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1.
PLoS Pathog ; 19(11): e1011741, 2023 Nov.
Article in English | MEDLINE | ID: mdl-37956166

ABSTRACT

A genomic signature for endosporulation includes a gene coding for a protease, YabG, which in the model organism Bacillus subtilis is involved in assembly of the spore coat. We show that in the human pathogen Clostridioidesm difficile, YabG is critical for the assembly of the coat and exosporium layers of spores. YabG is produced during sporulation under the control of the mother cell-specific regulators σE and σK and associates with the spore surface layers. YabG shows an N-terminal SH3-like domain and a C-terminal domain that resembles single domain response regulators, such as CheY, yet is atypical in that the conserved phosphoryl-acceptor residue is absent. Instead, the CheY-like domain carries residues required for activity, including Cys207 and His161, the homologues of which form a catalytic diad in the B. subtilis protein, and also Asp162. The substitution of any of these residues by Ala, eliminates an auto-proteolytic activity as well as interdomain processing of CspBA, a reaction that releases the CspB protease, required for proper spore germination. An in-frame deletion of yabG or an allele coding for an inactive protein, yabGC207A, both cause misassemby of the coat and exosporium and the formation of spores that are more permeable to lysozyme and impaired in germination and host colonization. Furthermore, we show that YabG is required for the expression of at least two σK-dependent genes, cotA, coding for a coat protein, and cdeM, coding for a key determinant of exosporium assembly. Thus, YabG also impinges upon the genetic program of the mother cell possibly by eliminating a transcriptional repressor. Although this activity has not been described for the B. subtilis protein and most of the YabG substrates vary among sporeformers, the general role of the protease in the assembly of the spore surface is likely to be conserved across evolutionary distance.


Subject(s)
Clostridioides difficile , Peptide Hydrolases , Humans , Peptide Hydrolases/metabolism , Clostridioides difficile/genetics , Clostridioides difficile/metabolism , Clostridioides , Spores, Bacterial/metabolism , Transcription Factors/metabolism , Endopeptidases/metabolism , Bacterial Proteins/metabolism , Bacillus subtilis/metabolism
2.
Nano Lett ; 23(7): 3030-3037, 2023 Apr 12.
Article in English | MEDLINE | ID: mdl-36989531

ABSTRACT

Optical properties of nanoparticle assemblies reflect distinctive characteristics of their building blocks and spatial organization, giving rise to emergent phenomena. Integrated experimental and computational studies have established design principles connecting the structure to properties for assembled clusters and superlattices. However, conventional electromagnetic simulations are too computationally expensive to treat more complex assemblies. Here we establish a fast, materials agnostic method to simulate the optical response of large nanoparticle assemblies incorporating both structural and compositional complexity. This many-bodied, mutual polarization method resolves limitations of established approaches, achieving rapid, accurate convergence for configurations including thousands of nanoparticles, with some overlapping. We demonstrate these capabilities by reproducing experimental trends and uncovering far- and near-field mechanisms governing the optical response of plasmonic semiconductor nanocrystal assemblies including structurally complex gel networks and compositionally complex mixed binary superlattices. This broadly applicable framework will facilitate the design of complex, hierarchically structured, and dynamic assemblies for desired optical characteristics.

3.
Chembiochem ; 24(4): e202200602, 2023 02 14.
Article in English | MEDLINE | ID: mdl-36454659

ABSTRACT

BP100 is a cationic undecamer peptide with antimicrobial and cell-penetrating activities. The orientation of this amphiphilic α-helix in lipid bilayers was examined under numerous conditions using solid-state 19 F, 15 N and 2 H NMR. At high temperatures in saturated phosphatidylcholine lipids, BP100 lies flat on the membrane surface, as expected. Upon lowering the temperature towards the lipid phase transition, the helix is found to flip into an upright transmembrane orientation. In thin bilayers, this inserted state was stable at low peptide concentration, but thicker membranes required higher peptide concentrations. In the presence of lysolipids, the inserted state prevailed even at high temperature. Molecular dynamics simulations suggest that BP100 monomer insertion can be stabilized by snorkeling lysine side chains. These results demonstrate that even a very short helix like BP100 can span (and thereby penetrate through) a cellular membrane under suitable conditions.


