Human Glucosylceramide Synthase at Work as Provided by "" Molecular Docking, Molecular Dynamics, and Metadynamics.

Glucosylceramide synthase (GCS) is an enzyme that catalyzes the first reaction of ceramide glycosylation in sphingolipid metabolism. It represents a primary target in the pharmacological treatment of some lysosomal storage diseases (LSDs), such as Gaucher and Niemann-Pick syndromes. In this study, starting from the model reported in the AlphaFold Protein Structure Database, the location and conformations of GCS substrates and cofactors have been provided by a step-by-step procedure, by which the functional manganese ion and the substrates have been inserted in the GCS structure through combined molecular docking and full-atomistic molecular dynamics approaches, including metadynamics.

Novel Mixed NOP/Opioid Receptor Peptide Agonists.

The nociceptin/orphanin FQ (N/OFQ)/N/OFQ receptor (NOP) system controls different biological functions including pain and cough reflex. Mixed NOP/opioid receptor agonists elicit similar effects to strong opioids but with reduced side effects. In this work, 31 peptides with the general sequence [Tyr/Dmt,Xaa]N/OFQ(1-13)-NH were synthesized and pharmacologically characterized for their action at human recombinant NOP/opioid receptors.

Structural determinants driving the binding process between PDZ domain of wild type human PALS1 protein and SLiM sequences of SARS-CoV E proteins.

Short Linear Motifs (SLiMs) are functional protein microdomains that typically mediate interactions between a short linear region in one protein and a globular domain in another. Surface Plasmon Resonance assays have been performed to determine the binding affinity between PDZ domain of wild type human PALS1 protein and tetradecapeptides representing the SLiMs sequences of SARS-CoV-1 and SARS-CoV-2 E proteins (E-SLiMs). SARS-CoV-2 E-SLiM binds to the human target protein with a higher affinity compared to SARS-CoV-1, showing a difference significantly greater than previously reported using the F318W mutant of PALS1 protein and shorter target peptides.

Improved binding of SARS-CoV-2 Envelope protein to tight junction-associated PALS1 could play a key role in COVID-19 pathogenesis.

The Envelope (E) protein of SARS-CoV-2 is the most enigmatic protein among the four structural ones. Most of its current knowledge is based on the direct comparison to the SARS E protein, initially mistakenly undervalued and subsequently proved to be a key factor in the ER-Golgi localization and in tight junction disruption. We compared the genomic sequences of E protein of SARS-CoV-2, SARS-CoV and the closely related genomes of bats and pangolins obtained from the GISAID and GenBank databases.

Ligand pathways in neuroglobin revealed by low-temperature photodissociation and docking experiments.

A combined biophysical approach was applied to map gas-docking sites within murine neuroglobin (Ngb), revealing snapshots of events that might govern activity and dynamics in this unique hexacoordinate globin, which is most likely to be involved in gas-sensing in the central nervous system and for which a precise mechanism of action remains to be elucidated. The application of UV-visible microspectroscopy , solution X-ray absorption near-edge spectroscopy and X-ray diffraction experiments at 15-40 K provided the structural characterization of an Ngb photolytic intermediate by cryo-trapping and allowed direct observation of the relocation of carbon monoxide within the distal heme pocket after photodissociation. Moreover, X-ray diffraction at 100 K under a high pressure of dioxygen, a physiological ligand of Ngb, unravelled the existence of a storage site for O in Ngb which coincides with Xe-III, a previously described docking site for xenon or krypton.

Microswitches for the Activation of the Nociceptin Receptor Induced by Cebranopadol: Hints from Microsecond Molecular Dynamics.

Cebranopadol (CBP) is a novel analgesic acting as agonist at the nociceptin (NOP) and μ-opioid (MOP) receptors, exhibiting high potency and efficacy as an antinociceptive and antihypersensitive drug. The binding conformation and the dynamical interactions of CBP with the NOP receptor have been investigated by molecular docking, molecular dynamics (MD) in the microsecond time scale, and hybrid quantum mechanics/molecular mechanics (QM/MM). CBP binds to the NOP receptor as a bidentate ligand of the aspartate D130 by means of both its fluoroindole and dimethyl nitrogens.

BBS9 gene in nonsyndromic craniosynostosis: Role of the primary cilium in the aberrant ossification of the suture osteogenic niche.

Nonsyndromic craniosynostosis (NCS) is the premature ossification of skull sutures, without associated clinical features. Mutations in several genes account for a small number of NCS patients; thus, the molecular etiopathogenesis of NCS remains largely unclear. Our study aimed at characterizing the molecular signaling implicated in the aberrant ossification of sutures in NCS patients.

"In silico" study of the binding of two novel antagonists to the nociceptin receptor.

Antagonists of the nociceptin receptor (NOP) are raising interest for their possible clinical use as antidepressant drugs. Recently, the structure of NOP in complex with some piperidine-based antagonists has been revealed by X-ray crystallography. In this study, a multi-flexible docking (MF-docking) procedure, i.

A Dynamic Picture of the Early Events in Nociceptin Binding to the NOP Receptor by Metadynamics.

