Nuclear resonance vibrational spectroscopy of a protein active-site mimic

Abstract

For many years, Mössbauer spectroscopy has been applied to measure recoilless absorption of x-ray photons by nuclei. Recently, synchrotron radiation sources have enabled the observation of weaker features separated from the recoilless resonance by the energy of vibrational quanta. This enables a form of vibrational spectroscopy with a unique sensitivity to the probe nucleus. Biological applications are particularly promising, because it is possible to selectively probe vibrations of a single atom at the active site of a complex biomolecule, while avoiding interference from the vibrations of thousands of other atoms. In contrast with traditional site-selective vibrational spectroscopies, nuclear resonance vibrational spectroscopy (NRVS) is not hampered by solvent interference and faces selection rule limitations only if the probe nucleus lies on a symmetry element. Here, we formulate a mathematical language appropriate for understanding NRVS measurements on molecular systems and apply it to analyse NRVS data recorded on ferrous nitrosyl tetraphenylporphyrin, Fe(TPP)(NO). This compound mimics the haem group found at the active site of many proteins involved in the biological usage of oxygen and nitric oxide. Measurements on such model compounds provide a baseline for evaluating the extent to which vibrations are localized at the active site of a protein, with the goal of elucidating the mechanisms of biological processes, such as intersite communication in allosteric proteins.

Vibrational dynamics of biological molecules: Multi-quantum contributions

“…1. In the harmonic approximation, these transitions dominate S (v) at low temperature and contribute a series of peaks, located at each of the normal mode frequencies v̄α, with areas [16] ϕ α = ( n α + 1 ) f ( ν R ν α ) ( k ⋅ e jα ) 2 (1) proportional to the mean squared displacement of the probe nucleus j along the direction k̂ of the X-ray beam. Here, n̄α = [exp(hcv̄α/k B T )1] -1 is the mean occupation number for mode α-at temperature T , and v̄R = 15.8 cm -1 is the recoil energy of 57 Fe nucleus at 14.4 keV.…”

“…The contributions of the first overtone (n α → n α +2), at energy 2v̄α, and combination (n α n α +1), (n β n β +1), at energy v̄α +v̄ , to→ → ν α + ν β , the total spectral area are given by [16] ϕ αα = 9 10 ϕ α 2 ∕ f (4) ϕ αβ = 3 5 ( ϕ α ϕ β ∕ f )( 1 + 2 cos 2 ξ αβ ) , (5) respectively, where ξ αβ is the angle between the Fe displacements in modes α and β.…”

“…5) [16]. An interesting consequence is that unresolved vibrational structure can affect the area of two-quantum features.…”

“…NRVS achieves the ultimate goal in selectivity, by targeting a single atom in a complex molecule. This method is particularly promising for characterizing the vibrational dynamics of 57 Fe in biological macromolecules [11,15,21,22,[25][26][27], and in small molecules designed to model protein active sites [16,19,20,24,28].…”

Condensed Matter Physics Using Nuclear Resonant Scattering

“…[93][94][95][96][97][98][99][100][101][102][103][104][105] This provides the opportunity to study the ligation and oxidation state of a specific site. The high brilliance of SR allows us to measure the PDOS even for small samples, i.e., measurements under extreme conditions in which the accessible sample space is severely limited are possible.…”