RNA-Protein Dynamics and Biocondensate Properties
RNA-protein interactions are the basis for numerous molecular control mechanisms in biology. In typical eukaryotic cells, more than 1500 different proteins interact with thousands of different RNAs. Molecular-level studies of RNA-protein interactions reveal relevance to the formation and nature of biomolecular condensates. The RNA-protein network is dynamic. That is, RNA-protein interactions change on biologically relevant time scales. Changes in the pattern of RNA-protein interactions at a single RNA binding site are ultimately determined by kinetic parameters, including the rate constants for protein binding and dissociation from a given RNA site. However, molecular dynamics (MD) simulations of protein-RNA complexes are more challenging than per-component simulations due to the strong electrostatic interactions and the delicate balance between various physical forces at the interface.
Fig. 1. The network of RNA and protein is determined by the dynamics of each interaction. (Licatalosi D D, et al., 2020)
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Understanding the principles of RNA-protein interactions is useful for both basic research and practical applications. We offer experimental techniques including X-ray crystallography and nuclear magnetic resonance (NMR) to analyze the structure of RNA-binding domains. Here, we focus on MD simulations of protein-RNA complexes by measuring aspects of RNA-protein interaction dynamics. CD BioSciences has technical platforms to assess cellular RNA-protein interaction dynamics that accompany biological processes over time scales of hours or longer, as well as to measure RNA-protein interaction dynamics in vitro.
Methods for Measuring RNA-Protein Interaction Dynamics in Cells
- Cross-linking and immunoprecipitation (CLIP) methods, for identifying RNAs that bind directly to specific proteins.
- RNA Antisense Purification (RAP), Comprehensive Identification of RBPs by Mass Spectrometry (CHIRP-MS), and Identification of Direct RNA Interacting Proteins (iDRiP), for the identification of proteins that bind directly to specific RNAs.
- RNA Interactome Capture (RIC) for global comparison of protein-RNA contact sites and identification of dynamic differences that may alter mRNA metabolism.
- Enhanced RIC (eRIC), which allows detection of dynamic changes in the RNA-binding proteome under different biological conditions.
Methods for Measuring RNA-Protein Interaction Dynamics In Vitro
- Electrophoretic gel displacement and filter combination technique, allowing physical separation of the RNA-protein complex from the free fraction to monitor the kinetics of RNA-protein interactions.
- UV absorption spectroscopy, circular dichroism, and fluorescence spectroscopy for monitoring RNA-protein interactions in solution.
- Fluorescence anisotropy measurements, fluorescence burst measurements, and fluorescence (Foerster) resonance energy transfer (FRET) for measuring the rate constants of RNA-protein interactions.
- Surface plasmon resonance, to measure RNA-protein interaction kinetic parameters.
- Enzymatic methods, allowing determination of the kinetic parameters of physical interactions between RNA and proteins.
- Single molecule fluorescence methods, for measuring the temporal trajectory of fluorescence changes of individual molecules or complexes.
- Optical and magnetic tweezers for measuring changes in the mechanical properties of individual molecules or complexes.
- High-throughput methods for measuring the kinetics of protein interactions with many RNA substrates in vitro.
Protein-RNA complexes have unusual and unique conformational changes, and MD modeling of proteins and RNAs as separate entities is complex. We can select the appropriate force field for your simulation by enhancing the RAN binding protein technique in solution and developing protein-RNA specific software for MD simulations as well as more complex RNA specific force fields.
Why Choose Us
- Cutting-edge techniques for measuring RNA-protein interaction kinetics.
- Translation can be tracked in real time, both intracellularly and in vitro.
- Enable measurement of RNA-protein interaction kinetics at high resolution in systems with multiple interacting components.
- Ensure accurate protein-RNA interface modeling.
Our range of technologies provides a large selection of tools for any researcher interested in understanding the kinetics of RNA-protein interactions. Based on the kinetic information obtained, we will also design kinetic prediction models of intracellular RNA-protein interactions. If you are interested in our services, please do not hesitate to contact us for more information.
Reference
- Licatalosi D D, et al. (2020) Approaches for measuring the dynamics of RNA-protein interactions[J]. Wiley Interdisciplinary Reviews: RNA. 11(1): e1565.
For research use only, not intended for any clinical use.
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