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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.
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Related Experiment Video

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

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

Published on: January 26, 2024

Conformational selection in protein binding and function.

Thomas R Weikl¹, Fabian Paul

¹Department of Theory and Bio-Systems, Max Planck Institute of Colloids and Interfaces, Science Park Golm, 14424, Potsdam, Germany.

Protein Science : a Publication of the Protein Society

|August 27, 2014

Summary

This summary is machine-generated.

Protein conformational selection is a key binding mechanism, especially for small molecules. This review highlights how binding and unbinding timescales dictate protein dynamics and function.

Keywords:

advanced nuclear magnetic resonance experiments binding kinetics conformational selection induced fit single-molecule fluorescence resonance energy transfer

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Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

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Published on: July 25, 2013

Area of Science:

Biochemistry
Molecular Biophysics
Structural Biology

Background:

Protein function relies on dynamic conformational changes.
Ligand binding can influence or be influenced by these protein dynamics.
Advanced Nuclear Magnetic Resonance (NMR) experiments reveal complex protein behaviors.

Purpose of the Study:

To review the concept of conformational selection in protein-ligand interactions.
To propose a unified view of conformational selection and induced-fit models.
To discuss experimental methods for characterizing these processes.

Main Methods:

Analysis of transition times and dwell times in protein conformational changes.
Comparison of timescales for ligand binding/unbinding versus protein conformational changes.
Review of advanced NMR and single-molecule fluorescence resonance energy transfer (smFRET) techniques.

Main Results:

Conformational selection requires fast ligand binding/unbinding relative to protein conformational dwell times.
A separation of timescales decouples binding events from conformational changes.
Conformational selection and induced-fit are inverse perspectives of the same phenomenon.
Large ligands can exhibit coupled conformational changes and binding events.

Conclusions:

The temporal ordering of binding and conformational changes determines whether a process is viewed as conformational selection or induced fit.
Experimental data from relaxation rates and exchange rates can elucidate these dynamics.
Understanding these mechanisms is crucial for comprehending protein function and designing drugs.