Journal of Proteomics & Bioinformatics
Open Access

Quantification of spatial correlations of fluorescent markers for studying protein-protein interactions

2^nd International Conference on Proteomics & Bioinformatics

July 2-4, 2012 Embassy Suites Las Vegas, USA

Vadim Zinchuk, Yong Wu, Olga Grossenbacher-Zinchuk and Enrico Stefani

Accepted Abstracts: J Proteomics Bioinform

Abstract :

Interaction of proteins via complex networks is one of the fundamental principles of cell and molecular biology and is the basis for the dynamic control of cellular metabolism. Proteins interact by direct binding, modification or by acting on a substrate and converting it. Binding of molecules to each other increases with the respective increase in their local concentrations, and it can be amplified when/if they are colocalized. It can be examined by detecting the overlap of fluorescent markers used to label them. The observed overlap is then quantified to serve as a measure of spatial correlation. We developed a technique to study protein-protein interactions by reducing the contribution of image background. Then, we applied a protein proximity index (PPI) and correlation coefficient (Rr) to estimate colocalization. Background heterogeneity is reduced by the median filtering procedure, comprising two steps, to reduce random noise and background, respectively. alternatively, background can be reduced by advanced thresholding. PPI provides separate values for each channel to characterize the contribution of each protein, whereas Rr determines the overall colocalization. The technique is demonstrated using computer-simulated and real biological images. Its advantage is that it significantly minimizes human bias and can be universally applied to various cell types in which there is a need to understand protein-protein interactions. It should be especially useful when studying membrane proteins as receptors and ion channels targeted by drugs.

Biography :

Vadim Zinchuk, M.D., Ph.D is a graduate of Kiev Medical University. For the last 10 years he is involved in the research in the fields of bioinformatics and quantitative medical biology. He currently works as Assistant Professor at the Department of Anatomy & Cell Biology, Kochi University, Kochi Japan. He has published more than 40 papers in international peer-reviewed journals.