Structural and biochemical characterization of Arabidopsis alcohol dehydrogenases reveals distinct functional properties but similar redox sensitivity

Alcohol dehydrogenases (ADHs) are a group of zinc-binding enzymes belonging to the medium-length dehydrogenase/reductase (MDR) protein superfamily. In plants, these enzymes fulfill important functions involving the reduction of toxic aldehydes to the corresponding alcohols (as well as catalyzing the reverse reaction, i.e., alcohol oxidation; ADH1) and the reduction of nitrosoglutathione (GSNO; ADH2/GSNOR). We investigated and compared the structural and biochemical properties of ADH1 and GSNOR from Arabidopsis thaliana. We expressed and purified ADH1 and GSNOR and determined two new structures, NADH-ADH1 and apo-GSNOR, thus completing the structural landscape of Arabidopsis ADHs in both apo- and holo-forms. A structural comparison of these Arabidopsis ADHs revealed a high sequence conservation (59% identity) and a similar fold. In contrast, a striking dissimilarity was observed in the catalytic cavity supporting substrate specificity and accommodation. Consistently, ADH1 and GSNOR showed strict specificity for their substrates (ethanol and GSNO, respectively), although both enzymes had the ability to oxidize long-chain alcohols, with ADH1 performing better than GSNOR. Both enzymes contain a high number of cysteines (12 and 15 out of 379 residues for ADH1 and GSNOR, respectively) and showed a significant and similar responsivity to thiol-oxidizing agents, indicating that redox modifications may constitute a mechanism for controlling enzyme activity under both optimal growth and stress conditions.

Characterization of chloroplast ribulose-5-phosphate-3-epimerase from the microalga Chlamydomonas reinhardtii

Carbon fixation relies on Rubisco and 10 additional enzymes in the Calvin-Benson-Bassham cycle. Epimerization of xylulose-5-phosphate (Xu5P) into ribulose-5-phosphate (Ru5P) contributes to the regeneration of ribulose-1,5-bisphosphate, the substrate of Rubisco. Ribulose-5-phosphate-3-epimerase (RPE, EC 5.1.3.1) catalyzes the formation of Ru5P, but it can also operate in the pentose-phosphate pathway by catalyzing the reverse reaction. Here, we describe the structural and biochemical properties of the recombinant RPE isoform 1 from Chlamydomonas (Chlamydomonas reinhardtii) (CrRPE1). The enzyme is a homo-hexamer that contains a zinc ion in the active site and exposes a catalytic pocket on the top of an α8β8 triose isomerase-type barrel as observed in structurally solved RPE isoforms from both plant and non-plant sources. By optimizing and developing enzyme assays to monitor the reversible epimerization of Ru5P to Xu5P and vice versa, we determined the catalytic parameters that differ from those of other plant paralogs. Despite being identified as a putative target of multiple thiol-based redox modifications, CrRPE1 activity is not affected by both reductive and oxidative treatments, indicating that enzyme catalysis is insensitive to possible redox alterations of cysteine residues. We mapped phosphorylation sites on the crystal structure, and the specific location at the entrance of the catalytic cleft supports a phosphorylation-based regulatory mechanism. This work provides an accurate description of the structural features of CrRPE1 and an in-depth examination of its catalytic and regulatory properties highlighting the physiological relevance of this enzyme in the context of photosynthetic carbon fixation.

Stearate-Coated Biogenic Calcium Carbonate from Waste Seashells: A Sustainable Plastic Filler

Waste seashells from aquaculture are a massive source of biogenic calcium carbonate (bCC) that can be a potential substitute for ground calcium carbonate and precipitated calcium carbonate. These last materials find several applications in industry after a surface coating with hydrophobic molecules, with stearate as the most used. Here, we investigate for the first time the capability of aqueous stearate dispersions to coat bCC powders from seashells of market-relevant mollusc aquaculture species, namely the oyster Crassostrea gigas, the scallop Pecten jacobaeus, and the clam Chamelea gallina. The chemical-physical features of bCC were extensively characterized by different analytical techniques. The results of stearate adsorption experiments showed that the oyster shell powder, which is the bCC with a higher content of the organic matrix, showed the highest adsorption capability (about 23 wt % compared to 10 wt % of geogenic calcite). These results agree with the mechanism proposed in the literature in which stearate adsorption mainly involves the formation of calcium stearate micelles in the dispersion before the physical adsorption. The coated bCC from oyster shells was also tested as fillers in an ethylene vinyl acetate compound used for the preparation of shoe soles. The obtained compound showed better mechanical performance than the one prepared using ground calcium. In conclusion, we can state that bCC can replace ground and precipitated calcium carbonate and has a higher stearate adsorbing capability. Moreover, they represent an environmentally friendly and sustainable source of calcium carbonate that organisms produce by high biological control over composition, polymorphism, and crystal texture. These features can be exploited for applications in fields where calcium carbonate with selected features is required.

Nanocrystalline and Amorphous Calcium Carbonate from Waste Seashells by Ball Milling Mechanochemistry Processes

Nanocrystalline calcium carbonate (CaCO3) and amorphous CaCO3 (ACC) are materials of increasing technological interest. Nowadays, they are mainly synthetically produced by wet reactions using CaCO3 reagents in the presence of stabilizers. However, it has recently been discovered that ACC can be produced by ball milling calcite. Calcite and/or aragonite are the mineral phases of mollusk shells, which are formed from ACC precursors. Here, we investigated the possibility to convert, on a potentially industrial scale, the biogenic CaCO3 (bCC) from waste mollusk seashells into nanocrystalline CaCO3 and ACC. Waste seashells from the aquaculture species, namely oysters (Crassostrea gigas, low-Mg calcite), scallops (Pecten jacobaeus, medium-Mg calcite), and clams (Chamelea gallina, aragonite) were used. The ball milling process was carried out by using different dispersing solvents and potential ACC stabilizers. Structural, morphological, and spectroscopic characterization techniques were used. The results showed that the mechanochemical process produced a reduction of the crystalline domain sizes and formation of ACC domains, which coexisted in microsized aggregates. Interestingly, bCC behaved differently from the geogenic CaCO3 (gCC), and upon long milling times (24 h), the ACC reconverted into crystalline phases. The aging in diverse environments of mechanochemically treated bCC produced a mixture of calcite and aragonite in a species-specific mass ratio, while the ACC from gCC converted only into calcite. In conclusion, this research showed that bCC can produce nanocrystalline CaCO3 and ACC composites or mixtures having species-specific features. These materials can enlarge the already wide fields of applications of CaCO3, which span from medical to material science.