Subject(s)
Molecular Dynamics Simulation , Peptides , Temperature , Peptides/chemistry , Cell Membrane/chemistry , Lipid Bilayers/chemistry , Magnetic Resonance Spectroscopy
4.
Proc Natl Acad Sci U S A ; 117(11): 5861-5872, 2020 03 17.
Article in English | MEDLINE | ID: mdl-32123101

ABSTRACT

The cytoskeletal protein actin polymerizes into filaments that are essential for the mechanical stability of mammalian cells. In vitro experiments showed that direct interactions between actin filaments and lipid bilayers are possible and that the net charge of the bilayer as well as the presence of divalent ions in the buffer play an important role. In vivo, colocalization of actin filaments and divalent ions are suppressed, and cells rely on linker proteins to connect the plasma membrane to the actin network. Little is known, however, about why this is the case and what microscopic interactions are important. A deeper understanding is highly beneficial, first, to obtain understanding in the biological design of cells and, second, as a possible basis for the building of artificial cortices for the stabilization of synthetic cells. Here, we report the results of coarse-grained molecular dynamics simulations of monomeric and filamentous actin in the vicinity of differently charged lipid bilayers. We observe that charges on the lipid head groups strongly determine the ability of actin to adsorb to the bilayer. The inclusion of divalent ions leads to a reversal of the binding affinity. Our in silico results are validated experimentally by reconstitution assays with actin on lipid bilayer membranes and provide a molecular-level understanding of the actin-membrane interaction.


Subject(s)
Actin Cytoskeleton/chemistry , Actin Cytoskeleton/metabolism , Lipid Bilayers/chemistry , Lipid Bilayers/metabolism , Actins/chemistry , Artificial Cells , Cell Membrane/chemistry , Cell Membrane/metabolism , Chemical Phenomena , Computational Biology , Computer Simulation , Cytoskeleton/chemistry , Cytoskeleton/metabolism , Ions/chemistry , Ions/metabolism , Models, Molecular , Molecular Dynamics Simulation , Protein Binding , Protein Conformation , Static Electricity
5.
Int J Mol Sci ; 23(6)2022 Mar 10.
Article in English | MEDLINE | ID: mdl-35328409

ABSTRACT

Severe Acute Respiratory Syndrome CoronaVirus-2 (SARS-CoV-2) is composed of four structural proteins and several accessory non-structural proteins. SARS-CoV-2's most abundant structural protein, Membrane (M) protein, has a pivotal role both during viral infection cycle and host interferon antagonism. This is a highly conserved viral protein, thus an interesting and suitable target for drug discovery. In this paper, we explain the structural nature of M protein homodimer. To do so, we developed and applied a detailed and robust in silico workflow to predict M protein dimeric structure, membrane orientation, and interface characterization. Single Nucleotide Polymorphisms (SNPs) in M protein were retrieved from over 1.2 M SARS-CoV-2 genomes and proteins from the Global Initiative on Sharing All Influenza Data (GISAID) database, 91 of which were located at the predicted dimer interface. Among those, we identified SNPs in Variants of Concern (VOC) and Variants of Interest (VOI). Binding free energy differences were evaluated for dimer interfacial SNPs to infer mutant protein stabilities. A few high-prevalent mutated residues were found to be especially relevant in VOC and VOI. This realization may be a game-changer to structure-driven formulation of new therapeutics for SARS-CoV-2.


Subject(s)
Coronavirus M Proteins/genetics , Genome, Viral/genetics , Mutation , Polymorphism, Single Nucleotide , SARS-CoV-2/genetics , Binding Sites/genetics , COVID-19/prevention & control , COVID-19/virology , Coronavirus M Proteins/chemistry , Coronavirus M Proteins/metabolism , Humans , Molecular Dynamics Simulation , Protein Binding , Protein Domains , Protein Multimerization , SARS-CoV-2/physiology
6.
Molecules ; 27(11)2022 Jun 06.
Article in English | MEDLINE | ID: mdl-35684575

