The Center
for Biophysical Sciences and Engineering (CBSE) (University-Wide Interdisciplinary
Director:
Established: 1986
The Center for Biophysical Sciences and Engineering (CBSE) is
dedicated to determination of structure-function relationships of biological
molecules supporting drug design methodology for chronic and infectious
diseases. With over 100 members
including 12+ PhD level crystallographers, the CBSE is one of the largest x-ray
crystallography units in the structural biology community.
Center Research
The CBSE has established research expertise in structural
biology to reflect its approach to structure based drug design and the impact
of structural genomics and proteomics in drug discovery. The facility provides structural biology
support from cloning and expression through structure determination and
combinatorial chemistry for researchers interested in macromolecular
structure-function relationships and drug discovery via intelligent
combinatorial design. Protein structural
information is used for the discovery and synthesis of complimentary compounds
that augment or inhibit the protein's biological activity for drug discovery applications. Our state-of-the-art
approach to developing small molecule drugs includes an integrated platform of
high-throughput (HTP) technologies providing structural solutions for both
aqueous and membrane proteins of interest.
Current drug development programs supported by the facility focus
on cancer, infectious diseases, cardiovascular disease, bacterial infections,
and immune response. The CBSE has a special
interest in crystallizing and solving membrane protein structures in
particular.
The CBSE operates a HTP Protein
Expression and Purification Facility for cloning and expressing proteins in
both prokaryotic and eukaryotic host systems on entire genomes, providing
molecular biology scale production and access to a core facility for large
scale growth of bacterial cultures. The
CBSE has expertise and ability to produce proteins of interest for researchers
in e. coli, baculovirus, yeast, and
the lentivirus system. Recombinatorial
cloning and streamlined approaches for refolding and purification of proteins
are employed to optimize results.
The HTP Protein Crystallization Facility
minimizes the time and amount of protein sample a researcher needs to obtain
diffraction quality crystals for structure determination. The Crystallization Facility includes a fully
integrated laboratory with HTP systems capable of rapidly generating hundreds
of specialized solutions for screens in nanoliter to microliter volumes. The laboratory maintains a total of four HTP
systems (employing hanging drop, sitting drop, batch, microchip free interface
diffusion and capillary counter diffusion methods) for crystallization and
co-crystallization trials, thus increasing throughput to over 20,000
experiments per day using nanoliter to microliter volumes. Sample requirements for initial screens start
at just 600 µg of protein. The HTP
protein crystallization and Co-Crystallization screening facility utilizes the
following integrated platform of systems:
·
A HTP automated system for rapid generation and
optimization of specialized solutions used in crystallization screens (Recipe
Maker™).
·
A new (2008) Rigaku Phoenix RE Liquid Handling System
for high throughput low volume protein crystallization experimentation.
·
Two automated HTP liquid dispensing systems for
submicroliter volumes (the custom built NanoScreen™ and the commercial
Cartesian HoneyBee™ System).
·
An automated microchip system for free interface
diffusion crystallization along with an automated imaging station for
microchips (a.k.a. the Fluidigm Topaz Microchip System™).
·
An automated HTP capillary counter diffusion system (the
HoneyComb by Genomic Solutions™).
·
A HTP automated system for optical recognition and
scoring of crystals (Crystal Score™).
·
A dynamically controlled crystal growth kinetic system
for optimization of crystal growth (Vapor Pro™).
·
The CBSE has also developed a neural network (utilizing
a predictive algorithm) for “in silico” screening of conditions. This neural network optimizes screening
conditions and has been shown to produce additional conditions that yield
larger, more suitable crystals for x-ray analysis. Success has been
demonstrated with the use of this virtual screening program for the
optimization of crystallization conditions, thus reducing amount of sample and
number of experiments needed to define high quality crystal growth. This technology supports efforts to find new
or optimize present conditions that improve crystal growth for both soluble and
in particular membrane proteins such as GPCR’s and Ion Channels.
·
HTP Self Interaction Chromatography, a customized HPLC
system for accurate protein-protein interaction experiments for the
determination of second virial coefficient measurements of proteins. Improved crystallization parameters for
proteins as well as optimizing solutions for the stabilization of protein
pharmaceutical formulations represents examples of protein solution phenomena
that can be measured with thermodynamics measurements of protein-protein
interactions. We can measure PPI through
the determination of the second virial coefficient. The CBSE has developed a - HTP analytical
method and automated system that allows users to quickly determine optimal
solutions.
