Search

The development of sustainable materials by employing natural and nontoxic resources has been attracting much attention over the previous years. In this work, we discuss for the first time the chemical combination between resorcinol diglycidyl ether (RDGE), an aromatic biobased thermosetting monomer, and polyhydroxybutyrate (PHB), a bioderived and biodegradable thermoplastic polyester. By this combination, we aimed to associate the high thermal stability of RDGE with a toughening effect by the aliphatic chains of PHB. The investigations on the mechanism of the cross-linking reaction and on the structural connectivity between the two components were realized by Fourier transform infrared (FTIR) and NMR spectroscopies. We found that the epoxide polymerization catalyzed by tertiary amines triggers the formation of crotonyl species by polyhydroxybutyrate cleavage. Two-dimensional NMR experiments show that polyhydroxybutyrate fragments covalently bind as side chains to the rigid aromatic network of the epoxide frame. The cross-linking between the two systems entails the formation of new ester and ether bonds. The obtained structures show a network homogeneity confirmed by a single

The nature of the nanoparticle-protein corona is emerging as a key aspect in determining the impact of nanomaterials on proteins and in general on the biological response. We previously demonstrated that citrate-stabilized gold nanoparticles (Cit-AuNPs) interact with β2-microglobulin (β2m) preserving the protein native structure. Moreover, Cit-AuNPs are able to hinder

The effect of extrinsic paramagnetic probes on NMR relaxation rates for surface mapping of proteins and other biopolymers is a widely investigated and powerful NMR technique. Here we describe a new application of those probes. It relies on the setting of the relaxation delay to generate magnetization equilibrium and off-equilibrium conditions, in order to tailor the extent of steady state signal recovery with and without the water-soluble nitroxide Tempol. With this approach it is possible to identify signals whose relaxation is affected by exchange processes and, from the relative assignments, to map the protein residues involved in association or conformational interconversion processes on a micro-to-millisecond time scale. This finding is confirmed by the comparison with the results obtained from relaxation dispersion measurements. This simple and convenient method allows preliminary inspection to highlight regions where structural or chemical exchange events are operative, in order to focus on quantitative subsequent determinations by transverse relaxation dispersion experiments or analogous NMR relaxation studies, and/or to gain insights into the predictions of calculations.

Herein, we compared the ability of linear and cyclic peptides generated in silico to target different protein sites: internal pockets and solvent-exposed sites. We selected human lysozyme (HuL) as a model target protein combined with the computational evolution of linear and cyclic peptides. The sequence evolution of these peptides was based on the PARCE algorithm. The generated peptides were screened based on their aqueous solubility and HuL binding affinity. The latter was evaluated by means of scoring functions and atomistic molecular dynamics (MD) trajectories in water, which allowed prediction of the structural features of the protein-peptide complexes. The computational results demonstrated that cyclic peptides constitute the optimal choice for solvent exposed sites, while both linear and cyclic peptides are capable of targeting the HuL pocket effectively. The most promising binders found in silico were investigated experimentally by surface plasmon resonance (SPR), nuclear magnetic resonance (NMR), and electrospray ionization mass spectrometry (ESI-MS) techniques. All tested peptides displayed dissociation constants in the micromolar range, as assessed by SPR; however, both NMR and ESI-MS suggested multiple binding modes, at least for the pocket binding peptides. A detailed NMR analysis confirmed that both linear and cyclic pocket peptides correctly target the binding site they were designed for.

Correction for ‘Exploring exchange processes in proteins by paramagnetic perturbation of NMR spectra’ by Yamanappa Hunashal et al., Phys. Chem. Chem. Phys., 2020, 22, 6247–6259, DOI: 10.1039/c9cp06950j.

Awareness about environmental impact of petroleum sourcing polymeric materials is leading to an increased interest sustainable materials manufacturing. Here we present the elaboration of fully bio-...