Nociceptin (NCC, also known as FQ (N/OFQ)) is the 17-amino acid neuropeptide, endogenous ligand for the G-protein-coupled receptor (NOP, also known as ORL-1). In this study, starting from the recently reported x-ray structure at pH 7 of NOP in complex with an antagonist, new insights, to our knowledge, on the binding geometry of NCC to NOP have been provided in silico. After a rigid docking of NCC in an α-helix conformation, molecular dynamics (MD) and metadynamics (METAD), a method for the analysis of free-energy surfaces (FES), were performed on the protein-peptide complex.

Vanadium K-edge XANES in vanadium-bearing model compounds: a full multiple scattering study.

A systematic study is presented on a set of vanadium-bearing model compounds, representative of the most common V coordination geometries and oxidation states, analysed by means of vanadium K-edge X-ray absorption near-edge spectroscopy calculations in the full multiple scattering (FMS) framework. Analysis and calibration of the free parameters of the theory under the muffin-tin approximation (muffin-tin overlap and interstitial potential) have been carried out by fitting the experimental spectra using the MXAN program. The analysis shows a correlation of the fit parameters with the V coordination geometry and oxidation state.

The non-octarepeat copper binding site of the prion protein is a key regulator of prion conversion.

The conversion of the prion protein (PrP(C)) into prions plays a key role in transmissible spongiform encephalopathies. Despite the importance for pathogenesis, the mechanism of prion formation has escaped detailed characterization due to the insoluble nature of prions. PrP(C) interacts with copper through octarepeat and non-octarepeat binding sites.

Intermediate states in the binding process of folic acid to folate receptor α: insights by molecular dynamics and metadynamics.

Folate receptor α (FRα) is a cell surface, glycophosphatidylinositol-anchored protein which has focussed attention as a therapeutic target and as a marker for the diagnosis of cancer. It has a high affinity for the dietary supplemented folic acid (FOL), carrying out endocytic transport across the cell membrane and delivering the folate at the acidic pH of the endosome. Starting from the recently reported X-ray structure at pH 7, 100 ns classical molecular dynamics simulations have been carried out on the FRα-FOL complex; moreover, the ligand dissociation process has been studied by metadynamics, a recently reported method for the analysis of free-energy surfaces (FES), providing clues on the intermediate states and their energy terms.

Quantitative analysis of deconvolved X-ray absorption near-edge structure spectra: a tool to push the limits of the X-ray absorption spectroscopy technique.

A deconvolution procedure has been applied to K-edge X-ray absorption near-edge structure (XANES) spectra of lanthanoid-containing solid systems, namely, hexakis(dmpu)praseodymium(III) and -gadolinium(III) iodide. The K-edges of lanthanoids cover the energy range 38 (La)-65 (Lu) keV, and the large widths of the core-hole states lead to broadening of spectral features, reducing the content of structural information that can be extracted from the raw X-ray absorption spectra. Here, we demonstrate that deconvolution procedures allow one to remove most of the instrumental and core-hole lifetime broadening in the K-edge XANES spectra of lanthanoid compounds, highlighting structural features that are lost in the raw data.

Distal-proximal crosstalk in the heme binding pocket of the NO sensor DNR.

In the opportunistic pathogen Pseudomonas aeruginosa the denitrification process is triggered by nitric oxide (NO) and plays a crucial role for the survival in chronic infection sites as a microaerobic-anaerobic biofilm. This respiratory pathway is transcriptionally induced by DNR, an heme-based gas sensor which positively responds to NO. Molecular details of the NO sensing mechanism employed by DNR are now emerging: we recently reported an in vitro study which dissected, for the first time, the heme-iron environment and identified one of the heme axial ligand (i.

Synergic role of nucleophosmin three-helix bundle and a flanking unstructured tail in the interaction with G-quadruplex DNA.

Nucleophosmin (NPM1) is a nucleocytoplasmic shuttling protein, mainly localized at nucleoli, that plays a number of functions in ribosome biogenesis and export, cell cycle control, and response to stress stimuli. NPM1 is the most frequently mutated gene in acute myeloid leukemia; mutations map to the C-terminal domain of the protein and cause its denaturation and aberrant cytoplasmic translocation. NPM1 C-terminal domain binds G-quadruplex regions at ribosomal DNA and at gene promoters, including the well characterized sequence from the nuclease-hypersensitive element III region of the c-MYC promoter.

Synthesis and characterization of different immunogenic viral nanoconstructs from rotavirus VP6 inner capsid protein.

In order to deliver low-cost viral capsomeres from a large amount of soluble viral VP6 protein from human rotavirus, we developed and optimized a biotechnological platform in Escherichia coli. Specifically, three different expression protocols were compared, differing in their genetic constructs, ie, a simple native histidine-tagged VP6 sequence, VP6 fused to thioredoxin, and VP6 obtained with the newly described small ubiquitin-like modifier (SUMO) fusion system. Our results demonstrate that the histidine-tagged protein does not escape the accumulation in the inclusion bodies, and that SUMO is largely superior to the thioredoxin-fusion tag in enhancing the expression and solubility of VP6 protein.

Structural and functional insights on folate receptor α (FRα) by homology modeling, ligand docking and molecular dynamics.

