When Metal Complexes Evolve, and a Minor Species is the Most Active: the Case of Bis(Phenanthroline)Copper in the Catalysis of Glutathione Oxidation and Hydroxyl Radical Generation.

Several copper-ligands, including 1,10-phenanthroline (Phen), have been investigated for anticancer purposes based on their capacity to bind excess copper (Cu) in cancer tissues and form redox active complexes able to catalyse the formation of reactive oxygen species (ROS), ultimately leading to oxidative stress and cell death. Glutathione (GSH) is a critical compound as it is highly concentrated intracellularly and can reduce and dissociate copper(II) from the ligand forming poorly redox-active copper(I)-thiolate clusters. Here we report that Cu-Phen speciation evolves in physiologically relevant GSH concentrations.

Predicting the Structure of Enzymes with Metal Cofactors: The Example of [FeFe] Hydrogenases.

The advent of deep learning algorithms for protein folding opened a new era in the ability of predicting and optimizing the function of proteins once the sequence is known. The task is more intricate when cofactors like metal ions or small ligands are essential to functioning. In this case, the combined use of traditional simulation methods based on interatomic force fields and deep learning predictions is mandatory.

Probing the Dynamic Landscape: From Static to Time-Resolved X-Ray Absorption Spectroscopy to Investigate Copper Redox Chemistry in Neurodegenerative Disorders.

Copper (Cu), with its ability to exist in various oxidation states, notably Cu(I) and Cu(II), plays a crucial role in diverse biological redox reactions. This includes its involvement in pathways associated with oxidative stress in neurodegenerative disorders such as Alzheimer's disease, Parkinson's disease, and Transmissible Spongiform Encephalopathies. This paper offers an overview of X-ray Absorption Spectroscopy (XAS) studies designed to elucidate the interactions between Cu ions and proteins or peptides associated with these neurodegenerative diseases.

Revisiting the pro-oxidant activity of copper: interplay of ascorbate, cysteine, and glutathione.

Copper (Cu) is essential for most organisms, but it can be poisonous in excess, through mechanisms such as protein aggregation, trans-metallation, and oxidative stress. The latter could implicate the formation of potentially harmful reactive oxygen species (O2•-, H2O2, and HO•) via the redox cycling between Cu(II)/Cu(I) states in the presence of dioxygen and physiological reducing agents such as ascorbate (AscH), cysteine (Cys), and the tripeptide glutathione (GSH). Although the reactivity of Cu with these reductants has been previously investigated, the reactions taking place in a more physiologically relevant mixture of these biomolecules are not known.

Probing protein stability: towards a computational atomistic, reliable, affordable, and improvable model.

We present an improved application of a recently proposed computational method designed to evaluate the change of free energy as a function of the average value of a suitably chosen collective variable in proteins. The method is based on a full atomistic description of the protein and its environment. The goal is to understand how the protein melting temperature changes upon single-point mutations, because the sign of the temperature variation will allow us to discriminate stabilizing vs.

The role of Zn ions in the interaction between SARS-CoV-2 orf7a protein and BST2/tetherin.

In this paper, we provide evidence that Zn ions play a role in the SARS-CoV-2 virus strategy to escape the immune response mediated by the BST2-tetherin host protein. This conclusion is based on sequence analysis and molecular dynamics simulations as well as X-ray absorption experiments [1].

Chasing the Elusive "In-Between" State of the Copper-Amyloid β Complex by X-ray Absorption through Partial Thermal Relaxation after Photoreduction.

The redox activity of Cu ions bound to the amyloid-β (Aβ) peptide is implicated as a source of oxidative stress in the context of Alzheimer's disease. In order to explain the efficient redox cycling between Cu -Aβ (distorted square-pyramidal) and Cu -Aβ (digonal) resting states, the existence of a low-populated "in-between" state, prone to bind Cu in both oxidation states, has been postulated. Here, we exploited the partial X-ray induced photoreduction at 10 K, followed by a thermal relaxation at 200 K, to trap and characterize by X-ray Absorption Spectroscopy (XAS) a partially reduced Cu-Aβ species different from the resting states.

A Thermodynamic Study on the Interaction between RH-23 Peptide and DMPC-Based Biomembrane Models.

Investigation of the interaction between drugs and biomembrane models, as a strategy to study and eventually improve drug/substrate interactions, is a crucial factor in preliminary screening. Synthesized peptides represent a source of potential anticancer and theragnostic drugs. In this study, we investigated the interaction of a novel synthesized peptide, called RH-23, with a simplified dimyristoylphosphatidylcholine (DMPC) model of the cellular membrane.

