Solution Biophysics Laboratory (SBL)

Solution Biophysics Laboratory

Introduction

The Solution Biophysics Laboratory (SBL), located in room 6.656 on the sixth floor of the Basic Science Building (BSB), was established in 1995. The purpose of the lab is to enhance solution biophysics research of SCSBMB core faculty members and UTMB collaborators. Instruction is given in the use of a variety of SBL instrumentation, including:

analytical ultracentrifugation
fluorescence
circular dichroism
dynamic light scattering
surface plasmon resonance
thermal denaturation high throughput analysis

SCSBMB faculty includes prominent researchers in the field of molecular biophysics and thermodynamics, and this core facility promotes the use of these techniques to solve research problems of a fundamental nature that may lead to a translational research objective. Solution molecular biophysics and thermodynamic techniques are used both as a primary research tool as well as means to structural studies (for example in the exploration of conditions for crystallization of proteins). Analytical ultracentrifugation studies of cytochrome p450 orthologues led to the successful crystallization and structure solution of the first open-form of a p450 (1).

Among the many research problems that can benefit from such studies include:

structure and function characterization of macromolecules
molecular mechanisms
protein stability issues
ligand binding thermodynamics
assay development
high throughput screening of protein or nucleic acid ligands

UTMB also pioneered the use of osmolytes in the stabilization of intrinsically unstructured regions of proteins (2) and the SBL has a long tradition of the use of protecting osmolytes in biophysical studies (3).

Instruments

Beckman-Coulter XL-A Analytical Ultra Centrifuge

Monitor the hydrodynamic properties of biomacromolecules and protein-protein interactions. Our XL-A analytical ultracentrifuge allows us to perform two basic types of experiments: sedimentation velocity (SV) and sedimentation equilibrium (SE). SV experiments leads to the determination of the sedimentation coefficient, s, which can provide information about the shape and molar mass of macromolecules in solution, as well as their size-distribution. This information can be used to analyze protein-protein interactions, the presence of oligomeric states, and conformational rearrangement of molecules. SE experiments is one of the best ways for determining the molecular weights of macromolecules and excellent for analysis of heterogeneity in solution. It is also one of the best techniques for obtaining equilibrium constants for self-associating systems.
Biacore T100

Our Surface Plasmon Resonance (SPR) Biacore T100 biosensor instrument is a high-throughput equipment that allows the study of protein-protein and protein-ligand kinetics and thermodynamics. Being fully automated, this instrument can be used in a 24/7 regime. It is especially well suited for the determination of k_on, k_off and Keq. When compared to similar techniques like isothermal titration calorimetry (ITC) it has reduced protein consumption.
Eppendorf epMotion 5075 Solution Robot
Routinely used for preparing samples and microplates for the thermofluor and also for the preparation of samples for the new Biacore T100.
Jasco J-815 Circular Dichroism Spectrometer
The Jasco J-815 Circular Dichroism Spectrometer housed in the SBL allows for the quick and easy determination of secondary and tertiary structures of protein samples. Thermodynamic data such as protein stability parameters and binding constants can also be obtained. Our instrument is able to perform a variety of experiments such as wavelength scans, temperature scans, and time courses. We have a set of different sized cuvettes to allow optimization of operating conditions, from high volume 1 cm cells to low volume "sandwich cells" especially suitable for "non-transparent" buffers.
The instrument includes software for instrument control, data acquisition, processing and publication quality presentations in a Windows environment. All experiment parameters are accessed through pull down menus. Control panels allow easy entry of all data acquisition parameters.
Malvern DLS
The Malvern mico V Dynamic Light Scattering instrument evaluates the hydrodynamic radius of macromolecules and macromolecular complexes in solution. DLS is often used in quality control of partical size, it is very sensitive to impurities in the sample, and can estimate the molecular weight of complexes. Intrinsically disordered proteins and their contraction and folding can be monitored using this technique.
MicroCal PEAQ-ITC from Malvern
Our isothermal titration calorimeter MicroCal PEAQ-ITC provides detailed analysis into binding energetics. The system has a 200 μL sample cell and provides direct measurement of the heat absorbed or evolved as a result of mixing precise amounts of reactants in liquid samples.
The washing module provides a quick and easy way to thoroughly clean both titration syringe and sample cell and data analysis can be performed quickly using the MicroCal PEAQ-ITC Analysis software using fitting models to calculate the stoichiometry (N), the binding constant (KD), enthalpy (ΔH), and entropy (ΔS) of the interaction.
Protein Thermal Shift Studies from Applied Biosystems
The Protein Thermal Shift assay can be performed quickly and in a high throughput fashion. This assay allows the user to test a large number of ligands looking for binding. Additionally it can be used to screen for buffers for crystallization conditions or for changes in stability when comparing mutants of a protein.
Refractometer
Used routinely to determine the concentration of the stock solutions of denaturants and osmolytes.
Spex Fluoromax Fluorometer
Fluorescence spectroscopy is well stablished technique to study protein folding and protein-protein, protein-ligand interactions. We can make use of both instrinsic or extrinsic fluorophores to follow changes in fluoresce emission due to changes in the chemical environment surrounding the fluorophore (such as due to addition of chaotropic agents typical in folding studies, or increasing concentrations of a binding partner). These changes in fluorescence emission allow us to obtain important thermodynamic information about the protein system such as binding constants and protein stability parameters.
ThermoFluor
This multipurpose high-throughput instrument can be used in an isothermal or thermal scan mode. It uses 384 well plates and in the thermal scan mode is designed to detect fluorescence of fluorophores that bind to the thermally denatured states of proteins. Ligands or solution conditions that stabilize the protein increase the melting temperature. Thus, the instrument can be used to optimize solution conditions for protein stability, assess binding constants of small ligands or protein binding partners to a particular protein. It can also be used for determining appropriate solution conditions for protein crystallization, enzyme assay development, or drug discovery.