Prediction of Thylakoid Lipid Binding Sites on Photosystem II

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

Supramolecular Nucleoside-Based Gel:Molecular Dynamics Simulation and Characterization of Its Nanoarchitecture and Self-Assembly Mechanism

Among the diversity of existing supramolecular hydrogels, nucleic acid-based hydrogels are of particular interest for potential drug delivery and tissue engineering applications because of their inherent biocompatibility. Hydrogel performance is directly related to the nanostructure and the self-assembly mechanism of the material, an aspect that is not well-understood for nucleic acid-based hydrogels in general and has not yet been explored for cytosine-based hydrogels in particular. Herein, we use a broad range of experimental characterization techniques along with molecular dynamics (MD) simulation to demonstrate the complementarity and applicability of both approaches for nucleic acid-based gelators in general and propose the self-assembly mechanism for a novel supramolecular gelator, N4-octanoyl-2′-deoxycytidine. The experimental data and the MD simulation are in complete agreement with each other and demonstrate the formation of a hydrophobic core within the fibrillar structures of these mainly water-containing materials. The characterization of the distinct duality of environments in this cytidine-based gel will form the basis for further encapsulation of both small hydrophobic drugs and biopharmaceuticals (proteins and nucleic acids) for drug delivery and tissue engineering applications

Exchange pathways of plastoquinone and plastoquinol in the photosystem II complex

Plastoquinone (PLQ) acts as an electron carrier between photosystem II (PSII) and the cytochrome b(6)f 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

Alignment of nanostructured tripeptide gels by directional ultrasonication

We demonstrate an in-situ ultrasonic approach to influence self-assembly across the supramolecular to micron length scales, showing enhancement of supramolecular interactions, chirality and orientation, which depends on the peptide sequence and solvent environment. This is the first successful demonstration of using oscillating pressure waves to generate anisotropic organo- and hydro- gels consisting of oriented tripeptides structures

Caught in the Act:Mechanistic Insight into Supramolecular Polymerization-Driven Self-Replication from Real-Time Visualization

Self-assembly features prominently in fields ranging from materials science to biophysical chemistry. Assembly pathways, often passing through transient intermediates, can control the outcome of assembly processes. Yet, the mechanisms of self-assembly remain largely obscure due to a lack of experimental tools for probing these pathways at the molecular level. Here, the self-assembly of self-replicators into fibers is visualized in real-time by high-speed atomic force microscopy (HS-AFM). Fiber growth requires the conversion of precursor molecules into six-membered macrocycles, which constitute the fibers. HS-AFM experiments, supported by molecular dynamics simulations, revealed that aggregates of precursor molecules accumulate at the sides of the fibers, which then diffuse to the fiber ends where growth takes place. This mechanism of precursor reservoir formation, followed by one-dimensional diffusion, which guides the precursor molecules to the sites of growth, reduces the entropic penalty associated with colocalizing precursors and growth sites and constitutes a new mechanism for supramolecular polymerization

Structural and Spectroscopic Properties of Assemblies of Self-Replicating Peptide Macrocycles

Self-replication at the molecular level is often seen as essential to the early origins of life. Recently a mechanism of self-replication has been discovered in which replicator self-assembly drives the process. We have studied one of the examples of such self-assembling self-replicating molecules to a high level of structural detail using a combination of computational and spectroscopic techniques. Molecular Dynamics simulations of self-assembled stacks of peptide-derived replicators provide insights into the structural characteristics of the system and serve as the basis for semiempirical calculations of the UV-vis, circular dichroism (CD) and infrared (IR) absorption spectra that reflect the chiral organization and peptide secondary structure of the stacks. Two proposed structural models are tested by comparing calculated spectra to experimental data from electron microscopy, CD and IR spectroscopy, resulting in a better insight into the specific supramolecular interactions that lead to self-replication. Specifically, we find a cooperative self-assembly process in which β-sheet formation leads to well-organized structures, while also the aromatic core of the macrocycles plays an important role in the stability of the resulting fibers

