Real-time observation of conformational fluctuations in Zn-substituted myoglobin by time-resolved transient hole-burning spectroscopy

Redox-state dependent blinking of single photosystem I trimers at around liquid-nitrogen temperature

Efficient light harvesting in a photosynthetic antenna system is disturbed by a ragged and fluctuating energy landscape of the antenna pigments in response to the conformation dynamics of the protein. This situation is especially pronounced in Photosystem I (PSI) containing red shifted chlorophylls (red Chls) with the excitation energy much lower than the primary donor. The present study was conducted to clarify light-harvesting dynamics of PSI isolated from Synechocystis sp. PCC6803 by using single-molecule spectroscopy at liquid‑nitrogen temperatures. Fluorescence emission at around 720 nm from the red Chls in single PSI trimers was monitored at 80-100 K. Intermittent variations in the emission intensities, so-called blinking, were frequently observed. Its time scale lay in several tens of seconds. The blinking amplitude depended on the redox state of the phylloquinone (A₁). Electrochromic shifts of Chls induced by the negative charge on A₁ were calculated based on the X-ray crystallographic structure. A Chl molecule, Chl-A839 (numbering according to PDB 5OY0), bound near A₁ was found to have a large electrochromic shift. This Chl has strong exciton coupling with neighboring Chl (A838) whose site energy was predicted to be determined by interaction with an arginine residue (ArgF84) [Adolphs et al., 2010]. A possible scenario of the blinking was proposed. Conformational fluctuations of ArgF84 seesaw the excitation-energy of Chl-A838, which perturbs the branching ratio of excitation-energy between the red Chl and the cationic form of P700 as a quencher. The electrochromic shift of Chl-A839 enhances the effect of the conformation dynamics of ArgF84.

Photosystem II does not possess a simple excitation energy funnel: time-resolved fluorescence spectroscopy meets theory

The experimentally obtained time-resolved fluorescence spectra of photosystem II (PS II) core complexes, purified from a thermophilic cyanobacterium Thermosynechococcus vulcanus, at 5–180 K are compared with simulations. Dynamic localization effects of excitons are treated implicitly by introducing exciton domains of strongly coupled pigments. Exciton relaxations within a domain and exciton transfers between domains are treated on the basis of Redfield theory and generalized Förster theory, respectively. The excitonic couplings between the pigments are calculated by a quantum chemical/electrostatic method (Poisson-TrEsp). Starting with previously published values, a refined set of site energies of the pigments is obtained through optimization cycles of the fits of stationary optical spectra of PS II. Satisfactorily agreement between the experimental and simulated spectra is obtained for the absorption spectrum including its temperature dependence and the linear dichroism spectrum of PS II core complexes (PS II-CC). Furthermore, the refined site energies well reproduce the temperature dependence of the time-resolved fluorescence spectrum of PS II-CC, which is characterized by the emergence of a 695 nm fluorescence peak upon cooling down to 77 K and the decrease of its relative intensity upon further cooling below 77 K. The blue shift of the fluorescence band upon cooling below 77 K is explained by the existence of two red-shifted chlorophyll pools emitting at around 685 and 695 nm. The former pool is assigned to Chl45 or Chl43 in CP43 (Chl numbering according to the nomenclature of Loll et al. Nature2005, 438, 1040) while the latter is assigned to Chl29 in CP47. The 695 nm emitting chlorophyll is suggested to attract excitations from the peripheral light-harvesting complexes and might also be involved in photoprotection.

Hole-burning spectroscopy as a probe of nano-environments and processes in biomolecules: a review

Hole-burning spectroscopy, a high-resolution spectroscopic technique, allows details of heterogeneous nano-environments in biological systems to be obtained from broad absorption bands. Recently, this technique has been applied to proteins, nucleic acids, cells, and substructures of water to probe the electrostatic conditions created by macromolecules and the surrounding solvent. Starting with the factors that obscure the homogeneous linewidth of a chromophore within an inhomogeneously broadened absorption or emission band, we describe properties and processes in biological systems that are reflected in the measured hole spectra. The technique also lends itself to the resolution of perturbation experiments, such as temperature cycling to elucidate energy landscape barriers, applied external electric fields (Stark effect) to measure net internal electric fields, and applied hydrostatic pressure to find the volume compressibility of proteins.

Coupling of protein and environment fluctuations

We review the concepts of protein dynamics developed over the last 35years and extend applications of the unified model of protein dynamics to heat flow and spatial fluctuations in hydrated myoglobin (Mb) powders. Differential scanning calorimetry (DSC) and incoherent neutron scattering (INS) data on hydration Mb powders are explained by the temperature-dependence of the hydration-shell β(h) process measured by dielectric relaxation spectroscopy (DRS). The unified model explains the temperature dependence of DSC and INS data as a kinetic effect due to a fixed experimental time window and a broad distribution of hydration-shell β(h) fluctuation rates. We review the slaving of large scale protein motions to the bulk solvent α process, and the metastability of Mb molecules in glass forming bulk solvent at low temperatures. This article is part of a Special Issue entitled: "Protein Dynamics: Experimental and Computational Approaches".

