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Conservation of Protein Domains Over Different Proteins

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...

Gene Evolution - Fast or Slow?

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...

Conserved Binding Sites

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...

Conservation of Protein Domains

Conservation of Protein Domains

Evolutionary Relationships through Genome Comparisons

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...

Multi-species Conserved Sequences

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...

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Related Experiment Video

Updated: Dec 14, 2025

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

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

Published on: July 14, 2015

The search of sequence variants using a constrained protein evolution simulation approach.

Pierre Tufféry¹, Sjoerd de Vries¹

¹Université de Paris, BFA, UMR 8251, CNRS, ERL U1133, Inserm, RPBS, F-75013 Paris, France.

Computational and Structural Biotechnology Journal

|July 23, 2020

Summary

This study introduces a novel sequence evolution method for protein engineering. It preserves local protein structure during substitutions, accurately predicting sequence diversity and guiding variant selection for enhanced properties.

Keywords:

Local structure Protein evolution Sequence optimization Structural alphabet

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Last Updated: Dec 14, 2025

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

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Area of Science:

Biochemistry
Computational Biology
Protein Science

Background:

Protein engineering and therapeutic peptide optimization require identifying critical sequence variants.
Substitutions must maintain protein structure and function while enhancing properties like stability or resistance.

Purpose of the Study:

Introduce a new sequence evolution approach focused on preserving local protein structure.
Demonstrate its ability to predict sequence diversity and guide site-specific substitutions.

Main Methods:

Developed a point-to-point control method for local structure preservation during sequence evolution.
Applied the approach to 6 mini-proteins and compared results to the Uniref repository.

Main Results:

The method intrinsically captures site-specific substitution rate heterogeneity.
Successfully reproduces observed sequence diversity from a single starting sequence.
Identifies specific positions and substitutions to avoid for maintaining structural integrity.

Conclusions:

Preserving local structure at each position is a key factor in protein sequence evolution.
This approach aids in selecting sequence variants for protein engineering and therapeutic peptide design.
Provides insights into structure-based sequence diversity and site-specific mutation constraints.