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Related Concept Videos

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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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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Conserved Binding Sites01:49

Conserved Binding Sites

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Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...
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Protein Organization01:24

Protein Organization

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Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
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Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

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Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to...
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Covalently Linked Protein Regulators02:04

Covalently Linked Protein Regulators

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Proteins can undergo many types of post-translational modifications, often in response to changes in their environment. These modifications play an important role in the function and stability of these proteins. Covalently linked molecules include functional groups, such as methyl, acetyl, and phosphate groups, and also small proteins, such as ubiquitin. There are around 200 different types of covalent regulators that have been identified.
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Related Experiment Video

Updated: Jan 17, 2026

Visualization of Protein-protein Interaction in Nuclear and Cytoplasmic Fractions by Co-immunoprecipitation and In Situ Proximity Ligation Assay
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RNA-protein interaction techniques - A historical and comparative analysis.

Sourabh Chakrabarty1, Sayan Roy1, Soumyadip Sarkar1

  • 1Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India.

Biochimica Et Biophysica Acta. Gene Regulatory Mechanisms
|September 13, 2025
PubMed
Summary
This summary is machine-generated.

This review details methods for studying RNA-protein interactions (RPI), crucial for understanding gene regulation. It covers techniques from Electrophoretic Mobility Shift Assay (EMSA) to CRISPR-based RNA-Protein interaction profiling (CBRIP).

Keywords:
Cross-linkingNon-cross-linkingRNA-binding proteinsRNA-protein interactions

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Area of Science:

  • Molecular Biology
  • Genetics
  • Biochemistry

Background:

  • RNAs, including messenger RNAs (mRNAs) and non-coding RNAs, regulate critical cellular processes.
  • RNA-binding proteins (RBPs) are key players in these regulatory mechanisms.
  • Understanding RNA-Protein interactions (RPI) is vital for deciphering gene expression and function.

Purpose of the Study:

  • To provide a comprehensive overview of methodologies used to study RNA-Protein interactions (RPI).
  • To discuss the historical development, strengths, weaknesses, and applications of various RPI techniques.
  • To consolidate RPI characterization methods based on their specific biological objectives.

Main Methods:

  • Electrophoretic Mobility Shift Assay (EMSA)
  • CRISPR-based RNA-Protein interaction profiling (CBRIP)
  • Diverse RNA- and protein-centric techniques for RPI elucidation.

Main Results:

  • A spectrum of RPI study techniques exists, from traditional to cutting-edge.
  • Each method possesses unique advantages and limitations impacting experimental outcomes.
  • Current applications of these techniques span various biological research areas.

Conclusions:

  • Method selection is critical for effectively investigating specific RPI-related biological questions.
  • This review serves as a guide to navigating the landscape of RPI analysis tools.
  • A consolidated understanding of RPI methodologies aids researchers in experimental design and interpretation.