Gold nanoparticles (AuNPs) have been proved to be ideal scaffolds to build nanodevices whose performance can be tuned by changing their coating. In particular, the interaction of AuNPs with proteins was revealed to be highly dependent on the physico-chemical properties of the gold cluster protecting monolayer. In this work we studied the behavior of three different alkanethiolate-coated AuNPs (AT-AuNPs) when they are incubated with a model amyloidogenic protein, β2-microglobulin (β2m), whose clinical relevance in dialysis-related amyloidosis (DRA) and structural properties are well known. To the aim we synthesized 6-mercaptohexanoic acid-coated AuNPs (MHA-AuNPs) and (11-mercaptoundecyl)-N,N,N-trimethylammonium bromide-coated AuNPs (MUTAB-AuNPs) of 7.5 nm diameter and 3-mercaptopropionic acid-coated AuNPs (MPA-AuNPs) of 3.6 nm diameter. To study the effects of the incubation with β2m of these NPs that differ in charge and dimension, we employed NMR, UV-vis and fluorescence spectroscopy, along with transmission electron microscopy (TEM). The three tested AuNP systems gave different results. We found that MHA-AuNPs precipitate with the protein into large agglomerates inducing β2m unfolding, MUTAB-AuNP precipitation is triggered by the protein that remains unchanged in solution, at least at the higher considered protein/NP ratio, and MPA-AuNPs interact preferentially with a localized region of the protein that stays essentially stably dissolved. These results stress the complexity of the bio-nano interface and the relevance and viability of the fine control of NP properties to master protein-NP interactions.

The need for thermosets from renewable resources is continuously increasing to find eco-friendly alternatives to petroleum-derived materials. Products obtained from biomass have shown to play an important role in this challenge. Here, we present the structural characterization of new biobased thermosets made of humins, a byproduct of lignocellulosic biorefinery, and glycidylated phloroglucinol coming from the biomass phenolic fraction. By employing attenuated total reflection-Fourier transform infrared and NMR spectroscopies, we elucidated the connections between these two systems, contributing to clarify their molecular structures and their reactivities. We demonstrated that the resin curing takes place through ether bond formation between humin hydroxyl functions and phloroglucinol epoxides. Besides cross-linking, humins show a complex rearrangement of their furanic structure through different concomitant chemical pathways depending on the reaction conditions.

Summary Inhibiting amyloid aggregation through high-turnover dynamic interactions could be an efficient strategy that is already used by small heat-shock proteins in different biological contexts. We report the interactions of three topologically non-trivial, zinc-templated metal-organic assemblies, a [2]catenane, a trefoil knot (TK), and Borromean rings, with two β2-microglobulin (β2m) variants responsible for amyloidotic pathologies. Fast exchange and similar patterns of preferred contact surface are observed by NMR, consistent with molecular dynamics simulations. In vitro fibrillation is inhibited by each complex, whereas the zinc-free TK induces protein aggregation and does not inhibit fibrillogenesis. The metal coordination imposes structural rigidity that determines the contact area on the β2m surface depending on the complex dimensions, ensuring in vitro prevention of fibrillogenesis. Administration of TK, the best protein-contacting species, to a disease-model organism, namely a Caenorhabditis elegans mutant expressing the D76N β2m variant, confirms the bioactivity potential of the knot topology and suggests new developments.

Pristine (as prepared) carbon nanotube (CNT) based substrates have been widely used to grow and interface neurons in culture. Nerve cells normally differentiate on CNTs and the synaptic networks, newly formed at the interface with this material, usually show an improved robustness in signal transfer. However manipulation of pristine CNTs is often prevented by their low dispersibility and tendency to aggregate in most solvents. This issue can be at least partially solved by adding solubilizing groups to the surface of CNT, which also helps improving their biocompatibility. It becomes therefore of crucial importance to determine whether chemically manipulated CNTs may maintain their performance in improving nerve signaling. Here we study and compare the impact in vitro on neuronal signaling of two classes of chemically modified multiwalled CNTs in reference to pristine CNTs, which are known to be a substrate able to boost neuronal growth and communication. We found that the extent of functionalization and the nature of the functional groups on MWNT sidewalls affect the conductivity and the biological effects of the final derivatives. This information is important for the future design of biointegrated devices.