Assembly of the Intraskeletal Coral Organic Matrix during Calcium Carbonate Formation

Scleractinia coral skeleton formation occurs by a heterogeneous process of nucleation and growth of aragonite in which intraskeletal soluble organic matrix molecules, usually referred to as SOM, play a key role. Several studies have demonstrated that they influence the shape and polymorphic precipitation of calcium carbonate. However, the structural aspects that occur during the growth of aragonite have received less attention. In this research, we study the deposition of calcium carbonate on a model substrate, silicon, in the presence of SOM extracted from the skeleton of two coral species representative of different living habitats and colonization strategies, which we previously characterized. The study is performed mainly by grazing incidence X-ray diffraction with the support of Raman spectroscopy and electron and optical microscopies. The results show that SOM macromolecules once adsorbed on the substrate self-assembled in a layered structure and induced the oriented growth of calcite, inhibiting the formation of vaterite. Differently, when SOM macromolecules were dispersed in solution, they induced the deposition of amorphous calcium carbonate (ACC), still preserving a layered structure. The entity of these effects was species-dependent, in agreement with previous studies. In conclusion, we observed that in the setup required by the experimental procedure, the SOM from corals appears to present a 2D lamellar structure. This structure is preserved when the SOM interacts with ACC but is lost when the interaction occurs with calcite. This knowledge not only is completely new for coral biomineralization but also has strong relevance in the study of biomineralization on other organisms.

Conformational Disorder Analysis of the Conditionally Disordered Protein CP12 from Arabidopsis thaliana in Its Different Redox States

CP12 is a redox-dependent conditionally disordered protein universally distributed in oxygenic photosynthetic organisms. It is primarily known as a light-dependent redox switch regulating the reductive step of the metabolic phase of photosynthesis. In the present study, a small angle X-ray scattering (SAXS) analysis of recombinant Arabidopsis CP12 (AtCP12) in a reduced and oxidized form confirmed the highly disordered nature of this regulatory protein. However, it clearly pointed out a decrease in the average size and a lower level of conformational disorder upon oxidation. We compared the experimental data with the theoretical profiles of pools of conformers generated with different assumptions and show that the reduced form is fully disordered, whereas the oxidized form is better described by conformers comprising both the circular motif around the C-terminal disulfide bond detected in previous structural analysis and the N-terminal disulfide bond. Despite the fact that disulfide bridges are usually thought to confer rigidity to protein structures, in the oxidized AtCP12, their presence coexists with a disordered nature. Our results rule out the existence of significant amounts of structured and compact conformations of free AtCP12 in a solution, even in its oxidized form, thereby highlighting the importance of recruiting partner proteins to complete its structured final folding.

Ribulose-1,5-bisphosphate regeneration in the Calvin-Benson-Bassham cycle: Focus on the last three enzymatic steps that allow the formation of Rubisco substrate

The Calvin-Benson-Bassham (CBB) cycle comprises the metabolic phase of photosynthesis and is responsible for carbon fixation and the production of sugar phosphates. The first step of the cycle involves the enzyme ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) which catalyzes the incorporation of inorganic carbon into 3-phosphoglyceric acid (3PGA). The following steps include ten enzymes that catalyze the regeneration of ribulose-1,5-bisphosphate (RuBP), the substrate of Rubisco. While it is well established that Rubisco activity acts as a limiting step of the cycle, recent modeling studies and experimental evidence have shown that the efficiency of the pathway is also impacted by the regeneration of the Rubisco substrate itself. In this work, we review the current understanding of the structural and catalytic features of the photosynthetic enzymes that catalyze the last three steps of the regeneration phase, namely ribose-5-phosphate isomerase (RPI), ribulose-5-phosphate epimerase (RPE), and phosphoribulokinase (PRK). In addition, the redox- and metabolic-based regulatory mechanisms targeting the three enzymes are also discussed. Overall, this review highlights the importance of understudied steps in the CBB cycle and provides direction for future research aimed at improving plant productivity.

Recovering and Exploiting Aragonite and Calcite Single Crystals with Biologically Controlled Shapes from Mussel Shells

Control over the shape and morphology of single crystals is a theme of great interest in fundamental science and for technological application. Many synthetic strategies to achieve this goal are inspired by biomineralization processes. Indeed, organisms are able to produce crystals with high fidelity in shape and morphology utilizing macromolecules that act as modifiers. An alternative strategy can be the recovery of crystals from biomineralization products, in this case, seashells. In particular, waste mussel shells from aquaculture are considered. They are mainly built up of single crystals of calcite fibers and aragonite tablets forming an outer and an inner layer, respectively. A simple mechanochemical treatment has been developed to separate and recover these two typologies of single crystals. The characterization of these single crystals showed peculiar properties with respect to the calcium carbonate from quarry or synthesis. We exploited these biomaterials in the water remediation field using them as substrate adsorbing dyes. We found that these substrates show a high capability of adsorption for anionic dye, such as Eosin Y, but a low capability of adsorption for cationic dyes, such as Blue Methylene. The adsorption was reversible at pH 5.6. This application represents just an example of the potential use of these biogenic single crystals. We also envision potential applications as reinforcing fillers and optical devices.

