Effect of protein packing structure on side-chain methyl rotor conformations

Abstract

Protein molecules undergo a series of conformational fluctuations ranging in degree from atomic vibrations to transient denaturation, even in physiological conditions^1,2. The rotational motions of amino acid side chains form an important subset of the types of fluctuation a protein can undergo. NMR^3–7 and molecular dynamics^8–10 have shown that methyl groups in proteins are not held in fixed positions, but spin rapidly around their rotor axes. The question then arises as to whether methyl groups in proteins predominantly adopt the ‘staggered’ conformation, favoured by the intrinsic barrier to rotation of these groups, or whether cooperative packing effects in the folded protein perturb the average configurations to higher torsional energy. We report here an investigation of the rotational conformations of the methyl groups of aliphatic side chains in the protein crambin by neutron diffraction. We find that in the time-averaged structure of this protein, the majority of methyl rotors adopt the staggered conformation. This is consistent with rotation being a quantized event consisting of rapid reorientations of ∼120° steps to positions of highest stability. The fact that the local environment does not dictate the low energy state of methyl groups suggests that within the seemingly close-packed interior structure of a protein, mutual packing accommodation occurs as a consequence of the inherent flexibility and small packing defects in protein structures.