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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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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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ER is the primary site for the maturation and folding of soluble and transmembrane secretory proteins. The calnexin cycle is a specific chaperone system that folds and assesses the confirmation of N-glycosylated proteins before they can exit the ER lumen. The primary players of this quality check pipeline are the lectins, ER-resident chaperones, and a glucosyl transferase enzyme. In case the calnexin system in the lumen fails to salvage a misfolded protein, it is transported to the cytoplasm...
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Foldy: An open-source web application for interactive protein structure analysis.

Jacob B Roberts1,2,3, Alberto A Nava1,2,4, Allison N Pearson1,2,5

  • 1Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, California, United States of America.

Plos Computational Biology
|February 2, 2024
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Summary
This summary is machine-generated.

Foldy is a cloud-based application making advanced AI structural biology tools accessible to biologists. It simplifies protein structure prediction and ligand docking, enhancing research efficiency.

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Area of Science:

  • Structural Biology
  • Computational Biology
  • Bioinformatics

Background:

  • Non-computational biologists face challenges accessing advanced AI tools for structural biology.
  • Existing tools may require significant computational resources and specialized expertise.

Purpose of the Study:

  • To introduce Foldy, a cloud-based application designed to democratize access to AI-driven structural biology tools.
  • To demonstrate Foldy's utility for protein structure prediction, annotation, and ligand docking.

Main Methods:

  • Foldy integrates AI tools like AlphaFold and DiffDock into a user-friendly interface.
  • The application supports cloud-based deployment and local configuration.
  • Case studies showcase applications in enzyme design and protein analysis.

Main Results:

  • Foldy enables prediction of protein structures up to 6000 amino acids and ligand docking.
  • The application facilitates visualization of Pfam annotations.
  • Comparative analysis highlights Foldy's practical data and computation management capabilities.

Conclusions:

  • Foldy serves as a valuable day-to-day tool for life science researchers.
  • The application enhances accessibility and efficiency of modern structural biology tools for a broader scientific audience.