Design study of a photon beamline for a soft X-ray FEL driven by high gradient acceleration at EuPRAXIA@SPARC_LAB

We are proposing a facility based on high gradient acceleration via x-band RF structures and plasma acceleration. We plan to reach an electron energy of the order of 1 GeV, suitable to drive a Free Electron Laser for applications in the so called "water window" (2 - 4 nm). A conceptual design of the beamline, from the photon beam from the undulators to the user experimental chamber, mainly focusing on diagnostic, manipulation and transport of the radiation is presented and discussed. We also briefly outline a user end station for coherent imaging, laser ablation and pump-probe experiments

Modeling the interplay of glycine protonation and multiple histidine binding of copper in the prion protein octarepeat subdomains

The octarepeat region of the prion protein can bind Cu(2+) ions up to full occupancy (one ion per octarepeat) at neutral pH. While crystallographic data show that the HGGG octarepeat subdomain is the basic binding unit, multiple histidine coordination at lower Cu occupancy has been reported by X-ray absorption spectroscopy, EPR, and potentiometric experiments. In this paper we investigate, with first principles Car-Parrinello simulations, the first step for the formation of the Cu low-level binding mode, where four histidine side chains are coordinated to the same Cu(2+) ion. This step involves the further binding of a second histidine to an already HGGG domain bonded Cu(2+) ion. The influence of the pH on the ability of Cu to bind two histidine side chains was taken into account by simulating different protonation states of the amide N atoms of the two glycines lying nearest to the first histidine. Multiple histidine coordination is also seen to occur when glycine deprotonation occurs and the presence of the extra histidine stabilizes the Cu-peptide complex. Though the stabilization effect slightly decreases with the number of deprotonated glycines (reaching a minimum when both N atoms of the two nearest glycines are available as Cu ligands), the system is still capable of binding the second histidine in a 4N tetrahedral (though slightly distorted) coordination, whose energy is very near to that of the crystallographic square-planar 3N1O coordination. This result suggests that at low metal concentration the reorganization energy associated with Cu(II)/Cu(I) reduction is small also at pH approximately 7, when glycines are deprotonated

A commentary on the inhibition of human TPC2 channel by the natural flavonoid naringenin: methods, experiments, and ideas

: Human endo-lysosomes possess a class of proteins called TPC channels on their membrane, which are essential for proper cell functioning. This protein family can be functionally studied by expressing them in plant vacuoles. Inhibition of hTPC activity by naringenin, one of the main flavonoids present in the human diet, has the potential to be beneficial in severe human diseases such as solid tumor development, melanoma, and viral infections. We attempted to identify the molecular basis of the interaction between hTPC2 and naringenin, using ensemble docking on molecular dynamics (MD) trajectories, but the specific binding site remains elusive, posing a challenge that could potentially be addressed in the future by increased computational power in MD and the combined use of microscopy techniques such as cryo-EM

Characterization of human frataxin missense variants in cancer tissues

Human frataxin is an iron binding protein involved in the mitochondrial Fe-S clusters assembly, a process fundamental for the functional activity of mitochondrial proteins. Decreased level of frataxin expression is associated with the neurodegenerative disease Friedreich ataxia. Defective function of frataxin may cause defects in mitochondria, leading to increased tumorigenesis. Tumour initiating cells show higher iron uptake, a decrease in iron storage and a reduced Fe-S clusters synthesis and utilization. In this study we selected, from COSMIC database, the somatic human frataxin missense variants found in cancer tissues p.D104G, p.A107V, p.F109L, p.Y123S, p.S161I, p.W173C, p.S181F, and p.S202F to analyze the effect of the single amino acid substitutions on frataxin structure, function and stability. The spectral properties, the thermodynamic and the kinetic stability, as well as the molecular dynamics of the frataxin missense variants found in cancer tissues point to local changes confined to the environment of the mutated residues. The global fold of the variants is not altered by the amino acid substitutions, however some of the variants show a decreased stability and a decreased functional activity in comparison to that of the wild type protein. This article is protected by copyright. All rights reserved

