Human aromatic amino acid decarboxylase is an asymmetric and flexible enzyme: Implication in aromatic amino acid decarboxylase deficiency.

Human aromatic amino acid decarboxylase (AADC) is a pyridoxal 5'-phosphate-dependent enzyme responsible for the biosynthesis of dopamine and serotonin, essential neurotransmitters involved in motor and cognitive abilities. Mutations in its gene lead to AADC deficiency, a monogenic rare neurometabolic childhood parkinsonism characterized by severe motor and neurodevelopmental symptoms. Here, for the first time, we solved the crystal structure of human holoAADC in the internal aldimine (1.9 Å) and in the external aldimine (2.4 Å) of the substrate analog L-Dopa methylester. In this intermediate, the highly flexible AADC catalytic loop (CL) is captured in a closed state contacting all protein domains. In addition, each active site, composed by residues of both subunits, is connected to the other through weak interactions and a central cavity. By combining crystallographic analyses with all-atom and coarse-grained molecular dynamics simulations, SAXS investigations and limited proteolysis experiments, we realized that the functionally obligate homodimeric AADC enzyme in solution is an elongated, asymmetric molecule, where the fluctuations of the CL are coupled to flexibility at the edge between the N-terminal and C-terminal domains. The structural integrity of this peripheral protein region is essential to catalysis, as assessed by both artificial and 37 AADC deficiency pathogenic variants leading to the interpretation that structural dynamics in protein regions far from the active site is essential for CL flexibility and the acquirement of a correct catalytically competent structure. This could represent the molecular basis for pathogenicity prediction in AADC deficiency.

pyGOMoDo: GPCRs modeling and docking with python.

MOTIVATION: We present pyGOMoDo, a Python library to perform homology modeling and docking, specifically designed for human GPCRs. pyGOMoDo is a python wrap-up of the updated functionalities of GOMoDo web server (https://molsim.sci.univr.it/gomodo). It was developed having in mind its usage through Jupyter notebooks, where users can create their own protocols of modeling and docking of GPCRs. In this article, we focus on the internal structure and general capabilities of pyGOMoDO and on how it can be useful for carrying out structural biology studies of GPCRs. RESULTS: The source code is freely available at https://github.com/rribeiro-sci/pygomodo under the Apache 2.0 license. Tutorial notebooks containing minimal working examples can be found at https://github.com/rribeiro-sci/pygomodo/tree/main/examples.

Exploring the Potential of Metal-Organic Frameworks for the Separation of Blends of Fluorinated Gases with High Global Warming Potential.

The research on porous materials for the selective capture of fluorinated gases (F-gases) is key to reduce their emissions. Here, the adsorption of difluoromethane (R-32), pentafluoroethane (R-125), and 1,1,1,2-tetrafluoroethane (R-134a) is studied in four metal-organic frameworks (MOFs: Cu-benzene-1,3,5-tricarboxylate, zeolitic imidazolate framework-8, MOF-177, and MIL-53(Al)) and in one zeolite (ZSM-5) with the aim to develop technologies for the efficient capture and separation of high global warming potential blends containing these gases. Single-component sorption equilibria of the pure gases are measured at three temperatures (283.15, 303.15, and 323.15 K) by gravimetry and correlated using the Tóth and Virial adsorption models, and selectivities toward R-410A and R-407F are determined by ideal adsorption solution theory. While at lower pressures, R-125 and R-134a are preferentially adsorbed in all materials, at higher pressures there is no selectivity, or it is shifted toward the adsorption R-32. Furthermore, at high pressures, MOF-177 shows the highest adsorption capacity for the three F-gases. The results presented here show that the utilization of MOFs, as tailored made materials, is promising for the development of new approaches for the selective capture of F-gases and for the separation of blends of these gases, which are used in commercial refrigeration.

Prevalence, risk factors and predictors of severity of neonatal thrombocytopenia in neonatal Intensive Care Units: a single center study.

