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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.
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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...
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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...
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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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Crystal Field Theory
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In complexation reactions, metal atoms or cations interact with ligands to form donor-acceptor adducts called metal complexes. Ligands that bind through one donor site are monodentate, ligands with two donor sites are bidentate, and those with more than two donor sites are polydentate ligands. For example, ethylene diamine is a bidentate ligand that binds through two nitrogen donor atoms, forming a five-membered ring. EDTA is a polydentate ligand that binds through four oxygen and two nitrogen...
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Anisotropic Friction in a Ligand-Protein Complex.

Wanhao Cai1, Miriam Jäger2, Jakob T Bullerjahn3

  • 1Institute of Physical Chemistry, University of Freiburg, Albertstr. 21, 79104 Freiburg, Germany.

Nano Letters
|March 22, 2023
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Summary

Researchers discovered a new type of molecular friction called anisotropic friction. This friction affects how strongly molecules like biotin-streptavidin bind, changing based on the direction of applied force.

Keywords:
atomic force microscopyfrictionligand-protein complexsingle moleculesteered molecular dynamics simulationtargeted molecular dynamics simulation

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Area of Science:

  • Biophysics
  • Molecular Dynamics
  • Surface Science

Background:

  • The influence of external directional forces on molecular friction remains largely unexplored.
  • Understanding molecular friction is crucial for biomolecular dynamics and interactions.

Purpose of the Study:

  • To investigate the force-driven dissociation of the biotin-streptavidin complex.
  • To identify and characterize a novel type of molecular friction: anisotropic friction.

Main Methods:

  • Atomic Force Microscopy (AFM)-based stereographic single-molecule force spectroscopy.
  • Targeted molecular dynamics simulations, including dissipation-corrected simulations based on Jarzynski's identity.
  • Analysis using Kramers' rate expression.

Main Results:

  • Identified anisotropic friction in the biotin-streptavidin complex, where friction and rupture force depend on the pulling angle.
  • Ruled out ligand solvation and protein-internal friction as causes for angle-dependent friction.
  • Observed free energy barrier heterogeneity along an orientation parameter, contributing to increased friction.

Conclusions:

  • Anisotropic friction is a previously undescribed phenomenon in molecular systems.
  • The heterogeneity of free energy barriers is a key factor driving anisotropic friction.
  • Anisotropic friction must be considered for a comprehensive understanding of biomolecular interactions and mechanical environments.