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Plastoquinone (PLQ) acts as an electron carrier between photosystem II (PSII) and the cytochrome b6f complex. To understand how PLQ enters and leaves PSII, here we show results of coarse grained molecular dynamics simulations of PSII embedded in the thylakoid membrane, covering a total simulation time of more than 0.5 ms. The long time scale allows the observation of many spontaneous entries of PLQ into PSII, and the unbinding of plastoquinol (PLQol) from the complex. In addition to the two known channels, we observe a third channel for PLQ/PLQol diffusion between the thylakoid membrane and the PLQ binding sites. Our simulations point to a promiscuous diffusion mechanism in which all three channels function as entry and exit channels. The exchange cavity serves as a PLQ reservoir. Our simulations provide a direct view on the exchange of electron carriers, a key step of the photosynthesis machinery., Plastoquinone (PLQ) shuttles electrons between photosystem II (PSII) and cytochrome b6f. Here the authors perform molecular dynamics simulations and propose that PLQ enters the exchange cavity of PSII by a promiscuous diffusion mechanism whereby three different channels each act as entry and exit points.

Stem cells are known to differentiate in response to the chemical and mechanical properties of the substrates on which they are cultured. Thus, supramolecular biomaterials with tunable properties are well suited for the study of stem cell differentiation. In this report, we exploited this phenomenon by combining stem cell differentiation in hydrogels with variable stiffness and metabolomics analysis to identify specific bioactive lipids that are uniquely used up during differentiation. To achieve this, we cultured perivascular stem cells on supramolecular peptide gels of different stiffness, and metabolite depletion followed. On soft (1 kPa), stiff (13 kPa), and rigid (32 kPa) gels, we observed neuronal, chondrogenic, and osteogenic differentiation, respectively, showing that these stem cells undergo stiffness-directed fate selection. By analyzing concentration variances of >600 metabolites during differentiation on the stiff and rigid gels (and focusing on chondrogenesis and osteogenesis as regenerative targets, respectively), we identified that specific lipids (lysophosphatidic acid and cholesterol sulfate, respectively), were significantly depleted. We propose that these metabolites are therefore involved in the differentiation process. In order to unequivocally demonstrate that the lipid metabolites that we identified play key roles in driving differentiation, we subsequently demonstrated that these individual lipids can, when fed to standard stem cell cultures, induce differentiation toward chondrocyte and osteoblast phenotypes. Our concept exploits the design of supramolecular biomaterials as a strategy for discovering cell-directing bioactive metabolites of therapeutic relevance.

The thylakoid membrane has a unique lipid composition, consisting mostly of galactolipids. These thylakoid lipids have important roles in photosynthesis. Here, we investigate to what extent these lipids bind specifically to the Photosystem II complex. To this end, we performed coarse-grain MD simulations of the Photosystem II complex embedded in a thylakoid membrane with realistic composition. Based on >85 μs simulation time, we find that monogalactosyldiacylglycerol and sulfoquinovosyldiacylglycerol lipids are enriched in the annular shell around the protein, and form distinct binding sites. From the analysis of residue contacts, we conclude that electrostatic interactions play an important role in stabilizing these binding sites. Furthermore, we find that chlorophyll a has a prevalent role in the coordination of the lipids. In addition, we observe lipids to diffuse in and out of the plastoquinone exchange cavities, allowing exchange of cocrystallized lipids with the bulk membrane and suggesting a more open nature of the plastoquinone exchange cavity. Together, our data provide a wealth of information on protein-lipid interactions for a key protein in photosynthesis.

In this article, we demonstrate the non-aqueous self-assembly of a low-molecular-mass organic gelator based on an electroactive p-type tetrathiafulvalene (TTF)-dipeptide bioconjugate. We show that a TTF moiety appended with diphenylalanine amide derivative (TTF-FF-NH2) self-assembles into one-dimensional nanofibers that further lead to the formation of self-supporting organogels in chloroform and ethyl acetate. Upon doping of the gels with electron acceptors (TCNQ/iodine vapor), stable two-component charge transfer gels are produced in chloroform and ethyl acetate. These gels are characterized by various spectroscopy (UV-vis-NIR, FTIR and CD), microscopy (AFM and TEM), rheology and cyclic voltammetry techniques. Furthermore, conductivity measurements performed on TTF-FF-NH2 xerogel nanofiber networks formed between gold electrodes on a glass surface indicate that these nanofibers show a remarkable enhancement in the conductivity after doping with TCNQ.

