The bending of hemagglutinin

Wit, C. J. W. de (2016) The bending of hemagglutinin. Bachelor's Thesis, Physics.

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Abstract

When an influenza virus tries to enter a cell, it has to fuse its viral membrane with the cell membrane. This fusion is mediated by a protein called hemagglutinin. hemagglutinin(HA) facilitates the fusion by bending into a hairpin configuration. In this study the bending region, called the hinge region, was simulated to elucidate the molecular dynamics(MD) and structures of this hinge region. To enhance the MD simulations, Hamiltonian replica exchange was used. Two implementations of Hamiltonian replica exchange where tested, a implementation using the free energy perturbation of GROMACS and a implementation using the plugin PLUMED. The methods where tested on an alanine dipeptide and a 3K(I) molecule. The PLUMED method was easiest to implement and had the fastest simulations, thus was used for the HA simulation. The hinge region was simulated from an initial straight, helical configuration. The histidine residue of the peptide was not protonated. After about 700 ns of simulation the peptide was in a folded configuration, in contrast to simulations done by Kalani et al.. The configuration switched between a helical folded structure and a non helical folded structure. In the folded configuration, the location of the histidine residue was on the outside of the folded structure, the location of the non polar residues was on the inside and the acid, polar and non polar residues on the outside of the structure. I propose that the bending of the hinge region is probably mediated by hydrophobic interactions and not by the protonation of the histidine residue.

Item Type:	Thesis (Bachelor's Thesis)
Degree programme:	Physics
Thesis type:	Bachelor's Thesis
Language:	English
Date Deposited:	15 Feb 2018 08:14
Last Modified:	15 Feb 2018 08:14
URI:	https://fse.studenttheses.ub.rug.nl/id/eprint/14287

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