Characterizing Structure and Free Energy Landscape of Proteins by NMR-guided Metadynamics

In the last two decades, a series of experimental and theoretical advances has made it possible to obtain a detailed understanding of the molecular mechanisms underlying the folding process of proteins. With the increasing power of computer technology, as well as with the improvements in force fields, atomistic simulations are also becoming increasingly important because they can generate highly detailed descriptions of the motions of proteins. A supercomputer specifically designed to integrate the Newton's equations of motion of proteins, Anton, has been recently able to break the millisecond time barrier. This achievement has allowed the direct calculation of repeated folding events for several fast-folding proteins and to characterize the molecular mechanisms underlying protein dynamics and function. However these exceptional resources are available only to few research groups in the world and moreover the observation of few event of a specific process is usually not enough to provide a statistically significant picture of the phenomenon. In parallel, it has also been realized that by bringing together experimental measurements and computational methods it is possible to expand the range of problems that can be addressed. For example, by incorporating structural informations as structural restraints in molecular dynamics simulations it is possible to obtain structural models of these transiently populated states, as well as of native and non-native intermediates explored during the folding process. By applying this strategy to structural parameters measured by nuclear magnetic resonance (NMR) spectroscopy, one can determine the atomic-level structures and characterize the dynamics of proteins. In these approaches the experimental information is exploited to create an additional term in the force field that penalizes the deviations from the measured values, thus restraining the sampling of the conformational space to regions close to those observed experimentally. In this thesis we propose an alternative strategy to exploit experimental information in molecular dynamics simulations. In this approach the measured parameters are not used as structural restraints in the simulations, but rather to build collective variables within metadynamics calculations. In metadynamics , the conformational sampling is enhanced by constructing a time-dependent potential that discourages the explorations of regions already visited in terms of specific functions of the atomic coordinates called collective variables. In this work we show that NMR chemical shifts can be used as collective variables to guide the sampling of conformational space in molecular dynamics simulations. Since the method that we discuss here enables the conformational sampling to be enhanced without modifying the force field through the introduction of structural restraints, it allows estimating reliably the statistical weights corresponding to the force field used in the molecular dynamics simulations. In the present implementation we used the bias exchange metadynamics method, an enhanced sampling technique that allows reconstructing the free energy as a simultaneous function of several variables. By using this approach, we have been able to compute the free energy landscape of two different proteins by explicit solvent molecular dynamics simulations. In the application to a well-structured globular protein, the third immunoglobulin-binding domain of streptococcal protein G (GB3), our calculation predicts the native fold as the lowest free energy minimum, identifying also the presence of an on-pathway compact intermediate with non-native topological elements. In addition, we provide a detailed atomistic picture of the structure at the folding barrier, which shares with the native state only a fraction of the secondary structure elements. The further application to the case of the 40-residue form of Amyloid beta, allows us another remarkable achievement: the quantitative description of the free energy landscape for an intrinsically disordered protein. This kind of proteins are indeed characterized by the absence of a well-defined three-dimensional structure under native conditions and are therefore hard to investigate experimentally. We found that the free energy landscape of this peptide has approximately inverted features with respect to normal globular proteins. Indeed, the global minimum consists of highly disordered structures while higher free energy regions correspond to partially folded conformations. These structures are kinetically committed to the disordered state, but they are transiently explored even at room temperature. This makes our findings particularly relevant since this protein is involved in the Alzheimer's disease because it is prone to aggregate in oligomers determined by the interaction of the monomer in extended beta-strand organization, toxic for the cells. Our structural and energetic characterization allows defining a library of possible metastable states which are involved in the aggregation process. These results have been obtained using relatively limited computational resources. The total simulation time required to reconstruct the thermodynamics of GB3 for example is about three orders of magnitude less than the typical timescale of folding of similar proteins, simulated also by Anton. We thus anticipate that the technique introduced in this thesis will allow the determination of the free energy landscapes of wide range of proteins for which NMR chemical shifts are available. Finally, since chemical shifts are the only external information used to guide the folding of the proteins, our methods can be also successfully applied to the challenging purpose of NMR structure determination, as we have demonstrated in a blind prediction test on the last CASD-NMR target

The Practice of ὀνοματοποιεῖν: Some Peculiar Statements in the Ancient Neoplatonic Commentators on Aristotle

