Thesis supervisor: Szilárd Fejér
Location of studies (in Hungarian): Csíkszereda Abbreviation of location of studies: Csík
Description of the research topic:
The Rous sarcoma virus (RSV) is a retrovirus that causes tumours in birds. The genetic material and the reverse transcriptase enzyme of the virus is packaged in a double protective shell: a nucleocapsid and a protein capsid (CA). The CA protein is capable of self-assembly into icosahedral shells, the units are connected through three protein-protein interfaces.1 The protein is capable to form polymorphic shells as well, structures such as spheroidal, tubular and planar CA assemblies have been described before.2 Changing the protein sequence, as well as the experimental conditions, affect greatly the self-assembly process.3
During our project we will investigate the in silico self-assembly of the CA protein with computational methods, in order to better understand the structural features that make this protein form such a variety of capsids.
1. Dimerization of RSV CA protein
Starting from the available 3D structures of the C-terminal and N-terminal parts of the protein (PDB: 1EOQ, 1EM9), we will investigate the two main protein domains. We will construct models for the complete CA protein, after which rigid docking will be carried out on the ZDOCK server, to sample the possible dimer structures. The best 2000 structures will be relaxed with AMBER, and the structures with the best binding energy will be compared to experimental interfaces. The same protocol will be used with other docking programs as well, to achieve consistency of results.
2. Modelling the CA protein with coarse-grained methods
The complete capsid can be modelled by coarse-graining the protein chains. We will replace the rigid parts of the protein with ellipsoids, with the aim to create a model which adequately describes the self-assembly of the virus capsid. The starting structures for coarse-graining will be the most stable dimers found during the previous step.
3. Evaluating capsid protein stability changes induced by mutation
The stability of dimers can be controlled by inducing point mutations of interface residues. By changing interface residues with amino acids of different type, we will create an array of possible point mutants. After energy minimization, we will select those mutants that have the largest effect on the calculated binding energies, and will subject these to molecular dynamics studies (AMBER PMEMD).
The stable dimers obtained during the first phase will also be subjected to long molecular dynamics runs on different temperatures. Evaluating these processes can yield new insight into the effect of mutations on self-assembly
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