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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...
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...
Ligand Binding Sites02:40

Ligand Binding Sites

Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...
Protein-protein Interfaces02:04

Protein-protein Interfaces

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 polypeptide...
RNA Structure01:19

RNA Structure

The basic structure of RNA consists of a string of ribonucleotides attached by phosphodiester bonds. Although most RNA is single-stranded, it can form complex secondary and tertiary structures. Such structures play essential roles in the regulation of transcription and translation.
Different Types of RNA Have the Same Basic Structure
There are three main types of ribonucleic acid (RNA) involved in protein synthesis: messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). All three...
RNA Structure01:23

RNA Structure

Overview
The basic structure of RNA consists of a five-carbon sugar and one of four nitrogenous bases. Although most RNA is single-stranded, it can form complex secondary and tertiary structures. Such structures play essential roles in the regulation of transcription and translation.
Different Types of RNA Have the Same Basic Structure
There are three main types of ribonucleic acid (RNA): messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). All three RNA types consist of a...

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Related Experiment Video

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Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells
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Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells

Published on: December 9, 2022

Predicting RNA-binding sites from the protein structure based on electrostatics, evolution and geometry.

Yao Chi Chen1, Carmay Lim

  • 1Department of Chemistry, National Tsing Hua University, Hsinchu 300, Taiwan.

Nucleic Acids Research
|February 16, 2008
PubMed
Summary

This study introduces a novel computational method to predict RNA-binding sites on proteins by identifying surface patches and clefts. The approach accurately identifies RNA-binding residues, aiding experimental validation and understanding protein-RNA interactions.

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Last Updated: Jul 7, 2026

Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells
10:34

Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells

Published on: December 9, 2022

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

RNA Secondary Structure Prediction Using High-throughput SHAPE
13:42

RNA Secondary Structure Prediction Using High-throughput SHAPE

Published on: May 31, 2013

Area of Science:

  • Biochemistry
  • Structural Biology
  • Computational Biology

Background:

  • RNA-binding proteins utilize surface features like helices, loops, or cavities to interact with RNA molecules.
  • Predicting these RNA-binding sites is crucial for understanding gene regulation and developing therapeutics.

Purpose of the Study:

  • To develop and validate a computational strategy for predicting RNA-binding residues on proteins.
  • To provide a prioritized list of candidate residues for experimental testing.

Main Methods:

  • The method identifies surface patches and clefts on protein structures.
  • Residues are scored based on electrostatic energy changes upon mutation and sequence conservation.
  • Input includes protein structure and homologous sequences.

Main Results:

  • The prediction method achieved high accuracy, correctly identifying RNA-binding sites in 81% of tested proteins.
  • Prediction accuracy was comparable using RNA-free or RNA-bound structures.
  • The approach successfully predicted binding sites even with protein conformational changes.

Conclusions:

  • The developed computational method is effective for predicting RNA-binding sites.
  • The strategy aids in prioritizing residues for experimental validation of RNA-protein interactions.
  • The findings are robust across different protein structures and RNA-binding states.