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

Abstract

Neutron scattering reveals a complex dynamics in polypeptide chains, with two main onsets of anharmonicity whose physical origin and biological role are still debated. In this study the dynamics of strategically selected homomeric polypeptides is investigated with elastic neutron scattering using different energy resolutions and compared with that of a real protein. Our data spotlight the dependence of anharmonic transition temperatures and fluctuation amplitudes on energy resolution, which we quantitatively explain in terms of a two-site model for the protein-hydration water energy landscape. Experimental data strongly suggest that the protein dynamical transition is not a mere resolution effect but is due to a real physical effect. Activation barriers and free energy values obtained for the protein dynamical transition allow us to make a connection with the two-well interaction potential of supercooledconfined water proposed to explain a low-density ! high-density liquid-liquid transition. DOI: 10.1103/PhysRevLett.109.128102 PACS numbers: 87.14.ef, 83.85.Hf, 87.15.HÀ Neutron scattering is a powerful technique to study protein dynamics and energetics. The structure factor SðE ¼ 0; Q; TÞ of elastic incoherent neutron scattering (EINS) is related to the time-position self correlation function of protein-solvent nuclei that, in turn, is related to the energy landscape of the system whose different tiers can be explored by the temperature dependence of the EINS signal. In particular, EINS on D 2 O-hydrated protein powders, which probes the mean square displacements (MSDs) of protein nonexchangeable H atoms, reveals two deviations from harmonic dynamics, at $100-150 K and at $220 K [1,2]. 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. Several interpretations of the PDT have been proposed: (i) a change in the protein structural flexibility in response to the glass transition of hydration water [8]; (ii) a result of the protein structural relaxation reaching the limit of the experimental frequency window [9][10][11]; (iii) the protein response to a fragile-to-strong dynamic crossover in the hydration water at 220 K where water structure makes a low density liquid ðLDLÞ ! high density liquid (HDL) transition [12]; (iv) a change in the thermodynamic resilience of the waterprotein system [13]. These models propose physical pictures partially alternative, demonstrating that the question has not been definitively settled yet: (i) and (ii) ascribe the PDT to a temperature dependent relaxation time crossing the instrumental time-scale; (iii) and (iv) interpret the PDT as ...

Hydration-dependent dynamic crossover phenomenon in protein hydration water

“…[12] is due to numerical errors in the data analysis protocol and can be ruled out with an improved analysis method. Magazù et al [16] and Schirò et al [19] draw opposite conclusions on the role that the dynamic crossover plays in the onset of the PDT with resolution-dependent neutron scattering experiments. Swenson et al [14], Pawlus et al [15], and Fenimore et al [18] propose that the appearance of the dynamic crossover in the hydration water is due to the existences of two different relaxation processes, the structural relaxation and a secondary relaxation, rather than a qualitative * Corresponding author: sowhsin@mit.edu change from an Arrhenius behavior to a super-Arrhenius behavior of the structural relaxation time.…”

“…This conjecture is under debate [16,19,27,28]. It is well known that most of proteins only function with sufficient hydration water.…”

“…This phenomenon is of particular interest, partially because (i) the crossover temperature T X of the hydration water is close to the transition temperature of the so-called protein dynamic transition (PDT) [13] T D and thus it is conjectured that the PDT is induced by the dynamic crossover of the hydration water [12] and (ii) this crossover is interpreted as an anomalous feature of the structural relaxation of the hydration water and is ascribed to the existence of the high-density liquid and low-density liquid phases in the supercooled water [12]. To date, this phenomenon and its physical implications are still largely debated [14][15][16][17][18][19]. Doster et al [17] state that the crossover observed in Ref.…”

Dynamical and orientational structural crossovers in low-temperature glycerol

“…1 is a mere coincidence, it is hard to see how it can be preserved at t r = 135 ps. One has to accept the conclusion that the kink in the MSD is not related to the observation window [32,41] and, instead, should be attributed to the softening of the liquid cage, with increasing temperature, in which a glycerol molecule finds itself for a relatively short time of ∼ 1 ps. The rattling inside the cage is followed by an escape and the onset of long-range diffusion, but this component simply adds to the main displacement achieved by the ballistic cage rattling.…”

“…(2) disappears and one gets an estimate of the mean square fluctuation (MSF) (δx) 2 from the linear slope of − ln(I(q, t r )) vs q 2 [29,32]. Otherwise one obtains half of the MSD (1/2) ∆x(t r ) 2 from the slope of − ln(I(q, t r )) vs q 2 .…”