Revisiting the optical properties of the FMO protein.
Ontology highlight
ABSTRACT:
SUBMITTER: Milder MT
PROVIDER: S-EPMC2882565 | biostudies-literature | 2010 Jun
REPOSITORIES: biostudies-literature
Publications
Revisiting the optical properties of the FMO protein.
Milder Maaike T W MT Brüggemann Ben B van Grondelle Rienk R Herek Jennifer L JL
Photosynthesis research 20100313 2-3
We review the optical properties of the FMO complex as found by spectroscopic studies of the Q ( y ) band over the last two decades. This article emphasizes the different methods used, both experimental and theoretical, to elucidate the excitonic structure and dynamics of this pigment-protein complex. ...[more]
Similar Datasets
Project description:We investigated a high-quality MgB2 thin film with a thickness of ~1000 nm on an Al2O3 substrate using optical spectroscopy. We measured the reflectance spectra of the film at various temperatures both below, and above, the superconducting transition temperature, T c [Formula: see text] 40 K. An earlier study showed that when the sample surface is exposed to air the optical properties of the surface change immediately, however, the saturated change is negligibly small in the far-infrared region. The optical conductivity spectrum in the normal state shows two (narrow and broad) Drude modes, with the narrow Drude mode being dominant in the low frequency region below 1000 cm-1. Our study, which uses a good-quality sample, provides more reliable data on the optical properties of MgB2, in a similar spectral range. The optical data is analyzed further using an extended Drude model, and the electron-phonon spectral density function, α 2 F(ω), is extracted. The spectral density function α 2 F(ω) features two peaks: a small one near 114 cm-1, and a strong peak around the 550 cm-1 where the B-B bond stretching phonon exists. Our data in the superconducting state does not show the expected energy shift of the onset of scattering associated with the α 2 F(ω) peaks.
| S-EPMC5567084 | biostudies-literature
Project description:For modern security, devices, individuals, and communications require unprecedentedly unique identifiers and cryptographic keys. One emerging method for guaranteeing digital security is to take advantage of a physical unclonable function. Surprisingly, native silk, which has been commonly utilized in everyday life as textiles, can be applied as a unique tag material, thereby removing the necessary apparatus for optical physical unclonable functions, such as an objective lens or a coherent light source. Randomly distributed fibers in silk generate spatially chaotic diffractions, forming self-focused spots on the millimeter scale. The silk-based physical unclonable function has a self-focusing, low-cost, and eco-friendly feature without relying on pre-/post-process for security tag creation. Using these properties, we implement a lens-free, optical, and portable physical unclonable function with silk identification cards and study its characteristics and reliability in a systemic manner. We further demonstrate the feasibility of the physical unclonable functions in two modes: authentication and data encryption.
| S-EPMC8752800 | biostudies-literature
Project description:The Fenna-Matthews-Olson (FMO) light-harvesting complex is now one of the primary model systems for the study of excitation energy transfer (EET). However, the mechanism of the EET in this system is still controversial. In this work, molecular dynamics simulations and the electrostatic-embedding quantum-mechanics/molecular-mechanics single-point calculations have been employed to predict the energy transfer pathways utilizing the polarized protein-specific charge (PPC), which provides a more realistic description of Coulomb interaction potential in the protein than conventional mean-field charge scheme. The recently discovered eighth pigment has also been included in this study. Comparing with the conventional mean-field charges, more stable structures of FMO complex were found under PPC scheme during molecular dynamic simulation. Based on the electronic structure calculations, an exciton model was constructed to consider the couplings during excitation. The results show that pigments 3 and 4 dominate the lowest exciton levels whereas the highest exciton level are mainly constituted of pigments 1 and 6. This observation agrees well with the assumption based on the spatial distribution of the pigments. Moreover, the obtained spectral density in this study gives a reliable description of the diverse local environment embedding each pigment.