Unravelling the regulation pathway of photosynthetic AB-GAPDH

Oxygenic phototrophs perform carbon fixation through the Calvin–Benson cycle. Different mechanisms adjust the cycle and the light-harvesting reactions to rapid environmental changes. Photosynthetic glyceraldehyde 3-phosphate dehydrogenase (GAPDH) is a key enzyme in the cycle. In land plants, different photosynthetic GAPDHs exist: the most abundant isoform is formed by A2B2 heterotetramers and the least abundant by A4 homotetramers. Regardless of the subunit composition, GAPDH is the major consumer of photosynthetic NADPH and its activity is strictly regulated. While A4-GAPDH is regulated by CP12, AB-GAPDH is autonomously regulated through the C-terminal extension (CTE) of its B subunits. Reversible inhibition of AB-GAPDH occurs via the oxidation of a cysteine pair located in the CTE and the substitution of NADP(H) with NAD(H) in the cofactor-binding site. These combined conditions lead to a change in the oligomerization state and enzyme inhibition. SEC–SAXS and single-particle cryo-EM analysis were applied to reveal the structural basis of this regulatory mechanism. Both approaches revealed that spinach (A2B2) n -GAPDH oligomers with n = 1, 2, 4 and 5 co-exist in a dynamic system. B subunits mediate the contacts between adjacent tetramers in A4B4 and A8B8 oligomers. The CTE of each B subunit penetrates into the active site of a B subunit of the adjacent tetramer, which in turn moves its CTE in the opposite direction, effectively preventing the binding of the substrate 1,3-bisphosphoglycerate in the B subunits. The whole mechanism is made possible, and eventually controlled, by pyridine nucleotides. In fact, NAD(H), by removing NADP(H) from A subunits, allows the entrance of the CTE into the active site of the B subunit, hence stabilizing inhibited oligomers.

Calcium carbonate: controlled synthesis, surface functionalization, and nanostructured materials

Calcium carbonate (CaCO₃) is an important inorganic mineral in biological and geological systems. Traditionally, it is widely used in plastics, papermaking, ink, building materials, textiles, cosmetics, and food. Over the last decade, there has been rapid development in the controlled synthesis and surface modification of CaCO₃, the stabilization of amorphous CaCO₃ (ACC), and CaCO₃-based nanostructured materials. In this review, the controlled synthesis of CaCO₃ is first examined, including Ca²⁺-CO₃^2- systems, solid-liquid-gas carbonation, water-in-oil reverse emulsions, and biomineralization. Advancing insights into the nucleation and crystallization of CaCO₃ have led to the development of efficient routes towards the controlled synthesis of CaCO₃ with specific sizes, morphologies, and polymorphs. Recently-developed surface modification methods of CaCO₃ include organic and inorganic modifications, as well as intensified surface reactions. The resultant CaCO₃ can then be further engineered via template-induced biomineralization and layer-by-layer assembly into porous, hollow, or core-shell organic-inorganic nanocomposites. The introduction of CaCO₃ into nanostructured materials has led to a significant improvement in the mechanical, optical, magnetic, and catalytic properties of such materials, with the resultant CaCO₃-based nanostructured materials showing great potential for use in biomaterials and biomedicine, environmental remediation, and energy production and storage. The influences that the preparation conditions and additives have on ACC preparation and stabilization are also discussed. Studies indicate that ACC can be used to construct environmentally-friendly hybrid films, supramolecular hydrogels, and drug vehicles. Finally, the existing challenges and future directions of the controlled synthesis and functionalization of CaCO₃ and its expanding applications are highlighted.

Structural snapshots of nitrosoglutathione binding and reactivity underlying S-nitrosylation of photosynthetic GAPDH

S-nitrosylation is a redox post-translational modification widely recognized to play an important role in cellular signaling as it can modulate protein function and conformation. At the physiological level, nitrosoglutathione (GSNO) is considered the major physiological NO-releasing compound due to its ability to transfer the NO moiety to protein thiols but the structural determinants regulating its redox specificity are not fully elucidated. In this study, we employed photosynthetic glyceraldehyde-3-phosphate dehydrogenase from Chlamydomonas reinhardtii (CrGAPA) to investigate the molecular mechanisms underlying GSNO-dependent thiol oxidation. We first observed that GSNO causes reversible enzyme inhibition by inducing S-nitrosylation. While the cofactor NADP⁺ partially protects the enzyme from GSNO-mediated S-nitrosylation, protein inhibition is not observed in the presence of the substrate 1,3-bisphosphoglycerate, indicating that the S-nitrosylation of the catalytic Cys149 is responsible for CrGAPA inactivation. The crystal structures of CrGAPA in complex with NADP⁺ and NAD⁺ reveal a general structural similarity with other photosynthetic GAPDH. Starting from the 3D structure, we carried out molecular dynamics simulations to identify the protein residues involved in GSNO binding. The reaction mechanism of GSNO with CrGAPA Cys149 was investigated by quantum mechanical/molecular mechanical calculations, which permitted to disclose the relative contribution of protein residues in modulating the activation barrier of the trans-nitrosylation reaction. Based on our findings, we provide functional and structural insights into the response of CrGAPA to GSNO-dependent regulation, possibly expanding the mechanistic features to other protein cysteines susceptible to be oxidatively modified by GSNO.

Multiscale analysis on otolith structural features reveals differences in ontogenesis and sex in Merluccius merluccius in the western Adriatic Sea

Otolith biomineralization results from biochemical processes regulated by the interaction of internal (physiological) and external (environmental) factors which lead to morphological and ultrastructural variability at intra- and interspecific levels. The aim of this study was to conduct a multi-scale analysis of the sagittal otoliths of the Merlucius merlucius (European hake) from the western Adriatic Sea in order to correlate otolith features with fish ontogeny and sex. We show that otoliths of sexually undifferentiated (non-sexed) individuals having a fish body total length (TL) less than 15 cm had faster growth in length, width, area, perimeter, volume and weight and a higher amount of organic matrix compared with otoliths of sexually differentiated individuals (females and males) having a fish size range of 15-50 cm. Most importantly, with increasing fish TL, female saccular otoliths contained a higher number of protuberances and rougher surface compared with male specimens, which showed more uniform mean curvature density. The differences between females and males discovered in this study could be associated with fish hearing adaptation to reproductive behavioural strategies during the spawning season. The outcomes of this research provide insights on how size and sex-related variations in otolith features may be affected by fish ecological and behavioural patterns.

