My approach to biophysics is to integrate principles from physics, physical chemistry and chemical/mechanical engineering to define mechanisms that drive important biochemical processes. To that end, my laboratory works in two parallel areas, structure and function of both membrane proteins and lipids, correlating the information gained in both approaches to give insight for future manipulation of cellular signaling pathways. The following is a summary of my research training, as well as specifics that I plan to carry forward in the questions that currently interest me.
Characterizing lipid phases that sequester membrane proteins for signal transduction. As a doctoral student under Dr. Christoph Naumann (IUPUI Chemistry), I learned how to use fluid flow dynamics of membrane proteins and lipids to ascertain structurally related function. Here we used protein lateral diffusion measured by single molecule techniques and fluorescence correlation spectroscopy to describe lipid affinity as a function of both the protein (function, structure, and activation by binding to agonist or antagonists) and lipid (fluidity/acyl chain packing, phase) (Siegel, Kimble-Hill et al. 2011). As a result, we were able to use confocal microscopy, single molecule fluorescence microscopy and atomic force microscopy to characterize the effect of reducing substrate related steric hindrances on membranes on lipid lateral mobility and bilayer morphology (Minner, Herring et al. 2013).
Describing the lipid platform that drives proteo-bicelle crystallization. As a postdoctoral fellow at Argonne National Laboratory, I learned small angle neutron and x-ray scattering techniques as applied to understanding the lipidic platform necessary for proteo-bicelle crystallization. We endeavored to determine whether the bicelle solution will change from ribbon-like lamellar structure to a cubic and/or micelle structure with the addition of OG or DM. We used small angle neutron scattering (SANS) to show that the bicelle structure changes as a function of OG/DM content, temperature, and total lyotrope concentration (Kimble-Hill, Singh et al. 2009).
Modulating aldehyde dehydrogenase (ALDH) activity. As a part of my postdoctoral training with Dr. Tom Hurley (IUSM Biochemistry), my work was focused on determining new ways to selectively modulate the function of ALDH family members. We utilized absorption/fluorescence spectroscopy to characterize the effect of small molecules on the function as well as x-ray diffraction of protein crystals to determine protein specific functional groups, as well as globular structural elements, which play a role in selective changes in functional behavior (Khanna, Chen et al. 2011, Parajuli, Kimble-Hill et al. 2011, Kimble-Hill, Parajuli et al. 2014). In combining information from a library of similar compounds, we reported structure activity relationships that give insight on how to optimize compounds to selectively modulate protein behavior in specific disease states.
Defining the molecular basis for Angiomotin (Amot) selective lipid affinity. I was awarded a K01 award from the National Cancer Institute that allowed me to develop an independent research program, which led to a current collaboration with Dr. Clark Wells (IUSM Biochemistry) to understand the role of Amot lipid binding in ductal cell hyperplasia/tumor genesis as Amot family members directly control the apical membrane organization and transcriptional cofactors sequestration to regulate cell growth. In this project, I have developed several lipid-based assays (fluorescence resonance energy transfer, lipid sedimentation, fluorescence spectroscopy, small angle scattering) for describing characterizing membrane binding, fusion, and reorganization events. Additionally, we have made inroads into determining the atomistic structure of these family members using a combination of computational modeling, SAXS and wide angle x-ray scattering (WAXS) measurements.
Additionally, I serve as the program coordinator for the IUPUI Post-Baccalaureate Research Education Program. As a Visiting Assistant Research Professor in the Department of Biochemistry and Molecular Biology, I mentor students in multiple undergraduate research programs including Life-Health Science Internship Program (LHSI), Bridges to the Baccalaureate, Undergraduate Research Opportunity Program (UROP), Diversity Scholars Research Program (DSRP), American Chemical Society Project Seed, Biology/Chemistry Department capstone classes, and Louis Stokes Alliances for Minority Participation (LSAMP).