TY  - CONF
AU  - Berg, Andrej
AU  - Peter, Christine
TI  - Conformational Analysis of Dual-Scale Simulations of Ubiquitin Chains
VL  - 50
CY  - Jülich
PB  - Forschungszentrum Jülich GmbH Zentralbibliothek, Verlag
M1  - FZJ-2020-01419
T2  - Publication Series of the John von Neumann Institute for Computing (NIC) NIC Series
SP  - 137 - 146
PY  - 2020
AB  - The analysis of large-scale simulations of (bio)molecular systems generated on high performance computer (HPC) clusters poses a challenge on its own due to the sheer amount of high-dimensional data. To make sense of these data and extract relevant information, techniques such as dimensionality reduction and clustering are used. They can be applied to characterise the sampling of conformational phase space as well as to bridge between simulations on different levels of resolution in multiscale setups. Here, we present an approach to analyse long-timescale simulations and to characterise conformational ensembles of flexibly-linked multidomain proteins using the example of differently covalently conjugated ubiquitin chains. We have analysed exhaustive coarse grained (CG) and atomistic simulations with the help of collective variables (CVs) that are particularly suitable to describe the mutual orientation of different subunits and the protein-protein interfaces between them. These data have been further processed through different dimensionality reduction techniques (relying on multidimensional-scaling like approaches as well as neural network autoencoders). The resulting low-dimensional maps have been used for the characterisation of conformational states and the quantitative comparison of conformational free energy landscapes (from simulations at different levels of resolution as well as of different chain types). With this multiscale simulation and analysis approach it is possible to identify characteristic properties of ubiquitin chains in solution which can be subsequently correlated with experimentally observed linkage- and chain length-specific behaviour.
T2  - NIC Symposium 2020
CY  - 27 Feb 2020 - 28 Feb 2020, Jülich (Germany)
Y2  - 27 Feb 2020 - 28 Feb 2020
M2  - Jülich, Germany
LB  - PUB:(DE-HGF)8 ; PUB:(DE-HGF)7
UR  - https://juser.fz-juelich.de/record/874409
ER  -