Date of Completion

Spring 5-1-2018

Project Advisor(s)

Eric May, Johann Peter Gogarten, Jose Gascon

University Scholar Major

Structural Biology and Biophysics

Disciplines

Biological and Chemical Physics

Abstract

Though eradicated in most of the world, poliovirus remains a common model virus for a family of mammalian viruses known as Picornaviruses. Despite the development of a vaccination, little is understood about the infection process, particularly the mechanism of cell entry. Experimental studies have attempted to elucidate the dynamics of this process and have proposed pathways focused on VP4, the smallest of the four peptides which makes up the viral capsid, and its interaction with the pentameric interfaces of the five fold axes. This study utilizes coarse-grained molecular dynamics to supplement these proposed mechanisms with simplified simulations which reduce the computational load while maintaining a reasonably accurate description of the system. We utilized artificial restraints to emulate the same externalization process predicted for VP4 successfully, showing a significant difference between capsids simulated with and without restraints. Analysis of the contacts VP4 peptides came into close proximity with during externalization revealed a high degree of interaction between VP1 and VP4 peptides, much higher than VP2 or VP3, even combined. This finding is in agreement with mechanisms proposed by prior studies which utilized traditional experimental techniques. Despite the agreement with the existing model, we noticed several anomalous motions with VP4 peptides which may signify an alternate pathway which is unrelated to interactions with VP1 peptides or the five-fold axes of the capsid structure.

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