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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...
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...
Protein Folding01:22

Protein Folding

Overview
Protein Organization01:24

Protein Organization

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.
The Equilibrium Binding Constant and Binding Strength02:18

The Equilibrium Binding Constant and Binding Strength

The equilibrium binding constant (Kb) quantifies the strength of a protein-ligand interaction. Kb can be calculated as follows when the reaction is at equilibrium:

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Related Experiment Video

Updated: Jun 1, 2026

A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

Relative solvent accessible surface area predicts protein conformational changes upon binding.

Joseph A Marsh1, Sarah A Teichmann

  • 1MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB20QH, UK. jmarsh@mrc-lmb.cam.ac.uk

Structure (London, England : 1993)
|June 8, 2011
PubMed
Summary
This summary is machine-generated.

Protein binding often causes significant conformational changes. A new measure, relative solvent accessible surface area, predicts these changes and reveals protein flexibility is linked to binding-induced alterations.

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Determination of Protein-ligand Interactions Using Differential Scanning Fluorimetry
13:26

Determination of Protein-ligand Interactions Using Differential Scanning Fluorimetry

Published on: September 13, 2014

Related Experiment Videos

Last Updated: Jun 1, 2026

A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

Determination of Protein-ligand Interactions Using Differential Scanning Fluorimetry
13:26

Determination of Protein-ligand Interactions Using Differential Scanning Fluorimetry

Published on: September 13, 2014

Area of Science:

  • Structural Biology
  • Biophysics
  • Computational Biology

Background:

  • Protein interactions are fundamental to biological processes.
  • Conformational changes are frequently observed during protein binding events.
  • Understanding these changes is key to deciphering molecular recognition.

Purpose of the Study:

  • To analyze the relationship between protein structures and binding-induced conformational changes.
  • To introduce a predictive measure for the magnitude of these conformational alterations.
  • To explore the link between protein flexibility and binding dynamics.

Main Methods:

  • Analysis of protein structures and their bound states.
  • Introduction and application of the relative solvent accessible surface area (rSASA) measure.
  • Examination of intrinsically disordered sequences in relation to conformational changes.

Main Results:

  • Relative solvent accessible surface area effectively predicts binding-induced conformational changes.
  • Large conformational changes are common in protein complexes.
  • Proteins undergoing significant conformational changes show enrichment of intrinsically disordered sequences.
  • rSASA of monomeric proteins serves as a proxy for protein flexibility.

Conclusions:

  • Relative solvent accessible surface area is a valuable tool for predicting protein conformational dynamics.
  • Protein flexibility, as indicated by rSASA, is strongly correlated with binding-induced conformational changes.
  • Findings support the conformational selection model in molecular recognition.