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An Average Solvent Electrostatic Configuration Protocol for QM/MM Free Energy Optimization: Implementation and

Yoelvis Orozco-Gonzalez1,2,3, Madushanka Manathunga3, María Del Carmen Marín4

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A new computational method accurately predicts light absorption in rhodopsin proteins. This free energy gradient approach optimizes chromophore geometry, providing reliable predictions for various rhodopsin systems.

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Area of Science:

  • Computational chemistry
  • Biophysics
  • Structural biology

Background:

  • Rhodopsins are crucial light-sensitive proteins.
  • Accurate prediction of their spectral properties (λmax) is challenging.
  • Understanding chromophore-protein interactions is key.

Purpose of the Study:

  • To develop and validate a novel atomistic methodology for free energy geometry optimization.
  • To accurately compute absorption maxima wavelengths (λmax) for rhodopsin systems.
  • To provide a versatile protocol applicable to various protein-ligand complexes.

Main Methods:

  • Utilized Nagaoka's Free Energy Gradient (FEG) within an Average Solvent Electrostatic Configuration (ASEC).
  • Employed sequential classical Molecular Dynamics (MD) and constrained Quantum Mechanics/Molecular Mechanics (QM/MM) geometry optimization.
  • Benchmarked using CASPT2//CASSCF/Amber level calculations.

Main Results:

  • Successfully reproduced λmax values for human cellular retinol binding protein II (hCRBPII) mutants.
  • Accurately predicted λmax trends for diverse wild-type rhodopsins across different organisms.
  • Validated the protocol on eubacterial rhodopsin mutants, showing limited absolute errors.

Conclusions:

  • The ASEC-FEG protocol offers a robust method for optimizing chromophore geometry in proteins.
  • This approach accurately predicts spectral properties (λmax) for rhodopsin-like systems.
  • The methodology is readily extendable to other protein-ligand systems.