Water-coupled low-frequency modes of myoglobin and lysozyme observed by inelastic neutron scattering

Abstract

Conformational changes of proteins often involve the relative motion of rigid structural domains. Normal mode analysis and molecular dynamics simulations of small globular proteins predict delocalized vibrations with frequencies below 20 cm(-1), which may be overdamped in solution due to solvent friction. In search of these modes, we have studied deuterium-exchanged myoglobin and lysozyme using inelastic neutron scattering in the low-frequency range at full and low hydration to modify the degree of damping. At room temperature, the hydrated samples exhibit a more pronounced quasielastic spectrum due to diffusive motions than the dehydrated samples. The analysis of the corresponding lineshapes suggests that water modifies mainly the amplitude, but not the characteristic time of fast protein motions. At low temperatures, in contrast, the dehydrated samples exhibit larger motional amplitudes than the hydrated ones. The excess scattering, culminating at 16 cm(-1), is suggested to reflect water-coupled librations of polar side chains that are depressed in the hydrated system by strong intermolecular hydrogen bonding. Both myoglobin and lysozyme exhibit ultra-low-frequency modes below 10 cm(-1) in the dry state, possibly related to the breathing modes predicted by harmonic analysis.

Solvent dependence of dynamic transitions in protein solutions

“…Rayleigh scattering of Möss-bauer radiation demonstrated an increase of dynamic amplitudes on hydration of myoglobin (28). This increase was also found in subsequent neutron work on lysozyme powders (29), and qualitatively similar results have been found in more recent neutron work on parvalbumin, lysozyme, myoglobin, and the bovine pancreatic trypsin inhibitor (23,(30)(31)(32)(33).It is clear from the above and other work that solvent affects protein dynamics at physiological temperatures. Therefore, a solvent dependence of the dynamic transition might be expected.…”

Excited-State Lifetimes of Far-Infrared Collective Modes in Proteins

“…Normal mode dynam-ics and relaxation calculations by Levitt et al [21] found that the low frequency collective modes where not strongly damped by the solvent because the amplitude of the modes was only 0.3 Å, less than the diameter of a water molecule and making macroscopic based hydrodynamic approximations questionable, while Go et al [22] found that the modes basically damped within one period of oscillation, that is, at the transform limited discussed above. The only experimental tests we have found concerning normal mode lifetimes comes from the work of Doerster et al, from studies of FIR emission of proteins when optically excited at optical wavelengths [24] and elastic scattering of neutrons from the collective boson peak seen below 100 cm −1 [25]. Figure 1 was an attempt to show how vibrational excitation of the reactive vibrational mode is a basic requisite for structural transition in a molecule (such as proteins) and its relation with transition rate.…”

Boson peak as a probe of quantum effects in a glassy state of biomolecules: The case of L-cysteine

“…Moreover, the damped librational character of a side-chain oscillations at low frequencies of proteins had been well described in the literature. [11,22,23] Thus one could argue that a damped harmonic oscillator model is a suitable way to express the inelastic light scattering related to the BP ,…”