Tunneling dynamics of side chains and defects in proteins, polymer glasses, and OH-doped network glasses

Identification of Residues Potentially Involved in Optical Shifts in the Water-Soluble Chlorophyll a-Binding Protein through Molecular Dynamics Simulations

Reversible light and thermally induced spectral shifts are universally observed in a wide variety of pigment-protein complexes at temperatures ranging from cryogenic to ambient. In this paper, we employed large-scale molecular dynamics (MD) simulations of a prototypical pigment-protein complex to better understand these shifts at a molecular scale. Although multiple mechanisms have been proposed over the years, no verification of these proposals via MD simulations has thus far been performed; our work represents the first step in this direction. From simulations of the water-soluble chlorophyll-binding protein complex, we determined that rearrangements of long hydrogen bonds were unlikely to be the origin of the multiwell landscape features necessary to explain observed spectral shifts. We also assessed small motions of amino acid residues and identified side chain rotations of some of these residues as likely candidates for the origin of relevant multiwell landscape features. The protein free-energy landscapes associated with side chain rotations feature energy barriers of around 1100-1600 cm-1, in agreement with optical spectroscopy results, with the most promising residue type associated with experimental signatures being serine, which possesses a symmetric triple-well landscape and moment of inertia of a relevant magnitude.

Probing Energy Landscapes of Cytochrome b6f with Spectral Hole Burning: Effects of Deuterated Solvent and Detergent

In non-photochemical spectral hole burning (NPHB) and spectral hole recovery experiments, cytochrome b₆f protein exhibits behavior that is almost independent of the deuteration of the buffer/glycerol glassy matrix containing the protein, apart from some differences in heat dissipation. On the other hand, strong dependence of the hole burning properties on sample preparation procedures was observed and attributed to a large increase of the electron-phonon coupling and shortening of the excited-state lifetime occurring when n-dodecyl β-d-maltoside (DM) is used as a detergent instead of n-octyl β-d-glucopyranoside (OGP). The data was analyzed assuming that the tunneling parameter distribution or barrier distribution probed by NPHB and encoded into the spectral holes contains contributions from two nonidentical components with accidentally degenerate excited state λ-distributions. Both components likely reflect protein dynamics, although with some small probability one of them (with larger md²) may still represent the dynamics involving specifically the -OH groups of the water/glycerol solvent. Single proton tunneling in the water/glycerol solvent environment or in the protein can be safely excluded as the origin of observed NPHB and hole recovery dynamics. The intensity dependence of the hole growth kinetics in deuterated samples likely reflects differences in heat dissipation between protonated and deuterated samples. These differences are most probably due to the higher interface thermal resistivity between (still protonated) protein and deuterated water/glycerol outside environment.

Low-temperature protein dynamics of the B800 molecules in the LH2 light-harvesting complex: spectral hole burning study and comparison with single photosynthetic complex spectroscopy

Previously published and new spectral hole burning (SHB) data on the B800 band of LH2 light-harvesting antenna complex of Rps. acidophila are analyzed in light of recent single photosynthetic complex spectroscopy (SPCS) results (for a review, see Berlin et al. Phys. Life Rev. 2007, 4, 64.). It is demonstrated that, in general, SHB-related phenomena observed for the B800 band are in qualitative agreement with the SPCS data and the protein models involving multiwell multitier protein energy landscapes. Regarding the quantitative agreement, we argue that the single-molecule behavior associated with the fastest spectral diffusion (smallest barrier) tier of the protein energy landscape is inconsistent with the SHB data. The latter discrepancy can be attributed to SPCS probing not only the dynamics of of the protein complex per se, but also that of the surrounding amorphous host and/or of the host-protein interface. It is argued that SHB (once improved models are developed) should also be able to provide the average magnitudes and probability distributions of light-induced spectral shifts and could be used to determine whether SPCS probes a set of protein complexes that are both intact and statistically relevant. SHB results are consistent with the B800 --> B850 energy-transfer models including consideration of the whole B850 density of states.

Microscopic Description of the Low-Temperature Anomalies in Silica and Lithium Silicate via Computer Simulations

Information about the nature of the low-temperature anomalies and in particular the properties of the tunneling systems in silica and lithium silica glasses are revealed via computer simulations. The potential energy landscape of these systems is systematically explored for adjacent pairs of local minima which may act as double-well potentials (DWPs) at low temperatures. Three different types of DWPs are distinguished, related to perfectly coordinated silica, intrinsic silica defects, and extrinsic defects. Their properties such as the spatial extension and the dipole moment are characterized in detail. Furthermore, the absolute number of tunneling systems, that is, symmetric DWPs, is estimated. The results are compared with dielectric echo, specific heat, and acoustic experiments on Suprasil I and Suprasil W. A semiquantitative agreement for all relevant features is obtained.

Characterization of tunneling systems in molecular versus polymer glasses by high-pressure photon echo spectroscopy

Intrinsic differences between tunneling two-level systems (TLSs) in molecular versus polymeric glasses are revealed by studying the effect of compression on TLS dynamics. Photon echo studies under variable low-temperature (1.1-2.3 K) and high-pressure (0-30 kbar) conditions have been performed to contrast the effect of compression on molecular [2-methyl-tetrahydrofuran (2MTHF)] versus polymer [Polymethylmethacrylate (PMMA)] glasses. The pressure-induced reduction in the magnitude of the optical dephasing rate of rhodamine 640 in a molecular glass (2MTHF) is found to be comparable to the volume decrease of the glass (e.g., approximately 20% at 30 kbar), indicating that TLSs in 2MTHF are associated with void space or low-density regions of the glass. In contrast, the relative pressure insensitivity observed for organic polymer glasses (PMMA) supports the idea that these TLSs are associated with side chain defects. The power-law exponent for the temperature-dependent dephasing in 2MTHF also decreased significantly at high pressure, suggesting a change in the form of the TLS density of states upon compression of the molecular glass.