An Atomistic View on the Mechanism of Diatom Peptide-Guided Biomimetic Silica Formation.

Deciphering nature's remarkable way of encoding functions in its biominerals holds the potential to enable the rational development of nature-inspired materials with tailored properties. However, the complex processes that convert solution-state precursors into solid biomaterials remain largely unknown. In this study, an unconventional approach is presented to characterize these precursors for the diatom-derived peptides R5 and synthetic Silaffin-1A1 (synSil-1A1). These molecules can form defined supramolecular assemblies in solution, which act as templates for solid silica structures. Using a tailored structural biology toolbox, the structure-function relationships of these self-assemblies are unveiled. NMR-derived constraints are employed to enable a recently developed fractal-cluster formalism and then reveal the architecture of the peptide assemblies in atomistic detail. Finally, by monitoring the self-assembly activities during silica formation at simultaneous high temporal and residue resolution using real-time spectroscopy, the mechanism is elucidated underlying template-driven silica formation. Thus, it is demonstrated how to exercise morphology control over bioinorganic solids by manipulating the template architectures. It is found that the morphology of the templates is translated into the shape of bioinorganic particles via a mechanism that includes silica nucleation on the solution-state complexes' surfaces followed by complete surface coating and particle precipitation.

Incorporation of Indoylated Phenylalanine Yields a Sub-Micromolar Selective Melanocortin-4 Receptor Antagonist Tetrapeptide.

The melanocortin family is involved in many physiological functions, including pigmentation, steroidogenesis, and appetite. The centrally expressed melanocortin-3 and melanocortin-4 receptors (MC3R and MC4R) possess overlapping but distinct roles in energy homeostasis. Herein, the third and fourth positions of a tetrapeptide lead compound [Ac-Arg-Arg-(pI)DPhe-Tic-NH2], previously reported to possess MC3R agonist and MC4R antagonist activities, were substituted with indoylated phenylalanine (Wsf/Wrf) residues in an attempt to generate receptor subtype selective compounds. At the third position, d-amino acids were required for melanocortin agonist activity, while both l- and d-residues resulted in MC4R antagonist activity. These results indicate that l-indoylated phenylalanine residues at the third position of the scaffold can generate MC4R over MC3R selective antagonist ligands, resulting in a substitution pattern that may be exploited for novel MC4R ligands that can be used to probe the in vivo activity of the MC4R without involvement of the MC3R.

The silica mineralisation properties of synthetic Silaffin-1A1 (synSil-1A1).

The synthetic monodisperse pentadecapeptide synSil-1A1 is a representative of the microdisperse mixture of the native silaffin natSil-1A1 produced by the diatom Cylindrotheca fusiformis. The octaphosphorylated zwitterionic synSil-1A1 is able to mineralise silica under slightly acidic conditions at pH 5.5, which is the physiologically relevant pH range assumed. Like the posttranslational modifications of the native silaffins, synSil-1A1 is functionalised on all four lysine and phosphorylated on all seven serine residues. We describe the synthesis of a trimethyl-δ-hydroxy-L-lysine building block, the incorporation of this choline-type amino acid in peptide synthesis and its phosphorylation, together with all further posttranslational modifications observed in the native silaffins. Quantitative structure-activity relationships from silicification experiments at high dilution reveal the unique mineralisation properties of the hyperphosphorylated peptide as a single substance and in interaction with long-chain polyamines (LCPA). Diffusion-ordered spectroscopy (DOSY) experiments reveal the formation of polyelectrolyte complexes (PEC) between synSil-1A1 and long-chain polyamines, which promotes the silicification process. The microdroplets have an overall balanced ratio of 100-150 cationic and the same number of anionic charges. The unique zwitterionic synSil-1A1 confirms the prevailing molecular model of biosilicification and validates it with quantitative data based on a single phosphopeptide species, avoiding the usual unphysiologically high concentrations of phosphate of many previous in vitro silicification experiments.

High five! Methyl probes at five ring positions of phenylalanine explore the hydrophobic core dynamics of zinc finger miniproteins.

