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Related Concept Videos

Conserved Binding Sites01:49

Conserved Binding Sites

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 analyses the...
Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

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 form...
Types of RNA01:23

Types of RNA

Overview
Three main types of RNA are involved in protein synthesis: messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). These RNAs perform diverse functions and can be broadly classified as protein-coding or non-coding RNA. Non-coding RNAs play important roles in the regulation of gene expression in response to developmental and environmental changes. Non-coding RNAs in prokaryotes can be manipulated to develop more effective antibacterial drugs for human or animal use.
RNA...
Leaky Scanning02:28

Leaky Scanning

During most eukaryotic translation processes, the small 40S ribosome subunit scans an mRNA from its 5' end until it encounters the first start AUG codon. The large 60S ribosomal subunit then joins the smaller one to initiate protein synthesis. The location of the translation initiation is largely determined by the nucleotides near the start codon as there may be multiple translation initiation sites present on the mRNA.  Marilyn Kozak discovered that the sequence RCCAUGG (where R stands for...
RNA Editing02:23

RNA Editing

RNA editing is a post-transcriptional modification where a precursor mRNA (pre-mRNA) nucleotide sequence is changed by base insertion, deletion, or modification. The extent of RNA editing varies from a few hundred bases, in mitochondrial DNA of trypanosomes, to a just single base, in nuclear genes of mammals. Even a single base change in the pre-mRNA can convert a codon for one amino acid into the codon for another amino acid or a stop codon. This type of re-coding can significantly affect the...
Directing Proteins to the Rough Endoplasmic Reticulum01:34

Directing Proteins to the Rough Endoplasmic Reticulum

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: Jun 23, 2026

Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins
11:34

Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins

Published on: August 9, 2019

Specific sequences within arginine-glycine-rich domains affect mRNA-binding protein function.

Anne E McBride1, Ana K Conboy, Shanique P Brown

  • 1Department of Biology, Bowdoin College, Brunswick, ME 04011, USA. amcbride@bowdoin.edu

Nucleic Acids Research
|May 21, 2009
PubMed
Summary
This summary is machine-generated.

Arginine-glycine (RG)-rich domains in RNA-binding proteins are crucial for function. This study reveals RG domain specificity, demonstrating that not all RG domains are interchangeable, impacting intracellular transport and mRNA splicing.

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Sample Preparation for Mass Spectrometry-based Identification of RNA-binding Regions
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Sample Preparation for Mass Spectrometry-based Identification of RNA-binding Regions

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Last Updated: Jun 23, 2026

Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins
11:34

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Published on: August 9, 2019

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions
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Sample Preparation for Mass Spectrometry-based Identification of RNA-binding Regions
10:52

Sample Preparation for Mass Spectrometry-based Identification of RNA-binding Regions

Published on: September 28, 2017

Area of Science:

  • Molecular Biology
  • Cell Biology
  • Biochemistry

Background:

  • Arginine methylation plays key roles in cellular processes like intracellular transport and mRNA splicing.
  • Methylated arginine-glycine (RG)-rich domains are prevalent in eukaryotic RNA-binding proteins.
  • The repetitive nature of RG domains raises questions about their specificity as interaction motifs.

Purpose of the Study:

  • To investigate the functional importance and specificity of RG-rich domains in RNA-binding proteins.
  • To determine if RG domains act as general interaction motifs or possess specific functions.
  • To utilize the Saccharomyces cerevisiae mRNA-binding protein Npl3 (ScNpl3) as a model system.

Main Methods:

  • Created chimeric forms of ScNpl3 by replacing its RG domain with RG domains from other proteins (ScGar1, ScNop1, CaNpl3).
  • Assessed the function of these chimeric proteins in S. cerevisiae cells lacking endogenous Npl3.
  • Evaluated protein self-association and nuclear localization of Npl3 and its chimeric variants.

Main Results:

  • The RG domain of ScNpl3 is essential for cellular growth, but the domain alone confers partial growth.
  • Chimeric proteins with RG domains from CaNpl3 retained significant ScNpl3 function.
  • Chimeric proteins with RG domains from ScGar1 and ScNop1 impaired ScNpl3 function and self-association, indicating RG domain specificity.
  • Specific RG sequences are required for Npl3 nuclear localization, though heterologous domains modulate transport.

Conclusions:

  • RG-rich domains exhibit specificity, meaning they are not universally interchangeable.
  • The specific sequences within RG domains dictate their function in RNA-binding proteins like Npl3.
  • RG domain specificity is critical for proper intracellular transport and mRNA splicing processes.