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One of the challenges of using the second law of thermodynamics to determine if a process is spontaneous is that it requires measurements of the entropy change for the system and the entropy change for the surroundings. An alternative approach involving a new thermodynamic property defined in terms of system properties only was introduced in the late nineteenth century by American mathematician Josiah Willard Gibbs. This new property is called the Gibbs free energy (G) (or simply the free...
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The spontaneity of a process depends upon the temperature of the system. Phase transitions, for example, will proceed spontaneously in one direction or the other depending upon the temperature of the substance in question. Likewise, some chemical reactions can also exhibit temperature-dependent spontaneities. To illustrate this concept, the equation relating free energy change to the enthalpy and entropy changes for the process is considered:
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Thermodynamic potentials are state functions that are extremely useful in analyzing a thermodynamic system. They have dimensions of energy. The four important thermodynamic potentials are internal energy, enthalpy, Helmholtz free energy, and Gibbs free energy. These thermodynamic potentials can be expressed using two of the following variables: pressure, volume, temperature, and entropy. These two variables are expressed as the rate of change of the thermodynamic potential with respect to other...
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The effective concentration of a species in a solution can be expressed precisely in terms of its activity. Activity considers the effect of electrolytes present in the vicinity of the species of interest and depends on the ionic strength of the solution. The activity of a species is expressed as the product of molar concentration and the activity coefficient of the species.
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A Transferable and Robust Computational Framework for Class A GPCR Activation Free Energies.

Simone Aureli1,2,3, Nicola Piasentin1,2, Thorben Fröhlking1,2,3

  • 1School of Pharmaceutical Sciences, University of Geneva, Rue Michel-Servet 1, CH-1206 Geneva, CH, Switzerland.

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Researchers developed a streamlined method to simulate G-protein coupled receptor (GPCR) activation. This approach simplifies defining collective variables (CVs) for molecular simulations, enabling robust free energy calculations and uncovering new insights into receptor activation mechanisms.

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Area of Science:

  • Biochemistry
  • Computational Biology
  • Pharmacology

Background:

  • G-protein coupled receptors (GPCRs) mediate crucial cellular functions, but simulating their activation is complex due to required local and global motion capture.
  • Previous methods for GPCR activation simulation, while successful for specific receptors like β1-adrenergic receptor (ADRB1), demanded extensive and error-prone collective variable (CV) refinement.

Purpose of the Study:

  • To introduce a streamlined and user-friendly strategy for defining CVs in molecular simulations of GPCR activation.
  • To reduce user intervention in the CV selection and refinement process while ensuring robust free energy convergence.
  • To apply the new method to pharmacologically relevant apo-GPCRs, specifically ADRB1 and the μ-opioid receptor.

Main Methods:

  • Developed an evolved strategy for defining collective variables (CVs) that minimizes user input.
  • Applied the enhanced CV definition strategy to molecular simulations of ADRB1 and the μ-opioid receptor.
  • Utilized a multiple replica enhanced sampling approach combined with the new CV strategy.

Main Results:

  • The new method successfully reconstructed free energies for ADRB1 activation, consistent with previous tailored approaches.
  • Novel biological insights into the activation mechanism of the μ-opioid receptor were obtained.
  • The strategy demonstrated robustness in achieving free energy convergence for both studied receptors.

Conclusions:

  • The proposed streamlined CV definition strategy is effective for simulating GPCR activation.
  • This method significantly reduces the complexity and potential for error in preparing molecular simulations of GPCRs.
  • The approach is readily applicable to other class A GPCRs, facilitating systematic studies of drug target activation mechanisms.