This paper shows the role of ὀνοματοποιεῖν in Neoplatonism and how this practice is ruled by an onto-logical canon. While ὀνοματοποιεῖν itself means the making of a brand new name, its usage is manifold. As Aristotle explains in Rh. III 2, poets take advantage of ὀνοματοποιεῖν to catch the undefined and give it a recognisable image, by means of a metaphorical name. In science, this practice, codified by Aristotle, is twofold: ὀνοματοποιεῖν meant both to re-semanticize words wellknown and to create names ex novo for things not discovered or studied yet. After analysing ὀνοματοποιεῖν’s recurrence in Aristotle, I illustrate that, according to Neoplatonic Commentators, impositio can be, both natural and technical, only of things in actuality, having a solid consistency. Intermediates between contraries, presumed relatives and powers as qualities are nameless – as  Philoponus notices in his In Categorias – since they haven’t an independent status and aren’t  definable. This bond between the original rhetorical practice and the ontological perspective, sketched in Int. 1, was strengthened by Alexander, who filled Aristotle’s gaps, stating that names signify things’ being, i.e. the form acquired in actuality

Propofol inhibits prokaryotic voltage-gated Na+ channels by promoting activation-coupled inactivation

Propofol is widely used in the clinic for the induction and maintenance of general anesthesia. As with most general anesthetics, however, our understanding of its mechanism of action remains incomplete. Local and general anesthetics largely inhibit voltage-gated Na+ channels (Navs) by inducing an apparent stabilization of the inactivated state, associated in some instances with pore block. To determine the biophysical and molecular basis of propofol action in Navs, we investigated NaChBac and NavMs, two prokaryotic Navs with distinct voltage dependencies and gating kinetics, by whole-cell patch clamp electrophysiology in the absence and presence of propofol at clinically relevant concentrations (2-10 μM). In both Navs, propofol induced a hyperpolarizing shift of the pre-pulse inactivation curve without any significant effects on recovery from inactivation at strongly hyperpolarized voltages, demonstrating that propofol does not stabilize the inactivated state. Moreover, there was no evidence of fast or slow pore block by propofol in a non-inactivating NaChBac mutant (T220A). Propofol also induced hyperpolarizing shifts of the conductance-voltage relationships with negligible effects on the time constants of deactivation at hyperpolarized voltages, indicating that propofol does not stabilize the open state. Instead, propofol decreases the time constants of macroscopic activation and inactivation. Adopting a kinetic scheme of Nav gating that assumes preferential closed-state recovery from inactivation, a 1.7-fold acceleration of the rate constant of activation and a 1.4-fold acceleration of the rate constant of inactivation were sufficient to reproduce experimental observations with computer simulations. In addition, molecular dynamics simulations and molecular docking suggest that propofol binding involves interactions with gating machinery in the S4-S5 linker and external pore regions. Our findings show that propofol is primarily a positive gating modulator of prokaryotic Navs, which ultimately inhibits the channels by promoting activation-coupled inactivation. © 2018 Yang et al

FSH treatment of male idiopathic infertility improves pregnancy rate: a meta-analysis

INTRODUCTION: The aim of this study is to comprehensively evaluate whether FSH administration to the male partner of infertile couples improves pregnancy rate, spontaneously and/or after assisted reproductive techniques (ART). METHODS: Meta-analysis of controlled clinical trials in which FSH was administered for male idiopathic infertility, compared with placebo or no treatment. Randomization was not considered as an inclusion criterion. RESULTS: We found 15 controlled clinical studies (614 men treated with FSH and 661 treated with placebo or untreated). Concerning the type of FSH, eight studies used recombinant FSH, whereas seven studies used purified FSH. Nine studies evaluated spontaneous pregnancy rate, resulting in an overall odds ratio (OR) of about 4.5 (CI: 2.17-9.33). Eight studies evaluated pregnancy rate after ART, showing a significant OR of 1.60 (CI: 1.08-2.37). Sub-dividing studies according to the FSH preparations (purified/recombinant), pregnancy rate improvement remained significant for each preparation. Eleven studies considered sperm quality after FSH treatment, finding a significant improvement of sperm concentration (2.66×10(6)/ml, CI: 0.47-4.84), but not of concentration of sperm with progressive motility (1.22×10(6)/ml, CI: -0.07 to 2.52). Three trials evaluated testicular volume, showing a non-significant increase in men treated (1.35 ml, CI: -0.44 to 3.14). CONCLUSION: The results of controlled clinical trials available in the literature indicate an improvement of pregnancy rate after FSH administration to the male partner of infertile couples, both spontaneously and after ART. However, the heterogeneity of studies, the high risk of bias and the lack of precise criteria to guide FSH administration limit the strength of these results. Future studies should be designed to identify the markers of FSH response which are helpful in the decision-making process. Meanwhile, the use of FSH in the treatment of male infertility should be cautious

