Replica Exchange Simulations of Folding in the YAP 1 Protein
Format
Oral Presentation
Abstract/Artist Statement
Proteins, or polypeptides, consist of multiple amino acid subunits that interact with each other through specific molecular properties. The disruption of these interactions by external influences – such as heating – can lead to denaturation (loss of structure and function) of a protein. Mother Nature has the capability to refold a denatured protein and thus restore its conformation and function about a million times each second; however, the largest and most capable computer in the world will be over a thousand times less able to imitate this task due to the inefficiencies of human knowledge. In order to approach what Mother Nature is able to do, I will combine modern molecular dynamics techniques with classical computational techniques to visualize the heating and refolding of a helical polypeptide. Implicit mathematical and physical constructs are applied to the simulations in order closely mimic the solvent properties of water. I will interpret structural and energetic analysis to determine the probability of the refolding of the helix. Since these simulations are carried-out in an aqueous environment, the results from our study could have relevance to various biotechnological and pharmaceutical endeavors, such as the battle against cancer and drug design and quality. I will examine a helical polypeptide fragment of the YAP1 protein, a gene product regulator active in defense genes in the yeast Saccharomyces cerevisiae, to complete this study.
Location
University of the Pacific, Classroom Building
Start Date
5-5-2007 9:00 AM
End Date
5-5-2007 12:30 PM
Replica Exchange Simulations of Folding in the YAP 1 Protein
University of the Pacific, Classroom Building
Proteins, or polypeptides, consist of multiple amino acid subunits that interact with each other through specific molecular properties. The disruption of these interactions by external influences – such as heating – can lead to denaturation (loss of structure and function) of a protein. Mother Nature has the capability to refold a denatured protein and thus restore its conformation and function about a million times each second; however, the largest and most capable computer in the world will be over a thousand times less able to imitate this task due to the inefficiencies of human knowledge. In order to approach what Mother Nature is able to do, I will combine modern molecular dynamics techniques with classical computational techniques to visualize the heating and refolding of a helical polypeptide. Implicit mathematical and physical constructs are applied to the simulations in order closely mimic the solvent properties of water. I will interpret structural and energetic analysis to determine the probability of the refolding of the helix. Since these simulations are carried-out in an aqueous environment, the results from our study could have relevance to various biotechnological and pharmaceutical endeavors, such as the battle against cancer and drug design and quality. I will examine a helical polypeptide fragment of the YAP1 protein, a gene product regulator active in defense genes in the yeast Saccharomyces cerevisiae, to complete this study.