A Metabolomic Perspective on Coeliac Disease

Metabolomics is an “omic” science that is now emerging with the purpose of elaborating a comprehensive analysis of the metabolome, which is the complete set of metabolites (i.e., small molecules intermediates) in an organism, tissue, cell, or biofluid. In the past decade, metabolomics has already proved to be useful for the characterization of several pathological conditions and offers promises as a clinical tool. A metabolomics investigation of coeliac disease (CD) revealed that a metabolic fingerprint for CD can be defined, which accounts for three different but complementary components: malabsorption, energy metabolism, and alterations in gut microflora and/or intestinal permeability. In this review, we will discuss the major advancements in metabolomics of CD, in particular with respect to the role of gut microbiome and energy metabolis

Context-Dependent Dynamics Lead to the Assembly of Functionally Distinct Microbial Communities

Niche construction through interspecific interactions can condition future community states on past ones. However, the extent to which such history dependency can steer communities towards functionally different states remains a subject of active debate. Using bacterial communities collected from wild pitchers of the carnivorous pitcher plant, Sarracenia purpurea, we test the effects of history on composition and function across communities assembled in synthetic pitcher plant microcosms. We find that the diversity of assembled communities is determined by the diversity of the system at early, pre-assembly stages. Species composition is also contingent on early community states, not only because of differences in the species pool, but also because the same species have different dynamics in different community contexts. Importantly, compositional differences are proportional to differences in function, as profiles of resource use are strongly correlated with composition, despite convergence in respiration rates. Early differences in community structure can thus propagate to mature communities, conditioning their functional repertoire

MODELING OF THE METAL BINDING SITES IN PROTEINS INVOLVED IN NEURODEGENERATION

Many proteins involved in the neurodegeneration processes are potential metalloproteins. In some of them the metal binding domain is flexible or unstructured (e.g. prion proteins, β-amyloid peptide, α-synuclein) resembling oligo-peptide chains. The regular protein structure usually has a critical impact on the binding ability of metal ion to protein scaffold, while in peptides with random structures the individual binding ability of the particular amino acid residue may decide about the peptide binding to metal ion

Copper binding to chicken and human prion protein amylodogenic regions: differences and similarities revealed by Ni2+ as a diamagnetic probe

Both human (h) and chicken (Ch) prion proteins (PrP) bind copper ions within the so called ‘‘tandem repeat” N-terminal region. Outside this region, hPrP possesses two additional copper binding sites, localized at His-96 and His-111 in the so called ‘‘amylodogenic” or neurotoxic region (residues 91–126). Also ChPrP possesses a similar region (ChPrP105140) containing two His (His-110 and His-124) and an identical hydrophobic tail of 15 amino acids rich in Ala and Gly. The copper binding abilities within such region of ChPrP were investigated by NMR, CD and potentiometry using Ni2+ as diamagnetic probe. The formation of diamagnetic metal complexes allowed to monitor the chemical shift and signal intensity variations and to determine the structural and kinetic features of the His-110 and His-124 metal binding sites. Finally a comparison between the hPrP and ChPrP metal binding abilities was performed. We found that the two prion proteins exhibited different copper and nickel preferences with the favoured metal binding sites localized at opposite His: His-110 for ChPrP, and His-111 for hPrP

Thermodynamic and spectroscopic investigation on the role of Met residues in CuII binding to the non-octarepeat site of the human prion protein

Among the common features shared by neurodegenerative diseases there is the central role played by specific proteins or peptides which accumulate in neurons as insoluble plaques or tangles, containing abnormal amounts of redox-active metal ions, like copper and iron. In the case of transmissible spongiform encephalopathies (TSE), the involved protein is known as "prion protein" (PrPC) since "prions" (proteinaceous and infectious) are the agents which make TSE transmissible. It is widely accepted that PrPC, in its wild-type form, can bind up to six Cu-II ions, four of them in the so-called "octarepeat domain" and the others in the "fifth (non-octarepeat) binding-site". The latter domain contains two His residues, acting as anchoring sites for Cu-II ions, and other potential binding residues, such as Lys and Met. While it is widely accepted that Lys residues do not take part in complex-formation, the role of methionines is still debated. In order to shed light on this issue, some peptides have been synthesized, either directly mimicking the sequence of the second half of the fifth binding site of human-PrPC (apo-form) or analogues where Met residues have been substituted by n-leucine. In addition, a series of short peptides, containing both His and Met residues in different relative positions, have been investigated, for the sake of comparison. Spectroscopic results, including NMR spectra of systems containing Ni-II as a probe for the paramagnetic Cu-II ion, agree on the exclusion of any direct interaction between the sulphur atom of Met residues and the Cu-II ion already bound to His-imidazole side-chains. However, thermodynamic data show that Met-109 somewhat contributes to stability of complex species and this can be attributed to different electronic and steric effects

Context-dependent dynamics lead to the assembly of functionally distinct microbial communities

Niche construction through interspecific interactions can condition future community states on past ones. However, the extent to which such history dependency can steer communities towards functionally different states remains a subject of active debate. Using bacterial communities collected from wild pitchers of the carnivorous pitcher plant, Sarracenia purpurea, we test the effects of history on composition and function across communities assembled in synthetic pitcher plant microcosms. We find that the diversity of assembled communities is determined by the diversity of the system at early, pre-assembly stages. Species composition is also contingent on early community states, not only because of differences in the species pool, but also because the same species have different dynamics in different community contexts. Importantly, compositional differences are proportional to differences in function, as profiles of resource use are strongly correlated with composition, despite convergence in respiration rates. Early differences in community structure can thus propagate to mature communities, conditioning their functional repertoire

The complex-formation behaviour of His residues in the fifth Cu2+ binding site of human Prion protein: a close look

Human Prion Protein (hPrPC) is able to bind up to six Cu2+ ions. Four of them can be allocated in the “octarepeat domain”, a region of the unstructured N-terminal domain containing four tandem-repetitions of the sequence PHGGGWGQ. It is widely accepted that the additional binding sites correspond to His-96 and His-111 residues. However, recent literature does not agree on the role and the behavior of these sites in Cu2+ complexation to hPrPC. In order to shed more light on this topic, some peptidic analogues of the PrP92-113 fragment were synthesized: (H96A)PrP92-113, (H111A)PrP92-113, (H96Nτ-Me-His)PrP92-113, (H111Nτ-Me-His)PrP92-113, (H96Nτ-Me-His)PrP92-100, (H111Nτ-Me-His)PrP106-113, where an alanine or a histidine methylated at the τ nitrogen atom of its imidazole ring have been substituted to His-96 or His-111. The first two ligands allowed to confirm that His-111 binding site is stronger than His-96 one: they act as independent sites even at Cu2+-ion substoichiometric levels. Neither multi-histidine binding nor bis-complex formation has been detected at neutral pH. Nτ methylation gave evidence that τ nitrogens of imidazole residues can participate in complex-formation only at acidic pH, where displacement of amidic protons by Cu2+ ions is not allowed. Finally, the length of the fragment does not look to have any significant influence on the behavior of the two His-96 and His-111 binding sites, from the point of view of neither the coordination geometry nor their relative strength