Adaptation processes in , an example of the light-induced optimization of the photosynthetic apparatus on hierarchical time scales.

Oxygenic photosynthesis in , one of a series of cyanobacteria producing red-shifted Chl , is adapted to varying light conditions by a range of diverse processes acting over largely different time scales. Acclimation to far-red light (FRL) above 700 nm over several days is mirrored by reversible changes in the Chl content. In several cyanobacteria that undergo FRL photoacclimation, Chl and Chl are directly involved in excitation energy transfer in the antenna system, form the primary donor in photosystem I (PSI), and are also involved in electron transfer within photosystem II (PSII), most probably at the Chl position, with efficient charge transfer happening with comparable kinetics to reaction centers containing Chl .

How electron tunneling and uphill excitation energy transfer support photochemistry in Halomicronema hongdechloris.

Halomicronema hongdechloris, the first cyanobacterium reported to produce the red-shifted chlorophyll f (Chl f) upon acclimation to far-red light, demonstrates remarkable adaptability to diverse light conditions. The photosystem II (PS II) of this organism undergoes reversible changes in its Chl f content, ranging from practically zero under white-light culture conditions to a Chl f: Chl a ratio of up to 1:8 when exposed to far-red light (FRL) of 720-730 nm for several days. Our ps time- and wavelength-resolved fluorescence data obtained after excitation of living H.

Effect of Molecular Dynamics and Internal Water Contact on the Photophysical Properties of Red pH-Sensitive Proteins.

The pH dependence of the absorption and (time-resolved) fluorescence of two red-shifted fluorescent proteins, mCardinal and mNeptune, was investigated. Decay-associated spectra were measured following fluorescence excitation at 470 nm in PBS buffer with a pH that ranged from 5.5 to 8.

Thermoresponsive swelling of photoacoustic single-chain nanoparticles.

NIR-fluorescent LCST-type single-chain nanoparticles (SCNPs) change their photophysical behaviour upon heating, caused by depletion of water from the swollen SCNP interiors. This thermoresponsive effect leads to a fluctuating photoacoustic (PA) signal which can be used as a contrast mechanism for PA imaging.

Light-Induced Conformational Flexibility of the Orange Carotenoid Protein Studied by Quasielastic Neutron Scattering with Illumination.

The orange carotenoid protein plays a vital role in the photoprotection of cyanobacteria and exhibits a significant structural change upon photoactivation. A rarely considered aspect is the importance of internal protein dynamics in facilitating the structural transition to the active state. In this study, we use quasielastic neutron scattering under (in situ) blue light illumination for the first time to directly probe the protein dynamics of the orange carotenoid protein in the dark-adapted and active states.

Tuning the Internal Compartmentation of Single-Chain Nanoparticles as Fluorescent Contrast Agents.

Controlling the internal structures of single-chain nanoparticles (SCNPs) is an important factor for their targeted chemical design and synthesis, especially in view of nanosized compartments presenting different local environments as a main feature to control functionality. We here design SCNPs bearing near-infrared fluorescent dyes embedded in hydrophobic compartments for use as contrast agents in pump-probe photoacoustic (PA) imaging, displaying improved properties by the location of the dye in the hydrophobic particle core. Compartment formation is controlled via single-chain collapse and subsequent crosslinking of an amphiphilic polymer using external crosslinkers in reaction media of adjustable polarity.

Residue-Specific Exchange of Proline by Proline Analogs in Fluorescent Proteins: How "Molecular Surgery" of the Backbone Affects Folding and Stability.

Replacement of proline (Pro) residues in proteins by the traditional site-directed mutagenesis by any of the remaining 19 canonical amino acids is often detrimental to protein folding and, in particular, chromophore maturation in green fluorescent proteins and related variants. A reasonable alternative is to manipulate the translation of the protein so that all Pro residues are replaced residue-specifically by analogs, a method known as selective pressure incorporation (SPI). The built-in chemical modifications can be used as a kind of "molecular surgery" to finely dissect measurable changes or even rationally manipulate different protein properties.

Coordination-Induced Band Gap Reduction in a Metal-Organic Framework.

Herein, we report on the synthesis of a microporous, three-dimensional phosphonate metal-organic framework (MOF) with the composition Cu (H -MTPPA)  ⋅ 2 NMP (H -MTPPA=methane tetra-p-phenylphosphonic acid and NMP=N-methyl-2-pyrrolidone). This MOF, termed TUB1, has a unique one-dimensional inorganic building unit composed of square planar and distorted trigonal bipyramidal copper atoms. It possesses a (calculated) BET surface area of 766.

