Simona Fermani

Nucleation and Growth from a Biomineralization Perspective

Biomineralization processes occur ubiquitously through a heterogeneous nucleation process. This despite the fact that nucleation follows a classical or no classical, two-step, pathway. In addition, in mineralizing organisms, the growth process can also take place through a classical path wherein instead of addition of single ions to the growing crystal nuclei, amorphous nanoparticles that crystallize on the growing crystal nuclei are utilized. After many years of evolution, organisms have established diverse strategies that follow the above principles. The molecular and structural details of those processes are for many aspects still unknown. In this chapter, a few representative cases among the most studied biominerals are presented. The final section is devoted to a summary of selected recent studies on the effect of ocean acidification on the biomineral synthesis and features.

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, uf8ffS- ) can react with H2 O2 leading to sulphenic acid formation (uf8ffSOH), 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, uf8ffSO2 H and uf8ffSO3 H, respectively), or alternatively, they can proceed towards further modifications including disulphide bond formation (uf8ffSSuf8ff), S-glutathionylation (uf8ffSSG) and sulphenamide formation (uf8ffSNuf8fe). 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

Dye pollution represents an important environmental concern, especially from textile industries in the South of Asia. On the other hand, biomass accumulation derived from mussel processing in alimentary industries is also an environmental problem. In this research, these two environmental issues are addressed by proposing the reuse of mussels protein anchoring threads, the byssus, as disposable material for dye water removal. The byssus was selected as substrate because it contains a distinctive variety of functional groups that can be exploited for diverse chemical interactions. This material was utilized in its native metaled state and in the de-metaled one, in order to study how the chemical state of the functional groups influences the adsorption properties of both anionic and cationic aromatic dyes. The results of comparative experiments of adsorption showed a higher uptake in the native metaled byssus for a model cationic dye, methylene blue, while the de-metaled byssus showed a higher uptake for a model anionic dye, Eosin Y. These results are considered in light of different uptake mechanisms, supported by the analyses of isotherm model parameters, in which diverse functional groups are involved as a function of substrate and dye chemical states.

Effects of magnesium and temperature control on aragonite crystal aggregation and morphology

In this study, the influence of Mg2+ on the aggregation and morphology of precipitated aragonite crystals is investigated at different temperatures. Different from some investigations described in the literature, aragonite precipitates in chemical systems in which Mg2+ acts specifically as crystal habit modifiers and not as polymorphic selectors. The results show that at increased Mg2+ concentration and temperature the aragonite crystals are less aggregated and that the amount of crystals sharing {110} faces and having larger extension of {001} faces increases. These outcomes may be relevant in biological, geochemical and technological contexts.

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.

Structural basis for the magnesium-dependent activation of transketolase from Chlamydomonas reinhardtii

BACKGROUNDnIn photosynthetic organisms, transketolase (TK) is involved in the Calvin-Benson cycle and participates to the regeneration of ribulose-5-phosphate. Previous studies demonstrated that TK catalysis is strictly dependent on thiamine pyrophosphate (TPP) and divalent ions such as Mg2+.nnnMETHODSnTK from the unicellular green alga Chlamydomonas reinhardtii (CrTK) was recombinantly produced and purified to homogeneity. Biochemical properties of the CrTK enzyme were delineated by activity assays and its structural features determined by CD analysis and X-ray crystallography.nnnRESULTSnCrTK is homodimeric and its catalysis depends on the reconstitution of the holo-enzyme in the presence of both TPP and Mg2+. Activity measurements and CD analysis revealed that the formation of fully active holo-CrTK is Mg2+-dependent and proceeds with a slow kinetics. The 3D-structure of CrTK without cofactors (CrTKapo) shows that two portions of the active site are flexible and disordered while they adopt an ordered conformation in the holo-form. Oxidative treatments revealed that Mg2+ participates in the redox control of CrTK by changing its propensity to be inactivated by oxidation. Indeed, the activity of holo-form is unaffected by oxidation whereas CrTK in the apo-form or reconstituted with the sole TPP show a strong sensitivity to oxidative inactivation.nnnCONCLUSIONnThese evidences indicate that Mg2+ is fundamental to allow gradual conformational arrangements suited for optimal catalysis. Moreover, Mg2+ is involved in the control of redox sensitivity of CrTK.nnnGENERAL SIGNIFICANCEnThe importance of Mg2+ in the functionality and redox sensitivity of CrTK is correlated to light-dependent fluctuations of Mg2+ in chloroplasts.

Influence of intra-skeletal coral lipids on calcium carbonate precipitation

Recent research studies have shown that the intra-skeletal organic matrix of corals contains lipids. This communication reports their characterization and their influence on calcium carbonate precipitation. In addition, their potential role in corals biomineralization is discussed.

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. Calcein is entrapped within calcite and aragonite and modifies the shape and morphology of both polymorphs. Moreover, in the presence of Mg2+, it inhibits aragonite formation in favor of magnesium calcite.

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.