The elucidation of internal dynamics in proteins is essential for the understanding of their stability and functionality. Breaking the symmetry of the degenerate rotation of the phenyl side chain provides additional structural information and allows a detailed description of the dynamics. Based on this concept, we propose a combination of synthetic and computational methods, to study the rotational mobility of the Phe ring in a sensitive zinc finger motif. The systematic methyl hopping around the phenylalanine ring yields o-, m-, p-tolyl and xylyl side chains that provide a vast array of additional NOE contacts, allowing the precise determination of the orientation of the aromatic ring. MD simulations and metadynamics complement these findings and facilitate the generation of free energy profiles for each derivative. Previous studies used a wide temperature window in combination with NMR spectroscopy to elucidate the side chain mobility of stable proteins. The zinc finger moiety exhibits a limited thermodynamic stability in a temperature range of only 40 K, making this approach impractical for this compound class. Therefore, we have developed a method that can be applied even to thermolabile systems and facilitates the detailed investigation of protein dynamics.

Tryptophan Analogues with Fixed Side-Chain Orientation: Expanding the Scope.

A generalized synthetic strategy is proposed here for the synthesis of asymmetric ß-indoylated amino acids by 8-aminoquinoline (8AQ)-directed C(sp3)-H functionalization of suitably protected precursors. Peptides containing one of the four stereoisomers of (indol-3-yl)-3-phenylalanine at position 2 of the parent peptide KwFwLL-NH2 (w=d-Trp) cover a wide range of activities as ghrelin receptor inverse agonists, among them the most active described until now. This application exemplarily shows how ß-indoylated amino acids can be used for the systematic variation of the position of an indole group in a bioactive peptide.

Covalent Linkage and Macrocylization Preserve and Enhance Synergistic Interactions in Catalytic Amyloids.

The self-assembly of short peptides into catalytic amyloid-like nanomaterials has proven to be a powerful tool in both understanding the evolution of early proteins and identifying new catalysts for practically useful chemical reactions. Here we demonstrate that both parallel and antiparallel arrangements of ß-sheets can accommodate metal ions in catalytically productive coordination environments. Moreover, synergistic relationships, identified in catalytic amyloid mixtures, can be captured in macrocyclic and sheet-loop-sheet species, that offer faster rates of assembly and provide more complex asymmetric arrangements of functional groups, thus paving the way for future designs of amyloid-like catalytic proteins. Our findings show how initial catalytic activity in amyloid assemblies can be propagated and improved in more-complex molecules, providing another link in a complex evolutionary chain between short, potentially abiotically produced peptides and modern-day enzymes.

Interactions of Long-Chain Polyamines with Silica Studied by Molecular Dynamics Simulations and Solid-State NMR Spectroscopy.

The investigation of molecular interactions between silica phases and organic components is crucial for elucidating the main steps involved in the biosilica mineralization process. In this respect, the structural characterization of the organic/inorganic interface is particularly useful for a deeper understanding of the dominant mechanisms of biomineralization. In this work, we have investigated the interaction of selectively 13C- and 15N-labeled atoms of organic long-chain polyamines (LCPAs) with 29Si-labeled atoms of a silica layer at the molecular level. In particular, silica/LCPA nanocomposites were analyzed by solid-state NMR spectroscopy in combination with all-atom molecular dynamics simulations. Solid-state NMR experiments allow the determination of 29Si-15N and 29Si-13C internuclear distances, providing the parameters for direct verification of atomistic simulations. Our results elucidate the relevant molecular conformations as well as the nature of the interaction between the LCPA and a silica substrate. Specifically, distances and second moments suggest a picture compatible with (i) LCPA completely embedded in the silica phase and (ii) the charged amino groups located in close vicinity of silanol groups.

Unexpected formation of a co-crystal containing the chalcone (E)-1-(5-chloro-thio-phen-2-yl)-3-(3-methyl-thio-phen-2-yl)prop-2-en-1-one and the keto-enol tautomer (Z)-1-(5-chloro-thio-phen-2-yl)-3-(3-methyl-thio-phen-2-yl)prop-1-en-1-ol.

The title crystal structure is assembled from the superposition of two mol-ecular structures, (E)-1-(5-chloro-thio-phen-2-yl)-3-(3-methyl-thio-phen-2-yl)prop-2-en-1-one, C12H9ClOS2 (93%), and (Z)-1-(5-chloro-thio-phen-2-yl)-3-(3-methyl-thio-phen-2-yl)prop-1-en-1-ol, C12H11ClOS2 (7%), 0.93C12H9ClOS2·0.07C12H11ClOS2. Both were obtained from the reaction of 3-methyl-thio-phene-2-carbaldehyde and 1-(5-chloro-thio-phen-2-yl)ethanone. In the extended structure of the major chalcone component, mol-ecules are linked by a combination of C-H⋯O/S, Cl⋯Cl, Cl⋯π and π-π inter-actions, leading to a compact three-dimensional supra-molecular assembly.

