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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...
Structural Protein Function01:56

Structural Protein Function

Structural proteins are a category of proteins responsible for functions ranging from cell shape and movement to providing support to major structures such as bones, cartilage, hair, and muscles. This group includes proteins such as collagen, actin, myosin, and keratin.
Collagen, the most abundant protein in mammals, is found throughout the body. In connective tissue, such as skin, ligaments, and tendons, it provides tensile strength and elasticity.  In bones and teeth, it mineralizes to form...
Structural Protein Function01:56

Structural Protein Function

Structural proteins are a category of proteins responsible for functions ranging from cell shape and movement to providing support to major structures such as bones, cartilage, hair, and muscles. This group includes proteins such as collagen, actin, myosin, and keratin.
Collagen, the most abundant protein in mammals, is found throughout the body. In connective tissue, such as skin, ligaments, and tendons, it provides tensile strength and elasticity.  In bones and teeth, it mineralizes to form...
Protein and Protein Structure02:15

Protein and Protein Structure

Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. Proteins may be structural, regulatory, contractile, or protective. They may serve in transport, storage, or membranes; or they may be toxins or enzymes. Their structures, like their functions, vary greatly. They are all, however, amino acid polymers arranged in a linear sequence.
A protein's shape is critical to its function. For example, an enzyme can...
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...
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...

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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

SiteBinder: an improved approach for comparing multiple protein structural motifs.

David Sehnal1, Radka Svobodová Vařeková, Heinrich J Huber

  • 1National Centre for Biomolecular Research, Faculty of Science and CEITEC-Central European Institute of Technology, Masaryk University Brno, Kamenice 5, 62500 Brno-Bohunice, Czech Republic.

Journal of Chemical Information and Modeling
|February 3, 2012
PubMed
Summary

A new software tool, SiteBinder, enables rapid and accurate multiple superimposition of large protein structural motif datasets. This method enhances the analysis of protein 3D structures, even with low sequence similarity, revealing conserved structural features.

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Area of Science:

  • Structural Biology
  • Bioinformatics
  • Computational Biology

Background:

  • The exponential growth of protein 3D structure data necessitates advanced tools for information extraction.
  • Current methods for analyzing large sets of protein structural motifs are often limited in scope and efficiency.

Purpose of the Study:

  • To develop and validate a robust software tool for the multiple superimposition of extensive protein structural motif collections.
  • To enable detailed structural comparisons, irrespective of sequence similarity, for enhanced biological insights.

Main Methods:

  • Development of a superimposition methodology employing systematic atom pairing searches and quaternion algebra for RMSD calculation.
  • Optimization of the search process using Protein Data Bank (PDB) annotations to reduce computational complexity.
  • Implementation of the methodology into a user-friendly web application, SiteBinder, capable of processing thousands of structures.

Main Results:

  • SiteBinder successfully superimposed 1000 experimentally determined structures for each of 32 eukaryotic linear motifs, demonstrating robustness and efficiency.
  • Analysis of PA-IIL sugar binding sites revealed conserved structures despite binding different sugars.
  • Superimposition of zinc finger motifs showed high conservation in the molecular structure near the Zn atom.
  • Comparison of BH3 domains supported a structural basis for functional segregation in BH3-only proteins.

Conclusions:

  • The SiteBinder software provides a powerful and versatile tool for analyzing large-scale protein structural data.
  • The methodology facilitates the discovery of conserved structural patterns crucial for understanding protein function and evolution.
  • Structural conservation identified in case studies highlights the utility of SiteBinder in diverse biological investigations.