Protein Flexibility and Conformational State: A Comparison of Collective Vibrational Modes of Wild-Type and D96N Bacteriorhodopsin

Abstract

Far infrared (FIR) spectral measurements of wild-type (WT) and D96N mutant bacteriorhodopsin thin films have been carried out using terahertz time domain spectroscopy as a function of hydration, temperature, and conformational state. The results are compared to calculated spectra generated via normal mode analyses using CHARMM. We find that the FIR absorbance is slowly increasing with frequency and without strong narrow features over the range of 2-60 cm(-1) and up to a resolution of 0.17 cm(-1). The broad absorption shifts in frequency with decreasing temperature as expected with a strongly anharmonic potential and in agreement with neutron inelastic scattering results. Decreasing hydration shifts the absorption to higher frequencies, possibly resulting from decreased coupling mediated by the interior water molecules. Ground-state FIR absorbances have nearly identical frequency dependence, with the mutant having less optical density than the WT. In the M state, the FIR absorbance of the WT increases whereas there is no change for D96N. These results represent the first measurement of FIR absorbance change as a function of conformational state.

Solute-induced retardation of water dynamics probed directly by terahertz spectroscopy

“…This calculation, which is carried out in terms of the vibrational modes of solvated lactose, is similar to that of Whitmire et al (45), who computed the low-temperature absorption spectrum of dehydrated bacteriorhodopsin in the terahertz region. In Fig.…”

“…Calculations of the normal modes were carried out with MOIL (53). In terms of the normal modes, the IR absorbance for a transition in mode ␣, with n␣ vibrational quanta to n ␣ ϩ 1 vibrational quanta can be estimated in terms of the mode-specific dipole derivative (45,58). We take the charges on the atoms to be fixed.…”

Ultra-sensitive detection of protein thermal unfolding and refolding using near-zone microwaves

“…5). A fixed number of peaks (7)(8)(9)(10)(11) were used to fit all return-loss scans in an unfolding/refolding series.…”

“…1) Experiments are performed on dry, but "hydrated" samples [3], [7], yielding results that may not be applicable to biomolecules in solution. 2) Results are qualitative rather than quantitative, i.e., a phenomenon is demonstrated, but its extent is not, or cannot, be further quantified [4].…”

Terahertz time-domain spectroscopy and imaging of artificial RNA

“…In the recent years there has been considerable interest in application of the terahertz frequency range (0.1 -5 THz) for detection and characterization of biological material, with emphasis on interaction between electromagnetic radiation and biological material [1,2,3], stand-off detection of biological warfare agents [4], analysis of low-frequency vibrations in RNA-and DNA strands [5,6] and proteins [9,10], as well as detection of skin cancer by THz imaging [7]. The interaction mechanism leading to absorption in the THz frequency range in biological material is still under debate, but it seems clear that intramolecular as well as intermolecular interactions mediated via hydrogen bonds and weak interactions such as van der Waals forces play an important role.…”