Phosphate-Silica Interactions in Diatom Biosilica and Synthetic Composites Studied by Rotational Echo Double Resonance (REDOR) NMR Spectroscopy.

Biosilica is a biogenic composite material produced by organisms like diatoms. Various biomolecules are tightly attached or incorporated into biosilica. Examples are special proteins termed silaffins and long-chain polyamines (LCPAs). Presumably, these biomolecules are involved in the biosilica formation process. Silaffins are highly phosphorylated zwitterions with LCPAs post-translationally attached to lysine residues. In the present work, we use distance-dependent solid-state NMR experiments, especially the 31P{29Si} Rotational Echo Double Resonance (REDOR) technique, to study the environment of phosphate moieties in biosilica and in vitro synthesized SiO2-based composites. In contrast to the heterogeneous mixtures of biomolecules found in native biosilica, the described in vitro silicification experiments make use of a single synthetic phosphopeptide and an LCPA of well-defined and uniform structure. The heteronuclear correlations measured from these silica composites provide reliable 31P-29Si dipolar second moments and information about the distribution of the phosphopeptide within the silica material. The calculated second moment indicates close contact between phosphopeptides and silica. The phosphopeptides are incorporated into the silica composite in a disperse manner. Moreover, the REDOR data acquired for diatom biosilica also imply that phosphate groups are part of the silica-organic interface in this material.

Defining the mobility range of a hinge-type connection using molecular dynamics and metadynamics.

A designed disulfide-rich ß-hairpin peptide that dimerizes spontaneously served as a hinge-type connection between proteins. Here, we analyze the range of dynamics of this hinge dimer with the aim of proposing new applications for the DNA-encodable peptide and establishing guidelines for the computational analysis of other disulfide hinges. A recent structural analysis based on nuclear magnetic resonance spectroscopy and ion mobility spectrometry revealed an averaged conformation in the hinge region which motivated us to investigate the dynamic behavior using a combination of molecular dynamics simulation, metadynamics and free energy surface analysis to characterize the conformational space available to the hinge. Principal component analysis uncovered two slow modes of the peptide, namely, the opening and closing motion and twisting of the two ß-hairpins assembling the hinge. Applying a collective variable (CV) that mimics the first dominating mode, led to a major expansion of the conformational space. The description of the dynamics could be achieved by analysis of the opening angle and the twisting of the ß-hairpins and, thus, offers a methodology that can also be transferred to other derivatives. It has been demonstrated that the hinge peptide's lowest energy conformation consists of a large opening angle and strong twist but is separated by small energy barriers and can, thus, adopt a closed and untwisted structure. With the aim of proposing further applications for the hinge peptide, we simulated its behavior in the sterically congested environment of a four-helix bundle. Preliminary investigations show that one helix is pushed out and a three-helix bundle forms. The insights gained into the dynamics of the tetra-disulfide peptide and analytical guidelines developed in this study may contribute to the understanding of the structure and function of more complex hinge-type proteins, such as the IgG antibody family.

Comparing the Hinge-Type Mobility of Natural and Designed Intermolecular Bi-disulfide Domains.

A pair of intermolecular disulfide bonds connecting two protein domains restricts their relative mobility in a systematic way. The bi-disulfide hinge cannot rotate like a single intermolecular disulfide bond yet is less restrained than three or more intermolecular disulfides which restrict the relative motion to a minimum. The intermediate mobility of bi-disulfide linked domains is characterized by their dominating opening and closing modes comparable to the mechanics of a door hinge on the macroscopic scale. Here we compare the central hinge region of Immunoglobulin G1 (IgG1) which is highly conserved among different species, with a recently designed hinge-type motif CHWECRGCRLVC from our lab, that was successfully used for the dimerization of the IgG1/κ-ab CL4 monocolonal antibody (mab). The minimal length of these synthetic hinges comprises only 12 amino acids, rendering them ideal models for computational studies. Well-tempered metadynamics was performed to adequately describe the available conformational space defined by the different hinges. In spite of the differences in amino acid composition and ring sizes, there are characteristic similarities of designed and natural hinges like the dependent mobility of the individual strands of each hinge domain.