Monitoring Risk Factors and Improving Adherence to Therapy in Patients With Chronic Kidney Disease (Smit-CKD Project): Pilot Observational Study.

Background: Chronic kidney disease is a major public health issue, with about 13% of the general adult population and 30% of the elderly affected. Patients in the last stage of this disease have an almost uniquely high risk of death and cardiovascular events, with reduced adherence to therapy representing an additional risk factor for cardiovascular morbidity and mortality. Considering the increased penetration of mobile phones, a mobile app could educate patients to autonomously monitor cardiorenal risk factors.

Metal Ion Binding in Wild-Type and Mutated Frataxin: A Stability Study.

This work studies the stability of wild-type frataxin and some of its variants found in cancer tissues upon Co binding. Although the physiologically involved metal ion in the frataxin enzymatic activity is Fe, as it is customarily done, Co is most often used in experiments because Fe is extremely unstable owing to the fast oxidation reaction Fe → Fe. Protein stability is monitored following the conformational changes induced by Co binding as measured by circular dichroism, fluorescence spectroscopy, and melting temperature measurements.

Is styrene competitive for dopamine receptor binding?

The potential role of styrene oxide in altering the dopaminergic pathway in the ear is investigated by means of molecular docking and molecular dynamics simulations. We estimate the binding affinity of both styrene oxide and dopamine to the dopaminergic receptor DrD2 by computing the free-energy difference, ∆, between the configuration where the ligand is bound to the receptor and the situation in which it is "infinitely" far away from it. The results show that the styrene oxide has a somewhat lower affinity for binding with respect to dopamine, which, however, may not be enough to prevent exogenous high concentration styrene oxide to compete with endogenous dopamine for DrD2 binding.

Modelling Protein Plasticity: The Example of Frataxin and Its Variants.

Frataxin (FXN) is a protein involved in storage and delivery of iron in the mitochondria. Single-point mutations in the gene lead to reduced production of functional frataxin, with the consequent dyshomeostasis of iron. FXN variants are at the basis of neurological impairment (the Friedreich's ataxia) and several types of cancer.

Aggregates Sealed by Ions.

The chapter draws a line connecting some recent results where the role of ions is found essential in sealing more or less pre-organized assemblies of macromolecules. We draw some dots along the line that starts from the effect of the ionic atmosphere and ends with the chemical bonds formed by multivalent ions acting as bridges between macromolecules. Many of these dots involve structurally disordered peptides and disordered regions of proteins.

Zn-Induced Interactions Between SARS-CoV-2 orf7a and BST2/Tetherin.

We present in this work a first X-ray Absorption Spectroscopy study of the interactions of Zn with human BST2/tetherin and SARS-CoV-2 orf7a proteins as well as with some of their complexes. The analysis of the XANES region of the measured spectra shows that Zn binds to BST2, as well as to orf7a, thus resulting in the formation of BST2-orf7a complexes. This structural information confirms the the conjecture, recently put forward by some of the present Authors, according to which the accessory orf7a (and possibly also orf8) viral protein are capable of interfering with the BST2 antiviral activity.

The apically incised coronally advanced surgical technique (AICAST) for periodontal regeneration in isolated defects: a case series.

Objectives: The aim of this retrospective case series was to report the performance up to 5 years of an innovative surgical design (the apically incised coronally advanced surgical technique [AICAST]) for the regenerative treatment of one- or two-walled intrabony periodontal lesions.

Method And Materials: After completion of standard step I to II periodontal therapy, nine isolated periodontal defects were treated through AICAST. The following clinical outcome measurements were collected before the surgical intervention and at the last available follow-up: probing pocket depth (PPD), recession depth (REC), and clinical attachment level (CAL).

Neurobiological underpinnings of cognitive subtypes in psychoses: A cross-diagnostic cluster analysis.

Schizophrenia and bipolar disorder include patients with different characteristics, which may hamper the definition of biomarkers. One of the dimensions with greater heterogeneity among these patients is cognition. Recent studies support the identification of different patients' subgroups along the cognitive domain using cluster analysis.

SARS-CoV-2 Virion Stabilization by Zn Binding.

Zinc plays a crucial role in the process of virion maturation inside the host cell. The accessory Cys-rich proteins expressed in SARS-CoV-2 by genes ORF7a and ORF8 are likely involved in zinc binding and in interactions with cellular antigens activated by extensive disulfide bonds. In this report we provide a proof of concept for the feasibility of a structural study of orf7a and orf8 proteins.

