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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...
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...
Gene Evolution - Fast or Slow?02:05

Gene Evolution - Fast or Slow?

The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
In contrast, regions which code...
Gene Evolution - Fast or Slow?02:05

Gene Evolution - Fast or Slow?

The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
In contrast, regions which code...
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 23, 2026

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

Published on: July 14, 2015

Using evolutionary information to find specificity-determining and co-evolving residues.

Grigory Kolesov1, Leonid A Mirny

  • 1Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA, USA.

Methods in Molecular Biology (Clifton, N.J.)
|April 22, 2009
PubMed
Summary
This summary is machine-generated.

Identifying specificity-determining residues (SDRs) and co-evolving residues (CERs) in proteins is crucial for understanding molecular recognition. New bioinformatics methods reveal distinct evolutionary patterns for SDRs and CERs, aiding in protein function analysis.

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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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In Vitro Directed Evolution of a Restriction Endonuclease with More Stringent Specificity
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In Vitro Directed Evolution of a Restriction Endonuclease with More Stringent Specificity

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Related Experiment Videos

Last Updated: Jun 23, 2026

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

Published on: July 14, 2015

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

In Vitro Directed Evolution of a Restriction Endonuclease with More Stringent Specificity
09:16

In Vitro Directed Evolution of a Restriction Endonuclease with More Stringent Specificity

Published on: March 25, 2020

Area of Science:

  • Molecular Biology
  • Bioinformatics
  • Evolutionary Biology

Background:

  • Protein interactions are fundamental to biological processes.
  • Specificity-determining residues (SDRs) mediate molecular recognition.
  • Distinguishing SDRs from other functionally important residues is challenging.

Purpose of the Study:

  • To develop and present novel bioinformatics methods for identifying SDRs and co-evolving residues (CERs).
  • To analyze the evolutionary patterns of SDRs and CERs in protein families.

Main Methods:

  • Utilized a Monte Carlo approach for statistical inference.
  • Developed two new methods to identify SDRs and CERs.
  • Applied methods to bacterial two-component systems and class Ia aminoacyl-tRNA synthetases.

Main Results:

  • Successfully identified specific evolutionary patterns for SDRs and CERs.
  • Results align with existing structural and experimental data.
  • Demonstrated distinct evolutionary characteristics of specificity-related residues.

Conclusions:

  • The developed methods effectively reveal evolutionary patterns of SDRs and CERs.
  • Protein specificity evolution exhibits complex and distinct patterns.
  • These findings enhance the understanding of molecular recognition mechanisms.