Calvin-Benson cycle regulation is getting complex

Oxygenic phototrophs use the Calvin-Benson cycle to fix CO₂ during photosynthesis. In the dark, glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and phosphoribulokinase (PRK), two enzymes of the Calvin-Benson cycle, form an inactive complex with the regulatory protein CP12, mainly under the control of thioredoxins and pyridine nucleotides. In the light, complex dissociation allows GAPDH and PRK reactivation. The GAPDH/CP12/PRK complex is conserved from cyanobacteria to angiosperms and coexists in land plants with an autoassembling GAPDH that is analogously regulated. With the recently described 3D structures of PRK and GAPDH/CP12/PRK, the structural proteome of this ubiquitous regulatory system has been completed. This outcome opens a new avenue for understanding the regulatory potential of photosynthetic carbon fixation by laying the foundation for its knowledge-based manipulation.

Wavy graphene sheets from electrochemical sewing of corannulene

The presence of non-hexagonal rings in the honeycomb carbon arrangement of graphene produces rippled graphene layers with valuable chemical and physical properties. In principle, a bottom-up approach to introducing distortion from planarity of a graphene sheet can be achieved by careful insertion of curved polyaromatic hydrocarbons during the growth of the lattice. Corannulene, the archetype of such non-planar polyaromatic hydrocarbons, can act as an ideal wrinkling motif in 2D carbon nanostructures. Herein we report an electrochemical bottom-up method to obtain egg-box shaped nanographene structures through a polycondensation of corannulene that produces a new conducting layered material. Characterization of this new polymeric material by electrochemistry, spectroscopy, electron microscopy (SEM and TEM), scanning probe microscopy, and laser desorption-ionization time of flight mass spectrometry provides strong evidence that the anodic polymerization of corannulene, combined with electrochemically induced oxidative cyclodehydrogenations (Scholl reactions), leads to polycorannulene with a wavy graphene-like structure.

A bottom-up synthesis of wavy graphene structures obtained through an anodic polymerization process, combined with an electrochemically triggered oxidative cyclodehydrogenation, of the bowl-shaped polyaromatic hydrocarbon corannulene.

Climate variation during the Holocene influenced the skeletal properties of Chamelea gallina shells in the North Adriatic Sea (Italy)

Understanding how marine taxa will respond to near-future climate changes is one of the main challenges for management of coastal ecosystem services. Ecological studies that investigate relationships between the environment and shell properties of commercially important marine species are commonly restricted to latitudinal gradients or small-scale laboratory experiments. This paper aimed to explore the variations in shell features and growth of the edible bivalve Chamelea gallina from the Holocene sedimentary succession to present-day thanatocoenosis of the Po Plain-Adriatic Sea system (Italy). Comparing the Holocene sub-fossil record to modern thanatocoenoses allowed obtaining an insight of shell variations dynamics on a millennial temporal scale. Five shoreface-related assemblages rich in C. gallina were considered: two from the Middle Holocene, when regional sea surface temperatures were higher than today, representing a possible analogue for the near-future global warming, one from the Late Holocene and two from the present-day. We investigated shell biometry and skeletal properties in relation to the valve length of C. gallina. Juveniles were found to be more porous than adults in all horizons. This suggested that C. gallina promoted an accelerated shell accretion with a higher porosity and lower density at the expense of mechanically fragile shells. A positive correlation between sea surface temperature and both micro-density and bulk density were found, with modern specimens being less dense, likely due to lower aragonite saturation state at lower temperature, which could ultimately increase the energetic costs of shell formation. Since no variation was observed in shell CaCO₃ polymorphism (100% aragonite) or in compositional parameters among the analyzed horizons, the observed dynamics in skeletal parameters are likely not driven by a diagenetic recrystallization of the shell mineral phase. This study contributes to understand the response of C. gallina to climate-driven environmental shifts and offers insights for assessing anthropogenic impacts on this economic relevant species.

Influence of proteins on mechanical properties of a natural chitin-protein composite

In many biogenic materials, chitin chains are assembled in fibrils that are wrapped by a protein fold. In them, the mechanical properties are supposed to be related to intra- and inter- interactions among chitin and proteins. This hypothesis has been poorly investigated. Here, this research theme is studied using the pen of Loligo vulgaris as a model material of chitin-protein composites. Chemical treatments were used to change the interactions involving only the proteic phase, through unfolding and/or degradation processes. Successively, structural and mechanical parameters were examined using spectroscopy, microscopy, X-ray diffractometry, and tensile tests. The data analysis showed that chemical treatments did not modify the structure of the chitin matrix. This allowed to derive from the mechanical test analysis the following conclusions: (i) the maximum stress (σ_max) relies on the presence of the disulfide bonds; (ii) the Young's modulus (E) relies on the overall correct folding of the proteins; (iii) the whole removal of proteins induces a decrease of E (> 90%) and σ_max (> 80%), and an increase in the maximum elongation. These observations indicate that in the chitin matrix the proteins act as a strengthener, which efficacy is controlled by the presence of disulfide bridges. This reinforcement links the chitin fibrils avoiding them to slide one on the other and maximizing their resistance and stiffness. In conclusion, this knowledge can explain the physio-chemical properties of other biogenic polymeric composites and inspire the design of new materials. STATEMENT OF SIGNIFICANCE: To date, no study has addressed on how proteins influence chitin-composite material's mechanical properties. Here we show that the Young's modulus and the maximum stress mainly rely on protein disulfide bonds, the inter-proteins ones and those controlling the folding of chitin-binding domains. The removal of protein matrix induce a reduction of Young's modulus and maximum stress, leaving the chitin matrix structurally unaltered. The measure of the maximum elongation shows that the chitin fibrils slide on each other only after removing the protein matrix. In conclusion, this research shows that the proteins act as a stiff matrix reinforced by di-sulfide bridges that link crystalline chitin fibrils avoiding them to slide one on the other.

