Protein dynamics at low temperatures

Determination of the spectral diffusion kernel of a protein by single-molecule spectroscopy

The spectral dynamics of individual bacterial light-harvesting-2 pigment-protein complexes have been studied at 1.4 K. The data provided the spectral diffusion kernel of the optical transitions of the embedded B800 bacteriochlorophyll a pigments. This kernel can be described by either a single Gaussian function or a superposition of Gaussian functions. Moreover, we found that the chromophores interact with two classes of TLSs that can be distinguished by their distance from the chromophore and are most likely located outside (class 1) and inside (class 2) the protein matrix.

Do Proteins at Low Temperature Behave as Glasses? A Single-Molecule Study

We have recorded long spectral diffusion trajectories from individual LH2 pigment-protein complexes from the purple bacterium Rhodobacter sphaeroides at 1.4 K. From these data, the spectral cumulants of the absorption lines of individual, protein-embedded BChl a pigments have been evaluated. It appears that the first and second cumulants cannot be described by the predictions of the well tested standard two-level system (TLS) model for spectral diffusion in glasses. The results of the present study clearly show that there is a fundamental difference between the relaxation behavior of our test protein and that of glasses.

Investigation of spectral diffusion in ribonuclease by photolabeling of intrinsic aromatic amino acids

Spectral diffusion dynamics in ribonuclease A was observed via the broadening of photochemical holes burned into the absorption spectrum of intrinsic tyrosine residues. Unlike previous results based on hole burning of chromophores in the pockets of heme proteins, where spectral diffusion develops according to a power law in time, the dynamics in ribonuclease follow a logarithmic law. The results suggest that the experiment preferentially labels the tyrosines located on the surface of the protein where the two-level system dynamics of the glass host matrix exert a strong influence.

Force modulating dynamic disorder: a physical model of catch-slip bond transitions in receptor-ligand forced dissociation experiments

Recent experiments found that some adhesive receptor-ligand complexes have counterintuitive catch-slip transition behaviors: the mean lifetimes of these complexes first increase (catch) with initial application of a small external force, and then decrease (slip) when the force is beyond some threshold. In this work we suggest that the forced dissociation of these complexes might be a typical rate process with dynamic disorder. The one-dimensional force modulating Agmon-Hopfield model is used to describe the transitions in the single-bond P-selectin glycoprotein ligand 1-P-selectin forced dissociation experiments, which were respectively performed in the constant force [Marshall, Nature (Landon) 423, 190 (2003)] and the ramping force [Evans, Proc. Natl. Acad. Sci. U.S.A 98, 11281 (2004)] modes. We find that, an external force can not only accelerate the bond dissociation, but also modulate the complex from the lower-energy barrier to the higher one; the catch-slip bond transition can arise from a particular energy barrier shape. The agreement between our calculation and the experimental data is satisfactory.

Aromatic substrate specificity of horseradish peroxidase C studied by a combined fluorescence line narrowing/energy minimization approach: the effect of localized side-chain reorganization

Horseradish peroxidase C binds a wide variety of small H-donor compounds such as benzohydroxamic acid (BHA) and 2-naphthohydroxamic acid (NHA). In this work, we use the Mg(II)-mesoporphyrin prosthetic group derivative as a spectroscopic probe of the active site and of the interaction with the substrates. We report on high-resolution fluorescence line-narrowed spectra which show that the effects of substrate binding on the electronic transitions are similar for both substrates and present data on the normal vibrational modes that are active in the vibronic spectra. Analysis of the vibrational frequencies shows that the Mg(II) ion is 5-coordinate in all cases, thus ruling out a solvent water as sixth ligand. The frequency shifts observed as a result of substrate binding are also indicative of a more rigid prosthetic group upon substrate binding. We present models for MgMP-HRP and its complexes with both substrates and compare the resulting structures on the basis of a modeling approach combining energy minimization to finite difference Poisson--Boltzmann calculations which partitions the various relative protein contributions to substrate binding. We show that the electrostatic potential of the prosthetic group is modified by the binding event. Analysis of the unbound and bound energy-minimized structures shows that the enzyme modulates substrate binding by subtle charge reorganization in the vicinity of the catalytic site and that this rearrangement is not attributable to significant secondary structure conformational changes but to side-chain reorganization.

Trehalose effect on low temperature protein dynamics: fluctuation and relaxation phenomena

We performed spectral diffusion experiments in trehalose-enriched glycerol/buffer-glass on horseradish peroxidase where the heme was replaced by metal-free mesoporphyrin IX, and compared them with the respective behavior in a pure glycerol/buffer-glass (Schlichter et al., J. Chem. Phys. 2000, 112:3045-3050). Trehalose has a significant influence: spectral diffusion broadening speeds up compared to the trehalose-free glass. This speeding up is attributed to a shortening of the correlation time of the frequency fluctuations most probably by preventing water molecules from leaving the protein interior. Superimposed to the frequency fluctuation dynamics is a relaxation dynamics that manifests itself as an aging process in the spectral diffusion broadening. Although the trehalose environment speeds up the fluctuations, it does not have any influence on the relaxation. Both relaxation and fluctuations are governed by power laws in time. The respective exponents do not seem to change with the protein environment. From the spectral dynamics, the mean square displacement in conformation space can be determined. It is governed by anomalous diffusion. The associated frequency correlation time is incredibly long, demonstrating that proteins at low temperatures are truly nonergodic systems.