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Related Concept Videos

Cooperative Allosteric Transitions01:58

Cooperative Allosteric Transitions

Cooperative allosteric transitions can occur in multimeric proteins, where each subunit of the protein has its own ligand-binding site. When a ligand binds to any of these subunits, it triggers a conformational change that affects the binding sites in the other subunits; this can change the affinity of the other sites for their respective ligands. The ability of the protein to change the shape of its binding site is attributed to the presence of a mix of flexible and stable segments in the...
Cooperative Allosteric Transitions01:58

Cooperative Allosteric Transitions

Cooperative allosteric transitions can occur in multimeric proteins, where each subunit of the protein has its own ligand-binding site. When a ligand binds to any of these subunits, it triggers a conformational change that affects the binding sites in the other subunits; this can change the affinity of the other sites for their respective ligands. The ability of the protein to change the shape of its binding site is attributed to the presence of a mix of flexible and stable segments in the...
Cooperative Allosteric Transitions01:58

Cooperative Allosteric Transitions

Cooperative allosteric transitions can occur in multimeric proteins, where each subunit of the protein has its own ligand-binding site. When a ligand binds to any of these subunits, it triggers a conformational change that affects the binding sites in the other subunits; this can change the affinity of the other sites for their respective ligands. The ability of the protein to change the shape of its binding site is attributed to the presence of a mix of flexible and stable segments in the...
Mutations in Microorganisms01:18

Mutations in Microorganisms

Mutations are heritable changes in an organism’s genome involving alterations in the base sequence of DNA or RNA. These changes can influence cellular processes and phenotypic traits, potentially transforming the unaltered wild type into a mutant form. Such changes, termed forward mutations, are pivotal in shaping the genetic diversity of organisms.RNA viruses exhibit the highest mutation rates due to the absence of robust proofreading mechanisms during genome replication. In contrast,...
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:
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 23, 2026

A Novel Saturation Mutagenesis Approach: Single Step Characterization of Regulatory Protein Binding Sites in RNA Using Phosphorothioates
11:49

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Characterizing the role of ensemble modulation in mutation-induced changes in binding affinity.

Anthony Manson1, Steven T Whitten, Josephine C Ferreon

  • 1Department of Biochemistry and Molecular Biology, and Sealy Center for Structural Biology and Biophysics, University of Texas Medical Branch, Galveston, Texas 77555, USA.

Journal of the American Chemical Society
|April 29, 2009
PubMed
Summary

Protein conformational fluctuations are crucial for biological functions like molecular recognition. Our study shows that analyzing these dynamics, particularly in SH3 domains, accurately predicts binding energetics and reveals insights into protein-ligand interactions.

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Mutagenesis and Functional Analysis of Ion Channels Heterologously Expressed in Mammalian Cells

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Area of Science:

  • Protein dynamics
  • Molecular recognition
  • Biophysics

Background:

  • Protein conformational fluctuations are essential for biological processes.
  • Understanding these dynamics aids in comprehending enzyme catalysis, molecular recognition, and allosteric signaling.

Purpose of the Study:

  • To investigate the role of conformational fluctuations in substrate/ligand recognition.
  • To analyze the binding reaction between an SH3 domain and its partner peptide.

Main Methods:

  • Enumerated SH3 domain fluctuations using a hard sphere collision model algorithm.
  • Calculated binding energetics with a structure-based energy function.
  • Applied principal coordinate analysis to computed ensembles to characterize conformational variations.

Main Results:

  • A simple model accurately reproduced mutation effects on SH3 binding energetics.
  • Conformational fluctuations in SH3, especially the RT loop, are diverse and approximated by random states.
  • Differences in binding affinity between mutants correlate with changes in principal modes of conformational variation.

Conclusions:

  • Dynamic protein loops can access a wide range of conformational states.
  • A comprehensive understanding of molecular recognition necessitates considering the full distribution of protein states.
  • This approach provides quantitative insights into protein-ligand interactions.