Acidic Monosaccharides become Incorporated into Calcite Single Crystals*

Carbohydrates, along with proteins and peptides, are known to represent a major class of biomacromolecules involved in calcium carbonate biomineralization. However, in spite of multiple physical and biochemical characterizations, the explicit role of saccharide macromolecules (long chains of carbohydrate molecules) in mineral deposition is not yet understood. In this study, we investigated the influence of two common acidic monosaccharides (MSs), the two simplest forms of acidic carbohydrates, namely glucuronic and galacturonic acids, on the formation of calcite crystals in vitro. We show here that the size, morphology, and microstructure of calcite crystals are altered when they are grown in the presence of these MSs. More importantly, these MSs were found to become incorporated into the calcite crystalline lattice and induce anisotropic lattice distortions, a phenomenon widely studied for other biomolecules related to CaCO₃ biomineralization, but never before reported in the case of single MSs. Changes in the calcite lattice induced by MSs incorporation were precisely determined by high-resolution synchrotron powder X-ray diffraction. We believe that the results of this research may deepen our understanding of the interaction of saccharide polymers with an inorganic host and shed light on the implications of carbohydrates for biomineralization processes.

Cholesterol derivatives make large part of the lipids from epidermal molts of the desert-adapted Gila monster lizard (Heloderma suspectum)

In order to understand the cutaneous water loss in the desert-adapted and venomous lizard Heloderma suspectum, the microscopic structure and lipid composition of epidermal molts have been examined using microscopic, spectroscopic and chemical analysis techniques. The molt is formed by a variably thick, superficial beta-layer, an extensive mesos-region and few alpha-cells in its lowermost layers. The beta-layer contains most corneous beta proteins while the mesos-region is much richer in lipids. The proteins in the mesos-region are more unstructured than those located in the beta-layer. Most interestingly, among other lipids, high contents of cholesteryl-β-glucoside and cholesteryl sulfate were detected, molecules absent or present in traces in other species of squamates. These cholesterol derivatives may be involved in the stabilization and compaction of the mesos-region, but present a limited permeability to water movements. The modest resistance to cutaneous water-loss of this species is compensated by adopting other physiological strategies to limit thermal damage and water transpiration as previous eco-physiological studies have indicated. The increase of steroid derivatives may also be implicated in the heat shock response, influencing the relative behavior in this desert-adapted lizard.

Supramolecular Hydrogels with Properties Tunable by Calcium Ions: A Bio-Inspired Chemical System

Boc-L-DOPA(OBn)₂-OH is a simple synthetic molecule that promotes hydrogelation through electrostatic and π-π stacking interactions. Hydrogelation can occur in alkaline conditions by the use of triggers. Four hydrogels were prepared varying the base, NaOH or Na₂CO₃, and the trigger, GdL or CaCl₂. When the hydrogel formed in the presence of Na₂CO₃ and CaCl₂, the concomitant production of CaCO₃ crystals occurred, generating an organic/inorganic composite material. It was observed that the hydrogel once self-assembled preserved its status even if the trigger, the calcium ions, was removed. The viscoelastic behavior of the hydrogels was analyzed through rheological experiments, which showed a solid-like behavior of the hydrogels. The corresponding xerogels were analyzed mainly by scanning electron microscopy (SEM) and synchrotron X-ray diffraction analysis (XRD). They showed differences in structure, morphology, and fiber organization according to their source. This research presents a hydrogel system that can be applied as a soft biomaterial for tissue engineering, cosmetics, food, and environmental science. Moreover, it represents a model for biomineralization studies in which the hydrogel structure can act as an analogue of the insoluble matrix that confines the calcification site, provides Ca²⁺, and preserves its structure.

Retinoic acid/calcite micro-carriers inserted in fibrin scaffolds modulate neuronal cell differentiation

The controlled release of cell differentiating agents is crucial in many aspects of regenerative medicine. Here we propose the use of hybrid calcite single crystals as micro-carriers for the controlled and localized release of retinoic acid, which is entrapped within the crystalline lattice. The release of retinoic acid occurs only in the proximity of stem cells, upon dissolution of the calcite hybrid crystals that are dispersed in the fibrin scaffold. These hybrid crystals provide a sustained dosage of the entrapped agent. The environment provided by this composite scaffold enables differentiation towards neuronal cells that form a three-dimensional neuronal network.

Redox Homeostasis in Photosynthetic Organisms: Novel and Established Thiol-Based Molecular Mechanisms

Significance: Redox homeostasis consists of an intricate network of reactions in which reactive molecular species, redox modifications, and redox proteins act in concert to allow both physiological responses and adaptation to stress conditions. Recent Advances: This review highlights established and novel thiol-based regulatory pathways underlying the functional facets and significance of redox biology in photosynthetic organisms. In the last decades, the field of redox regulation has largely expanded and this work is aimed at giving the right credit to the importance of thiol-based regulatory and signaling mechanisms in plants. Critical Issues: This cannot be all-encompassing, but is intended to provide a comprehensive overview on the structural/molecular mechanisms governing the most relevant thiol switching modifications with emphasis on the large genetic and functional diversity of redox controllers (i.e., redoxins). We also summarize the different proteomic-based approaches aimed at investigating the dynamics of redox modifications and the recent evidence that extends the possibility to monitor the cellular redox state in vivo. The physiological relevance of redox transitions is discussed based on reverse genetic studies confirming the importance of redox homeostasis in plant growth, development, and stress responses. Future Directions: In conclusion, we can firmly assume that redox biology has acquired an established significance that virtually infiltrates all aspects of plant physiology.

