Core Facilities
The departments and faculty participating in the Program in Biological Chemistry provide an impressive array of facilities and research instrumentation. Individual departments each possess facilities for routine physical measurements needed to support biochemical research. In addition, the major departments in the Program emphasize particular research areas and have the sophisticated instrumentation to support these activities. The major instruments (NMR, mass spectrometry, FT-IR, ESR, X-ray diffraction, supercomputer) are available to users campus-wide, and interdepartmental collaborations involving these instruments are encouraged. There are instruments available for UV-Vis, IR, CD, titration calorimetry, analytical ultracentrifugation, and polarimetry in participating departments. Groups in the Chemistry department are using scanning tunneling microscopy and atomic force microscopy to study the structure of biological macromolecules. For projects involving large-scale structures, a confocal microscope is located in the Biology department.
High Performance Computational Resources
Julio Facelli, Ph.D., Facility Supervisor
In addition to dedicated computational resources for biological chemistry research programs available in specific labs and departments, the Center for High Performance Computing (CHPC) provides training, software, and access to high performance computational resources or the larger campus community. Currently available hardware resources include an 8-node (32 processor) Compaq Sierra cluster with a QUADRIX switch and the Icebox cluster of ~303 nodes (388 processors) of Intel and AMD processors. Additional specialized servers are available for specific applications like large-scale statistics, molecular modeling, Genbank searches, etc. During the summer of 2003, a large NIH and University of Utah funded metacluster for bioinformatics ($2,000,000) came online. This includes a series of interconnected cluster computers including a high performance parallel cluster, a data-mining cluster, a visualization cluster, and a cycle farm. In addition, this metacluster integrates significant online storage capacity. In addition to hardware and software resources, the CHPC also provides advanced visualization capabilities including an AccessGrid node (allowing realtime video conferences to other AccessGrid nodes throughout the world) and training. For more information, see www.chpc.utah.edu.
DNA and Peptide Facility
Bob Shackmann, Ph.D., Facility Supervisor
This core offers investigators synthetic peptides for use in generating antibodies; and it also provides oligonucleotide synthesis services for use as primers in PCR experiments, hybridization studies, and for DNA sequencing. This core also offers Edman protein/peptide sequencing.
DNA Sequencing Facility
Helaman Escobar, Facility Supervisor
The DNA Sequencing Facility uses state-of-the-art capillary instrumentation to provide high throughput, low cost sequencing services to the University community. The facility offers custom sequencing of plasmid DNA, PCR products and large insert templates such as cosmids and BACs. The facility also offers complete single or double strand coverage of cloned DNA by primer walking and contig assembly. By utilizing a specialized laboratory information management system, the core offers electronic sample submission and data distribution, usually within 48 to 72 hours of sample submission.
Mass Spectrometry Facility
Chad Nelson, Ph.D., Facility Supervisor
This core provides mass spectrometry services and consultation to laboratories and other research groups. These measurements are utilized in a range of investigations involving molecular characterization, such as identification of mutagenized proteins from 1D or 2D gels, or characterization of potential anti-tumor agents. Molecular mass measurements are made with typical errors of +/– 0.25 Da at Mr 1,000, or +/– 2 Da at Mr 25kDa. Partial sequencing of small peptides can be carried out, at the 300 femtomole and higher level, in peptide mixtures or tryptic digests of proteins. Protein identification services include protein database searching using Sequest or Mascot software. Data are acquired using electrospray ionization LC/MS/MS techniques, or by matrix-assisted laser desorption ionization (MALDI) time-of-flight (TOF) mass spectrometry.
Biomolecular NMR Core Facility
Jack Shalicky, Ph.D., Facility Supervisor
This facility exists to facilitate the determination of new protein, nucleic acid, and natural product structures and to provide analytical NMR services to the Health Sciences community. The facility provides the necessary hardware and software for NMR data acquisition and analysis; it also has a centralized computing facility and detailed protocols for the various steps involved in biomolecular NMR structure determination. NMR instrumentation includes a Varian Unity 500 MHz NMR spectrometer, Varian Inova 600 MHz NMR spectrometers and a Varian Mercury 400. The NMR center also has several Sun and SGI workstations for offline data processing and biomolecular structure determination. Instrument schedules, rates, detailed instructions for using the facility, and instrument request forms are available on the website.
Protein Interaction Facility
David Myszka, Ph.D., Facility Supervisor
The Protein Interaction Facility provides easy access to advanced technologies used in characterizing binding interactions. Currently BIACORE 3000, 2000 and S51 optical biosensors are used to define the assembly state, affinity, and kinetics of an interaction. The advantage of optical biosensors is that they allow real-time analysis of molecular interactions without labeling requirements. This makes the technology applicable to the study of a wide variety of biological molecules including proteins, oligonucleotides, oligosaccharides and lipids.
Electron Microscopy Facility
Kurt Albertine, Ph.D., Facility Supervisor
This facility provides a variety of microscopy services to the basic science and clinical communities. Services and technical capabilities include light microscopy (brightfield, fluorescence, 3-D, etc.), transmission and scanning electron microscopy (quantitative morphology), histochemistry, immunohistochemistry, in situ hybridization, laser capture microscopy, PCR, RT-PCR and in situ PCR/RT.PCR.
X-ray Crystallography
The departments of Chemistry and Biochemistry are involved in structure determination using X-ray crystallography. High energy X-ray sources and computer interfaced detectors are used to obtain the high-quality diffraction data required to determine protein structures at high resolution. As described above, a large amount of computer resources are devoted to crystallographic refinement and to analyzing protein structures using molecular graphics systems.