Direct Evidence of the Amino Acid Side Chain and Backbone Contributions to Protein Anharmonicity

Abstract

Elastic incoherent neutron scattering has been used to study the temperature dependence of the mean-square displacements of nonexchangeable hydrogen atoms in powders of a series of homomeric polypeptides (polyglycine, polyalanine, polyphenylalanine and polyisoleucine) in comparison with myoglobin at the same hydration level (h = 0.2). The aim of the work was to measure the dynamic behavior of different amino acid residues separately and assess the contribution of each type of side chain to the anharmonic dynamics of proteins. The results provide direct experimental evidence that the first anharmonic activation, at approximately 150 K, is largely due to methyl group rotations entering the time window of the spectrometer used; however, contributions on the order of 10-20% from the motions of other groups (e.g., the phenolic ring and the methylene groups) are present. Our data also indicate that the dynamical transition occurring at approximately 230 K can be attributed, at least at the hydration level investigated, mainly to motions involving backbone fluctuations.

The “Protein Dynamical Transition” Does Not Require the Protein Polypeptide Chain

“…For the msd related to the dynamical transition, these contributions amount to about 0.04 Å 2 at room temperature, in good agreement with what is measured for polyglycine. 8 However, it should be considered that differences between the Mb and aa-m samples related to the side-chains environment, the amount of surface covered by water, the extent of polar/apolar interactions, and the presence of "free" carboxylic and amino groups, could also influence the amplitude of fluctuations. In order to further investigate the role of the polypeptide chain on protein dynamics, we performed inelastic incoherent neutron scattering experiments at a time-of-flight spectrometer with a resolution of 70 μeV fwhm.…”

Physical Origin of Anharmonic Dynamics in Proteins: New Insights From Resolution-Dependent Neutron Scattering on Homomeric Polypeptides

“…We study poly-glycine (poly-G) and poly-alanine (poly-A) in the dry state (where PDT does not occur) and at a hydration level (h ¼ 0:2 g D 2 O=g HP) low enough to get a signal attributable to protein nonexchangeable H atoms with a negligible D 2 O contribution [15], but high enough to allow the PDT. We have recently shown that hydrated poly-G undergoes only the PDT (no CH 3 are present) while dry poly-A shows only the MGA [3,4]: in this way we are able to study the resolution dependence of the two transitions, separately, avoiding their superposition. The MSD temperature dependence of these systems is compared to that of a representative globular protein, bovine serum albumin (BSA).…”

“…Molecular origin, physical nature and biological relevance of these ''transitions'' are still matter of discussion. The first one is attributed mainly to thermally activated motions of CH 3 methyl groups [1,[3][4][5][6] (for this reason hereon called methyl groups activation, MGA). The second one, called ''protein dynamical transition'' (PDT), has been first interpreted as a glasslike transition [2] directly correlated to the onset of biological activity [7], but this view has been later challenged.…”

“…week ending 21 SEPTEMBER 2012 protein dynamics observed with EINS [3,4]; this overcomes the problem posed by the intrinsic heterogeneity of proteins since it allows us to probe the dynamical behavior of each type of residue separately without neglecting the polymeric nature. We study poly-glycine (poly-G) and poly-alanine (poly-A) in the dry state (where PDT does not occur) and at a hydration level (h ¼ 0:2 g D 2 O=g HP) low enough to get a signal attributable to protein nonexchangeable H atoms with a negligible D 2 O contribution [15], but high enough to allow the PDT.…”

Dynamical properties of myoglobin in an ultraviscous water-glycerol solvent investigated with elastic neutron scattering and FTIR spectroscopy

“…As the temperature increases, new contributions to the dynamics can be triggered. Firstly, the activation of methyl group rotations can be observed [15,16], at temperature values varying from~100 to~180 K, depending on the experimental time resolution [7]. Further increasing the temperature, protein molecules start to fluctuate among different conformational substates, and these fluctuations bring about a steep increase in all measured dynamical properties of the system.…”