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Biochemistry Seminar – Dr. Phanourios Tamamis: “Biophysical Simulations and Calculations Bridging Gaps and “Provoking” Experiments”
September 18 @ 4:00 pm - 5:00 pm
Dr. Phanourios Tamamis
Department of Chemical Engineering
Texas A&M University
Title:”Biophysical Simulations and Calculations Bridging Gaps and “Provoking” Experiments”
Abstract: Biophysical simulations and calculations are increasingly becoming powerful tools in the fields of protein structure prediction and de novo protein design. Despite the continuous advancement of experimental methods, such tools have proved capable to bridge “gaps”, obtain information that is not accessible from experiments, and “provoke” new experiments. The talk will present an overview of problems of our research in specific areas, including amyloid peptide self-assembly and ligand-protein binding interactions, and highlight novel computational tools developed in our lab leading to the understanding of key biological axes or the discovery of novel biomaterials and potential therapeutics.
Amyloid peptide self-assembly is related to diseases such as diabetes II, Alzheimer’s and Parkinson’s. Our simulations provided insights into amyloid inhibition, disaggregation and sequestration of monomers, and among others uncovered the key structural and energetic determinants of amyloid sequestration by β-wrapins. Our findings can be used to design novel potent and multi-targeting β-wrapins which can potentially constitute novel promising therapeutics.
In addition, while amyloid self-assembly can be linked to diseases, amyloid nanostructures are highly attractive for the design of novel functional materials of the future. Despite the problems’ importance, the functionalization of such materials to bind to specific ions or compounds has been challenging, and relied upon scientists’ intuition. To resolve this, we developed the first computational protocol to functionalize amyloid materials, and we successfully implemented it for the design of materials with applications in separations, drug delivery and tissue engineering.
Furthermore, computational docking methods aim to predict how ligands bind to proteins, and are highly important to understand key biological axes and to discover new drugs. Nevertheless, existing methods face significant challenges in predictive accuracy and in studying protein conformational changes upon binding. We developed a novel computational protocol which uses biophysical principles to nearly exhaustively search the binding modes of a ligand in a protein’s binding pocket, and which can provide a highly-accurate prediction of the binding structure. The protocol will be demonstrated using example cases of structures delineated by our lab, provoking experiments which validated our findings.
Host: Michael Polymenis
Location: 108 Biochemistry Building (Bldg#1507)