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Understanding ligand binding in the guanidine-II riboswitch with the help of molecular simulation, enhanced sampling and machine learning

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Steuer-2-qvdc0gjv99w34.pdf
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2023

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Regulation of gene expression by riboswitches is prevalent in many bacteria. The binding of such small molecules is highly selective and leads to a conformational switch of the molecular architecture of the riboswitch, which in turn impacts the transcription or translation of the riboswitch-associated genes. Since their first discovery and validation in the early 2000s, riboswitches have been the subject of intense research, as they allow for new insights into bacterial physiology and offer immense potential for medicinal and biotechnological applications. In this thesis, a member of the guanidine sensing riboswitch family, the Guanidine-II (Gd-II) riboswitch, was investigated with the help of molecular dynamics simulations, enhanced sampling algorithms, and machine learning. The (un)binding event and the conformational states of single and dimerized Gd-II aptamers were studied in the presence and absence of the native ligand guanidinium and ligand analogs.

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Fachgebiet (DDC)
540 Chemie

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MD Simulation, RNA, Riboswitch, Computational Chemistry, Molecular Dynamics, Simulation, Guanidine, Guanidinium, EncoderMap, Machine Learning, Enhanced Sampling, Transition Path Sampling

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ISO 690STEUER, Jakob, 2023. Understanding ligand binding in the guanidine-II riboswitch with the help of molecular simulation, enhanced sampling and machine learning [Dissertation]. Konstanz: Universität Konstanz
BibTex
@phdthesis{Steuer2023-08-14Under-67670,
  year={2023},
  title={Understanding ligand binding in the guanidine-II riboswitch with the help of molecular simulation, enhanced sampling and machine learning},
  author={Steuer, Jakob},
  address={Konstanz},
  school={Universität Konstanz}
}
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Prüfungsdatum der Dissertation

April 18, 2023
Hochschulschriftenvermerk
Konstanz, Univ., Diss., 2023
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