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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’ 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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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 families are groups of homologous proteins; that is, they have similarities in amino acid sequences and three-dimensional structures. Protein families usually occur because of gene duplication, where an additional copy of a gene is inserted into the genome of an organism.   Mutations that change the amino acids but still allow the protein to be properly synthesized, will lead to new protein family members.   If these new proteins contain similar amino acids in key...
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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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A Protocol for Computer-Based Protein Structure and Function Prediction
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An Online Server for Geometry-Aware Protein Function Annotations Through Predicted Structure.

Jialin Zou1, Qianmu Yuan1,2, Yuedong Yang3

  • 1School of Computer Science and Engineering, Sun Yat-sen University, Guangzhou, Guangdong, China.

Methods in Molecular Biology (Clifton, N.J.)
|July 29, 2025
PubMed
Summary
This summary is machine-generated.

GPSFun is a new web server for protein function annotation, predicting binding sites, gene ontologies, and more. It addresses the gap in functional annotations for the growing number of protein sequences.

Keywords:
GPSFun web serverGene ontologiesLigand-binding sitesProtein function predictionProtein solubilitySubcellular locations

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Area of Science:

  • * Bioinformatics
  • * Computational Biology
  • * Structural Biology

Background:

  • * Determining protein functions is crucial for various biological research areas, including metagenomics, disease mechanism studies, and drug discovery.
  • * Current biochemical methods for protein function determination are often inefficient and expensive, creating a bottleneck in annotating the vast number of available protein sequences.

Purpose of the Study:

  • * To introduce GPSFun, a novel web server designed for fast and accurate protein sequence function annotation.
  • * To provide comprehensive, geometry-aware functional predictions, including ligand-binding sites, gene ontologies, subcellular localization, and protein solubility.

Main Methods:

  • * Development of a web server (GPSFun) for protein function annotation.
  • * Utilization of geometry-aware algorithms for predicting various functional attributes.
  • * Creation of a complementary database (GPSiteDB) from extensive Swiss-Prot annotations.

Main Results:

  • * GPSFun offers a user-friendly web interface for accessing detailed protein function annotations.
  • * The tool successfully annotated ligand-binding sites for over 568,000 Swiss-Prot proteins, forming the GPSiteDB database.
  • * Annotations include predictions for protein-binding sites, gene ontologies, subcellular locations, and protein solubility.

Conclusions:

  • * GPSFun provides a valuable and efficient resource for accelerating protein function annotation in biological research.
  • * The integrated GPSiteDB database offers a rich resource for exploring protein function and ligand-binding specificities.
  • * The developed methods enhance the understanding of protein roles in various biological contexts.