Dynamics in globular proteins: vibrational echo experiments

Influence of histidine tag attachment on picosecond protein dynamics

Polyhistidine affinity tags are routinely employed as a convenient means of purifying recombinantly expressed proteins. A tacit assumption is commonly made that His tags have little influence on protein structure and function. Attachment of a His tag to the N-terminus of the robust globular protein myoglobin leads to only minor changes to the electrostatic environment of the heme pocket, as evinced by the nearly unchanged Fourier transform infrared spectrum of CO bound to the heme of His-tagged myoglobin. Experiments employing two-dimensional infrared vibrational echo spectroscopy of the heme-bound CO, however, find that significant changes occur to the short time scale (picoseconds) dynamics of myoglobin as a result of His tag incorporation. The His tag mainly reduces the dynamics on the 1.4 ps time scale and also alters protein motions of myoglobin on the slower, >100 ps time scale, as demonstrated by the His tag's influence on the fluctuations of the CO vibrational frequency, which reports on protein structural dynamics. The results suggest that affinity tags may have effects on protein function and indicate that investigators of affinity-tagged proteins should take this into consideration when investigating the dynamics and other properties of such proteins.

Exploring the molecular origins of protein dynamics in the active site of human carbonic anhydrase II

We present three-pulse vibrational echo measurements of azide ion bound to the active site Zn of human carbonic anhydrase II (HCA II) and of two separate active-site mutants Thr199 --> Ala (T199A) and Leu198 --> Phe (L198F). Because structural motions of the protein active site influence the frequency of bound ligands, the differences in the time scales of the frequency-frequency correlation functions (FFCFs) obtained from global fits to each set of data allow us to make inferences about the time scales of the active site dynamics of HCA II. Surprisingly, the deletion of a potential electrostatic interaction in results in very little change in the FFCF, but the insertion of the bulky phenylalanine ring in causes much faster dynamics. We conclude that the fast, sub-picosecond time scale in the correlation function is attributable to hydrogen bond dynamics, and the slow, apparently static contribution is due to the conformational flexibility of Zn-bound azide in the active site.

Viscosity-dependent protein dynamics

Spectrally resolved stimulated vibrational echo spectroscopy is used to investigate the dependence of fast protein dynamics on bulk solution viscosity at room temperature in four heme proteins: hemoglobin, myoglobin, a myoglobin mutant with the distal histidine replaced by a valine (H64V), and a cytochrome c552 mutant with the distal methionine replaced by an alanine (M61A). Fructose is added to increase the viscosity of the aqueous protein solutions over many orders of magnitude. The fast dynamics of the four globular proteins were found to be sensitive to solution viscosity and asymptotically approached the dynamical behavior that was previously observed in room temperature sugar glasses. The viscosity-dependent protein dynamics are analyzed in the context of a viscoelastic relaxation model that treats the protein as a deformable breathing sphere. The viscoelastic model is in qualitative agreement with the experimental data but does not capture sufficient system detail to offer a quantitative description of the underlying fluctuation amplitudes and relaxation rates. A calibration method based on the near-infrared spectrum of water overtones was constructed to accurately determine the viscosity of small volumes of protein solutions.

Ultrafast dynamics of myoglobin without the distal histidine: stimulated vibrational echo experiments and molecular dynamics simulations

Ultrafast protein dynamics of the CO adduct of a myoglobin mutant with the polar distal histidine replaced by a nonpolar valine (H64V) have been investigated by spectrally resolved infrared stimulated vibrational echo experiments and molecular dynamics (MD) simulations. In aqueous solution at room temperature, the vibrational dephasing rate of CO in the mutant is reduced by approximately 50% relative to the native protein. This finding confirms that the dephasing of the CO vibration in the native protein is sensitive to the interaction between the ligand and the distal histidine. The stimulated vibrational echo observable is calculated from MD simulations of H64V within a model in which vibrational dephasing is driven by electrostatic forces. In agreement with experiment, calculated vibrational echoes show slower dephasing for the mutant than for the native protein. However, vibrational echoes calculated for H64V do not show the quantitative agreement with measurements demonstrated previously for the native protein.

