PhD topic in Interaction Protein-Protein and Protein-Membrane Research Group

6 Jan 2024
Job Information

Organisation/Company

CEITEC, Masaryk University

Research Field

Biological sciences » Biology
Biological sciences » Other
Chemistry » Biochemistry

Researcher Profile

First Stage Researcher (R1)

Country

Czech Republic

Application Deadline

18 Feb 2024 - 23:00 (UTC)

Type of Contract

Temporary

Job Status

Part-time

Offer Starting Date

1 Sep 2024

Is the job funded through the EU Research Framework Programme?

Not funded by an EU programme

Is the Job related to staff position within a Research Infrastructure?

No

Offer Description
Research group homepage:

https://vacha.ceitec.cz/

Topic titles:

• Regulation of protein liquid droplets during transcription
• Peptide Sequence Motifs for Selective Targeting of Pathogens

Requirements on candidates:

Outstanding candidates with experience in computer simulations and with an MSc/PhD degree in the fields of biophysics, soft matter physics, physical chemistry, computational chemistry, statistical mechanics, or related fields. Experience with molecular dynamics simulations (with GROMACS, CHARMM, NAMD, AMBER, LAMMPS, etc.) or other simulation techniques (Monte Carlo, DPD, etc.) at the atomistic or coarse-grained level would be an advantage.

1. Terminal RNA modifications in gene expression and viral infection

Supervisor: doc. RNDr. Robert Vácha, Ph.D.

Annotation:

Cells employ protein liquid droplets to form dynamic clusters, which function as nanoreactors or storages with the increased local concentration of specific protein components. These membrane-less organelles self-assemble based on weak protein-protein interactions of intrinsically disordered domains. However, the role of specific sequences remains elusive and the mixing between different protein droplets unexplored. This project is focused on the droplets involved in genome transcription, where posttranslational modifications control the droplet composition and regulate the transcription. Expected findings are not only important for the general knowledge but could also be useful in the design of new treatments because translocation malfunction is involved in numerous diseases including cancer. The research is strongly coupled to collaborations with excellent experimental teams and will be more closely discussed during the interview. The employed tools will contain multi-scale simulations using a wide range of advanced sampling techniques and development of protein parametrization.

APPLY: https://ls-phd.ceitec.cz/how-to-aplly/

 

2. The role of RNA modifying factors in human cancer

Supervisor: doc. RNDr. Robert Vácha, Ph.D.

Annotation: 

Antimicrobial peptides (AMPs) possess the ability to disrupt the membrane barrier function, effectively eliminating bacteria, viruses, and even cancer cells. Consequently, AMPs have emerged as promising candidates for the development of a new class of therapeutics. However, the majority of known AMPs exhibit toxic properties due to their origin from human-unfriendly sources, such as venoms. Our understanding of peptide targeting mechanisms towards specific pathogens and their membranes remains limited, hindering further peptide development. This ERC funded project aims to identify peptide sequence motifs that are responsible for selective targeting pathogens with respect to human cells. Apart from the differences in lipid composition of membranes, we will investigate the impact of membrane local curvature. The main tool for the study will be Molecular dynamics simulations with free energy calculations using Gromacs program package. These simulations will be complemented by in-house experiments providing crucial verification and feedback on peptide-membrane affinity. The acquired knowledge will guide the design of de novo peptides with enhanced pathogen-targeting specificity.

APPLY: https://ls-phd.ceitec.cz/how-to-aplly/

Requirements
Additional Information
Work Location(s)

Number of offers available

1

Company/Institute

CEITEC, Masaryk University

Country

Czech Republic

Geofield

Where to apply

Website

https://ls-phd.ceitec.cz/how-to-aplly/

STATUS: EXPIRED