In Vitro Coral Biomineralization under Relevant Aragonite Supersaturation Conditions

The biomineralization of corals occurs under conditions of high and low supersaturation with respect to aragonite, which corresponds to day- or night-time periods of their growth, respectively. Here, in vitro precipitation of aragonite in artificial seawater was investigated at a high supersaturation, allowing spontaneous nucleation and growth, as well as at low supersaturation conditions, which allowed only the crystal growth on the deliberately introduced aragonite seeds. In either chemical systems, soluble organic matrix (SOM) extracted from Balanophyllia europaea (light sensitive) or Leptopsammia pruvoti (light insensitive) was added. The analyses of the kinetic and thermodynamic data of aragonite precipitation and microscopic observations showed that, at high supersaturation, the SOMs increased the induction time, did not affect the growth rate and were incorporated within aggregates of nanoparticles. At low supersaturation, the SOMs affected the aggregation of overgrowing crystalline units and did not substantially change the growth rate. On the basis of the obtained results we can infer that at high supersaturation conditions the formation of nanoparticles, which is typically observed in the skeleton's early mineralization zone may occur, whereas at low supersaturation the overgrowth on prismatic seeds observed in the skeleton fiber zone is a predominant process. In conclusion, this research brings insight on coral skeletogenesis bridging physicochemical (supersaturation) and biological (role of SOM) models of coral biomineralization and provides a source of inspiration for the precipitation of composite materials under different conditions of supersaturation.

β-Chitin samples with similar microfibril arrangement change mechanical properties varying the degree of acetylation

Chitin is widespread in nature and is increasingly used in synthetic process for the production of new biomaterials. Chitin degree of acetylation, crystalline structure and microfibril arrangement differentiate chemical, physical and mechanical properties. Nevertheless, no information are available on the relationship between the mechanical properties and the degree of acetylation (DA) in chitin samples in which the microfibril arrangement does not change. Here, samples of β-chitin with decreasing DA, up to chitosan, were prepared using the squid pen of Loligo vulgaris. These samples were characterized by CP-MAS NMR spectroscopy, scanning electron microscopy, thermal analyses, synchrotron X-ray fiber diffraction and tensile tests. The results showed a similar microfibril arrangement decreasing the DA, except for the chitosan sample. The mechanical properties showed an increase of the maximum strain and a reduction of the maximum stress and Young's modulus, decreasing the DA. These changes, not linear with the DA, were related to structural changes at molecular structure level. The knowledge deriving from this study is of interest both for the understanding of the mechanical properties of chitinous biological samples, but also for the design and synthesis of new biomacromolecular materials.

Crystal Structure of Chloroplastic Thioredoxin f2 from Chlamydomonas reinhardtii Reveals Distinct Surface Properties

Protein disulfide reduction by thioredoxins (TRXs) controls the conformation of enzyme active sites and their multimeric complex formation. TRXs are small oxidoreductases that are broadly conserved in all living organisms. In photosynthetic eukaryotes, TRXs form a large multigenic family, and they have been classified in different types: f, m, x, y, and z types are chloroplastic, while o and h types are located in mitochondria and cytosol. In the model unicellular alga Chlamydomonas reinhardtii, the TRX family contains seven types, with f- and h-types represented by two isozymes. Type-f TRXs interact specifically with targets in the chloroplast, controlling photosynthetic carbon fixation by the Calvin⁻Benson cycle. We solved the crystal structures of TRX f2 and TRX h1 from C. reinhardtii. The systematic comparison of their atomic features revealed a specific conserved electropositive crown around the active site of TRX f, complementary to the electronegative surface of their targets. We postulate that this surface provides specificity to each type of TRX.

Structure and Function of Stony Coral Intraskeletal Polysaccharides

Polysaccharides represent a main weight fraction of the intraskeletal organic matrix of corals, but their structure, as well as their function in the calcification process, has been poorly investigated. This communication shows by a combination of techniques (nuclear magnetic resonance, Fourier transform infrared, and monosaccharide composition) that their key component is a 1→3 β-d glucuronic acid polymer and evidences its influence in vitro in the calcification process.

Aggregation Pathways of Native-Like Ubiquitin Promoted by Single-Point Mutation, Metal Ion Concentration, and Dielectric Constant of the Medium

Ubiquitin-positive protein aggregates are biomarkers of neurodegeneration, but the molecular mechanism responsible for their formation and accumulation is still unclear. Possible aggregation pathways of human ubiquitin (hUb) promoted by both intrinsic and extrinsic factors, are here investigated. By a computational analysis, two different hUb dimers are indicated as possible precursors of amyloid-like structures, but their formation is disfavored by an electrostatic repulsion involving Glu16 and other carboxylate residues present at the dimer interface. Experimental data on the E16V mutant of hUb shows that this single-point mutation, although not affecting the overall protein conformation, promotes protein aggregation. It is sufficient to shift the same mutation by only two residues (E18V) to regain the behavior of wild-type hUb. The neutralization of Glu16 negative charge by a metal ion and a decrease of the dielectric constant of the medium by addition of trifluoroethanol (TFE), also promote hUb aggregation. The outcomes of this research have important implications for the prediction of physiological parameters that favor aggregate formation.

Insights on the interaction of calcein with calcium carbonate and its implications in biomineralization studies

The effects of calcein, a fluorescent marker commonly used to assess mineral growth in calcifying organisms, on calcite and aragonite structure have been investigated.

Ecological relevance of skeletal fatty acid concentration and composition in Mediterranean scleractinian corals

The intra-skeletal fatty acid concentration and composition of four Mediterranean coral species, namely Cladocora caespitosa, Balanophyllia europaea, Astroides calycularis and Leptopsammia pruvoti, were examined in young and old individuals living in three different locations of the Mediterranean Sea. These species are characterized by diverse levels of organization (solitary or colonial) and trophic strategies (symbiotic or non-symbiotic). Fatty acids have manifold fundamental roles comprehensive of membrane structure fluidity, cell signaling and energy storage. For all species, except for B. europaea, the intra-skeletal fatty acid concentration was significantly higher in young individuals than in old ones. Moreover, fatty acid concentration was higher in colonial corals than in solitary ones and in the symbiotic corals compared to non-symbiotic ones. Analysis by gas chromatography-mass spectrometry (GC-MS) revealed that palmitic acid (16:0) was the most abundant fatty acid, followed by stearic (18:0) in order of concentration. Oleic acid (18:1) was detected as the third main component only in skeletons from symbiotic corals. These results suggest that, in the limits of the studied species, intra-skeletal fatty acid composition and concentration may be used for specific cases as a proxy of level of organization and trophic strategy, and eventually coral age.

