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Methyl•••Methyl Interactions in Proteins: Insights from Structural and Computational Studies.

Juhi Dutta1,2, Akshay Kumar Sahu1,2, Subhrakant Jena1,2

  • 1School of Chemical Sciences, National Institute of Science Education and Research (NISER), PO- Bhimpur-Padanpur, Via-Jatni, District- Khurda, Bhubaneswar PIN 752050, India.

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Methyl-methyl interactions in proteins are weak, driven by dispersion forces. These hydrophobic interactions are crucial for protein flexibility and drug interactions, with potential spectroscopic detection methods explored.

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Area of Science:

  • Supramolecular Chemistry
  • Biophysics
  • Computational Chemistry

Background:

  • Hydrophobic interactions, arising from the low affinity of nonpolar groups for water, are significant supramolecular forces.
  • London dispersion forces are well-established contributors to the stabilization of nonpolar complexes.
  • The precise origins of hydrophobic phenomena continue to be a subject of scientific debate.

Purpose of the Study:

  • To comprehensively investigate the nature and strength of methyl-methyl (CH3•••H3C) interactions within protein amino acid residues.
  • To elucidate the contributions of different forces to these interactions.
  • To explore potential experimental methods for characterizing these weak interactions.

Main Methods:

  • Utilized quantum mechanical calculations to analyze isolated mimetic dipeptide models.
  • Developed and employed custom Python code for data analysis.
  • Considered spectroscopic techniques like solution-phase 13C NMR and gas-phase terahertz (THz) spectroscopy.

Main Results:

  • Methyl-methyl interactions were found to be weak, with interaction energies ranging from -2.40 to -6.94 kJ/mol.
  • These interactions are primarily driven by dispersion forces, with a minor electrostatic contribution.
  • The cumulative effect of these weak interactions is vital for protein structure and function.

Conclusions:

  • Despite their individual weakness, CH3•••H3C interactions play a vital role in the flexibility of enzymatic centers and drug-protein interactions.
  • Experimental characterization of these weak interactions is challenging but feasible.
  • Solution-phase 13C NMR and gas-phase THz spectroscopy show promise for detecting and quantifying CH3•••H3C interactions.