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Related Concept Videos

Conserved Binding Sites01:49

Conserved Binding Sites

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 analyses the...
Ligand Binding Sites02:40

Ligand Binding Sites

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...
Ligand Binding Sites02:40

Ligand Binding Sites

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...
Ligand Binding and Linkage00:49

Ligand Binding and Linkage

Allosteric proteins have more than one ligand binding site; the binding of a ligand to any of these sites influences the binding of ligands to the other sites. When a protein is allosteric, its binding sites are called coupled or linked.  In the case of enzymes, the site that binds to the substrate is known as the active site and the other site is known as the regulatory site. When a ligand binds to the regulatory site, this leads to conformational changes in the protein that can influence the...
Ligand Binding and Linkage00:49

Ligand Binding and Linkage

Allosteric proteins have more than one ligand binding site; the binding of a ligand to any of these sites influences the binding of ligands to the other sites. When a protein is allosteric, its binding sites are called coupled or linked.  In the case of enzymes, the site that binds to the substrate is known as the active site and the other site is known as the regulatory site. When a ligand binds to the regulatory site, this leads to conformational changes in the protein that can influence the...
Protein-protein Interfaces02:04

Protein-protein Interfaces

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 polypeptide...

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Related Experiment Video

Updated: Jun 15, 2026

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions
06:50

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions

Published on: January 26, 2024

Feature-incorporated alignment based ligand-binding residue prediction for carbohydrate-binding modules.

Wei-Yao Chou1, Wei-I Chou, Tun-Wen Pai

  • 1Department of Computer Science, National Tsing Hua University, Hsinchu, Taiwan 300, Republic of China.

Bioinformatics (Oxford, England)
|March 2, 2010
PubMed
Summary
This summary is machine-generated.

We developed a feature-incorporated alignment (FIA) method to accurately identify ligand-binding residues in carbohydrate-binding modules (CBMs), even with low sequence identity. This computational approach improves understanding of protein-carbohydrate interactions.

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Area of Science:

  • Biochemistry
  • Structural Biology
  • Bioinformatics

Background:

  • Carbohydrate-binding modules (CBMs) exhibit conserved structures but low sequence identity, complicating functional analysis.
  • Accurate identification of ligand-binding residues is crucial for understanding protein-carbohydrate interactions.
  • Conventional alignment methods struggle with low sequence identity, hindering precise feature localization.

Purpose of the Study:

  • To develop a novel computational method for identifying functional ligand-binding residues in CBMs.
  • To improve the accuracy of sequence alignment for CBMs with low sequence identity.
  • To provide a tool for functional characterization of CBMs in the absence of 3D structural data.

Main Methods:

  • A feature-incorporated alignment (FIA) method was developed to flexibly align conserved signatures in CBMs.
  • An FIA-based target-template prediction model was implemented to identify ligand-binding residues.
  • The model was validated using Arabidopsis thaliana CBM45 and CBM53 sequences.

Main Results:

  • The FIA-based prediction model successfully identified ligand-binding residues on the surface of hypothetical structures.
  • FIA demonstrated significant improvement in estimating sequence similarity and identity for 808 sequences across 11 CBM families.
  • Performance was superior to six leading computational tools, as validated by Friedman rank test.

Conclusions:

  • Feature-incorporated alignment (FIA) is an effective method for analyzing CBMs with low sequence identity.
  • The FIA-based prediction model accurately identifies functional ligand-binding residues, aiding in understanding protein-carbohydrate binding mechanisms.
  • This approach enhances computational functional characterization of CBMs, particularly when 3D structural information is unavailable.