Biochemical basis of sulphenomics: how protein sulphenic acids may be stabilized by the protein microenvironment

Among protein residues, cysteines are one of the prominent candidates to ROS-mediated and RNS-mediated post-translational modifications, and hydrogen peroxide (H₂ O₂ ) is the main ROS candidate for inducing cysteine oxidation. The reaction with H₂ O₂ is not common to all cysteine residues, being their reactivity an utmost prerequisite for the sensitivity towards H₂ O₂ . Indeed, only deprotonated Cys (i.e. thiolate form, S^- ) can react with H₂ O₂ leading to sulphenic acid formation (SOH), which is considered as a major/central player of ROS sensing pathways. However, cysteine sulphenic acids are generally unstable because they can be further oxidized to irreversible forms (sulphinic and sulphonic acids, SO₂ H and SO₃ H, respectively), or alternatively, they can proceed towards further modifications including disulphide bond formation (SS), S-glutathionylation (SSG) and sulphenamide formation (SN). To understand why and how cysteine residues undergo primary oxidation to sulphenic acid, and to explore the stability of cysteine sulphenic acids, a combination of biochemical, structural and computational studies are required. Here, we will discuss the current knowledge of the structural determinants for cysteine reactivity and sulphenic acid stability within protein microenvironments.

Exploitation of mussel byssus mariculture waste as a water remediation material

The byssus is an alimentary industry waste with a unique combination of functional groups that has been successfully tested for the removal of charged aromatic dyes from water.

Tuning Cysteine Reactivity and Sulfenic Acid Stability by Protein Microenvironment in Glyceraldehyde-3-Phosphate Dehydrogenases of Arabidopsis thaliana

AIMS

Cysteines and H2O2 are fundamental players in redox signaling. Cysteine thiol deprotonation favors the reaction with H2O2 that generates sulfenic acids with dual electrophilic/nucleophilic nature. The protein microenvironment surrounding the target cysteine is believed to control whether sulfenic acid can be reversibly regulated by disulfide formation or irreversibly oxidized to sulfinates/sulfonates. In this study, we present experimental oxidation kinetics and a quantum mechanical/molecular mechanical (QM/MM) investigation to elucidate the reaction of H2O2 with glycolytic and photosynthetic glyceraldehyde-3-phosphate dehydrogenase from Arabidopsis thaliana (cytoplasmic AtGAPC1 and chloroplastic AtGAPA, respectively).

RESULTS

Although AtGAPC1 and AtGAPA have almost identical 3D structure and similar acidity of their catalytic Cys149, AtGAPC1 is more sensitive to H2O2 and prone to irreversible oxidation than AtGAPA. As a result, sulfenic acid is more stable in AtGAPA.

INNOVATION

Based on crystallographic structures of AtGAPC1 and AtGAPA, the reaction potential energy surface for Cys149 oxidation by H2O2 was calculated by QM. In both enzymes, sulfenic acid formation was characterized by a lower energy barrier than sulfinate formation, and sulfonate formation was prevented by very high energy barriers. Activation energies for both oxidation steps were lower in AtGAPC1 than AtGAPA, supporting the higher propensity of AtGAPC1 toward irreversible oxidation.

CONCLUSIONS

QM/MM calculations coupled to fingerprinting analyses revealed that two Arg of AtGAPA (substituted by Gly and Val in AtGAPC1), located at 8-15 Å distance from Cys149, are the major factors responsible for sulfenic acid stability, underpinning the importance of long-distance polar interactions in tuning sulfenic acid stability in native protein microenvironments.

Unravelling the shape and structural assembly of the photosynthetic GAPDH-CP12-PRK complex from Arabidopsis thaliana by small-angle X-ray scattering analysis

Oxygenic photosynthetic organisms produce sugars through the Calvin-Benson cycle, a metabolism that is tightly linked to the light reactions of photosynthesis and is regulated by different mechanisms, including the formation of protein complexes. Two enzymes of the cycle, glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and phosphoribulokinase (PRK), form a supramolecular complex with the regulatory protein CP12 with the formula (GAPDH-CP122-PRK)2, in which both enzyme activities are transiently inhibited during the night. Small-angle X-ray scattering analysis performed on both the GAPDH-CP12-PRK complex and its components, GAPDH-CP12 and PRK, from Arabidopsis thaliana showed that (i) PRK has an elongated, bent and screwed shape, (ii) the oxidized N-terminal region of CP12 that is not embedded in the GAPDH-CP12 complex prefers a compact conformation and (iii) the interaction of PRK with the N-terminal region of CP12 favours the approach of two GAPDH tetramers. The interaction between the GAPDH tetramers may contribute to the overall stabilization of the GAPDH-CP12-PRK complex, the structure of which is presented here for the first time.

Gains and losses of coral skeletal porosity changes with ocean acidification acclimation

Ocean acidification is predicted to impact ecosystems reliant on calcifying organisms, potentially reducing the socioeconomic benefits these habitats provide. Here we investigate the acclimation potential of stony corals living along a pH gradient caused by a Mediterranean CO2 vent that serves as a natural long-term experimental setting. We show that in response to reduced skeletal mineralization at lower pH, corals increase their skeletal macroporosity (features >10 μm) in order to maintain constant linear extension rate, an important criterion for reproductive output. At the nanoscale, the coral skeleton's structural features are not altered. However, higher skeletal porosity, and reduced bulk density and stiffness may contribute to reduce population density and increase damage susceptibility under low pH conditions. Based on these observations, the almost universally employed measure of coral biomineralization, the rate of linear extension, might not be a reliable metric for assessing coral health and resilience in a warming and acidifying ocean.

