B. Dutagaci

Complex Conformational Space of RNA Polymerase II C-Terminal Domain upon Phosphorylation

The paper explores the conformational space of RNA polymerase II CTD using enhanced sampling methods and examines how phosphorylation affects its structure.

Structural basis of transcription: RNA Polymerase II substrate binding and metal coordination at 3.0 A using a free-electron laser

This paper presents the structure of ATP-bound RNA Polymerase II at 3.0 Å resolution using a free-electron laser, revealing new insights into substrate binding and metal coordination in the active site.

Binding of Small Molecule Inhibitors to RNA Polymerase-Spt5 Complex Impacts RNA and DNA Stability

This study predicts SPI binding sites on Pol II-Spt5 and shows how strong binding affects RNA and DNA dynamics at the exit site.

Characterization of RNA Polymerase II Trigger Loop Mutations using Molecular Dynamics Simulations and Machine Learning

This study uses molecular dynamics and machine learning to analyze RNA Polymerase II trigger loop mutations, finding that ML can predict phenotypes from sequences and MD data reveals structural changes linked to mutation effects.

Protein-Nucleic Acid Interactions for RNA Polymerase II Elongation Factors by Molecular Dynamics Simulations

This study uses molecular dynamics simulations to analyze protein-nucleic acid interactions in SPT5 domains with DNA and RNA, showing force field accuracy and interaction networks affect dynamics.

Charge-Driven Phase Condensation of RNA and Proteins Suggests Broad Role of Phase Separation in Cytoplasmic Environments

This study shows that RNA and positively charged proteins can form phase-separated condensates through electrostatic complementarity, suggesting a broad role of phase separation in cytoplasmic environments.