Dynamic structure factor of vibrating fractals: Proteins as a case study

Abstract

We study the dynamic structure factor S(k,t) of proteins at large wave numbers k, kR(g)≫1, where R(g) is the gyration radius. At this regime measurements are sensitive to internal dynamics, and we focus on vibrational dynamics of folded proteins. Exploiting the analogy between proteins and fractals, we perform a general analytic calculation of the displacement two-point correlation functions, <[u(−>)(i)(t)-u(−>)(j)(0)](2)>. We confront the derived expressions with numerical evaluations that are based on protein data bank (PDB) structures and the Gaussian network model (GNM) for a few proteins and for the Sierpinski gasket as a controlled check. We use these calculations to evaluate S(k,t) with arrested rotational and translational degrees of freedom, and show that the decay of S(k,t) is dominated by the spatially averaged mean-square displacement of an amino acid. The latter has been previously shown to evolve subdiffusively in time, <[u(−>)(i)(t)-u(−>)(i)(0)](2)> ~t(ν), where ν is the anomalous diffusion exponent that depends on the spectral dimension d(s) and fractal dimension d(f). As a result, for wave numbers obeying k(2)<u(−>)(2)>≳1, S(k,t) effectively decays as a stretched exponential S(k,t)≃S(k)e(-(Γ(k)t)(β)) with β≃ν, where the relaxation rate is Γ(k)~(k(B)T/mω(o)(2))(1/β)k(2/β), T is the temperature, and mω(o)(2) the GNM effective spring constant describing the interaction between neighboring amino acids. The static structure factor is dominated by the fractal character of the native fold, S(k)~k(-d(f)), with negligible to marginal influence of vibrations. The analytical expressions are first confronted with numerically based calculations on the Sierpinski gasket, and very good agreement is found between simulations and theory. We then perform PDB-GNM-based numerical calculations for a few proteins, and an effective stretched exponential decay of the dynamic structure factor is found, albeit their relatively small size. However, when rotational and translational diffusion are added, we find that their contribution is never negligible due to finite size effects. While we can still attribute an effective stretching exponent β to the relaxation profile, this exponent is significantly larger than the anomalous diffusion exponent ν. We compare our theory with recent neutron spin-echo studies of myoglobin and hemoglobin and conclude that experiments in which the rotational and translational degrees of freedom are arrested, e.g., by anchoring the proteins to a surface, will improve the detection of internal vibrational dynamics.