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| - Can Proteins and Crystals Self-Catalyze Methyl Rotations?
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| - The χ (Cα−Cβ) torsional barrier in the dipeptide alanine (N-methyl-l-alanyl-N-methylamide) crystal wasinvestigated using ab initio calculations at various levels of theory, molecular mechanics, and moleculardynamics. For one of the two molecules in the asymmetric unit the calculations suggest that rotation aroundthe χ dihedral angle is catalyzed by the crystal environment, reducing by up to ∼2kT the torsional barrier inthe crystal with respect to that in the gas phase. This catalytic effect is present at both low and room temperatureand originates from a van der Waals destabilization of the minima in the methyl dihedral potential comingfrom the nonbonded environment of the side chain. Screening of a subset of the Protein Data Bank with apharmacophore model reproducing the crystal environment around this side chain methyl identified a proteincontaining an alanine residue with an environment similar to that in the crystal. Calculations indicate that thisχ torsional barrier is also reduced in the protein at low temperature but not at room temperature. This suggeststhat environment-catalyzed rotation of methyl groups can occur both in the solid phase and in native biologicalstructures, though this effect might be temperature-dependent. The relevance of this catalytic effect is discussedin terms of its natural occurrence and its possible contribution to the low-frequency vibrational modes ofmolecules.
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