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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...
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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 polypeptide...
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Protein Complex Assembly

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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.
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Analyzing Protein Architectures and Protein-Ligand Complexes by Integrative Structural Mass Spectrometry
07:33

Analyzing Protein Architectures and Protein-Ligand Complexes by Integrative Structural Mass Spectrometry

Published on: October 15, 2018

Modeling protein association mechanisms and kinetics.

Huan-Xiang Zhou1, Paul A Bates

  • 1Department of Physics and Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA.

Current Opinion in Structural Biology
|July 16, 2013
PubMed
Summary

Researchers have advanced protein association modeling, understanding physical factors affecting association rate constants (ka). New methods are emerging for calculating ka, especially for disordered proteins and in cellular environments.

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Area of Science:

  • Biochemistry
  • Computational Biology
  • Structural Biology

Background:

  • Protein association is fundamental to cellular functions.
  • Calculating association rate constants (ka) is crucial for understanding protein interactions.
  • Previous models have limitations in explaining the full spectrum of ka values.

Purpose of the Study:

  • To review advances in modeling protein association mechanisms.
  • To discuss methods for calculating association rate constants (ka).
  • To highlight progress in understanding protein binding kinetics in cellular contexts.

Main Methods:

  • Review of computational methods for protein association modeling.
  • Analysis of physical factors influencing association rate constants (ka).
  • Discussion of emerging techniques for ka calculations, including for disordered proteins.

Main Results:

  • Significant progress in understanding diffusion-limited association.
  • Development of promising methods for rate-limiting conformational changes.
  • Emergence of the 'dock-and-coalesce' mechanism for disordered proteins.
  • Advancements in modeling protein association in crowded cellular environments.

Conclusions:

  • A clearer understanding of physical factors governing protein association rate constants (ka).
  • The diffusion-limited half of the association problem is largely solved.
  • Promising methods are being developed for the conformational change-limited half.
  • Modeling protein association in cellular environments is advancing, aiding understanding of cellular functions.