The role of phosphopeptides in the mineralisation of silica.

We investigated the silicification activity of hyperphosphorylated peptides in combination with long-chain polyamines (LCPA). The bioinspired in vitro silicification experiments with peptides containing different amounts of phosphorylated serines showed structure-activity dependence by altering the amount and morphology of the silica precipitate. Our study provides an explanation for the considerable metabolic role of diatoms in the synthesis of hyperphosphorylated poly-cationic peptides such as natSil-1A1. The efficient late-stage phosphorylation of peptides yielded a synthetic heptaphosphopeptide whose silicification properties resemble those of natSil-1A1. As opposed to this, unphosphorylated poly-cationic peptides or LCPA require concentrations above 1 mM for silicification. Hyperphosphorylated peptides showed a linear dependence between the amount of dissolved peptides and the amount of precipitated silica in the concentration range below 1 mM. Under mildly acidic conditions and short precipitation times, the concentration of the added LCPA determined the size of the silica spheres.

Directed C(sp3)-H arylation of tryptophan: transformation of the directing group into an activated amide.

The 8-aminoquinoline (8AQ) directed C(sp3)-H functionalization was applied in the synthesis of ß-arylated tryptophan derivatives. The laborious protecting group reorganization towards α-amino acids compatible for solid phase peptide synthesis (SPPS) was cut short by the transformation of the directing group into an activated amide, which was either used directly in peptide coupling or in the gram scale synthesis of storable Fmoc-protected amino acids for SPPS. In this work, directed C-H activation and nonplanar amide chemistry complement each other for the synthesis of hybrids between phenylalanine and tryptophan with restricted side chain mobility.

The Synthesis, Characterization, Cytotoxic Activity Assessment and Structure-Activity Relationship of 4-Aryl-6-(2,5-dichlorothiophen-3-yl)-2-methoxypyridine-3-carbonitriles.

A series of 2-methoxypyridine-3-carbonitrile (5a-i)-bearing aryl substituents were successfully synthesized in good yields by the condensation of chalcones (4a-i) with malononitrile in basic medium. The condensation process, in most cases, offers a route to a variety of methoxypyridine derivatives (6a-g) as side products in poor yields. All new compounds were fully characterized using different spectroscopic methods. Mass ESI-HMRS measurements were also performed. Furthermore, these compounds were screened for their in vitro cytotoxicity activities against three cancer cell lines; namely, those of the liver (line HepG2), prostate (line DU145) and breast (line MBA-MB-231). The cytotoxicity assessment revealed that compounds 5d, 5g, 5h and 5i exhibit promising antiproliferative effects (IC50 1-5 µM) against those three cancer cell lines.

Reversible Covalent End-Capping of Collagen Model Peptides.

The combination of supramolecular aggregation of collagen model peptides with reversible covalent end-capping of the formed triple helix in a single experimental set-up yielded minicollagens, which were characterized by a single melting temperature. In spite of the numerous possible reaction intermediates, a specific synthetic collagen with a leading, middle and trailing strand is formed in a highly cooperative self-assembly process.

Synthesis, characterization, crystal structure and supra-molecularity of ethyl (E)-2-cyano-3-(3-methyl-thio-phen-2-yl)acrylate and a new polymorph of ethyl (E)-2-cyano-3-(thio-phen-2-yl)acrylate.

The synthesis, crystal structure and structural motif of two thio-phene-based cyano-acrylate derivatives, namely, ethyl (E)-2-cyano-3-(3-methyl-thio-phen-2-yl)acrylate (1), C11H11NO2S, and ethyl (E)-2-cyano-3-(thio-phen-2-yl)acrylate (2), C10H9NO2S, are reported. Derivative 1 crystallized with two independent molecules in the asymmetric unit, and derivative 2 represents a new monoclinic (C2/m) polymorph. The mol-ecular conformations of 1 and the two polymorphs of 2 are very similar, as all non-H atoms are planar except for the methyl of the ethyl groups. The inter-molecular inter-actions and crystal packing of 1 and 2 are described and compared with that of the reported monoclinic (C2/m) polymorph of derivative 2 [Castro Agudelo et al. (2017 ▸). Acta Cryst. E73, 1287-1289].

Side Chain Orientation of Tryptophan Analogues Determines Agonism and Inverse Agonism in Short Ghrelin Peptides.

