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Related Concept Videos

Protein Networks02:26

Protein Networks

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An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
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Assembly of Signaling Complexes01:30

Assembly of Signaling Complexes

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Multiprotein signaling complexes are formed in a dynamic process involving protein-protein interactions at the cytoplasmic domain of transmembrane receptors or enzymatic and non-enzymatic proteins associated with the receptor. These complexes ensure the activation and propagation of intracellular signals that regulate cell functions.
Interaction domains in cell signaling
Interaction domains recognize exposed features of their binding partners containing post-translationally modified sequences,...
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Ribosome Profiling02:24

Ribosome Profiling

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Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
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Protein-protein Interfaces02:04

Protein-protein Interfaces

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Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a...
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RNA-seq03:21

RNA-seq

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RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
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Directing Proteins to the Rough Endoplasmic Reticulum01:34

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The organelle-specific signaling sequences direct proteins synthesized in the cytosol to their final destination like ER, mitochondria, peroxisomes, etc. Some of the proteins directed to ER are then trafficked via vesicles to other organelles within the cell or the extracellular environment through the Golgi complex. For example, the rough ER synthesizes soluble proteins for transportation to the lysosomes or secretion out of the cell. It can also synthesize transmembrane proteins that can...
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Related Experiment Video

Updated: May 27, 2025

Transcriptome-Wide Profiling of Protein-RNA Interactions by Cross-Linking and Immunoprecipitation Mediated by FLAG-Biotin Tandem Purification
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Transcriptome-Wide Profiling of Protein-RNA Interactions by Cross-Linking and Immunoprecipitation Mediated by FLAG-Biotin Tandem Purification

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Dockground: The Resource Expands to Protein-RNA Interactome.

Keeley W Collins1, Matthew M Copeland1, Petras J Kundrotas1

  • 1Computational Biology Program, The University of Kansas, Lawrence, KS 66045, United States.

Journal of Molecular Biology
|February 16, 2025
PubMed
Summary
This summary is machine-generated.

Computational modeling aids in understanding protein-RNA interactions, crucial for cellular processes and disease research. The Dockground database now includes protein-RNA complexes to support this research.

Keywords:
molecular databasesmolecular recognitionprotein dockingprotein-RNA complexesstructural modeling

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Last Updated: May 27, 2025

Transcriptome-Wide Profiling of Protein-RNA Interactions by Cross-Linking and Immunoprecipitation Mediated by FLAG-Biotin Tandem Purification
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Transcriptome-Wide Profiling of Protein-RNA Interactions by Cross-Linking and Immunoprecipitation Mediated by FLAG-Biotin Tandem Purification

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Monitoring Protein-RNA Interaction Dynamics In Vivo at High Temporal Resolution Using χCRAC
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Novel RNA-Binding Proteins Isolation by the RaPID Methodology
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Area of Science:

  • Structural Biology
  • Computational Biology
  • Molecular Biology

Background:

  • RNA regulates cellular processes and binds proteins; dysregulation is linked to diseases like cancer.
  • Characterizing protein-RNA interactions structurally is vital for understanding molecular mechanisms.
  • RNA's flexibility complicates experimental structure determination, leading to a scarcity of available data.

Purpose of the Study:

  • To expand the Dockground resource for computational modeling of protein-RNA interactions.
  • To provide a comprehensive database of experimentally determined protein-RNA complexes.
  • To facilitate the development and benchmarking of structure-based modeling techniques for protein-RNA systems.

Main Methods:

  • Extended the Dockground database to include protein-RNA interactions.
  • Integrated new functionalities on the Dockground website (https://dockground.compbio.ku.edu/).
  • Enabled searching by various criteria, including redundancy removal at different similarity thresholds.
  • Implemented weekly updates with new structures from the Protein Data Bank.

Main Results:

  • The Dockground resource now contains a dedicated dataset for protein-RNA interactions.
  • The updated website offers enhanced search and data management capabilities.
  • The database is regularly updated, ensuring access to the latest structural information.
  • Facilitated computational modeling efforts by providing a valuable resource.

Conclusions:

  • The expanded Dockground database significantly enhances the study of protein-RNA interactions.
  • This resource supports the development of computational methods for structure-based modeling.
  • It aids researchers in understanding the structural basis of cellular processes and diseases involving RNA-binding proteins.