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Related Concept Videos

Protein-protein Interfaces02:04

Protein-protein Interfaces

Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a polypeptide...
Protein-Protein Interfaces02:04

Protein-Protein Interfaces

Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a polypeptide...
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...
Protein Networks02:26

Protein Networks

An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
Protein Networks02:26

Protein Networks

An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
Microbial Phylogeny01:28

Microbial Phylogeny

Understanding the evolutionary relationships among microorganisms is fundamental to microbial ecology and taxonomy. Phylogenetic trees are essential tools for inferring these relationships, relying primarily on comparative analyses of molecular sequences such as DNA, RNA, or proteins. In microbial studies, these trees typically depict the evolutionary paths of diverse bacterial and archaeal species by mapping genetic differences accumulated over time.Phylogenetic trees are composed of tips,...

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Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
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Published on: July 14, 2015

Joint evolutionary trees: a large-scale method to predict protein interfaces based on sequence sampling.

Stefan Engelen1, Ladislas A Trojan, Sophie Sacquin-Mora

  • 1Génomique Analytique, Université Pierre et Marie Curie-Paris 6, UMR S511, Paris, France.

Plos Computational Biology
|January 24, 2009
PubMed
Summary
This summary is machine-generated.

The Joint Evolutionary Trees (JET) method enhances protein interface prediction by analyzing evolutionary data with novel sampling and clustering techniques. This approach improves accuracy and efficiency for identifying critical protein residues involved in molecular interactions.

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Area of Science:

  • Computational Biology
  • Bioinformatics
  • Structural Biology

Background:

  • Protein interfaces are crucial for molecular recognition and biological function.
  • Existing methods for predicting protein interfaces face challenges with sequence alignment accuracy and data representation.

Purpose of the Study:

  • To introduce the Joint Evolutionary Trees (JET) method for improved protein interface residue prediction.
  • To enhance the sensitivity and computational efficiency of evolutionary trace analysis for identifying functionally important residues.

Main Methods:

  • JET employs Gibbs-like sampling of distance trees to mitigate errors from multiple sequence alignments and weakly homologous sequences.
  • A clustering method incorporating residue properties and conservation is used to identify and extend interaction sites on protein surfaces.
  • An iterative version, iJET, is developed for robust large-scale predictions, even with low evolutionary signal.

Main Results:

  • JET demonstrates significant improvements in performance and computational efficiency compared to existing methods like ET, Consurf, and Rate4Site.
  • The method was validated on diverse protein complexes, including heterodimers, homodimers, and transient complexes, as well as various protein families.
  • JET accurately predicts interaction sites across a wide range of biological molecules, including proteins, ligands, DNA, and RNA.

Conclusions:

  • The Joint Evolutionary Trees (JET) method offers a powerful and efficient approach for predicting protein-protein interaction sites.
  • JET's novel treatment of evolutionary information and advanced clustering provide higher accuracy and better adaptability for large-scale applications.
  • The iJET variant is particularly suitable for large-scale predictions, enhancing our understanding of molecular recognition and protein function.