Dynamics of proteins encapsulated in silica sol-gel glasses studied with IR vibrational echo spectroscopy

Spectrally resolved infrared stimulated vibrational echo spectroscopy is used to measure the fast dynamics of heme-bound CO in carbonmonoxy-myoglobin (MbCO) and -hemoglobin (HbCO) embedded in silica sol-gel glasses. On the time scale of approximately 100 fs to several picoseconds, the vibrational dephasing of the heme-bound CO is measurably slower for both MbCO and HbCO relative to that of aqueous protein solutions. The fast structural dynamics of MbCO, as sensed by the heme-bound CO, are influenced more by the sol-gel environment than those of HbCO. Longer time scale structural dynamics (tens of picoseconds), as measured by the extent of spectral diffusion, are the same for both proteins encapsulated in sol-gel glasses compared to that in aqueous solutions. A comparison of the sol-gel experimental results to viscosity-dependent vibrational echo data taken on various mixtures of water and fructose shows that the sol-gel-encapsulated MbCO exhibits dynamics that are the equivalent of the protein in a solution that is nearly 20 times more viscous than bulk water. In contrast, the HbCO dephasing in the sol-gel reflects only a 2-fold increase in viscosity. Attempts to alter the encapsulating pore size by varying the molar ratio of silane precursor to water (R value) used to prepare the sol-gel glasses were found to have no effect on the fast or steady-state spectroscopic results. The vibrational echo data are discussed in the context of solvent confinement and protein-pore wall interactions to provide insights into the influence of a confined environment on the fast structural dynamics experienced by a biomolecule.

Dynamics of hemoglobin in human erythrocytes and in solution: influence of viscosity studied by ultrafast vibrational echo experiments

Ultrafast spectrally resolved stimulated vibrational echo experiments are used to measure the vibrational dephasing of the CO stretching mode of hemoglobin-CO (HbCO) inside living human erythrocytes (red blood cells), in liquid solutions, and in a glassy matrix. A method is presented to overcome the adverse impact on the vibrational echo signal from the strong light scattering caused by the cells. The results from the cytoplasmic HbCO are compared to experiments on aqueous HbCO samples prepared in different buffers, solutions containing low and high concentrations of glycerol, and in a solid trehalose matrix. Measurements are also presented that provide an accurate determination of the viscosity at the very high Hb concentration that is found inside the cells. It is demonstrated that the dynamics of the protein, as sensed by the CO ligand, are the same inside the erythrocytes and in aqueous solution and are independent of the viscosity. In solutions that are predominantly glycerol, the dynamics are modified somewhat but are still independent of viscosity. The experiments in trehalose give the dynamics at infinite viscosity and are used to separate the viscosity-dependent dynamics from the viscosity-independent dynamics. Although the HbCO dynamics are the same in the red blood cell and in the equivalent aqueous solutions, differences in the absorption spectra show that the distribution of a protein's equilibrium substates is sensitive to small pH differences.

Fast protein dynamics probed with infrared vibrational echo experiments

IR vibrational echo experiments are used to study dynamics in myoglobin (Mb) by investigating the dephasing of the CO-stretching mode of CO bound at the active site of the protein (Mb-CO). The temperature dependence and the viscosity dependence of Mb-CO pure dephasing have been measured in several solvents. In low-temperature, glassy solvents, the pure dephasing has a power law temperature dependence, T(1.3), that reflects glasslike protein dynamics. In liquids, the temperature dependence is much steeper and arises from a combination of pure temperature dependence and the influence of decreasing solvent viscosity with increasing temperature. As the solvent viscosity decreases, the ability of the protein's surface to undergo topological fluctuations increases, which in turn increases the internal protein-structural fluctuations. The protein-structural motions are coupled to the CO bound at the active site by electric field fluctuations that accompany movements of polar residues. The dynamic electric field-coupling mechanism is tested by observing differences in the temperature dependence of the pure dephasing of Mb-CO mutations.

Two-dimensional time-frequency ultrafast infrared vibrational echo spectroscopy

2D spectrally resolved ultrafast (<200 fs) IR vibrational echo experiments were performed on Rh(CO)(2)acac [(acetylacetonato)dicarbonylrhodium (I)]. The 2D spectra display features that reflect the 0-1 and 1-2 transitions and the combination band transition of the symmetric (S) and antisymmetric (A) CO stretching modes. Three oscillations in the data arise from the frequency difference between the S and A modes (quantum beats) and the S and A anharmonicities. A new explanation is given for these "anharmonic" oscillations. Calculations show that spectral resolution enables the 0-1 and 1-2 dephasing to be measured independently.