TCBG Seminar

Simulations of Ligand Binding to Truncated Hemoglobins

Professor Kenneth W. Olsen
Department of Chemistry
Loyola University Chicago
Chicago, IL

Monday, March 12, 2007
3:00 pm (CT)
3269 Beckman Institute


The functions of proteins are usually dependent upon them binding other molecules. Proteins bind ligands for different reasons, for instance, regulating gene expression, enzymatic activity or transportation of the ligand. The shape of the binding site is complementary to the shape of the ligand to allow molecular interactions to occur. The molecular interaction between the ligand and protein may involve hydrogen bonding, van der Waals interactions, hydrophobic interactions and electrostatic interactions. When the binding site of a protein is buried in the interior of the protein, questions arise as to the pathway in which the ligand travels to bind. Myoglobin binds the ligand dioxygen. Myoglobin’s binding cavity is not visible from its exterior, giving no indication of how the ligand moves through the protein to bind. Truncated hemoglobins bind various ligands with their function still being a mystery. These proteins appear to have tunnel(s) potentially used by the ligand to bind. What is the reaction pathway between the reactant/unbound conformation and the product/bound conformation? In this talk, the reaction pathways for myoglobin and three different truncated hemoglobins will be examined using theoretical models. Two main algorithms utilized in this study are conjugate peak refinement and locally enhanced sampling molecular dynamics.

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