We describe two synthetic amino acids with inverted side chain stereochemistry, which induce opposite biological activity. Phe4 is an important part of the activation motif of ghrelin, and in short peptide inverse agonists such as KwFwLL-NH2 , the aromatic core is necessary for inactivation of the receptor. To restrict indole/phenyl mobility and simultaneously strengthen the interaction between peptide and receptor, we exchanged the natural monoaryl amino acids for diaryl amino acids derived from tryptophan. By standard solid-phase peptide synthesis, each of them was inserted into ghrelin or in the aromatic core of the inverse agonist. Both ghrelin analogues showed nanomolar activity, indicating sufficient space to accommodate the additional side chain. In contrast, diaryl amino acids in the inverse agonist had considerable influence on receptor signaling. Whereas the introduction of Wsf maintains inverse agonism of the peptide, Wrf shifts the receptor more to active states and can induce agonism depending on its introduction site.

Diamondoid Amino Acid-Based Peptide Kinase†A Inhibitor Analogues.

The incorporation of diamondoid amino acids (DAAs) into peptide-like drugs is a general strategy to improve lipophilicity, membrane permeability, and metabolic stability of peptidomimetic pharmaceuticals. We designed and synthesized five novel peptidic DAA-containing kinase inhibitors of protein kinase A using a sophisticated molecular dynamics protocol and solid-phase peptide synthesis. By means of a thermophoresis binding assay, NMR, and crystal structure analysis, we determined the influence of the DAAs on the secondary structure and binding affinity in comparison to the native protein kinase inhibitor, which is purely composed of proteinogenic amino acids. Affinity and binding pose are largely conserved. One variant showed 6.5-fold potency improvement, most likely related to its increased side chain lipophilicity. A second variant exhibited slightly decreased affinity presumably due to loss of hydrogen-bond contacts to surrounding water molecules of the first solvation shell.

A set of conformationally well-defined L/D-peptide epitopes provides a serological bar code for autoantibody subtypes.

Which conformational parameters lead to an antibody-affine peptide antigen? And in how many different conformations can we actually present the respective conformational epitope? To provide answers from a chemical point of view, we direct the bending and tethering of peptide backbones by the utilisation of a hydrophobic cluster, disulfides, and d-amino acids. Each mutation is employed pairwise on directly opposite sides of a ß-hairpin. In combination, these synthetic modules guide the formation of complementary ß-sheet-like structures, whereby the oppositely configured (l/d-)bi-disulfide pairs form with high regioselectivity. The conformational properties of the peptides are assessed by NMR spectroscopy and correlated with their antibody affinity in ELISA. From a pool of thus designed peptide antigens with distinctive complementary affinities against known rheumatoid arthritis (RA) autoantibodies, we select a set of epitopes for an immunoassay with sera of RA patients. We want to put emphasis on the idea, that the different conformational properties of the chosen antigens, containing the same epitope sequence, are mirrored in the distribution of autoantibody subtypes (or of the antibody polyclonality, respectively). Such directly comparable information can only be delivered by a set of peptides, rather than a single one. The hairpin-restriction technology of l/d-configured bi-disulfide amino acid pairs is not limited to RA but applicable to other shape-persistent hairpin motifs which are supposed to identify subgroups of protein receptors.

Hinge-Type Dimerization of Proteins by a Tetracysteine Peptide of High Pairing Specificity.

Dimeric disulfide-linked peptides are formed by the regioselective oxidative folding of thiol precursors containing the CX3CX2CX3C tetracysteine motif. Here, we investigate the general applicability of this peptide as a dimerization motif for different proteins. By recombinant DNA technology, the peptide CHWECRGCRLVC was loaded with proteins, and functional homodimers were obtained upon oxidative folding. Attached to the N-terminus of the dodecapeptide, the prokaryotic enzyme limonene epoxide hydrolase (LEH) completely forms a covalent antiparallel dimer. In a diatom expression system, the monoclonal antibody CL4 mAb is released in its functional form when its natural CPPC central parallel hinge is exchanged for the designed tetra-Cys hinge motif. To improve our understanding of the regioselectivity of tetra-disulfide formation, we provoked the formation of heterodimeric hinge peptides by mixing two different tetra-Cys peptides and characterizing the heterodimer by mass spectrometry and nuclear magnetic resonance spectroscopy.