Ligand-induced protein stabilization and enhanced molecular dynamics sampling techniques

Timo Schäfer, Andreas C. Joerger, John Spencer, Friederike Schmid and Giovanni Settanni ()
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Timo Schäfer: Johannes Gutenberg University, Department of Physics
Andreas C. Joerger: Johann Wolfgang Goethe University, Institute of Pharmaceutical Chemistry
John Spencer: University of Sussex, Department of Chemistry, School of Life Sciences
Friederike Schmid: Johannes Gutenberg University, Department of Physics
Giovanni Settanni: Johannes Gutenberg University, Department of Physics

A chapter in High Performance Computing in Science and Engineering '21, 2023, pp 3-17 from Springer

Abstract: Abstract Molecular dynamics (MD) simulations provide an increasingly important instrument to study protein-materials interaction phenomena, thanks to both the constant improvement of the available computational resources and the refinement of the modeling methods. Here, we summarize the results obtained along two different research directions within our project. First, we show how MD simulations of several cancer mutants of the DNA-binding domain of the tumor suppressor protein p53 allowed to establish the destabilizing effect of the mutations as well as the stabilizing effects of bound ligands. Second, we report on the development of a new reweighting technique for metadynamics simulations that speeds up convergence and may provide an advantage in the case of simulation of large systems.

Date: 2023
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DOI: 10.1007/978-3-031-17937-2_1

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