Project Description:
Opening for a Ph.D. student in the Molecular and Cellular Modelling group at the ZMBH and Heidelberg Institute for Theoretical Studies (HITS) (http://www.h-its.org/mcm).
The cellular environment is chock-full of diffusing molecules. How this crowded and confined environment influences the dynamic behaviour and specific interactions of biomolecules is not well understood. We are developing Brownian dynamics methodology to simulate the diffusional association of biomolecules. This in implemented in our SDA software ( http://mcm.h-its.org/sda). We have used this approach to compute biomolecular association rates, to dock macromolecules, and to simulate the diffusive and association properties of concentrated protein solutions in the presence of surfaces. This methodology can be coupled with atomic-detail molecular dynamics simulations as well as biochemical network modelling in a multi-scale approach. The project will involve the development and application of the Brownian dynamics simulation methodology to understand how protein-protein interactions are influenced by a macromolecularly crowded environment and how the approach may aid the design of proteins for therapeutic applications.
References:
Michael Martinez, Neil J. Bruce, Julia Romanowska, Daria B. Kokh, Musa Ozboyaci, Xiaofeng Yu, Mehmet Ali Öztürk, Stefan Richter and Rebecca C. Wade. SDA 7: A modular and parallel implementation of the simulation of diffusional association software. J. Comput. Chem., (2015) 36:1631-1645
Mehmet Ali Öztürk, Georgi V. Pachov, Rebecca C. Wade and Vlad Cojocaru Conformational selection and dynamic adaptation upon linker histone binding to the nucleosome. Nucl. Acids Res. (2016), 44:6599-6613.
Nadinath B. Nillegoda, Janine Kirstein, Anna Szlachcic, Mykhaylo Berynskyy, Antonia Stank, Florian Stengel, Kristin Arnsburg, Xuechao Gao, Annika Scior, Ruedi Aebersold, D. Lys Guilbride, Rebecca C. Wade, Richard I. Morimoto, Matthias P. Mayer and Bernd Bukau. Crucial HSP70 co-chaperone complex unlocks metazoan protein disaggregation. Nature, (2015) 524:247–251.
Methods that will be used:
Computational molecular modelling and simulation, Brownian and molecular dynamics simulation.
Collaboration Partners (optional):
Profile of candidate’s qualification:
Candidates should possess a Master’s Degree or equivalent qualification in biophysics, biochemistry, molecular biotechnology, or a related discipline. Candidates should preferably have a strong theoretical background, experience in biomolecular modelling and simulation, possess excellent programming skills, and have a genuine interest in interdisciplinary research.
Keywords:
Molecular modelling and simulation
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