Folate receptor α (FRα) is a cell surface, glycophosphatidylinositol (GPI)-anchored protein with a high affinity for its ligand partner, which is highly expressed in malignant cells and has been selected as a therapeutic target and marker for the diagnosis of cancer. No direct structural information is available from either X-ray diffraction or NMR on the post-translational structure of this disulfide-rich protein. Three-dimensional models of the FRα structure have been derived with the recent homology modeling packages, using the crystal structure of the riboflavin-binding protein (RfBP) as a template.

Dioxygen oxidation Cu(II) → Cu(III) in the copper complex of cyclo(Lys-dHis-βAla-His): a case study by EXAFS and XANES approach.

A former spectroscopic study of Cu(II) coordination by the 13-membered ring cyclic tetrapeptide c(Lys-dHis-βAla-His) (DK13), revealed the presence, at alkaline pH, of a stable peptide/Cu(III) complex formed in solution by atmospheric dioxygen oxidation. To understand the nature of this coordination compound and to investigate the role of the His residues in the Cu(III) species formation, Cu K-edge XANES, and EXAFS spectra have been collected for DK13 and two other 13-membered cyclo-peptides: the diastereoisomer c(Lys-His-βAla-His) (LK13), and c(Gly-βAla-Gly-Lys) (GK13), devoid of His residues. Comparison of pre-edge peak features with those of Cu model compounds, allowed us to get information on copper oxidation state in two of the three peptides, DK13 and GK13: DK13 contains only Cu(III) ions in the experimental conditions, while GK13 binds only with Cu(II).

Effects of the pathological Q212P mutation on human prion protein non-octarepeat copper-binding site.

Prion diseases are a class of fatal neurodegenerative disorders characterized by brain spongiosis, synaptic degeneration, microglia and astrocytes activation, neuronal loss and altered redox control. These maladies can be sporadic, iatrogenic and genetic. The etiological agent is the prion, a misfolded form of the cellular prion protein, PrP(C).

Local structure and dynamics of hemeproteins by X-ray absorption near edge structure spectroscopy.

X-ray absorption near edge structure (XANES) spectroscopy is a synchrotron radiation technique sensitive to the local structure and dynamics around the metal site of a heme containing protein. Advances in detection techniques and theoretical/computational platforms in the last 15 years allowed the use of XANES as a quantitative probe of the key structural determinants driving functional changes, both in a concerted way with protein crystallography and EXAFS (extended X-ray absorption fine structure), or as a stand-alone method to apply in the crystal state as well as in solution. Moreover, the local dynamics of the heme site has been deeply investigated, on one hand, coupling XANES to classical photolysis experiments at cryogenic temperatures; on the other hand, the intrinsic property of the synchrotron radiation to induce radiolysis events, has been exploited to investigate specific cryotrapped intermediates, using X-rays both as a pump and a probe.

Unusual heme binding properties of the dissimilative nitrate respiration regulator, a bacterial nitric oxide sensor.

Aims: In the opportunistic pathogen Pseudomonas aeruginosa, nitric oxide (NO) triggers the respiration of nitrate (denitrification), thus allowing survival in chronic infection sites as a microaerobic-anaerobic biofilm. The NO-dependent induction of denitrification is mediated by the dissimilative nitrate respiration regulator (DNR), a transcription factor forming a stable complex with heme, which is required to sense the physiological messenger (i.e.

Ligand binding intermediates of nitrosylated human hemoglobin induced at low temperature by X-ray irradiation.

Under prolonged X-ray irradiation, the ferrous heme of nitrosylated human adult hemoglobin derivative (HbNO) undergoes a reversible transition generating a 5-coordinate species, due to release of the Fe-NO bond. The overall process can be investigated using X-ray absorption near edge structure (XANES) spectroscopy. In this work, Fe K-edge XANES spectra were measured at T < 15 K, pH 9.

X-ray-induced lysis of the Fe-CO bond in carbonmonoxy-myoglobin.

By using X-ray absorption near edge structure (XANES) spectroscopy, we show that under prolonged exposure to Synchrotron X-rays, at T < 10 K, the Fe-heme in carbonmonoxy-myoglobin (MbCO) undergoes a slow two-state transition process. The final spectrum is nearly identical to that of the classical photoproduct (Mb*CO) obtained by UV-visible light illumination at 15 K. By increasing the temperature, the starting spectrum of MbCO is recovered at T > 100 K, demonstrating that the process is reversible and no damage occurred at the heme site in the time course of the experiment.

Dynamic investigation of protein metal active sites: interplay of XANES and molecular dynamics simulations.

The effect of structural disorder on the X-ray absorption near-edge structure (XANES) spectrum of a heme protein has been investigated using the dynamical description of the system derived from molecular dynamics (MD) simulations. The XANES spectra of neuroglobin (Ngb) and carbonmonoxy-neuroglobin (NgbCO) have been quantitatively reproduced, starting from the MD geometrical configurations, without carrying out any optimization in the structural parameter space. These results provide an important experimental validation of the reliability of the potentials used in the MD simulations and accordingly corroborate the consistency of the structural dynamic information on the metal center, related to its biological function.