Structural Biology Shared Resource
- Macromolecular X-ray Crystallography
- Nuclear Magnetic Resonance Facility
- Molecular Modeling Facilities
Jan F. Chlebowski, Ph.D.
Resource Director
(804) 828-1023
jfchlebo@vcu.edu
The Structural Biology Shared Resource represents a coalescence of resources critical to the determination and utilization of structural information in addressing problems of significance in cancer research. With the sequencing of the major mammalian genomes, the frontier of biology has shifted from sequence to function and to the functional genomics and the closely related structural genomics initiatives. Developments in both hardware and software in computational technology allow the information intrinsic to a three-dimensional structure (e.g., the size, shape, electrostatic charge distribution, hydrophobic/hydrophilic characteristics of ligand binding sites on macromolecules) to be used for design of pharmaceutic agents.
The field of structure-based drug design has undergone cycles of acceptance by the pharmaceutical industry and biotech, but the type of information that comes out of such studies has been consistently of interest to academic scientists. Computational methods, termed molecular modeling or computational chemistry, are also now recognized as extremely powerful tools for predicting molecular architecture on the basis of sequence information. Interpretation of the consequences of mutagenesis is enhanced by orders of magnitude if structural information at atomic resolution is available.
One focus of the Resource is aiding in the understanding of the mechanism of an enzymatic reaction by illustrating the structure of proteins. In particular, Massey scientists in both the Molecular Cancer Therapeutics and Cancer Cell Biology programs are interested in protein: protein interactions and the downstream events precipitated by the docking of one protein onto another. The potential for interactive research is nowhere greater than in this area.
The Resource offers instrumentation, computer hardware and software, and support personnel for the determination of molecular structures and the utilization of structural information in cancer research. The shared resource encompasses three related components: X-ray Crystallography, Nuclear Magnetic Resonance and Molecular Modeling. These facilities are clustered in dedicated space to facilitate access and consultation with the support team.
Macromolecular X-ray Crystallography
H. Tonie Wright, Ph.D.
Director
(804) 828-6139
xrdproc@vcu.edu
The crystallographic facility carries out structure determination of biological macromolecules through collaborations with Massey Cancer Center members and other investigators at VCU. Structures of enzymes involved with one carbon metabolism, fatty acid biosynthesis, drug resistance, RNA processing and modification, as well as structures of RNA and DNA-protein complexes are examples of recent projects. The core facility works closely with the user from the earliest stages of macromolecule expression and purification through interpretation and correlation of the determined structure with solution and biological properties of the molecule.
The crystallography core facility is housed in the Institute of Structural Biology and Drug Discovery, located near the Massey Cancer Center within the Virginia BioTechnology Research Park. The Institute has contiguous dedicated laboratory space for crystal growth and handling and for data collection. The former contains incubators, microscopes, glove box and wet laboratory space and the latter houses the data collection facility. Virtually all macromolecular crystallography data are now collected using a Raxis-IV++ imaging plate system, MicroMax-007 high frequency rotating anode, Blue Max-Flux Confocal optical system, X-stream cryogenic system, RAXIS-IV++ 2 stage and Windows-based CrystalClear software for data acquisition and processing.
For development of projects, please consult with the facility director for more detailed information.
Nuclear Magnetic Resonance Facility
J. Neel Scarsdale, Ph.D.
Director
(804) 828-7147
jscarsda@vcu.edu
Nuclear magnetic resonance (NMR) has long served as a key analytical tool in the characterization of the chemical and 3-D structure of biomedical relevance. This includes applications in the characterization of synthetic and naturally occurring therapeutic candidates (drugs) as well as sophisticated applications allowing the determination of the 3-D structure of small proteins and nucleic acids. More recently, NMR methods have seen innovative applications in the analysis of whole cell extracts for the purpose of analyzing changes in metabolite levels associated with drug therapies and the search for biomarkers associated with specific disease states. Available resources allow the exploration of these varied applications.
