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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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Energy Diagrams, Transition States, and Intermediates02:13

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Free-energy diagrams, or reaction coordinate diagrams, are graphs showing the energy changes that occur during a chemical reaction. The reaction coordinate represented on the horizontal axis shows how far the reaction has progressed structurally. Positions along the x-axis close to the reactants have structures resembling the reactants, while positions close to the products resemble the products.  Peaks on the energy diagram represent stable structures with measurable lifetimes, while...
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Thermodynamics: Activity Coefficient01:24

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Activity is the measure of the effective concentration of the species in solution. It can be expressed as the product of the molar concentration of the species and its activity coefficient. The activity coefficient is a dimensionless quantity and depends on the total ionic strength of the solution.
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The free energy change for a reaction that occurs under the standard conditions of 1 bar pressure and at 298 K is called the standard free energy change. Since free energy is a state function, its value depends only on the conditions of the initial and final states of the system. A convenient and common approach to the calculation of free energy changes for physical and chemical reactions is by use of widely available compilations of standard state thermodynamic data. One method involves the...
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Free Energy Changes for Nonstandard States03:25

Free Energy Changes for Nonstandard States

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The free energy change for a process taking place with reactants and products present under nonstandard conditions (pressures other than 1 bar; concentrations other than 1 M) is related to the standard free energy change according to this equation:
 
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Calculating the Equilibrium Constant02:46

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The equilibrium constant for a reaction is calculated from the equilibrium concentrations (or pressures) of its reactants and products. If these concentrations are known, the calculation simply involves their substitution into the Kc expression.
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This study introduces a novel method for atomistic simulations to explore rare transitions between metastable states. The approach efficiently samples transition states, aiding in understanding complex molecular dynamics.

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Area of Science:

  • Computational Chemistry
  • Molecular Dynamics
  • Statistical Mechanics

Background:

  • Atomistic simulations face challenges in studying rare transitions between long-lived metastable states.
  • Understanding these transitions is crucial for various scientific disciplines.

Purpose of the Study:

  • To develop a method for exploring the transition state ensemble in atomistic simulations.
  • To provide a systematic approach for analyzing and interpreting simulation results.

Main Methods:

  • The proposed method utilizes the committor function and its variational principle.
  • A self-consistent procedure is employed to find the minimum, requiring only initial and final state information.
  • Efficient sampling of numerous transition state configurations is enabled from the outset.

Main Results:

  • The method allows for extensive sampling of transition state configurations.
  • A detailed analysis of the transition state ensemble is performed using the variational principle.
  • Degrees of freedom most involved in the transition are quantitatively ranked.

Conclusions:

  • The developed method facilitates a systematic interpretation of simulation data.
  • It enables the construction of efficient, physics-informed collective variables for future studies.
  • This approach enhances the study of kinetic bottlenecks in molecular systems.