Polymeric peptide pigments with sequence-encoded properties

Melanins are a family of heterogeneous polymeric pigments that provide ultraviolet (UV) light protection, structural support, coloration, and free radical scavenging. Formed by oxidative oligomerization of catecholic small molecules, the physical properties of melanins are influenced by covalent and noncovalent disorder. We report the use of tyrosine-containing tripeptides as tunable precursors for polymeric pigments. In these structures, phenols are presented in a (supra-)molecular context dictated by the positions of the amino acids in the peptide sequence. Oxidative polymerization can be tuned in a sequence-dependent manner, resulting in peptide sequence–encoded properties such as UV absorbance, morphology, coloration, and electrochemical properties over a considerable range. Short peptides have low barriers to application and can be easily scaled, suggesting near-term applications in cosmetics and biomedicine

Structure, dynamics and applications of peptide-based nanomaterials

Peptide-based nanomaterials have rapidly gained interest over the last 10 years, because of their potential uses in biomedicine, nanotechnology and catalysis. Short peptides can readily self-assemble into ordered structures on the nanometer length scale. The design rules for these constructs are not fully understood yet, which is a key issue in engineering new functional nanomaterials. This thesis discusses how infrared spectroscopy and computational chemistry can contribute to the understanding of structure and dynamics of peptide-based selfassembled systems. Quantum mechanical calculations will be discussed in the light of determining stacking interactions between aromatic peptide amphiphiles and predicting their infrared absorptions bands. Furthermore, in case studies of various peptides, both IR spectroscopy and all-atom MD are demonstrated to be sensitive to small changes in the supramolecular structure as a consequence of variations in the amino acid side chains of the peptides under study. However, currently all-atom MD is still somewhat limited by computational costs and the specific assignments of the bands in IR spectra are not always clear. With a lower level of detail in MD simulations, information relevant to the time and length scales of the process of self-assembly can be obtained. The coarse-grain simulation protocol developed here shows good agreement with experiments in terms of predicting a peptide's propensity to aggregate and can reproduce morphological features of self-assembled systems. Finally, these peptide-based materials are applied in encapsulating an enzyme active site mimic that is of relevance for the cheap, environmentally friendly production of hydrogen as a fuel. Using time-resolved infrared spectroscopy it is shown that the hydrogel environment formed by a short, amphiphilic peptide protected the enzyme 15 mimic both from degradation by oxygen and UV irradiation. This type of peptide scaffolding for hydrogenase mimics has potential in creating an artificial enzyme for the reversible oxidation of hydrogen.Peptide-based nanomaterials have rapidly gained interest over the last 10 years, because of their potential uses in biomedicine, nanotechnology and catalysis. Short peptides can readily self-assemble into ordered structures on the nanometer length scale. The design rules for these constructs are not fully understood yet, which is a key issue in engineering new functional nanomaterials. This thesis discusses how infrared spectroscopy and computational chemistry can contribute to the understanding of structure and dynamics of peptide-based selfassembled systems. Quantum mechanical calculations will be discussed in the light of determining stacking interactions between aromatic peptide amphiphiles and predicting their infrared absorptions bands. Furthermore, in case studies of various peptides, both IR spectroscopy and all-atom MD are demonstrated to be sensitive to small changes in the supramolecular structure as a consequence of variations in the amino acid side chains of the peptides under study. However, currently all-atom MD is still somewhat limited by computational costs and the specific assignments of the bands in IR spectra are not always clear. With a lower level of detail in MD simulations, information relevant to the time and length scales of the process of self-assembly can be obtained. The coarse-grain simulation protocol developed here shows good agreement with experiments in terms of predicting a peptide's propensity to aggregate and can reproduce morphological features of self-assembled systems. Finally, these peptide-based materials are applied in encapsulating an enzyme active site mimic that is of relevance for the cheap, environmentally friendly production of hydrogen as a fuel. Using time-resolved infrared spectroscopy it is shown that the hydrogel environment formed by a short, amphiphilic peptide protected the enzyme 15 mimic both from degradation by oxygen and UV irradiation. This type of peptide scaffolding for hydrogenase mimics has potential in creating an artificial enzyme for the reversible oxidation of hydrogen