Protein–nucleic acids interactions: new ways of connecting structure, dynamics and function

Abstract

Molecular machines that act on nucleic acids, DNA and RNA are at the heart of the field of cellular information processing. A coherent description of the interactions involved in their assembly, activities and regulation affords a quantitative understanding of how transcription factors and DNA repair proteins find their unique targets among millions of nonspecific sequences and undamaged DNA bases, how the intricate choreography of DNA replication, recombination and repair and gene expression is regulated, how viral particles self-assemble and how chromosomes are organized inside living cells. These important questions are not easy to answer for the following reasons:(1) transactions between proteins and nucleic acids commonly involve extended surfaces with multiple interaction epitopes, and the resulting macromolecular assemblies are non-homogenous and dynamic; (2) the structures of multicomponent protein-DNA and protein-RNA complexes are often refractory to analysis by traditional X-ray crystallography and nuclear magnetic resonance (NMR). New techniques, clever adaptations and combinations of the state-of-the-art approaches are therefore needed.Our selection of speakers cover exciting new developments, both technological and conceptual, in determining the structures of protein-DNA and protein-RNA

Reaction Coordinate and Thermodynamics of Base Flipping in RNA

“…Interactions between nucleic acids and proteins play an essential role in various cellular processes including post-transcriptional modifications, − repair mechanisms, , and replication. , Some proteins bind to nucleic acids without introducing significant structural changes, but in other cases, binding is associated with large distortions in the structures of nucleic acids. Among other examples are enzymes that bind to nucleic acids upon opening of a specific base pair to perform a chemical reaction on the target base. , It means that the bases involved in chemical modifications have to be accessible to enzymes, preferably in a flipped out (extrahelical) state.…”

Exploring the Nature of Hydrogen Bonding between RNA and Proteins: A Comprehensive Analysis of RNA : Protein Complexes

“…The phenomenon of biomolecular recognition entails the interaction between two biologically-relevant entities, and encompasses a number of important processes in biochemistry, that include drug:receptor interactions, [1] protein:protein interactions [2] and protein:nucleic acid interactions. [3] Noncovalent interactions are specifically suited for biomolecular recognition. Owing to their importance, a significant number of studies in the last decade have analyzed the distribution of noncovalent interactions involved in biomolecular recognition.…”

Quantitation of nucleoprotein complexes by UV absorbance and Bradford assay

“…Interactions between nucleic acids and proteins are at the heart of the field of cellular information processing, such as DNA replication, DNA transcription, DNA translation, and post-translational regulation (Gao et al . 2019 ; Spies and Smith 2017 ). Therefore, exploring the interactions between proteins and nucleic acids is of particular interest in the fields of biology, clinical medicine, and chemistry (Gao et al .…”