The NMR facility is currently located in the basement of McGuire Hall on the VCU Medical Center campus, close to Massey Cancer Center. Five contiguous rooms house a 500 MHz instrument and a 300 MHz instrument. As part of the university plan for enhancement of structural biology, both of these instruments will be replaced in the next period. The target is for acquisition of a 700 MHz instrument and a new 300 MHz instrument to update the current facilities.
The equipment resources of the facility are:
500 MHz instrument:Varian Unity + 500, three RF channels with waveform generators on all channels, single axis pulsed field gradients, Ultra-NMR (39 channel) shims; high stability temperature controller. The magnet is equipped with vibration isolation legs and an FTS systems Air/Air chiller is used for precooling the VT air for low temperature runs.
Three probes are available:
- Nallorac Z-spec 31P,13C,15N,1H quadruple resonance gradient probe
- Varian Indirect detect gradient probe with tunable X-channel (15N-31P)
- Varian triple resonance (13C,15N,1H) gradient probe
300 MHz NMR: A second 300 MHz instrument is available in the same suite which serves the needs for individuals involved in chemical synthesis or investigation of low MW compounds; this instrument is aVarian Gemini 2000 300 MHz 13C,1H instrument with Sun Ultra-5 workstation as a front end. Probe Varian 13C,1H dual nucleus probe (observe carbon, decouple 1H).
The facility includes a data processing area with a Silicon Graphics Indigo II workstation, the on-site availability of which allows prolonged data processing (often a requirement for multidimensional NMR experiments) to be conducted without use of the on-board workstation for the high-field instrument.
Access to, and use of, the resources including training and collaborative projects are arranged through the facility director.
Molecular Modeling Facilities
Glen E. Kellogg, Ph.D.
Director
(804) 828-6452
gkellogg@vcu.edu
Molecular modeling resources provide both the hardware for the display and analysis of structures as well as the computational and analytical software that is required for the reduction of data for analysis in terms of molecular properties. This includes the assessment of molecular properties critical in the application of methods of rational drug design as well as the identification of binding sites on macromolecular structures, the “docking” of molecules with each other based on steric, electronic and polar characteristics, and assessment of molecular energetics. The resources included here are critical to and integrated with the other two components of the structural biology shared resource.
Hardware for molecular modeling used by the Resource is primarily located on the second floor of the Virginia BioTechnology Research Park (BioTech One) in space allocated to the Institute for Structural Biology and Drug Design. Most of the faculty members located in the Institute are members of the Cancer Center and participants in Massey’s programs and program activities. The current site was planned and designed specifically for molecular modeling with special lighting, electrical, communications and HVAC features.
The computing hardware and software of the Molecular Modeling Facility are, at present, as follows:
Computers and printers
- Three Silicon Graphics Octane2 graphics workstations.
- Three Silicon Graphics Fuel graphics workstations.
- One Silicon Graphics Octane graphics workstation.
- Eight Silicon Graphics O2 graphics workstations.
- One Silicon Graphics Indigo II graphics workstation.
- Linux File server (Red Hat 9.0).
- Xerox/Tektronix Phaser 7750 color laser printer.
- Hewlett-Packard LaserJet 9000 printer.
Shared network resources
- TB RAID disk system.
- 1.5 TB RAID system.
- DLT (300 gB) tape drive.
Modeling software
- Sybyl (20 simultaneous users).
- InsightII/Discover (10 simultaneous users).
- GRID.
- HINT.
- Molconn-Z.
- DOCK.
- GOLD.
- Flex-X.
- DGEOM.
- O.
- Chain.
- Felix.
Development software
- FORTRAN and C/C++ (Irix and ESV).
- Power FORTRAN and Power C (for SGI multiprocessor systems).
- Open Interface (Biosym integration tools).
Databases include
- NCI 3D molecular database.
- Pomona MedChem Database.
A vital component to the success of the facility is that new applications and modeling approaches are being developed in-house. This capability and expertise permits an extra measure of flexibility in approaching solutions to computational problems as they arise in the context of the research objectives of the Massey Cancer Center membership.
Access to, and use of, the resources are arranged through the facility director.