Efficacy of follicle-stimulating hormone treatment in male idiopathic infertility: a meta-analysis

Study question: To comprehensively evaluate whether follicle stimulating hor- mone (FSH) administration to the male partner of idiopathic infertile couples improves pregnancy rate, both spontaneous and after assisted reproductive tech- nique (ART), using a meta-analytic approach and including controlled clinical trial. Summary answer: The administration of FSH to infertile men is reported in the literature since 1991, improving fertilisation and pregnancy rate. A significant increase in pregnancy rate after ART and male treatment with FSH was already shown in several studies, since FSH improves the sperm quality. FSH treatment could improve sperm quality and pregnancy rate in idiopathic infertile men. What is known already: The Cochrane Collaboration recently estimated the overall effect of FSH treatment of the man in couples attending ART, enrolled in randomised, controlled, clinical-trials. That meta-analysis demonstrated that FSH treatment significantly improves spontaneous pregnancy rate, whereas no improvement of pregnancy rate was observed after ART, using fixed and strict inclusion criteria. They excluded all trials in which the randomization was not provided leading to potential loss of useful information that could help clini- cians in their routinely practice. Study design, size, duration: We conducted a comprehensive literature search for controlled clinical trials in which FSH was administered for male idiopathic infertility, compared with placebo or no treatment. The randomization was not considered as inclusion criterion. We considered studies in which men with idiopathic infertility or subfertility were enrolled, chronicallty treated with any type of FSH, compared with placebo or no treatment. Participants/materials, setting, methods: We found 15 controlled clinical stud- ies. Concerning the type of FSH, eight studies included in the meta-analysis used recombinant FSH, whereas seven studies used purified FSH. Pregnancy rate, when evaluated, was considered spontaneous or after ART. Selected trials gave details about 1275 infertile-men, 614 treated with FSH and 661 not-treated. Main results and the role of chance: Among the 15 studies included, nine studies evaluated the spontaneous pregnancy rate, resulting in an overall im- provement of about 4.5 (CI 2.17–9.33 and I2 = 0%) (p < 0.001). Eight stud- ies evaluated pregnancy rate after ART, showing a significant improvement of about 1.60 (CI 1.08–2.37 and I2 = 43%) (p = 0.002). Sub-dividing studies ac- cording to the FSH preparations (purified or recombinant), the pregnancy rate improvement remained significant (p = 0.007 and p = 0.002, respectively). Elev- en studies considered sperm quality after FSH treatment, finding a significant improvement of sperm concentration (mean improvement of 2.66x106 millions/ mL, with CI 0.47–4.84, p = 0.02), but not of sperm motility (mean improvement of 1.22x106 millions/mL, with CI -0.07–2.52, p = 0.06). Finally, three trials evaluated testicular volume, showing a non-significant increase in men treated (mean increase of 1.35 mL, with CI -0.44–3.14, p = 0,14). Limitations, reason for caution: The heterogeneity of studies, together with the high risk of biases in this field of research could limit the strength of these results. Wider implications of the findings: The results of controlled clinical trials available in literature indicate an improvement of pregnancy rate after FSH ad- ministration to the male partner of infertile couples, both spontaneous and after ART. Study funding/competing interest(s): Funding by University(ies) – University of Modena and Reggio Emilia. Trial registration number: NA. Keywords: FSH, idiopathic male infertility, reproductio

Pensiero e linguaggio dell'essere nel Commentario di Giovanni Filopono alle categorie di Aristotele. Introduzione, testo, traduzione e commento

