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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 form...

Conservation of Protein Domains

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...

Protein-Drug Binding: Determination Methods

Protein-Drug Binding: Determination Methods

Determining protein-drug binding can be achieved through indirect and direct methods, each providing valuable insights into the interaction between proteins and drugs.
Indirect methods involve isolating the bound drug from its free form in biological samples such as blood, serum, or plasma. These techniques aim to measure the percentage of drugs bound to proteins. Equilibrium dialysis is a commonly used method where the free drug concentration at equilibrium is measured by separating the bound...

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 analyses the...

Protein Dynamics in Living Cells

Protein Dynamics in Living Cells

Different fluorescence-based techniques are used to study the protein dynamics in living cells. These techniques include FRAP, FRET, and PET.
Fluorescent recovery after photobleaching (FRAP) is a fluorescent-protein-based detection technique used to quantify protein movement rates within the cell. This method exposes a small portion of the cell to an intense laser beam. The laser beam causes permanent photobleaching of the fluorophore-tagged proteins in the exposed region. As the bleached...

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...

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Related Experiment Video

Updated: Jun 1, 2026

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

New methods to measure residues coevolution in proteins.

Hongyun Gao¹, Yongchao Dou, Jialiang Yang

¹School of Mathematical Sciences, Dalian University of Technology, Dalian, People’s Republic of China.

BMC Bioinformatics

|May 27, 2011

Summary

New methods improve protein coevolution analysis by incorporating amino acid background and physicochemical properties. These approaches better quantify residue covariation, revealing new insights into evolutionary pressures.

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Area of Science:

Biophysics
Computational Biology
Bioinformatics

Background:

Protein coevolution is often measured by site covariation.
Existing methods primarily use mutual information (MI) based on residue frequencies.
These methods can be influenced by amino acid evolutionary pressures.

Purpose of the Study:

To develop novel measures for quantifying protein residue covariation.
To incorporate biological constraints, such as amino acid background distribution and physicochemical properties.
To improve the accuracy and biological relevance of coevolution analysis.

Main Methods:

Introduced Mutual Information with Amino Acid Background distribution (MIB) to account for background frequencies.
Developed Mutual Information of Physicochemical properties (MIP) to assess property covariation.
Proposed MIBP by combining MIB and MIP for a comprehensive analysis.
Applied new measures to the conn(k) indicator to identify covariation signals.

Main Results:

The MIB measure effectively removes the influence of amino acid evolutionary pressure.
MIB provides a more biologically relevant measure of residue coevolution.
MIP analysis reveals covariation based on physicochemical properties as a novel aspect of coevolution.
The new measures successfully identified covariation signals in protein sites.

Conclusions:

Incorporating amino acid background distribution enhances coevolution analysis by mitigating evolutionary pressure effects.
The MIB measure offers a more biologically informed perspective on residue coevolution.
Covariation of physicochemical properties represents a significant, previously unexploited source of coevolution information.