Lab Coordinator: Dr. Robert Latour
The
Biomolecular Interactions Laboratory is located in the Rhodes
Engineering Research Center. The laboratory has 800 sq. ft. of wet
laboratory space with work benches, sinks, refrigerator/freezer, and
fume-hoods for experimental work, and an adjacent laboratory section
for computational chemistry based modeling modeling.
The laboratory is dedicated to the study of the thermodynamics of biomolecular interactions with emphasis upon nonspecific protein-surface and specific protein-receptor interactions. These interactions are of central importance in a very broad range of biomedical engineering and biotechnology applications. Medical applications include tissue and blood biocompatibility, tissue calcification, celluar viability and control for tissue engineering, and resistance to bacterial adhesion for the prevention of infection. Biotechnology applications include the development of biosensors and decontamination agents for chem/bio defense and food safety applications, biomolecular recovery and separation, biofouling resistant surfaces, and fundamental studies of aquatic biomineralization.
The laboratory is dedicated to the study of the thermodynamics of biomolecular interactions with emphasis upon nonspecific protein-surface and specific protein-receptor interactions. These interactions are of central importance in a very broad range of biomedical engineering and biotechnology applications. Medical applications include tissue and blood biocompatibility, tissue calcification, celluar viability and control for tissue engineering, and resistance to bacterial adhesion for the prevention of infection. Biotechnology applications include the development of biosensors and decontamination agents for chem/bio defense and food safety applications, biomolecular recovery and separation, biofouling resistant surfaces, and fundamental studies of aquatic biomineralization.
Figure 1. Biacore-X Surface Plasmon Resonance Spectroscopy (SPR) Instrument. SPR spectroscopy provides real-time kinetic data for biomolecule-surface adsorption processes. This instrument serves as our primary experimental tool for studying protein-surface and protein-ligand interactions.
Figure
2. Molecular model (MSI, InsightII) of
an array of methyl-terminated alkane thiol
molecules [S-(CH2)15-CH3]
depicting a self-assembled monolayer (SAM) formed on a gold surface.
(yellow=sulfur, green=carbon, white=hydrogen)
Figure 3. Molecular model of a 9-residue peptide over an OH-SAM surface in water with 140 mM Na+ and Cl- constructed for molecular dynamics simulations (CHARMM & VMD software).
Figure
4. 30 kDa fragment of fibrinogen
(blood clotting protein) over aCOOH
SAM surface-initial position prior
to molecular dynamics simulations.
Model size: 107Å x
90Å x 105Å. Water molecules
not shown for clarity. (GROMACS & VMD
software)
Facilities
Biomolecular Interactions Experimental Laboratory
(510/512 Rhodes Research Center)
(510/512 Rhodes Research Center)
This laboratory is dedicated to studies that are being conducted to quantitatively measure molecular-level aspects related to the orientation, conformation, and bioactivity of adsorbed peptides and proteins to surfaces as a function of surface chemistry. As described below, our experimental studies are specifically designed and coordinated to support the development of computational chemistry methods for the accurate simulation of protein adsorption behavior.
The central components of this laboratory are a surface plasmon resonance (SPR) spectroscopy instrument (Biacore X, Biacore, Inc.) for adsorption kinetics and thermodynamics studies, a Reichert AR700 temperature controlled automatic refractometer (precision refractive index measurement for SPR bulk shift subtraction), a JASCO J-810 circular dichroism spectropolarimeter with Peltier temperature control for protein secondary structure analysis, a variable angle spectroscopic ellipsometer (GES5, SOPRA Inc.) for SAM surface and protein adsorption characterization, and a computerized contact angle instrument and image analysis system (CAM 200 instrument, KSV Instruments Ltd.) for surface characterization.
The central components of this laboratory are a surface plasmon resonance (SPR) spectroscopy instrument (Biacore X, Biacore, Inc.) for adsorption kinetics and thermodynamics studies, a Reichert AR700 temperature controlled automatic refractometer (precision refractive index measurement for SPR bulk shift subtraction), a JASCO J-810 circular dichroism spectropolarimeter with Peltier temperature control for protein secondary structure analysis, a variable angle spectroscopic ellipsometer (GES5, SOPRA Inc.) for SAM surface and protein adsorption characterization, and a computerized contact angle instrument and image analysis system (CAM 200 instrument, KSV Instruments Ltd.) for surface characterization.
Biomolecular Interactions Modeling Laboratory
(407 Rhodes Research Center)
(407 Rhodes Research Center)
The computational chemistry
facility provides the means to theoretically
assess molecular behavior to complement
the experimental studies described
above (see Figures 2 - 4). Computational
recourses include PC workstations networked
with a 300+ node Linux cluster that
is fully staffed and maintained through
the College of Engineering and Science
at Clemson University. The molecular
modeling facility includes BioMedCAChe
(Fujitsu), Materials Studio and Insight
II (Accelrys), AMBER, BOSS, CHARMM,
and GROMACS software capabilities.
Collaborators
Our
computational research program is
being conducted in close collaboration
with top experimental groups around
the country, including:
RESBIO at
Rutgers University
NESAC/BIO at the University of Washington
the Garcia lab at Georgia Tech
CAEFF at Clemson University
and our own experimental group in the Bioengineering Department at Clemson
Our research program focuses on the development of molecular modeling capabilities for the accurate simulation of the adsorption of peptides and proteins to surfaces as a function of surface chemistry. Our primary focus involves the development of the CHARMM molecular simulation program and force field for this application under NIH support. Projects are being conducted in collaboration with a list of modeling colleagues, including:
Dr. Steven Stuart and Dr. Brian Dominy
(Clemson University, Department of Chemistry)
Dr.
David Bruce (Clemson University, Dept. of Chemical & Biomolecular
Engineering)
Dr. Doyle Knight (Rutgers University)
Dr. William Welsh (Univ of Medicine & Dentistry of New
Jersey, Director of the
Informatics Institute)
Dr. Bernard Brooks (Chief
of the Laboratory of Computational
Biology at the NHLBI, NIH)
Dr. Alexander MacKerell (University of Maryland - Baltimore, School of
Pharmacy)
RESBIO at
Rutgers UniversityNESAC/BIO at the University of Washingtonthe Garcia lab at Georgia TechCAEFF at Clemson Universityand our own experimental group in the Bioengineering Department at Clemson
Our research program focuses on the development of molecular modeling capabilities for the accurate simulation of the adsorption of peptides and proteins to surfaces as a function of surface chemistry. Our primary focus involves the development of the CHARMM molecular simulation program and force field for this application under NIH support. Projects are being conducted in collaboration with a list of modeling colleagues, including:
Dr. Steven Stuart and Dr. Brian Dominy
(Clemson University, Department of Chemistry)Dr.
David Bruce (Clemson University, Dept. of Chemical & Biomolecular
Engineering)Dr. Doyle Knight (Rutgers University)Dr. William Welsh (Univ of Medicine & Dentistry of New
Jersey, Director of the
Informatics Institute)Dr. Bernard Brooks (Chief
of the Laboratory of Computational
Biology at the NHLBI, NIH)Dr. Alexander MacKerell (University of Maryland - Baltimore, School of
Pharmacy)