BACKGROUND: Thrombocytopenia is a common hematological disorder seen in the neonatal period, especially in newborns admitted to the Neonatal Intensive Care Unit (NICU). The clinical and laboratorial presentation is heterogeneous, with different underlying causes and risk factors. There are still few studies about some possible risk factors and their influence on the newborn's clinical outcome. The aim of this study was to assess the prevalence, risk factors and predictors of severity of thrombocytopenia in a level III NICU. METHODS: The present analysis was the retrospective study of newborns with thrombocytopenia (platelet count less than 150×109/L) admitted from January 1, 2008, to December 31, 2017. Patients included newborns admitted after the first 72 hours of life and those with thrombocytopenia related to surgical intervention were excluded. RESULTS: Out of 187 neonates with thrombocytopenia, a total of 134 neonates were included in the study, corresponding to a prevalence of 3.3%. One hundred fourteen (85%) neonates had an early onset presentation (EOT), and 20 (15%) neonates had a late onset presentation (LOT); 68 (50.7%) neonates had severe and 66 (49.3%) had non-severe thrombocytopenia. Sepsis was identified as an independent predictor of LOT. Sepsis by gram-negative bacteria was identified as an independent predictor for severe thrombocytopenia. CONCLUSIONS: Identification of risk factors, early diagnosis and treatment of the underlying causes are crucial for a better approach of neonatal thrombocytopenia. A strong association between sepsis and sepsis by gram-negative bacteria with LOT and severe thrombocytopenia, respectively, enhances the importance of nosocomial sepsis control in NICU.

Effect of the Heteroaromatic Antenna on the Binding of Chiral Eu(III) Complexes to Bovine Serum Albumin.

The cationic enantiopure (R,R) and luminescent Eu(III) complex [Eu(bisoQcd)(H2O)2] OTf (with bisoQcd = N,N'-bis(2-isoquinolinmethyl)-trans-1,2-diaminocyclohexane N,N'-diacetate and OTf = triflate) was synthesized and characterized. At physiological pH, the 1:1 [Eu(bisoQcd)(H2O)2]+ species, possessing two water molecules in the inner coordination sphere, is largely dominant. The interaction with bovine serum albumin (BSA) was studied by means of several experimental techniques, such as luminescence spectroscopy, isothermal titration calorimetry (ITC), molecular docking (MD), and molecular dynamics simulations (MDS). In this direction, a ligand competition study was also performed by using three clinically established drugs (i.e., ibuprofen, warfarin, and digitoxin). The nature of this interaction is strongly affected by the type of the involved heteroaromatic antenna in the Eu(III) complexes. In fact, the presence of isoquinoline rings drives the corresponding complex toward the protein superficial area containing the tryptophan residue 134 (Trp134). As the main consequence, the metal center undergoes the loss of one water molecule upon interaction with the side chain of a glutamic acid residue. On the other hand, the similar complex containing pyridine rings ([Eu(bpcd)(H2O)2]Cl with bpcd = N,N'-bis(2-pyridylmethyl)-trans-1,2-diaminocyclohexane N,N'-diacetate) interacts more weakly with the protein in a different superficial cavity, without losing the coordinated water molecules.

Batch chromatography with recycle lag. I-Concept and design.

This is the first of a two-part study in which we explore the concept of batch chromatography with recycle lag, concluding with the design, construction, and experimental validation of a prototype that embodies the physical realization of this concept. Moreover, the apparatus is simple to set up in particular in view of large-scale applications. Here the theory behind batch chromatography with recycle lag is revisited and extended, with emphasis on the mathematical formulation and procedure for deriving the single-column batch analogue of any variant of multicolumn simulated countercurrent chromatography. By resorting to selected examples, namely GE Healthcare Bio-science's three-column periodic countercurrent chromatography, Novasep's sequential multicolumn chromatography, and a few hypothetical multicolumn processes, we discuss how the theory can be operationalized. Finally, we conclude by describing the design of a device or apparatus-an eluate recycling device (ERD)-to physically realize the proposed concept. The ERD implements an approximate "first in, first out" method for organizing and manipulating the to-be-recycled fractions of eluate collected from the chromatography column, where the oldest (first) amount fluid, or 'head' of the fraction, is the first to exit and be recycled to the column.