| S-EPMC4661465 | biostudies-literature
Project description:NGC 4151 is the brightest Seyfert 1 nucleus in X-rays. It was the first object to show short time delays in the Fe K band, which were attributed to relativistic reverberation, providing a new tool for probing regions at the black hole scale. Here, we report the results of a large XMM-Newton campaign in 2015 to study these short delays further. Analyzing high quality data that span time scales between hours and decades, we find that neutral and ionized absorption contribute significantly to the spectral shape. Accounting for their effects, we find no evidence for a relativistic reflection component, contrary to early work. Energy-dependent lags are significantly measured in the new data, but with an energy profile that does not resemble a broad iron line, in contrast to the old data. The complex lag-energy spectra, along with the lack of strong evidence for a relativistic spectral component, suggest that the energy-dependent lags are produced by absorption effects. The long term spectral variations provide new details on the variability of the narrow Fe Kα line. We find that its variations are correlated with, and delayed with respect to, the primary X-ray continuum. We measure a delay of τ=3.3-0.7+1.8 days, implying an origin in the inner broad line region (BLR). The delay is half the Hβ line delay, suggesting a geometry that differs slightly from the optical BLR.
| S-EPMC7472994 | biostudies-literature
Project description:A recently engineered mutant of cyan fluorescent protein (WasCFP) that exhibits pH-dependent absorption suggests that its tryptophan-based chromophore switches between neutral (protonated) and charged (deprotonated) states depending on external pH. At pH 8.1, the latter gives rise to green fluorescence as opposed to the cyan color of emission that is characteristic for the neutral form at low pH. Given the high energy cost of deprotonating the tryptophan at the indole nitrogen, this behavior is puzzling, even if the stabilizing effect of the V61K mutation in proximity to the protonation/deprotonation site is considered. Because of its potential to open new avenues for the development of optical sensors and photoconvertible fluorescent proteins, a mechanistic understanding of how the charged state in WasCFP can possibly be stabilized is thus important. Attributed to the dynamic nature of proteins, such understanding often requires knowledge of the various conformations adopted, including transiently populated conformational states. Transient conformational states triggered by pH are of emerging interest and have been shown to be important whenever ionizable groups interact with hydrophobic environments. Using a combination of the weighted-ensemble sampling method and explicit-solvent constant pH molecular dynamics (CPHMD(MS?D)) simulations, we have identified a solvated transient state, characterized by a partially open ?-barrel where the chromophore pKa of 6.8 is shifted by over 20 units from that of the closed form (6.8 and 31.7, respectively). This state contributes a small population at low pH (12% at pH 6.1) but becomes dominant at mildly basic conditions, contributing as much as 53% at pH 8.1. This pH-dependent population shift between neutral (at pH 6.1) and charged (at pH 8.1) forms is thus responsible for the observed absorption behavior of WasCFP. Our findings demonstrate the conditions necessary to stabilize the charged state of the WasCFP chromophore (namely, local solvation at the deprotonation site and a partial flexibility of the protein ?-barrel structure) and provide the first evidence that transient conformational states can control optical properties of fluorescent proteins.
| S-EPMC4394632 | biostudies-literature
Project description:The study of the optical properties of graphene oxide (GO) is crucial in designing functionalized GO materials with specific optical properties for various applications such as (bio) sensors, optoelectronics, and energy storage. The present work aims to investigate the electronic transitions, optical bandgap, and absorption coefficient of GO under different conditions. Specifically, the study examines the effects of drying times ranging from 0 to 120 h while maintaining a fixed temperature of 80°C and low temperatures ranging from 40℃ to 100℃, with a constant drying time of 24 h. Our findings indicate that exposing the GO sample to a drying time of up to 120 h at 80°C can lead to a reduction in the optical bandgap, decreasing it from 4.09 to 2.76 eV. The π-π* transition was found to be the most affected, shifting from approximately 230 nm at 0 h to 244 nm after 120 h of drying time. Absorption coefficients of 3140-5507 ml mg-1 m-1 were measured, which are similar to those reported for exfoliated graphene dispersions but up to two times higher, confirming the improved optical properties of GO. Our findings can provide insights into determining the optimal temperature and duration required for transforming GO into its reduced form for a specific application through extrapolation. The study is complemented by analyzing the elemental composition, surface morphology change, and electrical properties.
