chen H, Gu Z, Zhang H, Chen,
W, Lowther, WT, and Chen YQ (2012) Expression and purification of integral
membrane fatty acid desaturases. PLoS One 8, e58139.
- Pryor EE Jr, Wozniak DJ, Hollis T (2012) Crystallization of Pseudomonas aeruginosa AmrZ protein:
development of a comprehensive method for obtaining and optimization of
protein-DNA crystals. Acta Crystallogr Sect F Struct Biol Cryst Commun 68:985-993.
- Salsbury FR Jr, Poole LB,
Fetrow JS. (2012) Electrostatics
of cysteine residues in proteins: parameterization and validation of a simple
model. Proteins 80:2583-2591.
- Orebaugh CD, Fye JM, Harvey S, Hollis T, Wilkinson JC, Perrino FW
(2013) The TREX1 C-terminal region controls cellular localization through
ubiquitination. J Biol Chem 288:
- Negureanu L, Salsbury FR Jr (2013) Destabilization of the MutSα's
protein-protein interface due to binding to the DNA adduct induced by
anticancer agent carboplatin via molecular dynamics simulations. J
Mol Model 19:4969-14989.
- Ghosh S, Salsbury FR Jr, Horita DA, Gmeiner WH. (2013) Cooperative stabilization of
Zn(2+):DNA complexes through netropsin binding in the minor groove of
FdU-substituted DNA. J Biomol Struct Dyn 31:1301-1310.
AC, Qian J, Reisz JA, Furdui CM, and Lowther WT (2013) Molecular basis for the
resistance of human mitochondrial 2-Cys peroxiredoxin 3 to hyperoxidation. J
Biol Chem 288, 29714-29723.
- Fye JM, Coffin SR, Orebaugh CD, Hollis T, Perrino FW (2014) The Arg-62 Residues of the TREX1
Exonuclease Act Across the Dimer Interface Contributing to Catalysis in the
Opposing Protomers. J Biol Chem, PMID: 24616097, in press.
- Stuart CH, Horita DA,
Thomas MJ, Salsbury FR Jr,
Lively MO, Gmeiner WH.(2014), Site-Specific DNA-Doxorubicin
Conjugates Display Enhanced Cytotoxicity to Breast Cancer Cells. Bioconjug