Role of solvent for the dynamics and the glass transition of proteins

For the first time, a systematic investigation of the glass transition and its related dynamics of myoglobin in water-glycerol solvent mixtures of different water contents is presented. By a combination of broadband dielectric spectroscopy and differential scanning calorimetry (DSC), we have studied the relation between the protein and solvent dynamics with the aim to better understand the calorimetric glass transition, T(g), of proteins and the role of solvent for protein dynamics. The results show that both the viscosity related α-relaxation in the solvent as well as several different protein relaxations are involved in the calorimetric glass transition, and that the broadness (ΔT(g)) of the transition depends strongly on the total amount of solvent. The main reason for this seems to be that the protein relaxation processes become more separated in time with decreasing solvent level. The results are compared to that of hydrated myoglobin where the hydration water does not give any direct contribution to the calorimetric T(g). However, the large-scale α-like relaxation in the hydration water is still responsible for the protein dynamics that freeze-in at T(g). Finally, the dielectric data show clearly that the protein relaxation processes exhibit similar temperature dependences as the α-relaxation in the solvent, as suggested for solvent-slaved protein motions.

A unified model of protein dynamics

Protein functions require conformational motions. We show here that the dominant conformational motions are slaved by the hydration shell and the bulk solvent. The protein contributes the structure necessary for function. We formulate a model that is based on experiments, insights from the physics of glass-forming liquids, and the concepts of a hierarchically organized energy landscape. To explore the effect of external fluctuations on protein dynamics, we measure the fluctuations in the bulk solvent and the hydration shell with broadband dielectric spectroscopy and compare them with internal fluctuations measured with the Mössbauer effect and neutron scattering. The result is clear. Large-scale protein motions are slaved to the fluctuations in the bulk solvent. They are controlled by the solvent viscosity, and are absent in a solid environment. Internal protein motions are slaved to the beta fluctuations of the hydration shell, are controlled by hydration, and are absent in a dehydrated protein. The model quantitatively predicts the rapid increase of the mean-square displacement above approximately 200 K, shows that the external beta fluctuations determine the temperature- and time-dependence of the passage of carbon monoxide through myoglobin, and explains the nonexponential time dependence of the protein relaxation after photodissociation.

The red-edge effects: 30 years of exploration

In 1970, three laboratories independently made a discovery that, for aromatic fluorophores embedded into different rigid and highly viscous media, the spectroscopic properties do not conform to classical rules. The fluorescence spectra can depend on excitation wavelength, and the excited-state energy transfer, if present, fails at the "red" excitation edge. These red-edge effects were related to the existence of excited-state distribution of fluorophores on their interaction energy with the environment and the slow rate of dielectric relaxation of this environment. In these conditions the site-selection can be provided by variation of the energy of illuminating light quanta, and the behaviour of selected species can be followed as a function of time and other variables. These observations found extensive application in different areas of research: colloid and polymer science, molecular biophysics, photochemistry and photobiology. In particular, they led to the development of very productive methods of studying the dynamics of dielectric relaxations in protein and membranes, using the tryptophan emission and the emission of a variety of probes. These studies were extended to the time domain with the observation of new site-selective effects in emission intensity and anisotropy decays. They stimulated the emergence and development of cryogenic energy-selective and single-molecular techniques that became valuable tools in their own right in chemistry and biophysics research. Site-selection effects were discovered for electron-transfer and proton-transfer reactions if they depended on the dynamics of the environment. This review is focused on the progress in the field of red-edge effects, their applications and prospects.

Time-resolved hole-burning study on myoglobin: fluctuation of restricted water within distal pocket

We have studied the equilibrium fluctuation dynamics of Zn-substituted myoglobin and its His64-->Leu (H64L) mutant in the pH range from 5 to 9 by using time-resolved transient-hole-burning (TRTHB) spectroscopy. In the H64L mutant, we have observed a largely reduced width of the absorption spectrum and only a slight temporal shift of the hole-burning spectrum. These observations both reflect the suppressed conformational fluctuation in the mutant. On the other hand, the pH-dependent change in the absorption spectrum could not be solely explained by the change in the protonation state of His64 induced by the pH change. These results suggest that although the fluctuation dynamics observed by the TRTHB experiment of the native sample mainly reflects the conformational motion around His64, the interconversion process of His64 between its protonated and unprotonated states has a minor contribution. Instead, we have proposed a tentative interpretation that the motion of the water molecule around His64 is the main source of the observed dynamics in the TRTHB technique.

Conformational fluctuation of native-like and molten-globule-like cytochrome c observed by time-resolved hole burning

Nanosecond to millisecond conformational fluctuations of Zn-substituted cytochrome c (ZnCytc) have been studied by the time-resolved transient hole-burning method. The investigation of low-temperature dynamics has been made on the ZnCytc solution sample in a water-glycerol mixture. The conformational fluctuations in the native-like and the molten-globule (MG)-like states have been compared for the aqueous solution samples at room temperature. ZnCytc in the MG-like state has been prepared by adding 200 mM NaClO4 to the protein solution with a pH of 2.1, and the formation of the MG-like state has been confirmed by both the far-UV CD and the visible absorption spectra. The hole spectrum of ZnCytc has been found to consist of two nearly degenerate components, that is, the Qx and Qy bands. The temporal change in the Qx component hole spectrum has been extracted by fitting the observed hole spectrum to the three-Gaussian form. The experimental results for ZnCytc dissolved in a water-glycerol mixture have revealed that the conformational fluctuation of ZnCytc is suppressed around 200 K, which is nearly the same temperature as the glass-like transition point of Zn-substituted myoglobin (ZnMb) and also as the glass-transition point of the solvent. This supports the idea of the solvent-induced glass-like transition of a protein. It has been also found that at physiological temperatures the time scale of the conformational fluctuation of ZnCytc lies around a few tens of nanoseconds, which is 2-3 orders of magnitude faster than that of ZnMb. The experimental results for the aqueous solution samples have shown that the difference between the native-like and the MG-like states is not conspicuous. However, they are indicative of the appearance of the slower conformational fluctuation in the MG-like state.