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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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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’ 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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A Protocol for Computer-Based Protein Structure and Function Prediction
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An easy-to-use three-dimensional protein-structure-prediction online platform "DPL3D" based on deep learning

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  • 1NewInsyght Biotech (Guangdong) Co., Ltd. DongGuan 523000, China.

Current Research in Structural Biology
|January 27, 2025
PubMed
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Predicting mutant protein structures is crucial for understanding diseases. DPL3D is a new platform that visualizes these 3D protein structures, aiding biological discovery and clinical applications.

Keywords:
Gene mutationProtein three-dimensional structureStructural biology

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Area of Science:

  • Structural Biology
  • Computational Biology
  • Genomics

Background:

  • Protein structure changes, often due to missense mutations, can cause diseases.
  • Accurate prediction of mutant protein structures is limited by data availability.
  • Existing methods for assessing mutation impact rely heavily on evolutionary conservation.

Purpose of the Study:

  • To develop a user-friendly platform for predicting and visualizing mutant protein 3D structures.
  • To integrate advanced computational protein structure prediction tools.
  • To provide clinicians and researchers with accessible structural biology information.

Main Methods:

  • Utilized AlphaFold 2, RoseTTAFold, RoseTTAFold All-Atom, and trRosettaX-Single for structure prediction.
  • Compiled a database of 210,180 molecular structures, including 52,248 human proteins.
  • Implemented interactive 2D and 3D structure visualization using LiteMol.

Main Results:

  • Developed the DPL3D platform (http://nsbio.tech:3000) for mutant protein structure prediction and visualization.
  • Enabled automated and manual interactive visualization of protein structures.
  • Provided access to a large-scale database of protein structural information.

Conclusions:

  • DPL3D facilitates the utilization of structural biology information by clinicians and researchers.
  • The platform enhances the ability to study the impact of mutations on protein structure and function.
  • Accelerates biological discovery through easy retrieval of large-scale protein structural data.