Photosystem II (PSII) is one of the key protein complexes in photosynthesis. We introduce a coarse grained model of PSII and present the analysis of 60 µs molecular dynamics simulations of PSII in both monomeric and dimeric form, embedded in a thylakoid membrane model that reflects its native lipid composition. We describe in detail the setup of the protein complex and the many natural cofactors, and characterize their mobility. Overall we find that the protein subunits and cofactors are more flexible towards the periphery of the complex, as well as near the PLQ exchange cavity and at the dimer interface. Of all cofactors, β-carotenes show the highest mobility. Some of the β-carotenes diffuse in and out of the protein complex via the thylakoid membrane. In contrast to the PSII dimer, the monomeric form adopts a tilted conformation in the membrane, with strong interactions between the soluble PsbO subunit and the glycolipid headgroups. Interestingly, the tilted conformation causes buckling of the membrane. Together, our results provide an unprecedented view of PSII dynamics on a microsecond time scale. Our data may be used as basis for the interpretation of experimental data as well as for theoretical models describing exciton energy transfer.

The coassembly of small molecules is a useful means of increasing the complexity and functionality of their resultant supramolecular constructs in a modular fashion. In this study, we explore the assembly and coassembly of serine surfactants and tyrosine-leucine hydrogelators, capped at the N-termini with either fluorenyl-9-methoxycarbonyl (Fmoc) or pyrene. These systems all exhibit self-assembly behavior, which is influenced by aromatic stacking interactions, while the hydrogelators also exhibit β-sheet-type arrangements, which reinforce their supramolecular structures. We provide evidence for three distinct supramolecular coassembly models; cooperative, disruptive, and orthogonal. The coassembly mode adopted depends on whether the individual constituents (I) are sufficiently different, such that effective segregation and orthogonal assembly occurs; (II) adhere to a communal mode of self-assembly; or (III) act to compromise the assembly of one another via incorporation and disruption. We find that a greater scope for controllable coassembly exists within orthogonal systems; which show minimal relative changes in the native gelator's supramolecular structure by Fourier transform infrared spectroscopy (FTIR), circular dichroism (CD), and fluorescence spectroscopy. This is indicative of the segregation of orthogonal coassembly constituents into distinct domains, where surfactant chemical functionality is presented at the surface of the gelator's supramolecular fibers. Overall, this work provides new insights into the design of modular coassembly systems, which have the potential to augment the chemical and physical properties of existing gelator systems.

The development of multidimensional spectroscopic tools capable of resolving site-specific information about proteins and enzymes in the solution phase is an important aid to our understanding of biomolecular mechanisms, structure, and dynamics. Nicotinamide adenine dinucleotide (NAD) is a common biological substrate and so offers significant potential as an intrinsic vibrational probe of protein-ligand interactions but its complex molecular structure and incompletely characterized infrared spectrum currently limit its usefulness. Here, we report the FTIR spectroscopy of the oxidized and reduced forms of NAD at a range of pD values that relate to the "folded" and "unfolded" forms of the molecules that exist in solution. Comparisons with structural analogs and the use of density functional theory simulations provide a full assignment of the observed modes and their complex pD dependencies. Finally, ultrafast two-dimensional infrared spectra of the oxidized and reduced forms of NAD are reported and their usefulness as biomolecular probes is discussed.

Several short peptide sequences are known to self-assemble into supramolecular nanostructures with interesting properties. In this study, coarse-grained molecular dynamics is employed to rapidly screen all 400 dipeptide combinations and predict their ability to aggregate as a potential precursor to their self-assembly. The simulation protocol and scoring method proposed allows a rapid determination of whether a given peptide sequence is likely to aggregate (an indicator for the ability to self-assemble) under aqueous conditions. Systems that show strong aggregation tendencies in the initial screening are selected for longer simulations, which result in good agreement with the known self-assembly or aggregation of dipeptides reported in the literature. Our extended simulations of the diphenylalanine system show that the coarse-grain model is able to reproduce salient features of nanoscale systems and provide insight into the self-assembly process for this system.

