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Protein-protein Interfaces02:04

Protein-protein Interfaces

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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 Networks02:26

Protein Networks

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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.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
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Conserved Binding Sites01:49

Conserved Binding Sites

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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.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...
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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.
The primary structure of a protein is its amino acid sequence....
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Ligand Binding Sites02:40

Ligand Binding Sites

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Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...
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Related Experiment Video

Updated: May 17, 2025

Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions
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Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions

Published on: January 26, 2024

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Predictions from Deep Learning Propose Substantial Protein-Carbohydrate Interplay.

Samuel W Canner1, Ronald L Schnaar2,3, Jeffrey J Gray1,4

  • 1Program in Molecular Biophysics, Johns Hopkins University, Baltimore, MD, United States.

Biorxiv : the Preprint Server for Biology
|March 31, 2025
PubMed
Summary
This summary is machine-generated.

We developed computational tools, Protein interaction of Carbohydrates Predictor (PiCAP) and Carbohydrate Protein Site Identifier 2 (CAPSIF2), to identify protein-carbohydrate interactions. These tools predict carbohydrate binding proteins and their interaction sites with high accuracy, revealing widespread interactions in key proteomes.

Keywords:
Glycancarbohydrateglycomeinteractomelectomeproteome

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Area of Science:

  • Biochemistry and Molecular Biology
  • Computational Biology
  • Bioinformatics

Background:

  • Identifying protein-carbohydrate interactions is crucial for understanding biological processes, yet experimental methods are resource-intensive.
  • Current estimates suggest only 1.5-5% of proteins bind carbohydrates, contrasting with the 50-70% of proteins known to be glycosylated.
  • A significant gap exists in accurately predicting carbohydrate-binding proteins and their interaction sites.

Purpose of the Study:

  • To develop novel computational tools for predicting protein-carbohydrate binding and identifying specific interaction sites.
  • To establish a robust dataset for training and validating predictive models for protein-carbohydrate interactions.
  • To assess the prevalence of carbohydrate-binding proteins across different proteomes and investigate their biological relevance.

Main Methods:

  • Developed the Protein interaction of Carbohydrates Predictor (PiCAP), a neural network model trained on known carbohydrate binders and non-binders.
  • Created the Carbohydrate Protein Site Identifier 2 (CAPSIF2) model to predict specific protein residues involved in carbohydrate binding.
  • Utilized a curated dataset including known binders, DNA-binding proteins, cytoskeletal components, antibodies, and small-molecule binders for training and validation.

Main Results:

  • PiCAP achieved 90% balanced accuracy in predicting protein-level carbohydrate binding/non-binding.
  • CAPSIF2 demonstrated a Dice coefficient of 0.57 for residue-level predictions, outperforming existing models.
  • Application to human neural cells and proteomes (E. coli, M. musculus, H. sapiens) predicted 35-40% of proteins bind carbohydrates.

Conclusions:

  • PiCAP and CAPSIF2 are effective computational tools for predicting protein-carbohydrate interactions and binding sites.
  • A substantial portion of proteins across various proteomes are predicted to engage in carbohydrate binding.
  • These findings highlight the significant role of protein-carbohydrate interactions in cellular functions and open avenues for further research.