ABSTRACT

Scaffolds based on biopolymers and nanomaterials with appropriate mechanical properties and high biocompatibility are desirable in tissue engineering. Therefore, polylactic acid (PLA) nanocomposites were prepared with ceramic nanobioglass (PLA/n-BGs) at 5 and 10 wt.%. Bioglass nanoparticles (n-BGs) were prepared using a sol-gel methodology with a size of ca. 24.87 ± 6.26 nm. In addition, they showed the ability to inhibit bacteria such as Escherichia coli (ATCC 11775), Vibrio parahaemolyticus (ATCC 17802), Staphylococcus aureus subsp. aureus (ATCC 55804), and Bacillus cereus (ATCC 13061) at concentrations of 20 w/v%. The analysis of the nanocomposite microstructures exhibited a heterogeneous sponge-like morphology. The mechanical properties showed that the addition of 5 wt.% n-BG increased the elastic modulus of PLA by ca. 91.3% (from 1.49 ± 0.44 to 2.85 ± 0.99 MPa) and influenced the resorption capacity, as shown by histological analyses in biomodels. The incorporation of n-BGs decreased the PLA crystallinity (from 7.1% to 4.98%) and increased the glass transition temperature (Tg) from 53 °C to 63 °C. In addition, the n-BGs increased the thermal stability due to the nanoparticle's intercalation between the polymeric chains and the reduction in their movement. The histological implantation of the nanocomposites and the cell viability with HeLa cells higher than 80% demonstrated their biocompatibility character with a greater resorption capacity than PLA. These results show the potential of PLA/n-BGs nanocomposites for biomedical applications, especially for long healing processes such as bone tissue repair and avoiding microbial contamination.


Subject(s)
Nanocomposites , Polyesters , Escherichia coli , HeLa Cells , Humans , Nanocomposites/chemistry , Polyesters/chemistry , Polyesters/pharmacology , Tissue Engineering
7.
J Chem Inf Model ; 61(1): 335-346, 2021 01 25.
Article in English | MEDLINE | ID: mdl-33400529

ABSTRACT

Nucleotides are structural units relevant not only in nucleic acids but also as substrates or cofactors in key biochemical reactions. The size- and timescales of such nucleotide-protein interactions fall well within the scope of coarse-grained molecular dynamics, which holds promise of important mechanistic insight. However, the lack of specific parameters has prevented accurate coarse-grained simulations of protein interactions with most nucleotide compounds. In this work, we comprehensively develop coarse-grained parameters for key metabolites/cofactors (FAD, FMN, riboflavin, NAD, NADP, ATP, ADP, AMP, and thiamine pyrophosphate) in different oxidation and protonation states as well as for smaller molecules derived from them (among others, nicotinamide, adenosine, adenine, ribose, thiamine, and lumiflavin), summing up a total of 79 different molecules. In line with the Martini parameterization methodology, parameters were tuned to reproduce octanol-water partition coefficients. Given the lack of existing data, we set out to experimentally determine these partition coefficients, developing two methodological approaches, based on 31P-NMR and fluorescence spectroscopy, specifically tailored to the strong hydrophilicity of most of the parameterized compounds. To distinguish the partition of each relevant protonation species, we further potentiometrically characterized the protonation constants of key molecules. This work successfully builds a comprehensive and relevant set of computational models that will boost the biochemical application of coarse-grained simulations. It does so based on the measurement of partition and acid-base physicochemical data that, in turn, covers important gaps in nucleotide characterization.


Subject(s)
Molecular Dynamics Simulation , Nucleotides , Hydrophobic and Hydrophilic Interactions , Octanols , Water
8.
Nano Lett ; 20(5): 4007-4013, 2020 05 13.
Article in English | MEDLINE | ID: mdl-32357005

ABSTRACT

Nanocrystal gelation provides a powerful framework to translate nanoscale properties into bulk materials and to engineer emergent properties through the assembled microstructure. However, many established gelation strategies rely on chemical reactions and specific interactions, e.g., stabilizing ligands or ions on the nanocrystals' surfaces, and are therefore not easily transferable. Here, we report a general gelation strategy via nonspecific and purely entropic depletion attractions applied to three types of metal oxide nanocrystals. The gelation thresholds of two compositionally distinct spherical nanocrystals agree quantitatively, demonstrating the adaptability of the approach for different chemistries. Consistent with theoretical phase behavior predictions, nanocrystal cubes form gels at a lower polymer concentration than nanocrystal spheres, allowing shape to serve as a handle to control gelation. These results suggest that the fundamental underpinnings of depletion-driven assembly, traditionally associated with larger colloidal particles, are also applicable at the nanoscale.