These complimentary technologies
position the CBSE to rapidly pursue structural information for every protein in
a target genome. Researchers at the CBSE
have successfully
pioneered new technologies in support of drug discovery programs that have led
to the design of pharmaceuticals for preclinical and clinical trials developed
to treat chronic and infectious diseases such as T-cell mediated diseases, acute
coronary syndromes, influenza, Bacillus
anthracis (anthrax infection), bacterial vaginosis, and other emerging
infections.
The CBSE has unparalleled capacity in
the area of collecting x-ray diffraction data and analyzing these coordinates for
3D structure determination of proteins and protein drug complexes. Since 1997, UAB has been a member of the
Southeast Regional Collaborative Access Team (SERCAT) with dedicated access to
two of the most powerful beamlines at the Argonne National Laboratory in
The Laboratory of Medicinal and Combinatorial
Chemistry (LMCC) identifies and optimizes lead compounds against selected and newly defined
biological targets. The LMCC works with
the x-ray crystal structure of protein drug targets to perform “in silico”
virtual screening and protein structure-directed ligand design. This capability has considerable advantages for
the design and development of clinically relevant compounds for pharmaceutical
design. Two synthetic laboratories are
specifically designed for parallel, solution phase chemistry and house the robotic
synthesizer along with other equipment to support parallel library
synthesis.
The CBSE Biomolecular
Physics laboratory provides complimentary techniques used by researchers in support
of both crystallization and lead compound development. The CBSE Biomolecular Analysis Group currently
uses biocalorimetry data and other biophysical tools to advance the early
stages of lead compound design and optimization when the focus is on improving
affinity for the macromolecular target.
Calorimetry techniques determine relevant thermodynamic parameters
necessary to correlate structure with energetics. These energetic consequences per se, can
affect the mechanism of action.
Knowledge of how these thermodynamic parameters of binding vary with
different lead structures and chemical analogs can direct choices for further
chemical modification. The laboratory includes
four high sensitivity calorimeters (isothermal and differential scanning
calorimeters); two Biosensor BiaCore 2000; and an OLIS rapid scanning
spectrophotometer for circular dichroism, fluorescence, fluorescence
polarization and uv/vis for kinetic, stopped-flow, and temperature scanning.
Isothermal Titration Calorimetry and
Differential Scanning Calorimetry can advance research with applications in: 1)
protein engineering, detecting misfolded domains; 2) proteomics, energetic
domain architecture; 3) optimization of crystallization conditions, 4) biopharmaceutical
formulations; 5) drug discovery: developing universal assay for lead
identification, development; and 6) understanding the importance of functional
groups, salvation, hydrophobicity, and conformation.
A HTP Screening Facility
rapidly identifies active compounds in chemical libraries with high statistical
accuracy to advance initial leads for drug design. The facility provides a platform of
flexibility and rich functionality for HTP research applications. Numerous biochemical and molecular biology
experiments are performed, such as compound library screening, enzymatic
activity,
The Center’s history also includes the designation in 1986
from NASA as a
In 1990, the Engineering Division was
brought in-house to develop new technologies and support the scientific
community in the design and operation of both laboratory and microgravity
experiments. The Engineering Division is
a full-service organization capable of providing technical services and
turn-key systems to our customers. Our
capabilities in hardware and software development cover mechanical, electrical,
and software design, fabrication, assembly, test, and operations. As one of the nation's leading developers in
cold stowage hardware for use in microgravity and exploration, the Engineering
Division provides services in systems engineering, safety and verification
documentation/closeout, crew training, launch-site support, mission operations,
and recovery. The Engineering Division
offers expertise in the following areas: 1) Mechanical Hardware (prototype)
Development; 2) Electrical Engineering; 3) Software Development; 4) Metrology;
5) Procurement, Fabrication and Assembly; 6) Research Machine Shop; and 7)
Systems Engineering.
The Engineering Division occupies 18,000 square feet. There is specialized facility space supports
hardware assembly and system testing, remote operations for payloads on-board
Shuttle or ISS, and computer/network internal support functions. The following labs are ISO 9001:2000 Certified:
1) the Fabrication/Assembly/Test Labs, 2) the 100k Class Clean Room, 3) the
Prototyping Lab, and 4) the Metrology Hardware machining and fabrication is
performed through the Research Machine Shop and is available to the entire UAB
community as well.
For
additional information:
Director:
Email: delucas@cbse.uab.edu
Approved by:
Date: April 30, 2008
Click here to return to the SOM
Research Web Site's home page.