Batch chromatography with recycle lag. II-Physical realization and experimental validation.

This is the second of a two-part study in which we explore the concept of batch chromatography with recycle lag, concluding with the design, construction, and experimental validation of a prototype-an eluate recycling device (ERD)-that embodies the physical realization of this concept. The ERD implements an approximate "first in, first out" method of organizing and manipulating the to-be-recycled fractions of eluate collected from the chromatography column, where the oldest (first) amount fluid, or 'head' of the fraction, is the first to exit and be recycled back to the column. Moreover, the apparatus is simple to set up in particular in view of large-scale applications. Here we detail the construction of the ERD and assembly of a setup to interconnect the ERD and a chromatography column. Through the coordinated operation of two-way valves and two-position six-port switching valves it is possible to implement a diverse set of configurations or operating modes interconnecting the chromatography column and the ERD. The setup is validated experimentally with success using the separation of a nucleoside mixture by reversed phase chromatography as a model problem. It is also shown that by redesigning the fluid distributor using 3D printing technology the ERD performance can be improved.

The importance of intramolecular hydrogen bonds on the translocation of the small drug piracetam through a lipid bilayer.

The number of hydrogen bond donors and acceptors is a fundamental molecular descriptor to predict the oral bioavailability of small drug candidates. In fact, the most widely used oral bioavailability rules (such as the Lipinsky's rule-of-five and the Veber rules) make use of this molecular descriptor. It is generally assumed that hydrogen bond donors and acceptors impact on passive diffusion across cell membranes, a fundamental event during drug absorption and distribution. Although the relationship between the number of these motifs and the probability of having good oral bioavailability has been studied and described for more than 20 years, little attention has been given to their spatial distribution in the molecule. In this paper, we used molecular dynamics to describe the effect of intramolecular hydrogen bonding on the passive diffusion of a small drug (piracetam) through a lipid membrane. The results indicated that the formation of an intramolecular hydrogen bond decreases the barrier for translocation by ca. 4 kcal mol-1 and increases the permeability of the tested molecule, partially compensating the desolvation penalty arising from the penetration of the drug into the biological membrane core. This effect was apparent in simulations where the formation of this interaction was prevented with the help of modified potentials, and in simulations with a similar compound to piracetam that was not able to form this intramolecular hydrogen bond due to a larger distance between the hydrogen bond donor and acceptor groups. These results were also supported by coarse-grained methods, which are becoming an important resource for sampling a larger chemical space of molecules, with reduced computational effort. Furthermore, entropy and enthalpy derived profiles were also obtained as the compounds translocated across the membrane, suggesting that, even though the process of formation of internal hydrogen bonds is entropically unfavorable, the enthalpic gain is such that the formation of these interactions is beneficial for the passive diffusion across cell membranes.

Challenges of electric swing adsorption for CO(2) capture.

This work focuses on the application of electric swing adsorption (ESA) as a selective postcombustion technique to capture and concentrate CO(2) from flue gases of power plants. The initial application should be the capture of CO(2) from flue gases of combined cycle natural gas (NGCC) power plants: the CO(2) content ranges from 3-5 %, with up to 12 % of oxygen. Several challenges to deploy this process for a large-scale application are pointed out. Materials such as amine-modified resins or zeolites should be good candidates for this process (indirect ESA) because they exhibit good loadings at low partial pressures of CO(2). The process design should take into account the temperature increase due to adiabatic operation, pushing the effective loadings to values around 20 % of maximum loading. Several process operations are suggested in order to improve the CO(2) purity and recovery and also to integrate the ESA process with other sources of heat, which may have an important impact in energy consumption.