| S-EPMC10397392 | biostudies-literature
Project description:The objective of the study is to assess the safety and technical feasibility of a new imaging system, used during colorectal resection surgery, named Trident in version 1.0, which could be used by the surgeon during colorectal procedures to obtain information on intestinal tissue oxygenation.
| 68418 | ecrin-mdr-crc
Project description:The flavin-containing monooxygenase (FMO) family of enzymes oxygenates nucleophilic xenobiotics and endogenous substances. Human FMO3 and FMO5 are the predominant FMO forms in adult liver. These enzymes are naturally membrane-bound, and recombinant proteins are commercially available as microsomal preparations from insect cells (i.e., Supersome FMO). As an alternative, FMO3 has previously been expressed as a soluble protein, through use of an N-terminal maltose-binding protein (MBP) fusion. In the current study, MBP fusions of both human FMO3 and FMO5 were prepared to >90% purity in the presence of detergent and characterized for biochemical and kinetic parameters, and the parameters were compared with those of Supersome FMO samples. Although MBP-FMO enzymes afforded lower rates of turnover than the corresponding Supersome FMOs, both types of FMO showed identical substrate dependencies and similar responses to changes in assay conditions. Of interest, the FMO3 enzymes showed a 2-fold activation of k(cat)/K(m) in the presence of Triton X-100. Oligomeric analysis of MBP-FMO3 also showed disassociation from a high-order oligomeric form to a monomeric status in the presence of Triton X-100. This report serves as the first direct comparison between Supersome FMOs and the corresponding MBP fusions and the first report of a detergent-based activation of k(cat)/K(m) that corresponds to changes in oligomerization.
| S-EPMC2993457 | biostudies-literature
Project description:Significant protein rearrangement upon excitation and energy transfer in Fenna-Matthews-Olson protein of Prosthecochloris aestuarii results in a modified energy landscape, which induces more changes in pigment site energies than predicted by the "standard" hole-burning theory. The energy changes are elucidated by simulations while investigating the effects of site-dependent disorder, both static (site-energy distribution widths) and dynamic (spectral density shapes). The resulting optimized site energies and their fluctuations are consistent with relative differences observed in inhomogeneous widths calculated by recent molecular dynamic simulations. Two sets of different spectral densities reveal how their shapes affect the population dynamics and distribution of exciton lifetimes. Calculations revealed the wavelength-dependent distributions of exciton lifetimes (T 1) in the femtosecond to picosecond time frame. We suggest that the calculated multimodal and asymmetric wavelength-dependent T 1 distributions offer more insight into the interpretation of resonant hole-burned (HB) spectra, kinetic traces in two-dimensional (2D) electronic spectroscopy experiments, and widely used global analyses in fitting data from transient absorption experiments.
| S-EPMC7931385 | biostudies-literature
Project description:Experimental findings of long-lived quantum coherence in the Fenna-Matthews-Olson (FMO) complex and other photosynthetic complexes have led to theoretical studies searching for an explanation of this unexpected phenomenon. Extending in this regard our own earlier calculations, we performed simulations of the FMO complex in a glycerol-water mixture at 310 K as well as 77 K, matching the conditions of earlier 2D spectroscopic experiments by Engel et al. The calculations, based on an improved quantum procedure employed by us already, yielded spectral densities of each individual pigment of FMO, in water and glycerol-water solvents at ambient temperature that compare well to prior experimental estimates. Due to the slow solvent dynamics at 77 K, the present results strongly indicate the presence of static disorder, i.e., disorder on a time scale beyond that relevant for the construction of spectral densities.
| S-EPMC3714603 | biostudies-literature