Calcite Single Crystals as Hosts for Atomic-Scale Entrapment and Slow Release of Drugs

Doxorubicin (DOX)/CaCO3 single crystals act as pH responsive drug carrier. A biomimetic approach demonstrates that calcite single crystals are able, during their growth in the presence of doxorubicin, to entrap drug molecules inside their lattice along specific crystallographic directions. Alterations in lattice dimensions and microstructural parameters are determined by means of high-resolution synchrotron powder diffraction measurements. Confocal microscopy confirms that doxorubicin is uniformly embedded in the crystal and is not simply adsorbed on the crystal surface. A slow release of DOX was obtained preferentially in the proximity of the crystals, targeting cancer cells.

Calcium carbonate crystallization in tailored constrained environments

This research shows that by tailoring the assembly of lecithin molecules it is possible to modulate the texture, polymorphism, size and shape of calcium carbonate crystals.

Customizing properties of β-chitin in squid pen (gladius) by chemical treatments

The squid pen (gladius) from the Loligo vulgaris was used for preparation of β-chitin materials characterized by different chemical, micro- and nano-structural properties that preserved, almost completely the macrostructural and the mechanical ones. The β-chitin materials obtained by alkaline treatment showed porosity, wettability and swelling that are a function of the duration of the treatment. Microscopic, spectroscopic and synchrotron X-ray diffraction techniques showed that the chemical environment of the N-acetyl groups of the β-chitin chains changes after the thermal alkaline treatment. As a consequence, the crystalline packing of the β-chitin is modified, due to the intercalation of water molecules between β-chitin sheets. Potential applications of these β-chitin materials range from the nanotechnology to the regenerative medicine. The use of gladii, which are waste products of the fishing industry, has also important environmental implications.

Evidence of structural variability among synthetic and biogenic vaterite

Recently, the results of experimental and theoretical investigations have revealed that, in vaterite, two or even more crystalline structures coexist. In this communication we report evidence of diverse vaterite structures in biogenic samples of different origin. In addition, it is shown that the synthetic vaterite precipitated in the presence of poly-l-aspartate has structures similar to those of biogenic samples.

Thioredoxin-dependent redox regulation of chloroplastic phosphoglycerate kinase from Chlamydomonas reinhardtii

In photosynthetic organisms, thioredoxin-dependent redox regulation is a well established mechanism involved in the control of a large number of cellular processes, including the Calvin-Benson cycle. Indeed, 4 of 11 enzymes of this cycle are activated in the light through dithiol/disulfide interchanges controlled by chloroplastic thioredoxin. Recently, several proteomics-based approaches suggested that not only four but all enzymes of the Calvin-Benson cycle may withstand redox regulation. Here, we characterized the redox features of the Calvin-Benson enzyme phosphoglycerate kinase (PGK1) from the eukaryotic green alga Chlamydomonas reinhardtii, and we show that C. reinhardtii PGK1 (CrPGK1) activity is inhibited by the formation of a single regulatory disulfide bond with a low midpoint redox potential (-335 mV at pH 7.9). CrPGK1 oxidation was found to affect the turnover number without altering the affinity for substrates, whereas the enzyme activation appeared to be specifically controlled by f-type thioredoxin. Using a combination of site-directed mutagenesis, thiol titration, mass spectrometry analyses, and three-dimensional modeling, the regulatory disulfide bond was shown to involve the not strictly conserved Cys(227) and Cys(361). Based on molecular mechanics calculation, the formation of the disulfide is proposed to impose structural constraints in the C-terminal domain of the enzyme that may lower its catalytic efficiency. It is therefore concluded that CrPGK1 might constitute an additional light-modulated Calvin-Benson cycle enzyme with a low activity in the dark and a TRX-dependent activation in the light. These results are also discussed from an evolutionary point of view.

Biomineralization control related to population density under ocean acidification

Anthropogenic CO₂ is a major driver of current environmental change in most ecosystems¹, and the related ocean acidification (OA) is threatening marine biota². With increasing pCO₂, calcification rates of several species decrease³, although cases of up-regulation are observed⁴. Here, we show that biological control over mineralization relates to species abundance along a natural pH gradient. As pCO₂ increased, the mineralogy of a scleractinian coral (Balanophyllia europaea) and a mollusc (Vermetus triqueter) did not change. In contrast, two calcifying algae (Padina pavonica and Acetabularia acetabulum) reduced and changed mineralization with increasing pCO₂, from aragonite to the less soluble calcium sulphates and whewellite, respectively. As pCO₂ increased, the coral and mollusc abundance was severely reduced, with both species disappearing at pH < 7.8. Conversely, the two calcifying and a non-calcifying algae (Lobophora variegata) showed less severe or no reductions with increasing pCO₂, and were all found at the lowest pH site. The mineralization response to decreasing pH suggests a link with the degree of control over the biomineralization process by the organism, as only species with lower control managed to thrive in the lowest pH.

C60@Lysozyme: direct observation by nuclear magnetic resonance of a 1:1 fullerene protein adduct

Integrating carbon nanoparticles (CNPs) with proteins to form hybrid functional assemblies is an innovative research area with great promise for medical, nanotechnology, and materials science. The comprehension of CNP-protein interactions requires the still-missing identification and characterization of the 'binding pocket' for the CNPs. Here, using Lysozyme and C60 as model systems and NMR chemical shift perturbation analysis, a protein-CNP binding pocket is identified unambiguously in solution and the effect of the binding, at the level of the single amino acid, is characterized by a variety of experimental and computational approaches. Lysozyme forms a stoichiometric 1:1 adduct with C60 that is dispersed monomolecularly in water. Lysozyme maintains its tridimensional structure upon interaction with C60 and only a few identified residues are perturbed. The C60 recognition is highly specific and localized in a well-defined pocket.