Plasma-generated X-ray pulses: betatron radiation opportunities at EuPRAXIA@SPARC_LAB

EuPRAXIA is a leading European project aimed at the development of a dedicated, groundbreaking, ultra-compact accelerator research infrastructure based on novel plasma acceleration concepts and laser technology and on the development of their users’ communities. Within this framework, the Laboratori Nazionali di Frascati (LNF, INFN) will be equipped with a unique combination of an X-band RF LINAC generating high-brightness GeV-range electron beams, a 0.5 PW class laser system and the first fifth-generation free electron laser (FEL) source driven by a plasma-based accelerator, the EuPRAXIA@SPARC_LAB facility. Wiggler-like radiation emitted by electrons accelerated in plasma wakefields gives rise to brilliant, ultra-short X-ray pulses, called betatron radiation. Extensive studies have been performed at the FLAME laser facility at LNF, INFN, where betatron radiation was measured and characterized. The purpose of this paper is to describe the betatron spectrum emitted by particle wakefield acceleration at EuPRAXIA@SPARC_LAB and provide an overview of the foreseen applications of this specific source, thus helping to establish a future user community interested in (possibly coupled) FEL and betatron radiation experiments. In order to provide a quantitative estimate of the expected betatron spectrum and therefore to present suitable applications, we performed simple simulations to determine the spectrum of the betatron radiation emitted at EuPRAXIA@SPARC_LAB. With reference to experiments performed exploiting similar betatron sources, we highlight the opportunities offered by its brilliant femtosecond pulses for ultra-fast X-ray spectroscopy and imaging measurements, but also as an ancillary tool for designing and testing FEL instrumentation and experiments

Theoretical Study of Vibrational Properties of Peptides: Force Fields in Comparison and Ab Initio Investigation

Infrared (IR) spectroscopy is a valuable tool to obtain information about protein secondary structure. The far-infrared (FIR) spectrum is characterized by a complex combination of different molecular contributions which, for small molecules, may be interpreted with the help of quantum-mechanical (QM) calculations. Unfortunately, the high computational cost of QM calculations makes them inapplicable to larger molecules, such as proteins and peptides. In this work, we present a theoretical study on the secondary structure, molecular properties, and vibrational spectra of different peptides, using both a classical and a QM approach. Our results show that the amide I main peak value, and related quantities, such as dipole strength (DS) and transition dipole moment (TDM), depends on protein secondary structure; in particular, from QM calculations arises that α-rich molecular systems present lower intensities than β-rich ones. Furthermore, it is possible to decouple and identify the intensity of the different contributions of the inter- and intra-molecular motions which characterize the FIR spectrum, starting from the results obtained with QM calculations

Cu Involvement In Prion Oligopeptide Stability: Experiments And Numerical Simulations

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The role of metals in amyloid aggregation: A test case for ab initio simulations

First principle ab initio molecular dynamics simulations of the Car-Parrinello type have proved to be of invaluable help in understanding the microscopic mechanisms of chemical bonding both in solid state physics and in structural biophysics. In this work we present as test cases the study of the Cu coordination mode in two especially important examples: Prion protein and beta-amyloids. Using medium size PC-clusters as well as larger parallel platforms, we are able to deal with systems comprising 300 to 500 atoms and 1000 to 1500 electrons for as long as 2 - 3 ps. We present structural results which confirm indications coming from NMR and XAS data

Probing the Dynamic Landscape: from Static to Time‐Resolved X‐ray Absorption Spectroscopy to Investigate Copper Redox Chemistry in Neurodegenerative Disorders

Copper (Cu), capable of existing in various oxidation states, notably Cu(I) and Cu(II), plays a pivotal 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. The emphasis lies on the technique's specificity, revealing the local coordination environment, and on its sensitivity to Cu oxidation states. Furthermore, the paper focuses on XAS applications targeting the characterization of intermediate reaction states and explores the opportunities arising from recent advancements in time-resolved XAS at ultra-bright synchrotron and free electron laser radiation sources