2013 - 2014This work’s goal is not only to detect the originality of the philoponian Commentary on Aristotle’s Categories, but also to show that logic is an autonomous discipline which studies the reality of being as practical and theoretical sciences do. First of all I proposed the text of the Commentary according to Busse’s edition of 1898, introduced by an editorial note, explaining that the text published has been followed faithfully, except for some interventions reported in footnotes, interventions flowing from the critical apparatus of Busse himself or aiming to correct typographical errors and oversights. The translation’s goal is mainly to prepare the ground for its detailed exegesis. The text’s reading shows that Philoponus’ In Categorias is a personal elaboration of the scholastic tradition in the light of the Commentator’s methodical brilliance, that stands out from Ammonius for theoretical breadth and depth, as well as for accuracy of certain considerations. Categories are shown not only as a logical text but also as a systematic tool of great importance. Philoponus shows that all disciplines, theoretical and practical, are closely related to logic, by which philosophers discern truth from falsehood and right from wrong. This thesis allow you to observe carefully in Philoponus’s treaty all interdisciplinary relationships, digressions and theoretical insights in support of this theory. The study of pre-propositional logic has as object simple beings signified by simple words through simple thoughts: homological correspondence between these three planes of reality is the foundation of Aristotle’s philosophy and of Philoponus’ recovery. Aristotle, this is clear from the Commentary, was, according to Philoponus, a platonic, among the best disciples of the Master. [edited by Author]XIII n.s

Talking about sex: erectile dysfunction in the oncology patient

: Cancer-related diagnosis and treatments can profoundly affect every aspect of an individual's life. The negative impact on the sexual sphere can manifest with onset or worsening of the most frequent male form of sexual dysfunction, that is the erectile dysfunction (ED), with an estimated incidence ranging from 40 to 100% in patients living with cancer. Cancer and ED are strictly related for many reasons. First, the psychological distress, the so-called 'Damocles syndrome', afflicting cancer patients contributes to ED onset. Second, all cancer therapies can variably lead to sexual dysfunction, even more than the disease itself, having both direct or indirect effects on sexual life. Indeed, alongside pelvic surgery and treatments directly impairing the hypothalamus-pituitary-gonadal axis, the altered personal-body-image frequently experienced by people living with cancer may represent a source of distress contributing to sexual dysfunction. It is undeniable that sexual issues are currently neglected or at least under-considered in the oncological setting, mainly due to the subjective lack of preparation experienced by healthcare professionals and to scant information provided to oncological patients on this topic. To overcome these management problems, a new multidisciplinary medical branch called 'oncosexology' was set up. The aim of this review is to comprehensively evaluate ED as an oncology-related morbidity, giving new light to sexual dysfunction management in the oncological setting

Propofol inhibits the voltage-gated sodium channel NaChBac at multiple sites.

Voltage-gated sodium (NaV) channels are important targets of general anesthetics, including the intravenous anesthetic propofol. Electrophysiology studies on the prokaryotic NaV channel NaChBac have demonstrated that propofol promotes channel activation and accelerates activation-coupled inactivation, but the molecular mechanisms of these effects are unclear. Here, guided by computational docking and molecular dynamics simulations, we predict several propofol-binding sites in NaChBac. We then strategically place small fluorinated probes at these putative binding sites and experimentally quantify the interaction strengths with a fluorinated propofol analogue, 4-fluoropropofol. In vitro and in vivo measurements show that 4-fluoropropofol and propofol have similar effects on NaChBac function and nearly identical anesthetizing effects on tadpole mobility. Using quantitative analysis by 19F-NMR saturation transfer difference spectroscopy, we reveal strong intermolecular cross-relaxation rate constants between 4-fluoropropofol and four different regions of NaChBac, including the activation gate and selectivity filter in the pore, the voltage sensing domain, and the S4-S5 linker. Unlike volatile anesthetics, 4-fluoropropofol does not bind to the extracellular interface of the pore domain. Collectively, our results show that propofol inhibits NaChBac at multiple sites, likely with distinct modes of action. This study provides a molecular basis for understanding the net inhibitory action of propofol on NaV channels. © 2018 Wang et al

Short term Leydig cell stimulation by LH and hCG in man with central hypogonadism

Short term Leydig cell stimulation by LH and hCG in man with central hypogonadis