Molecular dynamics simulations of protein-nucleotide interaction (A16*)

• Subject Area: Biophysics
• Term: from 2018 to 2022
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 105286809

We will use molecular dynamics (MD) simulations to study conformational transitions of RNA polymerase II (Pol II) and of several members of the RNA helicase family. Specifically, we aim to derive energetically and sterically feasible pathways for DNA opening and loading into the catalytic cleft of Pol II. By means of SAXS-guided MD simulations and free energy calculations, we aim to reveal the mechanisms involved in RNA loading and RNA sliding by RNA helicases.

• DFG Programme: Collaborative Research Centres
• Subproject of: SFB 860: Integrative Structural Biology of Dynamic Macromolecular Assemblies
• Applicant Institution: Georg-August-Universität Göttingen
• Project Head: Professor Dr. Jochen Hub