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Related Concept Videos

Cooperative Allosteric Transitions01:58

Cooperative Allosteric Transitions

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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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Communication01:03

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Communication between two animals occurs when one animal transmits an information signal that causes a change in the animal that receives the information. Organisms communicate with one another in a host of different ways. Signals can be auditory, chemical, visual, tactile, or a combination of these. Communication is a critical behavioral adaptation that promotes survival, growth, and reproduction.
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Dynamic Equilibrium02:20

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A reversible chemical reaction represents a chemical process that proceeds in both forward (left to right) and reverse (right to left) directions. When the rates of the forward and reverse reactions are equal, the concentrations of the reactant and product species remain constant over time and the system is at equilibrium. A special double arrow is used to emphasize the reversible nature of the reaction. The relative concentrations of reactants and products in equilibrium systems vary greatly;...
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The free energy change for a process may be viewed as a measure of its driving force. A negative value for ΔG represents a driving force for the process in the forward direction, while a positive value represents a driving force for the process in the reverse direction. When ΔGrxn is zero, the forward and reverse driving forces are equal, and the process occurs in both directions at the same rate (the system is at equilibrium).
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Equilibrium calculations for systems involving multiple equilibria are often complex. For example, to calculate the solubility of a sparingly soluble salt in an aqueous solution in the presence of a common ion, one must consider all the equilibria in this solution. Calculations for these systems can be complicated and tedious, so a systematic approach with a series of steps is often helpful. The process is detailed below.
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Spatiotemporal Control of Protein Activity through Optogenetic Allosteric Regulation
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A non-equilibrium approach to allosteric communication.

Gerhard Stock1, Peter Hamm2

  • 1Biomolecular Dynamics, Institute of Physics, Albert Ludwigs University, Freiburg, Germany stock@physik.uni-freiburg.de.

Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
|May 9, 2018
PubMed
Summary

Allosteric transitions in proteins are dynamic processes that share similarities with protein folding but are order-order transitions. Non-equilibrium experiments and simulations offer a promising approach to study these dynamics.

Keywords:
allosteric transitiondownhill foldingdynamic contentfree-energy landscapenon-equilibrium molecular dynamics simulationstime-resolved vibrational spectroscopy

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Area of Science:

  • Biophysics
  • Structural Biology
  • Computational Biology

Background:

  • Protein folding dynamics are well-understood, but allosteric transition dynamics remain challenging to describe.
  • Small structural changes and experimental difficulties hinder direct observation of allosteric transitions.

Purpose of the Study:

  • To outline a description for the dynamics of allosteric communication in proteins.
  • To investigate the dynamical features of allosteric transitions using a model system.

Main Methods:

  • Utilized pump-probe experiments and non-equilibrium molecular dynamics simulations.
  • Studied a photoswitchable PDZ2 domain as a model for allosteric transitions.
  • Calculated the dynamical content of both experimental and simulation data.

Main Results:

  • Allosteric communication exhibits properties similar to downhill protein folding.
  • The transition was characterized as an 'order-order' process.
  • Experimental and simulation data showed remarkable agreement.

Conclusions:

  • Non-equilibrium experiments and simulations are effective for studying allosteric dynamics.
  • Allosteric communication involves multiscale and hierarchical dynamics.
  • The study provides insights into the nature of 'allosteric pathways'.