Background: The interaction between proteins and nanoparticles is a very relevant subject because of the potential applications in medicine and material science in general. Further interest derives from the amyloidogenic character of the considered protein, &beta, 2-microglobulin (&beta, 2m), which may be regarded as a paradigmatic system for possible therapeutic strategies. Previous evidence showed in fact that gold nanoparticles (AuNPs) are able to inhibit &beta, 2m fibril formation in vitro. Methods: NMR (Nuclear Magnetic Resonance) and ESR (Electron Spin Resonance) spectroscopy are employed to characterize the paramagnetic perturbation of the extrinsic nitroxide probe Tempol on &beta, 2m in the absence and presence of AuNPs to determine the surface accessibility properties and the occurrence of chemical or conformational exchange, based on measurements conducted under magnetization equilibrium and non-equilibrium conditions. Results: The nitroxide perturbation analysis successfully identifies the protein regions where protein-protein or protein-AuNPs interactions hinder accessibility or/and establish exchange contacts. These information give interesting clues to recognize the fibrillation interface of &beta, 2m and hypothesize a mechanism for AuNPs fibrillogenesis inhibition. Conclusions: The presented approach can be advantageously applied to the characterization of the interface in protein-protein and protein-nanoparticles interactions.

Purpose The ex-vivo normothermic perfusion in Heart Transplantation (HTx) allows to expand the donor pool by reducing the ischemic time and providing graft evaluation. Aim of the study was to compare the traditional cold storage (CS) and ex-vivo normothermic perfusion (EVP) in HTx employing marginal donors. Methods Since 2011, 87 HTx employing marginal donors (age>55 years; expected ischemic time>4h; LVEF 14mm; drug abuse; cardiac arrest; CAD) in standard recipients has been performed, CS was utilized in 70 cases (80%) and EVP in 17 (20%). Pre-operative data, survival and complications at short and long term were analysed. Endomyocardial biopsies were collected at time of organ retrieval (T0), before implantation (T1) and after aortic declamping (T2) for light and electron mycroscopy. Blood samples were collected at T0 and T2 from coronary sinus and peripheral vein for metabolomic evaluation . Results Preoperative data were similar in the two groups. Three organs (15%) were considered not suitable for HTx after EVP. Ischemic time and surgical time were shorter in EVP group, which showed a better short and long term survival: a 5-year survival of 100% vs. 94%, 82% and 73% at 30-day, 1 and 5 years respectively in CS group (p=0.06) and less overall complications (65% vs. 89%, p=0.02). In CS group, endomyocardial biopsies showed a tendency for more prominent myocardial damage after heart reperfusion, especially underlined by mitochondrial and organelles dysfunction (figure1). Conclusion EVP permits to exclude not suitable grafts, to reduce complications and to obtain optimal HTx survival. Pathological findings show a tendency for better myocardial protection.

Protein aggregation including the formation of dimers and multimers in solution, underlies an array of human diseases such as systemic amyloidosis which is a fatal disease caused by misfolding of native globular proteins damaging the structure and function of affected organs. Different kind of interactors can interfere with the formation of protein dimers and multimers in solution. A very special class of interactors are nanoparticles thanks to the extremely efficient extension of their interaction surface. In particular citrate-coated gold nanoparticles (cit-AuNPs) were recently investigated with amyloidogenic protein $\beta$2-microglobulin ($\beta$2m). Here we present the computational studies on two challenging models known for their enhanced amyloidogenic propensity, namely $\Delta$N6 and D76N $\beta$2m naturally occurring variants, and disclose the role of cit-AuNPs on their fibrillogenesis. The proposed interaction mechanism lies in the interference of the cit-AuNPs with the protein dimers at the early stages of aggregation, that induces dimer disassembling. As a consequence, natural fibril formation can be inhibited. Relying on the comparison between atomistic simulations at multiple levels (enhanced sampling molecular dynamics and Brownian dynamics) and protein structural characterisation by NMR, we demonstrate that the cit-AuNPs interactors are able to inhibit protein dimer assembling. As a consequence, the natural fibril formation is also inhibited, as found in experiment., Comment: Published by RSC, under a Creative Commons Attribution 3.0 Unported Licence

Protein fibrillation is involved in many serious diseases, and protein oligomers are proved to be precursors of amyloid fibrils. NMR and QCMD experiments allowed us to establish that the interaction between citrate-stabilized gold nanoparticles and a paradigmatic amyloidogenic protein, β2-microglobulin, is able to interfere with protein association into oligomers.