Arylphosphonate-Tethered Porphyrins: Fluorescence Silencing Speaks a Metal Language in Living Enterocytes*.

We report the application of a highly versatile and engineerable novel sensor platform to monitor biologically significant and toxic metal ions in live human Caco-2 enterocytes. The extended conjugation between the fluorescent porphyrin core and metal ions through aromatic phenylphosphonic acid tethers generates a unique turn off and turn on fluorescence and, in addition, shifts in absorption and emission spectra for zinc, cobalt, cadmium and mercury. The reported fluorescent probes p-H TPPA and m-H TPPA can monitor a wide range of metal ion concentrations via fluorescence titration and also via fluorescence decay curves.

Fluorescent and Water Dispersible Single-Chain Nanoparticles: Core-Shell Structured Compartmentation.

Single-chain nanoparticles (SCNPs) are highly versatile structures resembling proteins, able to function as catalysts or biomedical delivery systems. Based on their synthesis by single-chain collapse into nanoparticular systems, their internal structure is complex, resulting in nanosized domains preformed during the crosslinking process. In this study we present proof of such nanocompartments within SCNPs via a combination of electron paramagnetic resonance (EPR) and fluorescence spectroscopy.

Courses Based on iGEM/BIOMOD Competitions Are the Ideal Format for Research-Based Learning of Xenobiology.

Synthetic biology and especially xenobiology, as emerging new fields of science, have reached an intellectual and experimental maturity that makes them suitable for integration into the university curricula of chemical and biological disciplines. Novel scientific fields that include laboratory work are perfect playgrounds for developing highly motivating research-based teaching modules. We believe that research-based learning enriched by digital tools is the best approach for teaching new emerging essentials of academic education.

Phosphonate Metal-Organic Frameworks: A Novel Family of Semiconductors.

Herein, the first semiconducting and magnetic phosphonate metal-organic framework (MOF), TUB75, is reported, which contains a 1D inorganic building unit composed of a zigzag chain of corner-sharing copper dimers. The solid-state UV-vis spectrum of TUB75 reveals the existence of a narrow bandgap of 1.4 eV, which agrees well with the density functional theory (DFT)-calculated bandgap of 1.

Red, Orange, Green: Light- and Temperature-Dependent Color Tuning in a Cyanobacteriochrome.

Cyanobacteriochromes (CBCRs) are photoreceptor proteins that photoconvert between two parent states and thereby regulate various biological processes. An intriguing property is their variable ultraviolet-visible (UV-vis) absorption that covers the entire spectral range from the far-red to the near-UV region and thus makes CBCRs promising candidates for optogenetic applications. Here, we have studied Slr1393, a CBCR that photoswitches between red- and green-absorbing states (Pr and Pg, respectively).

Solution Structure and Conformational Flexibility in the Active State of the Orange Carotenoid Protein: Part I. Small-Angle Scattering.

Orange carotenoid proteins (OCPs) are photoswitchable macromolecules playing an important role in nonphotochemical quenching of excess energy in cyanobacterial light harvesting. Upon absorption of a blue photon (450-500 nm), OCPs undergo a structural change from the ground state OCP to the active state OCP, but high-resolution structures of the active state OCP are not yet available. Here, we use small-angle scattering methods combined with simulation tools to determine low-resolution structures of the active state at low protein concentrations via two approaches: first, directly by in situ illumination of wild-type OCP achieving a turnover to the active state of >90% and second, by using the mutant OCP anticipated to mimic the active state structure.

Solution Structure and Conformational Flexibility in the Active State of the Orange Carotenoid Protein. Part II: Quasielastic Neutron Scattering.

Orange carotenoid proteins (OCPs), which are protecting cyanobacterial light-harvesting antennae from photodamage, undergo a pronounced structural change upon light absorption. In addition, the active state is anticipated to boost a significantly higher molecular flexibility similar to a "molten globule" state. Here, we used quasielastic neutron scattering to directly characterize the vibrational and conformational molecular dynamics of OCP in its ground and active states, respectively, on the picosecond time scale.

Melanoidin formed from fructosylalanine contains more alanine than melanoidin formed from d-glucose with L-alanine.

In this study the elemental compositions of melanoidin formed at 160 °C from d-glucose (Glc) and l-alanine (Ala) as well as from fructosylalanine - the corresponding Amadori rearrangement product - were compared. Specific chemical bonds were probed by FTIR spectroscopy. This approach tackles the different chemical pathways for melanoidin formation via the Amadori rearrangement in contrast to the reaction from Glc/Ala.

Vinylene-Linked Covalent Organic Frameworks by Base-Catalyzed Aldol Condensation.

