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Center for Nonlinear Studies |
Well-known for its role in regulating the coagulation cascade, heparin is a highly sulfated, flexible polysaccharide and one of the most negatively charged molecules in the human body, with an average net charge of -2.7 per disaccharide. Heparin has a large number of functions in the body that are mediated through interactions with proteins, likely through specific sequences of heparin. However, modeling these interactions is challenging, since there is no established method for modeling heparin. Furthermore, designing heparin sequences for particular functions in terms of structure-function relationships is difficult, since the conformational ensembles of these sequences are not known. Molecular dynamics (MD) simulations can provide insight on the conformational ensembles of heparin. Within MD simulations, there are two competing parameter sets available for modeling heparin, known as GLYCAM06 and CHARMM36. By comparison to experimental data, this study shows evidence that GLYCAM06 is the superior parameter set for describing heparin. Understanding heparin’s sequence-conformation relationship will provide insight on how to design heparin for a particular function, thus paving the way for optimizing heparin’s usefulness as a medical drug. This talk is a part of the student seminar series. Multiple ten minute talks starting at 2:00pm
Host: Angel Garcia