Structural Biology
Structural Biology Core
The Structural Biology Core facility in the Department of Molecular Medicine is designed to support researchers in their drug discovery and structure-based drug design efforts. With the computing power of the USF Research Computing Central Instructional and Research Computing Environment (CIRCE) or Amazon Web Services (AWS), researchers can use DOCK 3.7 to virtually screen the ~ 1.5 billion compounds contained in the ZINC database to identify novel small molecule leads against their targets. Then, using the core’s Cytiva Biacore S200 Surface Plasmon Resonance (SPR) instrument or BioTek Cytation 5 plate reader, researchers can validate compounds identified and purchased from virtual screening. The Biacore S200 is Cytiva’s most sensitive SPR instrument, and specifically designed to characterize the interactions involved in LMW/fragment-based drug discovery. The core is also open to working with researchers to utilize their own assays for hit validation. From there, researchers have access to the core’s full array of protein crystallization equipment in order to capture a crystal structure of validated hits in complex with their targets.
This crystallization equipment includes:
- The Art Robbins Instruments Crystal Phoenix Liquid Handling Robot and the SPT Labtech Mosquito Xtal3, which allow researchers to quickly screen their protein of interest against an array of crystallization conditions and identify initial hits,
- The Formulatrix Rock Imager 1000 Crystal Imager, which serves as both an incubator for screening trays and as an imager. The Rock Imager can automatically image screening trays on set schedules, using visible, polarized, and UV light, and help to quickly identify new protein crystals.
- The Formulatrix Formulator 16, which can be used to aid in optimization of crystallization conditions, allows for the creation of novel crystallization screens that can be designed by researchers. The core also possesses all the necessary equipment to enable researchers to freeze and ship crystals to national beamlines for data collection. As part of the Southeast Regional Collaborative Access Team (SER-CAT) at Argonne National Laboratory, the core has access to regular beamtimes at the Advanced Photon Source (APS), where crystal datasets can be collected in as little as three minutes. If required, the core can also aid in the solving and refinement of crystal structures.
As a USF core facility, the staff can provide user training, experimental design support, and sample preparation/analysis.
Services Offered:
- Virtual screening/molecular modeling
- Protein purification
- Protein crystal screening/optimization
- X-ray data collection
- Solution/refinement of crystal structures
- Surface Plasmon Resonance (SPR)
- Hit validation
Location and Contact Information:
The Structural Biology Core facility is located in MDC 3524.
For questions, please contact:
Yu Chen, Ph.D.
ychen1@usf.edu
Eric Lewandowski, Ph.D.
elewand2@usf.edu
Additional team members:
Jesper Madsen, Ph.D.
jespermadsen@usf.edu
Ya-Tzu Li
li19@usf.edu
Drug Discovery
The Biacore S200 is Cytiva’s most sensitive SPR instrument and is specifically designed to detect (down to 0.1 RU) and characterize interactions of LMW analytes in drug discovery applications. The S200 supports the use of 96 and 384 well plates, as well as individual tubes depending on the application. Sensor chips used on the S200 contain four flow cells, thus allowing for the linkage and testing of up to four different ligands.
The Cytation 5 is an automated plate reader that can facilitate UV-Vis absorbance detection, luminescence, and filter/monochromator-based fluorescence assays. The built in Peltier cooling module helps keep the temperature in the reader stable and leads to more consistent results. The core also possesses a green filter cube for the Cytation 5 that allows for Fluorescence Polarization assays to be run. The reader supports up to 1,536 well plates and has a built-in shaker.
Structure-Based Drug Design
The AKTA Pure FPLC (Fast Protein Liquid Chromatography) system allows for the rapid purification of proteins, peptides, etc... The system is suitable for running affinity, ion exchange, hydrophobic interaction, and size-exclusion chromatography columns and the F9-C fraction collector can conveniently dispense samples into 96 well deep-well plates for easy collection and analysis. Additionally, the S9 Sample Pump allows for the loading of large sample volumes onto columns at up to 50 mL/min.
The Phoenix and Xtal3 are high-throughput crystallization screening robots that allow researchers to quickly screen their protein of interest against commercially available crystallization screening kits, or screens developed in house. The Xtal3 can set up screening drops as small as 50 nL, thus allowing researchers to use a minimal amount of precious sample. The core regularly keeps the following commercial crystallization screens in stock, but researchers can also provide their own for use:
- Rigaku JCSG+
- Rigaku Berkeley
- Rigaku Top96
- NeXtal PEGs II Suite
- NeXtal AmSO4 Suite
The Rock Imager is an automatic crystal imaging system/hotel that can store up to 970 screening trays at 20° C and image the trays on a set schedule. This eliminates the need for researchers to manually look through every screening drop and allows for rapid identification of screening hits. An array of imaging schedules are available to track crystal growth over the span of a few days, or up to three months. The Rock Imager is equipped with visible, polarized, and UV objectives for easy determination of protein crystals vs. salt crystals. Additionally, crystallization conditions identified on the Rock Imager can be automatically sent to the Formulator 16 to create customized optimization screens that can be used on the Phoenix.
The Formulator 16 is a liquid handler that utilizes microfluidics to dispense (down to 200 nL) up to 16 different reagents and create custom crystal screening/optimization screens. Crystallization conditions can be automatically uploaded from the Rock Imager and used to design a tailored optimization screen to improve crystal size/quality.
User Fees
| Academic User |
Industry User |
|
| Protein Purification | ||
| AKTA Pure (unassisted)1 |
$10/hr | $20/hr |
| AKTA Pure (assisted) | $30/hr | $50/hr |
| Training |
$25/hr |
$45/hr |
|
Crystallization Robots |
||
| ARI Phoenix or Xtal3 |
$20/per screen |
$35/per screen |
| Formulatrix Formulator |
$25/per screen |
$40/per screen |
|
Supply Fee (if using Core solutions/supplies) |
$10/each |
$17/each |
|
Crystal Imaging |
||
|
Formulatrix Rock Imager (28 days/visible and UV) |
$3/per tray |
$10/per tray |
|
Crystal Data Collection |
||
| SERCAT-ID/BM2 |
$250/hour |
$500/hour |
|
Data Refinement/Solution |
||
|
Solution and refinement of crystal structure |
$40/hour |
$80/hour |
| SPR3 | ||
| Biacore S200 (unassisted) |
$30/hour |
$60/hour |
| Biacore S200 (assisted) |
$60/hour |
$120/hour |
| Training Supplies4 |
$726/each |
|
| Training |
$40/hour |
$95/hour |
| Supply Fee5 | $50 | |
| Overnight Chip Rehydration5 |
$50 |
|
1 Training required.
2 Includes crystal freezing, shipping, and data collection time.
3 User buys sensor chips and supplies. Training required for unassisted use.
4 Training cost includes cost of Getting Started Kit and one (1) Series S CM5 sensor chip
5 One-time fee
*Per project pricing also available for discussion.