Two 2D covalent organic frameworks (COFs) linked by vinylene (-CH=CH-) groups (V-COF-1 and V-COF-2) are synthesized by exploiting the electron deficient nature of the aromatic s-triazine unit of C -symmetric 2,4,6-trimethyl-s-triazine (TMT). The acidic terminal methyl hydrogens of TMT can easily be abstracted by a base, resulting in a stabilized carbanion, which further undergoes aldol condensation with multitopic aryl aldehydes to be reticulated into extended crystalline frameworks (V-COFs). Both V-COF-1 (with terepthalaldehyde (TA)) and V-COF-2 (with 1,3,5-tris(p-formylphenyl)benzene (TFPB)) are polycrystalline and exhibit permanent porosity and BET surface areas of 1341 m  g and 627 m  g , respectively.

PCA-based identification and differentiation of FTIR data from model melanoidins with specific molecular compositions.

Melanoidins formed from different carbohydrates, such as d-glucose, d-fructose, and d-xylose, and their typical degradation products, such as hydroxymethylfurfural, furfural, glyoxal, and methylglyoxal, with l-alanine were analyzed with Fourier transform infrared spectroscopy (FTIR). Characteristic infrared bands were identified representing spectral differences between the investigated melanoidin species due to their different molecular compositions. With the help of principal components analysis (PCA) the IR data allowed for a fast discrimination between the different model melanoidins.

Molecular insights into antibiotic resistance - how a binding protein traps albicidin.

The worldwide emergence of antibiotic resistance poses a serious threat to human health. A molecular understanding of resistance strategies employed by bacteria is obligatory to generate less-susceptible antibiotics. Albicidin is a highly potent antibacterial compound synthesized by the plant-pathogenic bacterium Xanthomonas albilineans.

Photosynthesis supported by a chlorophyll f-dependent, entropy-driven uphill energy transfer in Halomicronema hongdechloris cells adapted to far-red light.

The phototrophic cyanobacterium Halomicronema hongdechloris shows far-red light-induced accumulation of chlorophyll (Chl) f, but the involvement of the pigment in photosynthetic energy harvesting by photosystem (PS) II is controversially discussed. While H. hongdechloris contains negligible amounts of Chl f in white-light culture conditions, the ratio of Chl f to Chl a is reversibly changed up to 1:8 under illumination with far-red light (720-730 nm).

Antimicrobial Peptides Produced by Selective Pressure Incorporation of Non-canonical Amino Acids.

Nature has a variety of possibilities to create new protein functions by modifying the sequence of the individual amino acid building blocks. However, all variations are based on the 20 canonical amino acids (cAAs). As a way to introduce additional physicochemical properties into polypeptides, the incorporation of non-canonical amino acids (ncAAs) is increasingly used in protein engineering.

Engineering 'Golden' Fluorescence by Selective Pressure Incorporation of Non-canonical Amino Acids and Protein Analysis by Mass Spectrometry and Fluorescence.

Fluorescent proteins are fundamental tools for the life sciences, in particular for fluorescence microscopy of living cells. While wild-type and engineered variants of the green fluorescent protein from Aequorea victoria (avGFP) as well as homologs from other species already cover large parts of the optical spectrum, a spectral gap remains in the near-infrared region, for which avGFP-based fluorophores are not available. Red-shifted fluorescent protein (FP) variants would substantially expand the toolkit for spectral unmixing of multiple molecular species, but the naturally occurring red-shifted FPs derived from corals or sea anemones have lower fluorescence quantum yield and inferior photo-stability compared to the avGFP variants.

The impact of the phytochromes on photosynthetic processes.

This review describes the phytochrome system in higher plants and cyanobacteria and its role in regulation of photosynthetic processes and stress protection of the photosynthetic apparatus. A relationship between the content of the different phytochromes, the changes in the ratios of the physiologically active forms of phytochromes to their total pool and the resulting influence on photosynthetic processes is reviewed. The role of the phytochromes in the regulation of the expression of genes encoding key photosynthetic proteins, antioxidant enzymes and other components involved in stress signaling is elucidated.

Structural characterization of melanoidin formed from d-glucose and l-alanine at different temperatures applying FTIR, NMR, EPR, and MALDI-ToF-MS.

The aim of this study was to identify specific chemical bonds and characteristic structures in melanoidins formed from d-glucose and l-alanine between 130 and 200 °C. The results might be used to control the type and amount of melanoidin produced during food processing. For this purpose, complementary techniques, such as FTIR, NMR, EPR, and MALDI-ToF, were employed.