9.
Molecules ; 26(16)2021 Aug 06.
Article in English | MEDLINE | ID: mdl-34443341

ABSTRACT

In recent decades, the number of patients requiring biocompatible and resistant implants that differ from conventional alternatives dramatically increased. Among the most promising are the nanocomposites of biopolymers and nanomaterials, which pretend to combine the biocompatibility of biopolymers with the resistance of nanomaterials. However, few studies have focused on the in vivo study of the biocompatibility of these materials. The electrospinning process is a technique that produces continuous fibers through the action of an electric field imposed on a polymer solution. However, to date, there are no reports of chitosan (CS) and polyvinyl alcohol (PVA) electrospinning with carbon nano-onions (CNO) for in vivo implantations, which could generate a resistant and biocompatible material. In this work, we describe the synthesis by the electrospinning method of four different nanofibrous membranes of chitosan (CS)/(PVA)/oxidized carbon nano-onions (ox-CNO) and the subdermal implantations after 90 days in Wistar rats. The results of the morphology studies demonstrated that the electrospun nanofibers were continuous with narrow diameters (between 102.1 nm ± 12.9 nm and 147.8 nm ± 29.4 nm). The CS amount added was critical for the diameters used and the successful electrospinning procedure, while the ox-CNO amount did not affect the process. The crystallinity index was increased with the ox-CNO introduction (from 0.85% to 12.5%), demonstrating the reinforcing effect of the nanomaterial. Thermal degradation analysis also exhibited reinforcement effects according to the DSC and TGA analysis, with the higher ox-CNO content. The biocompatibility of the nanofibers was comparable with the porcine collagen, as evidenced by the subdermal implantations in biological models. In summary, all the nanofibers were reabsorbed without a severe immune response, indicating the usefulness of the electrospun nanocomposites in biomedical applications.


Subject(s)
Carbon/chemistry , Chitosan/chemistry , Electricity , Materials Testing , Membranes, Artificial , Nanocomposites/chemistry , Polyvinyl Alcohol/chemistry , Animals , Nanocomposites/toxicity , Oxidation-Reduction , Rats
10.
J Community Psychol ; 49(5): 1134-1152, 2021 07.
Article in English | MEDLINE | ID: mdl-33393077

ABSTRACT

This study offers a qualitative comparison of risk factors for youth violence from the perspectives of community stakeholders in a low-income, urban community experiencing elevated rates of violence. One-on-one interviews were conducted with 36 community stakeholders across three key categories: 10 community residents who cared for youth living in the community, 15 program or service providers, and 11 leaders in community agencies and organizations. A grounded theory approach was used for data collection and analysis to extract themes that emerged from the question, "What are the things in the community that lead to youth violence?" While there was significant overlap in stakeholders' beliefs about precursors to youth violence, important differences also emerged. In order for youth violence prevention strategies to be successful, they must consider and address risk factors identified by community stakeholders involved in the implementation and sustainability.


Subject(s)
Poverty , Violence , Adolescent , Humans , Risk Factors , Violence/prevention & control
11.
Molecules ; 25(10)2020 May 14.
Article in English | MEDLINE | ID: mdl-32423061

ABSTRACT

Scaffold development for cell regeneration has increased in recent years due to the high demand for more efficient and biocompatible materials. Nanomaterials have become a critical alternative for mechanical, thermal, and antimicrobial property reinforcement in several biopolymers. In this work, four different chitosan (CS) bead formulations crosslinked with glutaraldehyde (GLA), including titanium dioxide nanoparticles (TiO2), and graphene oxide (GO) nanosheets, were prepared with potential biomedical applications in mind. The characterization of by FTIR spectroscopy, X-ray photoelectron spectroscopy (XRD), thermogravimetric analysis (TGA), energy-dispersive spectroscopy (EDS) and scanning electron microscopy (SEM), demonstrated an efficient preparation of nanocomposites, with nanoparticles well-dispersed in the polymer matrix. In vivo, subdermal implantation of the beads in Wistar rat's tissue for 90 days showed a proper and complete healing process without any allergenic response to any of the formulations. Masson's trichrome staining of the histological implanted tissues demonstrated the presence of a group of macrophage/histiocyte compatible cells, which indicates a high degree of biocompatibility of the beads. The materials were very stable under body conditions as the morphometry studies showed, but with low resorption percentages. These high stability beads could be used as biocompatible, resistant materials for long-term applications. The results presented in this study show the enormous potential of these chitosan nanocomposites in cell regeneration and biomedical applications.