Dealing with Cu reduction in X-ray absorption spectroscopy experiments.

In this paper we prove in the exemplary case of the amyloid-β peptide in complex with Cu(ii) that at the current low temperatures employed in XAS experiments, the time needed for collecting a good quality XAS spectrum is significantly shorter than the time after which structural damage becomes appreciable. Our method takes advantage of the well-known circumstance that the transition of Cu from the oxidized to the reduced form under ionizing radiation can be quantified by monitoring a characteristic peak in the pre-edge region. We show that there exists a sufficiently large time window in which good XAS spectra can be acquired before the structure around the oxidized Cu(ii) ion reorganizes itself into the reduced Cu(i) "resting" structure.

Multi-scale theoretical approach to X-ray absorption spectra in disordered systems: an application to the study of Zn(ii) in water.

We develop a multi-scale theoretical approach aimed at calculating from first principles X-ray absorption spectra of liquid solutions and disordered systems. We test the method by considering the paradigmatic case of Zn(ii) in water which, besides being relevant in itself, is also of interest for biology. With the help of classical molecular dynamics simulations we start by producing bunches of configurations differing for the Zn(ii)-water coordination mode.

Designing effective anticancer-radiopeptides. A Molecular Dynamics study of their interaction with model tumor and healthy cell membranes.

One of the greatest merit of the use of radiopeptides in oncology is their selectivity which, however, brings about the drawback that each radiopeptide is specific for a given tumor type. To overcome this problem the direction currently taken in drug design is that of radiolabelling peptide hormones (or their analogues), relying on their intrinsic ability to bind to specific receptors in precise areas of the human body, at the cost, however, of a poor selectivity against healthy cells. We present here an extensive Molecular Dynamics study of a promising alternative inspired by the mechanism through which antimicrobial peptides interact with the negatively charged bacterial membranes.

Human insulin fibrillogenesis in the presence of epigallocatechin gallate and melatonin: Structural insights from a biophysical approach.

Fibrillogenesis of monomeric human insulin in the presence or absence of (-)-epigallocatechin-3-gallate and melatonin was here investigated using a multi-technique approach. Results from Raman and Infrared spectroscopy pointed out that a high content of intermolecular β-sheet aggregates is formed after long-term incubation. However, near UV experiments, Dynamic Light Scattering, Thioflavin-T fluorescence measurements and Atomic Force Microscopy revealed that the kinetics from native-to-fibrillar state of insulin is hampered only in the presence of (-)-epigallocatechin-3-gallate.

The effect of β-sheet breaker peptides on metal associated Amyloid-β peptide aggregation process.

Far-UV Circular Dichroism experiments and Atomic Force Microscopy tomography are employed to assess the impact of β-sheet breakers on the Aβ peptide aggregation process in the presence of Cu or Zn transition metals. In this work we focus on two specific 5-amino acids long β-sheet breakers, namely the LPFFD Soto peptide, already known in the literature, and the LPFFN peptide recently designed and studied by our team. We provide evidence that both β-sheet breakers are effective in reducing the Aβ aggregation propensity, even in the presence of metal ions.

Single-Nucleotide Polymorphism of PPARγ, a Protein at the Crossroads of Physiological and Pathological Processes.

Genome polymorphisms are responsible for phenotypic differences between humans and for individual susceptibility to genetic diseases and therapeutic responses. Non-synonymous single-nucleotide polymorphisms (nsSNPs) lead to protein variants with a change in the amino acid sequence that may affect the structure and/or function of the protein and may be utilized as efficient structural and functional markers of association to complex diseases. This study is focused on nsSNP variants of the ligand binding domain of PPARγ a nuclear receptor in the superfamily of ligand inducible transcription factors that play an important role in regulating lipid metabolism and in several processes ranging from cellular differentiation and development to carcinogenesis.

Role of dietary antioxidant (-)-epicatechin in the development of β-lactoglobulin fibrils.

Under specific physico-chemical conditions β-lactoglobulin is seen to form fibrils structurally highly similar to those that are formed by the amyloid-like proteins associated with neurodegenerative disorders, such as Alzheimer and Parkinson diseases. In the present study we provide insights on the possible role that the dietary flavonoid (-)-epicatechin plays on β-lactoglobulin fibril formation. Fibril formation is induced by keeping β-lactoglobulin solutions at pH2.