Our Methods
Synthesis & Biophysical Characterization
Biology
Computation
Every project in the lab begins with organic synthesis, and we employ methods, including classical organic chemistry transformations, (asymmetric) transition-metal catalyzed chemistry, and microwave-assisted polypeptide synthesis. We then systematically probe the molecular frameworks created, employing quantitative biophysical and physical organic methods. Those include nuclear magnetic resonance (N.B. UCSC received a brand new 800 MHz instrument in May 2016) circular dichroism, dynamic light scattering, isothermal titration calorimetry and small-angle X-ray scattering (SLAC facilities, Stanford). We benefit greatly from the existence of the state-of-the-art screening center at UCSC, and collaborate with the Ayzner lab on synchrotron-related experiments.
Molecules that show interesting properties in cell-free systems are studied in the biologically relevant setting. Neurodegeneration being a major area of interest for the lab, we focus our cell culture studies mostly on brain cells – neurons and astrocytes. Neuroinflammation constitutes a major contribution to neurodegenerative disorders, and the crosstalk with the immune system, including Nuclear Factor Kappa B signaling, hence, also of high interest. We furthermore collaborate with electrophysiologists to elucidate molecular mechanisms of action of the compounds we synthesize, in hippocampal slices (long-term potentiation experiments).
We employ density functional theory, as well as molecular dynamics simulations to gain deeper insight into structural and functional properties of the frameworks under investigation. The continuous crosstalk between experiment and theory gives rise to an intellectually stimulating environment with great learning opportunities for the students. Computational work is typically performed by Prof. Raskatov himself, but highly motivated students are encouraged to inquire.