Laboratory. The Fesik lab consists of about 4,000 sq. ft. with bench space and seating capacity for 28 researchers. The lab contains all the necessary equipment to perform molecular and cell biology experiments, protein purifications, sample preparation, and medicinal chemistry. It contains eight fume hoods, a cell culture room with four biohoods, a room housing the fermentor, and a shared cold room. In addition, the Fesik Lab has access to NMR spectrometers, X-ray equipment, and a crystallization robot in the structural biology core facility, instrumentation in the High Throughput Screening Core and Mass Spectrometry Core, and additional equipment in the Vanderbilt Institute of Chemical Biology’s Chemical Synthesis Core and other chemistry labs on campus (Professors Sulikowski, Lindsley, and Johnston).
Protein preparation. The lab contains all the necessary equipment to clone, express, and purify proteins such as an Eppendorf MasterCycler for running PCR and two E-Gel iBase and E-Gel Safe Imager systems for DNA agarose gel electrophoresis and collection. Other related equipment includes: a -80 °C freezer to store competent cells and proteins; a -20 °C freezer to store enzymes, plasmids and reagents; a bench-top and floor model refrigerated shaker/incubator; a BioFlo 415 fermentor for cell culture growth; bench-top and floor model centrifuges for cell harvesting; and a APV 2000 cell homogenizer for lysing cells.
X-ray crystallography. Crystallization screens are designed and prepared using the Hamilton Microlab Star liquid handling workstations, and protein crystallization drops are set up with the nano-dispensing Mosquito robot. The crystallization plates are stored in three vibration-free crystallization incubators capable of temperature programming, and crystals are observed using an Olympus SXZ16 stereomicroscope equipped with a 5MP digital camera. Additionally, cryogenic tools, dewars, and a dry shipper from VWR are used for cryo-crystallography and synchrotron data collection. X-ray crystallographic experiments will be performed using a Bruker Microstar high brilliance rotating anode X-ray generator, an Oxford XCalibur sealed tube generator with CCD detector, or a synchrotron. Vanderbilt owns a 1/2 share of the Life Sciences Collaborative Access Team (LS-CAT) beamline which provides over 40 days of synchrotron experiments per year.
We have a wide selection of polymer supported or resin-bound reagents and scavengers (e.g. PSTrisamine, MP-carbonate, PS-DCC, etc) to enable parallel chemistry, faster reaction workups and purifications. We also have access to an automated mass directed Agilent HPLC system that will be used for the purification of large libraries of compounds. In addition, through the Vanderbilt Institute of Chemical Biology’s Chemical Synthesis Core, the chemistry team has access to additional specialized equipment, including a Varian Polaris 211 analytical HPLC system with PDA and autosampler dedicated to chiral analyses, a Varian Prepstar SD1 preparative scale HPLC dedicated to chiral purifications, three large capacity chiral preparatory columns, a Parr hydrogenator, and an Autopol III automatic polarimeter.Selected additional instrumentation, such as gas chromatographs, an ozonizer, and a high pressure hydrogenation apparatus, among others, is also available at need from the groups of Professors Sulikowski, Lindsley, and Johnston, which are located in close proximity. Within the Mass Spectrometry Core facility, 41 mass spectrometers, including MALDI and TOF instruments, are available for non-routine experiments.
Computing. Each member of the Fesik lab has a Macintosh computer and access to a number of standard computing programs. In addition, three linux work stations are available in the lab for molecular modeling and docking experiments. The lab members have access via subscription to a number of shared software packages, including the Molecular Operating Environment (MOE), the ChemCart database containing the Vanderbilt compound collection, and Pipeline Pilot, via the HTS Core and/or the Center for Structural Biology. High performance and throughput computing are handled by three primary systems. The Advanced Computing Center for Research and Education (ACCRE) maintains a 1200-processor compute cluster with 1.5GB of RAM per processor. The CSB faculty typically access ~15% of ACCRE. The facility is operated by ACCRE staff, who are supported through user fees. The Center for Structural Biology (CSB), of which Dr. Fesik is a member, maintains additional high performance computing resources: an SGI Altix system with 32 Intel Itanium2 CPUs and 64GB of RAM, and a 25-node cluster with 624GB of RAM and 200 Intel Nehalem processor cores interconnected with a 40 Gbit Infiniband fabric. These systems are all interconnected to a 20TB highperformance gigabit Ethernet network-attached storage system which facilitates data sharing between all the above computing resources and local workstations. These CSB facilities are operated by the CSB Computing Core, which is responsible for supporting all local computing resources. This group keeps the central computers and network updated, trouble-shoots, coordinates for outside repair and service contracts, does regular data backups and maintains shared software and databases, remote access into the network, color and black-and-white laser printers, and a data management system for short-term and archival file storage. The CSB Computing Core is supported through a system of user fees. Access to a comprehensive suite of continually updated and optimized structural biology software packages is provided through the SBGrid consortium, which charges an annual fee for this service.