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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...
Cooperative Binding of Transcription Regulators02:13

Cooperative Binding of Transcription Regulators

Transcriptional regulators bind to specific cis-regulatory sequences in the DNA to regulate gene transcription. These cis-regulatory sequences are very short, usually less than ten nucleotide pairs in length. The short length means that there is a high probability of the exact same sequence randomly occurring throughout the genome.  Since regulators can also bind to groups of similar sequences, this further increases the chances of random binding. Transcriptional regulators form dimers that...
Cooperative Binding of Transcription Regulators02:13

Cooperative Binding of Transcription Regulators

Transcriptional regulators bind to specific cis-regulatory sequences in the DNA to regulate gene transcription. These cis-regulatory sequences are very short, usually less than ten nucleotide pairs in length. The short length means that there is a high probability of the exact same sequence randomly occurring throughout the genome.  Since regulators can also bind to groups of similar sequences, this further increases the chances of random binding. Transcriptional regulators form dimers that...
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...
Multi-species Conserved Sequences02:51

Multi-species Conserved Sequences

Next-generation sequencing technologies have created large genomic databases of a variety of animals and plants. Ever since the human genome project was completed, scientists studied the genome of primates, mammals, and other phylogenetically distant living beings. Such large-scale  studies have provided new insights into the evolutionary relationship between organisms.
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved DNA...

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Related Experiment Video

Updated: Jun 20, 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

RNA-binding residues in sequence space: conservation and interaction patterns.

Ruth V Spriggs1, Susan Jones

  • 1Department of Chemistry and Biochemistry, School of Life Sciences, John Maynard-Smith Building, University of Sussex, Falmer, Brighton, BN1 9QG, UK.

Computational Biology and Chemistry
|August 25, 2009
PubMed
Summary
This summary is machine-generated.

Identifying RNA-binding proteins (RBPs) is crucial. This study analyzes the evolutionary conservation of RNA-binding residues (RBRs) to develop sequence patterns for discovering novel RBPs, outperforming traditional homology searches.

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Last Updated: Jun 20, 2026

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

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Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
07:08

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

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Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions
06:50

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions

Published on: January 26, 2024

Area of Science:

  • Biochemistry and Molecular Biology
  • Bioinformatics
  • Genomics

Background:

  • RNA-binding proteins (RBPs) are essential for cellular functions, but many remain uncharacterized.
  • Sequence homology is limited in identifying functional proteins, especially orphan open reading frames (ORFs).
  • Novel methods for protein function annotation beyond sequence similarity are needed.

Purpose of the Study:

  • To characterize RNA-binding residues (RBRs) based on evolutionary conservation and sequence patterns.
  • To evaluate the potential of these characteristics for identifying RBPs from sequence data.
  • To develop sequence patterns for predicting RBP function in uncharacterized proteins.

Main Methods:

  • Comparative analysis of residue conservation in 261 RBPs, distinguishing RBRs from non-RBRs and specific vs. non-specific RBRs.
  • Construction of RBR sequence patterns derived from known protein-RNA structures.
  • Application of sequence patterns to differentiate RNA-binding from non-RNA-binding sequences and predict functions for hypothetical proteins.

Main Results:

  • RBRs are significantly more conserved than other surface residues.
  • RBRs involved in hydrogen bonding to the RNA backbone exhibit higher conservation than those binding to RNA bases.
  • Developed sequence patterns achieved high precision (>80%) and recall, outperforming homology searches.
  • Two family-specific patterns showed high predictive value (>=85% precision) for identifying potential RBPs.

Conclusions:

  • Evolutionary conservation patterns of RBRs can be leveraged for RBP identification.
  • Sequence pattern analysis offers a powerful alternative to homology-based methods for RBP discovery.
  • This approach successfully identified potential novel RBPs requiring experimental validation.