Frataxin (FXN) is a protein involved in storage and delivery of iron in the mitochondria. Single-point mutations in the FXN 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. By using altruistic metadynamics in conjunction with the maximal constrained entropy principle, we estimate the change of free energy in the protein unfolding of frataxin and of some of its pathological mutants. The sampled configurations highlight differences between the wild-type and mutated sequences in the stability of the folded state. In partial agreement with thermodynamic experiments, where most of the analyzed variants are characterized by lower thermal stability compared to wild type, the D104G variant is found with a stability comparable to the wild-type sequence and a lower water-accessible surface area. These observations, obtained with the new approach we propose in our work, point to a functional switch, affected by single-point mutations, of frataxin from iron storage to iron release. The method is suitable to investigate wide structural changes in proteins in general, after a proper tuning of the chosen collective variable used to perform the transition.

EuPRAXIA is a leading European project aimed at the development of a dedicated, ground-breaking, 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.

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. destabilizing mutations in protein sequences. In this refined application the method is based on altruistic well-tempered metadynamics, a variant of multiple-walkers metadynamics. The resulting metastatistics is then modulated by the maximal constrained entropy principle. The latter turns out to be especially helpful in free-energy calculations as it is able to alleviate the severe limitations of metadynamics in properly sampling folded and unfolded configurations. In this work we apply the computational strategy outlined above in the case of the bovine pancreatic trypsin inhibitor, a well-studied small protein, which is a reference for computer simulations since decades. We compute the variation of the melting temperature characterizing the folding-unfolding process between the wild-type protein and two of its single-point mutations that are seen to have opposite effect on the free energy changes. The same approach is used for free energy difference calculations between a truncated form of frataxin and a set of five of its variants. Simulation data are compared to in vitro experiments. In all cases the sign of the change of melting temperature is reproduced, under the further approximation of using an empirical effective mean-field to average out protein-solvent interactions.