The speed and angular distribution of O atoms arising from the photofragmentation of C(5)H(8)-O(2), the isoprene-oxygen van der Waals complex, in the wavelength region of 213-277 nm has been studied with the use of a two-color dissociation-probe method and the velocity map imaging technique. Dramatic enhancement in the O atoms photo-generation cross section in comparison with the photodissociation of individual O(2) molecules has been observed. Velocity map images of these "enhanced" O atoms consisted of five channels, different in their kinetic energy, angular distribution, and wavelength dependence. Three channels are deduced to be due to the one-quantum excitation of the C(5)H(8)-O(2) complex into the perturbed Herzberg III state ((3)Δ(u)) of O(2). This excitation results in the prompt dissociation of the complex giving rise to products C(5)H(8)+O+O when the energy of exciting quantum is higher than the complex photodissociation threshold, which is found to be 41740 ± 200 cm(-1) (239.6±1.2 nm). This last threshold corresponds to the photodissociation giving rise to an unexcited isoprene molecule. The second channel, with threshold shifted to the blue by 1480 ± 280 cm(-1), corresponds to dissociation with formation of rovibrationally excited isoprene. A third channel was observed at wavelengths up to 243 nm with excitation below the upper photodissociation threshold. This channel is attributed to dissociation with the formation of a bound O atom C(5)H(8)-O(2) + hv → C(5)H(8)-O(2)((3)Δ(u)) → C(5)H(8)O + O and/or to dissociation of O(2) with borrowing of the lacking energy from incompletely cooled complex internal degrees of freedom C(5)H(8)*-O(2) + hv → C(5)H(8)*-O(2)((3)Δ(u)) → C(5)H(8) + O + O. The kinetic energy of the O atoms arising in two other observed channels corresponds to O atoms produced by photodissociation of molecular oxygen in the excited a (1)Δ(g) and b (1)Σ(g)(+) singlet states as the precursors. This indicates the formation of singlet oxygen O(2)(a (1)Δ(g)) and O(2)(b (1)Σ(g)(+)) after excitation of the C(5)H(8)-O(2) complex. Cooperative excitation of the complex with a simultaneous change of the spin of both partners (1)X-(3)O(2) + hν → (3)X-(1)O(2) → (3)X + (1)O(2) is suggested as a source of singlet oxygen O(2)(a (1)Δ(g)) and O(2)(b (1)Σ(g)(+)). This cooperative excitation is in agreement with little or no vibrational excitation of O(2)(a (1)Δ(g)), produced from the C(5)H(8)-O(2) complex as studied in the current paper as well as from the C(3)H(6)-O(2) and CH(3)I-O(2) complexes reported in our previous paper [Baklanov et al., J. Chem. Phys. 126, 124316 (2007)]. The formation of O(2)(a (1)Δ(g)) from C(5)H(8)-O(2) was observed at λ(pump) = 213-277 nm with the yield going down towards the long wavelength edge of this interval. This spectral profile is interpreted as the red-side wing of the band of a cooperative transition (1)X-(3)O(2) + hν → (3)X(T(2))-(1)O(2)(a (1)Δ(g)) in the C(5)H(8)-O(2) complex.

Peptide based 2D nanostructures of micronscale size in both X and Y dimensions are extremely rare because amino acid chirality favours helical structures, and nucleation-growth mechanisms usually favour uni-directional growth. We demonstrate the production of extended two-dimensional (2D) peptide nanostructuresvia the thermolysin catalysed condensation of Fmoc protected hydrophilic amino acid (serine, Fmoc-S) and a hydrophobic amino acid ester (phenylalanine, F-OMe). We propose that lateral self-assembly is enabled by the reversible nature of the system, favouring the thermodynamic product (extended sheets) over kinetically favoured 1 dimensional structures. Fmoc-SF-OMe forms extended arrays of β-sheet structures interlock via π-stacking between Fmoc groups. We propose that, due to its alternating hydrophilic/hydrophobic amino acid sequence, amphiphilic sheets presenting either phenyl or hydroxyl functionality are formed that assemble pair-wise, thereby shielding hydrophobic groups from the aqueous environment. Formation of these structures was supported by fluorescence emission spectroscopy, FTIR and XRD analysis and molecular mechanics minimization. At enhanced enzyme concentrations, hierarchical self-assembly was observed giving rise to spherulitic structures, with the number of spherulites dictated by enzyme concentration.