Keck Biophysics Facility

• Characterization of biomolecular interactions.

  We offer several orthogonal technologies for characterization of biomolecular interactions in terms of affinity, specificity, stoichiometry. These tools include micro-calorimeters as well as surface plasmon resonance and bio-layer interferometry instruments, which are used for validation and optimization of drug candidates from high-throughput screens, for rational drug design and structure-activity studies.

• Characterization of exosomes, viruses, and synthetic nanoparticles.

  We offer technologies, including static and dynamic light scattering and nano-particle tracking analysis, that can determine size distribution and concentration of biological exosomes, virus particles and liposomes as well as synthetic nano devices that are engineered for drug/gene delivery, bio-sensing and bio-imaging purposes.

• Characterization of biological and synthetic macromolecules.

  We have a sophisticated set of spectrometers and fluorimeters that can be used for examining the purity, stability, solubility and structural and conformational integrity of proteins, nucleic acids and synthetic polymers. These assays are essential to structure-activity studie and are also commonly employed for characterization of target antigens, crystallization efforts and as quality control in preclinical studies involving engineered proteins or therapeutic antibodies.

• Characterization of suspensions of small drugs, peptides and micro RNAs.

  We offer stability testing, measurements of solubility, purity, heterogeneity and ratiometric content of solutions and suspensions. These analyses are important for enhancing the quality, safety and efficiency of therapeutic reagents. Small-scale purification by HPLC or size exclusion chromatography and lyophilization services are also available.

• Imaging and quantitation of fluorescent, absorbance, phosphorescent and chemiluminescent signals from gels, blots or multiple well plates.

  These capabilities are used in a broad range of projects including quantitative protein expression and protein interaction assays in normal and malignant cells, validation of genetic profiling studies and antibody-based detection tests.

• Bio-layer Interferometer: Characterization of macromolecular interactions (affinity and kinetics) for hit validation and optimization
• Differential Scanning Calorimeter: Thermal analysis of proteins, lipids, nucleic acids, nanoparticles and micellar systems for protein engineering and stability studies
• Isothermal Titration Calorimeter: Characterization of molecular interactions (affinity, thermodynamics, stoichiometry) for drug screening studies, target validation
• Circular Dichroism Spectrophotometer: Secondary and tertiary structure evaluation of proteins, peptides, nucleic acids and synthetic polymers, chirality measurements
• Dynamic Light Scattering: Measurements of hydrodynamic radii, utilized in solubility and stability assays
• Fluorescence Plate Reader: Fluorescence-based assays and screens in 96 well plates
• Fluorescence Polarization System: Characterization of high-affinity protein-drug/peptide interactions, hit validation studies
• Micro-Volume Full-Spectrum Fluorimeter: Quantification of nucleic acids and fluorescent molecules in microvolume samples
• Steady State Photon Counting Fluorimeter: Structural and dynamic characterization of biological and synthetic polymers, nucleic acids, proteins and nanostructures
• High-Pressure Liquid Chromatography: Separation and characterization of bio-macromolecules and small molecules in complex mixtures
• Digital Imager: Digital imaging of fluorescent and dye-stained gels
• Freeze-Dry System: Freeze-drying suspensions of biomolecules, organic compounds and cell extracts
• Size Exclusion Chromatography with Light Scattering: Separation and l characterization (molar mass, hydrodynamic radius, polydispersity index) of complex mixtures
• Nanoparticle Tracking Analysis: Hydrodynamic radius measurement of micro and nanostructures (gold/silver particles, exosomes, liposomes, micelles)
• NIR Fluorescence and Chemiluminescence Digital Imager: Imaging chemiluminescent and NIR fluorescent western blots, gels and multi-wheel plates
• qPCR system: MicroRNA analysis, single nucleotide polymorphism genotyping, copy number variation analysis
• Multi-Channel Surface Plasmon Resonance: Label-free, real time quantitative measurements of molecular interactions for structure-function analyses, hit validation and kinetics guided drug optimization studies
• Laser Imager: Imaging and quantitation of radioisotopic and UV-Vis fluorescent signals in gels, blots and plates
• Double-beam Spectrophotometer: UV-Vis-NIR measurements (absorbance, transmittance and reflectance) of liquid and solid samples and tissues

Structural characterization of therapeutic targets

Histone deacetylases (HDACs) are a class of enzymes responsible for erasing acetylation marks from chromatin and facilitating a transcriptionally-repressed state. Several small-molecule inhibitors of HDAC1 and HDAC2 have been previously identified in high-throughput screens and developed into cancer therapeutics. However, these inhibitors disrupt several cellular pathways involving related HDAC enzymes and show high cytotoxicity and severe adverse effects. Since HDAC proteins are involved in several multiprotein corepressor complexes, each with distinct functional roles, next generation inhibitors with targeted functional specificity could be designed based on structural and functional characterization of these complexes. The Radhakrishnan (CEND) and Modragon (CAPS) groups examined the role of two main proteins, Sin3A and Sds3, in HDAC1 recruitment and assembly of the core Sin3L/Rpd3L complex. Based on structural information and functional studies, specific regions and residues critical for these interactions were identified. The study also showed that Sds3 dimerizes, forming an anti-parallel coiled-coil dimer via two adjacent segments of its polypeptide chain and that BRMS1 (breast cancer metastasis suppressor dimerizes in a similar manner The facility's isothermal titration calorimetry (ITC) and size exclusion chromatography with light scattering (SEC-MALS) instruments were used to determine the affinity and stoichiometry of these complexes and the effects of specific mutations at the Sin3A-Sds3 and Sds3 dimer interface Reference: Clark et. al. Proc Natl Acad Sci USA, 112:E3669, 2015 PMCID PMC4507224

Support of drug development studies

Activin is a small protein associated with several disease conditions, including cancer-related cachexia. In late-stage murine cancer models, inhibition of activin with either follistatin or with RIIA receptor protein has been shown to reverse cachexia effects. Based on the crystal structure of the activin-follistatin complex, the groups of Woodruff (CCS) and Scheidt (CAPS) collaborated in work that identified a number of potential small-molecule activin antagonists through in silico screening (J. Med. Chem. 58:5637, 2015). The Keck Facility's Bio-layer Interferometry (BLI) instrument was used to test potential leads for their ability to bind activin with high specificity and to inhibit the activin-RIIA interaction in a dose-dependent manner. These biophysical data correlated with functional studies, in which the lead compound NUCC-555 was shown to inhibit activin A-mediated cell proliferation in ex vivo ovary cultures. These findings lay the foundation for future work aimed at optimizing lead compounds as potential small-molecule therapeutics to target cancer-related cachexia and other activin-mediated diseases.

Reference: Zhu et. al. J. Med. Chem. 58:5637, 2015. PMCID: PMC4635973

A sortable list of publications from our facility can be found on our website.

All manuscripts and grants presenting work supported by this core should include the following acknowledgement:

We thank the Robert H. Lurie Comprehensive Cancer Center of Northwestern University in Chicago, IL for the use of the Keck Biophysics resources. The Lurie Cancer Center is supported in part by a NCI Cancer Center Support Grant #P30 CA060553.