Apr 20th, 1:00 PM - 4:00 PM


Prediction of the Structure of an Unknown Collagen Type IX-Like Protein Using Homologous Computational Chemical Calculations

Faculty Sponsor

Dr. Jeffrey Peloquin


A functional homologue of the NC4 domain of Collagen type IX, referred to as Col11a1NTD, has been isolated and subjected to initial characterization. While a crystal structure of the NC4 domain is available, no such structure is available for Col11a1NTD. In order to determine if Col11a1NTD has a structure similar to that of the NC4 domain, we are using the computational chemical program AMBER to predict the structure of Col11a1NTD via a molecular dynamics calculation. Initial biochemical analysis of Col11a1NTD has predicted a number of amino acids forming two distinct zinc cation binding sites. These two putative binding sites will be evaluated to determine which site most likely represents the true binding site, functional under the physiological conditions of the cell surface. The results of this computational study will serve to refine the predictions from the biochemical studies and allow us to make hypotheses regarding structure and function that can be tested experimentally.