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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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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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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.
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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.
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Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
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Arpeggio: A Web Server for Calculating and Visualising Interatomic Interactions in Protein Structures.

Harry C Jubb1, Alicia P Higueruelo1, Bernardo Ochoa-Montaño1

  • 1Department of Biochemistry, Sanger Building, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK.

Journal of Molecular Biology
|December 15, 2016
PubMed
Summary

Arpeggio is a web server that visualizes molecular interactions between proteins, DNA, and small molecules. It aids drug design and mutation impact studies by detailing various interatomic contacts and aromatic interactions.

Keywords:
drug designmolecular recognitionprotein interactionsprotein–ligand interactionsprotein–protein interactions

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Area of Science:

  • Structural Biology
  • Computational Biology
  • Drug Discovery

Background:

  • Molecular recognition relies on specific interatomic interactions.
  • Visualizing these interactions is crucial for drug design and understanding mutation effects.

Purpose of the Study:

  • To present Arpeggio, a web server for calculating and visualizing molecular interactions.
  • To provide insights into molecular recognition events and aid in structure-based drug design.

Main Methods:

  • Arpeggio calculates various interactions: van der Waals', ionic, carbonyl, metal, hydrophobic, halogen bonds, hydrogen bonds, and specific atom-aromatic ring (cation-π, donor-π, halogen-π, carbon-π) and aromatic ring-aromatic ring (π-π) interactions.
  • It processes user-submitted macromolecule structures.
  • PyMOL session files are downloadable for high-quality image generation.

Main Results:

  • Arpeggio successfully calculates a comprehensive range of interatomic and aromatic interactions.
  • The tool facilitates the generation of publication-quality visualizations of these interactions.
  • User-submitted structures can be analyzed for detailed interaction profiles.

Conclusions:

  • Arpeggio offers a user-friendly platform for exploring molecular interactions.
  • It serves as a valuable tool for researchers in structural biology, computational chemistry, and drug discovery.
  • The visualization capabilities aid in understanding molecular recognition and guiding therapeutic development.