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Related Concept Videos

Protein Organization01:24

Protein Organization

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Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
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Protein Organization01:13

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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.
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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.
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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...
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DAMA: a method for computing multiple alignments of protein structures using local structure descriptors.

Paweł Daniluk1, Tymoteusz Oleniecki2, Bogdan Lesyng3

  • 1Bioinformatics Laboratory, Mossakowski Medical Research Centre, Polish Academy of Sciences, 02-106 Warsaw, Poland.

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|August 16, 2021
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Summary

Protein structure alignment is challenging. DAMA, a new computational tool, effectively aligns multiple protein structures using local 3D descriptors, improving evolutionary analysis and functional similarity identification.

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Area of Science:

  • Computational structural biology
  • Bioinformatics
  • Protein structure analysis

Background:

  • Protein structure is more conserved than sequence, aiding evolutionary and functional studies.
  • Accurate multiple structure alignment is crucial but computationally difficult.

Purpose of the Study:

  • Develop and apply DAMA, a novel computational environment for multiple protein structure alignment.
  • Improve the analysis of residue conservation and identification of structural patterns.

Main Methods:

  • DAMA utilizes local 3D structure descriptors and nearest-neighbor environments.
  • An effective heuristic approach addresses the NP-complete multiple alignment problem.
  • The algorithm identifies the largest consistent ensemble of similar descriptors.

Main Results:

  • DAMA captures biologically significant similarities in test sets, including protein kinases.
  • The method accurately identifies equivalent residues, aiding in understanding protein similarity.
  • DAMA outperforms other methods, especially with strict similarity measures (QC) and difficult cases.

Conclusions:

  • DAMA provides an effective solution for multiple protein structure alignment.
  • The tool enhances the discovery of evolutionary relationships and functional similarities.
  • DAMA is available online and via Linux binaries.