| dc.contributor.advisor | Tůma, Roman | |
| dc.contributor.author | Halbeisen, Marco | |
| dc.date.accessioned | 2025-03-06T08:58:36Z | |
| dc.date.available | 2025-03-06T08:58:36Z | |
| dc.date.issued | 2022 | |
| dc.date.submitted | 2022-05-12 | |
| dc.identifier.uri | https://dspace.jcu.cz/handle/20.500.14390/46852 | |
| dc.description.abstract | In this bachelor thesis the focus was on the study of non-structural proteins of the tick-borne encephalitis virus involved in the replicatory process of the virus. Non-structural protein number 3 (NS3) and number 5 (NS5) contain a helicase and an RNA-dependent RNA polymerase domain, respectively, and play a crucial role in the life cycle of the virus. Therefore, they are of interest to develop a potential antiviral drug inhibiting the replication of the pathogen. It has been found that these two proteins form a dimer during the replication of the viral RNA. The aim of the thesis was to identify the exact interaction of the two proteins with existing hydrogen-deuterium mass spectroscopy data as well as modelling the RNA into the complexes. The research was conducted by using computational biology tools including homology modelling using MODELLER, manual modelling in PyMOL and Chimera as well as Molecular Dynamics Simulations in GROMACS. | cze |
| dc.format | 67 | |
| dc.format | 67 | |
| dc.language.iso | eng | |
| dc.publisher | Jihočeská univerzita | cze |
| dc.rights | Bez omezení | |
| dc.subject | PyMOL | cze |
| dc.subject | Homology modelling | cze |
| dc.subject | Molecular dynamics simulation | cze |
| dc.subject | site directed mutagenesis | cze |
| dc.subject | PyMOL | eng |
| dc.subject | Homology modelling | eng |
| dc.subject | Molecular dynamics simulation | eng |
| dc.subject | site directed mutagenesis | eng |
| dc.title | Modelling of tick borne enecephalitis virus (TBEV) proteins and their complexes | cze |
| dc.title.alternative | Modelling of tick borne enecephalitis virus (TBEV) proteins and their complexes | eng |
| dc.type | bakalářská práce | cze |
| dc.identifier.stag | 63828 | |
| dc.description.abstract-translated | In this bachelor thesis the focus was on the study of non-structural proteins of the tick-borne encephalitis virus involved in the replicatory process of the virus. Non-structural protein number 3 (NS3) and number 5 (NS5) contain a helicase and an RNA-dependent RNA polymerase domain, respectively, and play a crucial role in the life cycle of the virus. Therefore, they are of interest to develop a potential antiviral drug inhibiting the replication of the pathogen. It has been found that these two proteins form a dimer during the replication of the viral RNA. The aim of the thesis was to identify the exact interaction of the two proteins with existing hydrogen-deuterium mass spectroscopy data as well as modelling the RNA into the complexes. The research was conducted by using computational biology tools including homology modelling using MODELLER, manual modelling in PyMOL and Chimera as well as Molecular Dynamics Simulations in GROMACS. | eng |
| dc.date.accepted | 2022-06-15 | |
| dc.description.department | Přírodovědecká fakulta | cze |
| dc.thesis.degree-discipline | Biological Chemistry | cze |
| dc.thesis.degree-grantor | Jihočeská univerzita. Přírodovědecká fakulta | cze |
| dc.thesis.degree-name | Bc. | |
| dc.thesis.degree-program | Biological Chemistry | cze |
| dc.description.grade | Dokončená práce s úspěšnou obhajobou | cze |
| dc.description.defence | <p>Prof. Grubhoffer welcame the student, the commission members, and the audience. The student presented the basics of TBEV replication, polyprotein production and processing, and information on the two studied proteins NS3 and NS5 and their subdomains. Next, the student presented the flow of his work, modelling and studies on both proteins and their subdomains, proposed site-directed mutagenesis and production of mutated proteins. Finally, the results were discussed.</p>
<p>Co-supervisor Dr Franta presented the review of the supervisor assoc. prof. Tůma, followed by the opponent Libor Hejduk, MSc. The student answered all the questions. Then he answered questions regarding the phosphate release assay.</p>
<p>4x excellent - final excellent.</p>
<p>The commission suggests this work an Award by the head of the Dept. of Chemistry.</p> | cze |