Nanoparticles have repeatedly been shown to enhance fibril formation when assayed with amyloidogenic proteins. Recently, however, evidence casting some doubt about the generality of this conclusion started to emerge. Therefore, to investigate further the influence of nanoparticles on the fibrillation process, we used a naturally occurring variant of the paradigmatic amyloidogenic protein β

Nanoparticles have repeatedly been shown to enhance fibril formation when assayed with amyloidogenic proteins. Recently, however, evidence casting some doubt about the generality of this conclusion started to emerge. Therefore, to investigate further the influence of nanoparticles on the fibrillation process, we used a naturally occurring variant of the paradigmatic amyloidogenic protein β2-microglobulin (β2m), namely D76N β2m where asparagine replaces aspartate at position 76. This variant is responsible for aggressive systemic amyloidosis. After characterizing the interaction of the variant with citrate-stabilized gold nanoparticles (Cit-AuNPs) by NMR and modeling, we analyzed the fibril formation by three different methods: thioflavin T fluorescence, native agarose gel electrophoresis and transmission electron microscopy. The NMR evidence indicated a fast-exchange interaction involving preferentially specific regions of the protein that proved, by subsequent modeling, to be consistent with a dimeric adduct interacting with Cit-AuNPs. The fibril detection assays showed that AuNPs are able to hamper D76N β2m fibrillogenesis through an effective interaction that competes with protofibril formation or recruitment. These findings open promising perspectives for the optimization of the nanoparticle surface to design tunable interactions with proteins.

The oriented immobilization of proteins, key for the development of novel responsive biomaterials, relies on the availability of effective probes. These are generally provided by standard approaches based on in vivo maturation and in vitro selection of antibodies and/or aptamers. These techniques can suffer technical problems when a non-immunogenic epitope needs to be targeted. Here we propose a strategy to circumvent this issue by in silico design. In our method molecular binders, in the form of cyclic peptides, are computationally evolved by stochastically exploring their sequence and structure space to identify high-affinity peptides for a chosen epitope of a target globular protein: here a solvent-exposed site of β2-microglobulin (β2m). Designed sequences were screened by explicit solvent molecular dynamics simulations (MD) followed by experimental validation. Five candidates gave dose-response surface plasmon resonance signals with dissociation constants in the micromolar range. One of them was further analyzed by means of isothermal titration calorimetry, nuclear magnetic resonance, and 250 ns of MD. Atomic-force microscopy imaging showed that this peptide is able to immobilize β2m on a gold surface. In short, we have shown by a variety of experimental techniques that it is possible to capture a protein through an epitope of choice by computational design.

The use of binary blends of hydrogenated and fluorinated alkanethiolates represents an interesting approach to the construction of anisotropic hybrid organic–inorganic nanoparticles since the fluorinated and hydrogenated components are expected to self-sort on the nanoparticle surface because of their reciprocal phobicity. These mixed monolayers are therefore strongly non-ideal binary systems. The synthetic routes we explored to achieve mixed monolayer gold nanoparticles displaying hydrogenated and fluorinated ligands clearly show that the final monolayer composition is a non-linear function of the initial reaction mixture. Our data suggest that, under certain geometrical constraints, nucleation and growth of fluorinated domains could be the initial event in the formation of these mixed monolayers. The onset of domain formation depends on the structure of the fluorinated and hydrogenated species. The solubility of the mixed monolayer nanoparticles displayed a marked discontinuity as a function of the monolayer composition. When the fluorinated component content is small, the nanoparticle systems are fully soluble in chloroform, at intermediate content the nanoparticles become soluble in hexane and eventually they become soluble in fluorinated solvents only. The ranges of monolayer compositions in which the solubility transitions are observed depend on the nature of the thiols composing the monolayer.