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Related Concept Videos

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...
Protein Complexes with Interchangeable Parts01:57

Protein Complexes with Interchangeable Parts

Groups of proteins may form a complex where each protein in this complex has a different role in the overall execution of the complex’s function. Often some of the proteins in the complex can be replaced by a closely related variant to give a complex that contains many of the same components yet is functionally distinct.
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order to...
Protein Complexes with Interchangeable Parts01:57

Protein Complexes with Interchangeable Parts

Groups of proteins may form a complex where each protein in this complex has a different role in the overall execution of the complex’s function. Often some of the proteins in the complex can be replaced by a closely related variant to give a complex that contains many of the same components yet is functionally distinct.
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order to...
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...

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Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
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An integrated system for studying residue coevolution in proteins.

Kevin Y Yip1, Prianka Patel, Philip M Kim

  • 1Department of Computer Science, Yale University, 51 Prospect Street, New Haven, CT 06511, USA.

Bioinformatics (Oxford, England)
|December 7, 2007
PubMed
Summary

This study introduces an online system for comparing residue coevolution scoring functions in protein structures. It offers over 100 variations and preprocessing options to enhance coevolution signal detection and analysis.

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Area of Science:

  • Computational Biology
  • Structural Bioinformatics
  • Protein Science

Background:

  • Residue coevolution is crucial for understanding protein structures.
  • Numerous scoring functions exist, but their comparative performance and weaknesses are unclear.
  • Algorithmic complexities hinder the implementation and comparison of these functions.

Purpose of the Study:

  • To develop an integrated online system for comparative analysis of residue coevolution scoring functions.
  • To provide a comprehensive platform for evaluating the strengths and weaknesses of different coevolution quantification methods.
  • To facilitate the study of relationships between coevolution scores and protein structural features.

Main Methods:

  • Developed an online system implementing a wide range of commonly used coevolution scoring functions.
  • Included methods such as Statistical Coupling Analysis (SCA), Explicit Likelihood of Subset Variation (ELSC), mutual information, and correlation-based approaches.
  • Integrated data preprocessing options: sequence weighting, residue grouping, and filtering of sequences, sites, and site pairs, resulting in over 100 scoring variations.

Main Results:

  • The system enables comparative analyses of over 100 variations of coevolution scoring functions.
  • Preprocessing options enhance the sensitivity and specificity of coevolution signal detection.
  • The system facilitates the correlation of coevolution scores with inter-residue distances from crystal structures.

Conclusions:

  • The developed online system provides a valuable resource for researchers studying protein structures through residue coevolution.
  • It simplifies the comparison and application of diverse coevolutionary analysis methods.
  • The system aids in understanding protein structural principles by linking coevolutionary signals to physical proximity.