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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...
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...
Conservation of Protein Domains02:26

Conservation of Protein Domains

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...
Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...

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Demonstration of the Sequence Alignment to Predict Across Species Susceptibility Tool for Rapid Assessment of Protein Conservation
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Demonstration of the Sequence Alignment to Predict Across Species Susceptibility Tool for Rapid Assessment of Protein Conservation

Published on: February 10, 2023

Using genome-wide protein sequence data to predict amino acid conservation.

Peter Palenchar1, Mathew Mount, Douglas Cusato

  • 1Department of Chemistry, Rutgers University, 315 Penn St, Camden, NJ 08102-1411, USA. peterpal@crab.rutgers.edu

The Protein Journal
|September 17, 2008
PubMed
Summary

Predicting essential amino acids in unique proteins is challenging. This study identifies five key "conservation factors" from primary sequences that effectively predict amino acid conservation in Escherichia coli and yeast proteins.

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

  • * Computational Biology
  • * Bioinformatics
  • * Molecular Evolution

Background:

  • * Multiple sequence alignments are standard for identifying critical amino acids in conserved proteins.
  • * Unique or rare proteins lack sufficient homologous sequences for effective alignment-based analysis.
  • * Novel methods are needed to predict functionally important amino acids in proteins with limited evolutionary data.

Purpose of the Study:

  • * To investigate the relationship between amino acid conservation and sequence-derived factors in Escherichia coli proteins.
  • * To identify predictive factors for amino acid conservation beyond traditional sequence alignments.
  • * To develop a predictive model for conserved amino acids in proteins lacking extensive homologous sequences.

Main Methods:

  • * Analyzed the correlation between amino acid conservation and five factors: identity, N-terminal neighbor, C-terminal neighbor, local hydropathy, and local net charge.
  • * Utilized primary sequence data from Escherichia coli proteins.
  • * Developed a scoring system combining these factors to predict amino acid conservation.

Main Results:

  • * Four of the five investigated factors (excluding amino acid identity) showed significant relationships with conservation for specific amino acids.
  • * A combined score using all five factors demonstrated statistically significant predictive value for conserved amino acids.
  • * The predictive model was effective for both intra-species (E. coli) and inter-species (Saccharomyces cerevisiae) comparisons.

Conclusions:

  • * Five sequence-derived factors, termed
  • conservation factors
  • , can predict amino acid conservation.
  • * This approach offers a viable method for analyzing proteins with limited sequence alignments.
  • * The findings have implications for understanding protein function and evolution in diverse organisms.