Presentation material from Kanchan Garai

Equipments bought 1.Fluorometer equipped with excitation and emission monochromators for wavelength scanning, a polarizer and analyzer pair for fluorescence anisotropy measurements. The sensitivity is high enough to detect 1.0 attomolar for fluorescein dye. 2.Components for Fluorescence Correlation Spectroscopy (FCS): We are in the process of setting up an FCS in my lab. We have already obtained the optomechanics components. The orders have been placed for the rest of the components such as the digital correlator, filters, objective lenses and avalanche photo diode detectors. 3.Future plan: We plan to build a superresolution microscope using stochastic optical reconstruction microscopy (STORM). We will also buy an atomic force microscope (AFM) soon.

Publications and grant applications Published: Garai K, Verghese PB, Baban B, Holtzman DM, Frieden C. The Binding of Apolipoprotein E to Oligomers and Fibrils of Amyloid-β Alters the Kinetics of Amyloid Aggregation. Biochemistry Oct 14;53(40): doi: /bi In prep: Holehouse AS, Garai K, Lyle N, Vitalis A, and Pappu RV. Quantitative assessments of the distinct contributions of polypeptide backbone amides versus sidechain groups to chain expansion via chemical denaturation Grant application to India-USA collaborative research on Diabetes Title: Biophysical studies to determine the role of apolipoprotein E on aggregation of IAPP in Type 2 diabetes and Amyloid-beta in Alzheimer's disease. Primary Investigator: Dr. Kanchan Garai at TIFR-Hyderabad Co-investigator: Prof. PK Madhu at TIFR-Hyderabad USA collaborator: Dr. Jan Bieschke at Washington University in St. Louis Submitted on 18 th September, 2014

Research plan: Proteins amyloids in disease, functions and in nanobiotechnology Role of apolipoprotein E (apoE) on amyloid aggregation in Alzheimer’s disease and Type2 diabetes. ApoE is a functional protein but how it influences Alzeimer’s and Type2 diabetes is unknown. We will perform biophysical experiments to unravel the molecular mechanisms of the role of apoE on aggregation of amyloid beta peptide in Alzheimer’s and of IAPP in Type 2 diabetes. Interaction of apoE with amyloid beta fibrils. The white dots are apoE labeled with nanogold particles. The fibrillar structures are amyloid beta fibers. Garai et al, Biochemistry, 2014 Solution NMR structure of apolipoprotein E3. adapted from Chen et al, PNAS, 2012.

Mechanism of bacterial biofilm formation: Many bacteria produce amyloid fibers known as curli which play important roles in bacterial biofilm formation. Bacterial biofilms enable bacteria strong resistance to external stresses such as antibiotics. The amyloid protein CsgA is the major and CsgB is the minor component of the curli fibers. We are interested to understand the synergistic self-assembly of CsgA and CsgB in curli formation leading to formation of the biofils. Design and synthesis smart nanobiomaterial using protein self-assembly: The nanometer dimension of the amyloid fibers and their high stability makes them suitable candidate for development functional materials. We are working to develop protein hydrogels and metal nanowires using amyloids as template. Curli fibers from e.coli. (Evans and Chapman, BBA, 2014)