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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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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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Protein Visualizer 2.0: Intuitive and Interactive Visualization of Protein Topology and Co/Post-Translational

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  • 1Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada.

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Summary
This summary is machine-generated.

Protein Visualizer 2.0 offers a novel web-based tool for analyzing human protein topology and post-translational modifications. It visualizes key structural features, aiding in the assessment of conflicts and revealing hidden relationships for detailed protein studies.

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Area of Science:

  • Biochemistry
  • Structural Biology
  • Bioinformatics

Background:

  • Protein structure and function are critically influenced by topology and post-translational modifications (PTMs).
  • Existing visualization tools like PyMOL, iCn3D, UniProt PTM, and Protter offer detailed protein analysis but lack integrated visualization of topology with key PTM-related features.
  • This gap hinders comprehensive studies on the interplay between protein structure, modifications, and function.

Discussion:

  • Protein Visualizer 2.0 is a new web-based tool designed to visualize the topology of all human proteins alongside crucial features like N-glycosylation, disulfide bonds, and their potential free sites.
  • The tool facilitates the identification of potential conflicts between predicted protein topology and known co/post-translational modifications.
  • It enables the discovery of previously unrecognized relationships among these diverse structural elements.

Key Insights:

  • Integrated visualization of protein topology with N-glycosylation and disulfide bond features.
  • Assessment of conflicts between predicted topology and PTMs.
  • Unveiling of hidden structural relationships for enhanced protein analysis.

Outlook:

  • Potential for broader application in studying protein structure-function relationships across different organisms.
  • Facilitation of hypothesis generation in proteomics and drug discovery.
  • Advancement of our understanding of protein regulation and cellular processes.