Subject(s)
Chitosan/chemistry , Graphite/chemistry , Nanocomposites/chemistry , Nanoparticles/chemistry , Tissue Scaffolds , Titanium/chemistry , Animals , Biocompatible Materials , Cell Survival/drug effects , Chitosan/pharmacology , Graphite/pharmacology , Histiocytes/cytology , Histiocytes/drug effects , Histiocytes/physiology , Male , Nanocomposites/ultrastructure , Nanoparticles/ultrastructure , Rats , Rats, Wistar , Skin/cytology , Skin/drug effects , Tissue Engineering/methods , Titanium/pharmacology
12.
Molecules ; 25(5)2020 Mar 07.
Article in English | MEDLINE | ID: mdl-32155970

ABSTRACT

The design of scaffolding from biocompatible and resistant materials such as carbon nanomaterials and biopolymers has become very important, given the high rate of injured patients. Graphene and carbon nanotubes, for example, have been used to improve the physical, mechanical, and biological properties of different materials and devices. In this work, we report the grafting of carbon nano-onions with chitosan (CS-g-CNO) through an amide-type bond. These compounds were blended with chitosan and polyvinyl alcohol composites to produce films for subdermal implantation in Wistar rats. Films with physical mixture between chitosan, polyvinyl alcohol, and carbon nano-onions were also prepared for comparison purposes. Film characterization was performed with Fourier Transformation Infrared Spectroscopy (FTIR), Thermogravimetric Analysis (TGA), Differential Scanning Calorimetry (DSC), Tensile strength, X-ray Diffraction Spectroscopy (XRD), and Scanning Electron Microscopy (SEM). The degradation of films into simulated body fluid (SBF) showed losses between 14% and 16% of the initial weight after 25 days of treatment. Still, a faster degradation (weight loss and pH changes) was obtained with composites of CS-g-CNO due to a higher SBF interaction by hydrogen bonding. On the other hand, in vivo evaluation of nanocomposites during 30 days in Wistar rats, subdermal tissue demonstrated normal resorption of the materials with lower inflammation processes as compared with the physical blends of ox-CNO formulations. SBF hydrolytic results agreed with the in vivo degradation for all samples, demonstrating that with a higher ox-CNO content increased the stability of the material and decreased its degradation capacity; however, we observed greater reabsorption with the formulations including CS-g-CNO. With this research, we demonstrated the future impact of CS/PVA/CS-g-CNO nanocomposite films for biomedical applications.


Subject(s)
Nanocomposites/chemistry , Prostheses and Implants , Animals , Biocompatible Materials/chemistry , Calorimetry, Differential Scanning , Carbon , Chitosan/chemistry , Hydrogen-Ion Concentration , Microscopy, Electron, Scanning , Nanocomposites/administration & dosage , Nanocomposites/therapeutic use , Polyvinyl Alcohol/chemistry , Rats, Wistar , Spectroscopy, Fourier Transform Infrared , Spectrum Analysis, Raman , Tensile Strength , Thermogravimetry , X-Ray Diffraction
13.
Molecules ; 25(7)2020 Apr 07.
Article in English | MEDLINE | ID: mdl-32272702

ABSTRACT

The development of new biocompatible materials for application in the replacement of deteriorated tissues (due to accidents and diseases) has gained a lot of attention due to the high demand around the world. Tissue engineering offers multiple options from biocompatible materials with easy resorption. Chitosan (CS) is a biopolymer derived from chitin, the second most abundant polysaccharide in nature, which has been highly used for cell regeneration applications. In this work, CS films and Ruta graveolens essential oil (RGEO) were incorporated to obtain porous and resorbable materials, which did not generate allergic reactions. An oil-free formulation (F1: CS) and three different formulations containing R. graveolens essential oil were prepared (F2: CS-RGEO 0.5%; F3: CS+RGEO 1.0%; and F4: CS+RGEO 1.5%) to evaluate the effect of the RGEO incorporation in the mechanical and thermal stability of the films. Infrared spectroscopy (FTIR) analyses demonstrated the presence of RGEO. In contrast, X-ray diffraction (XRD) and differential scanning calorimetry (DSC) analysis showed that the crystalline structure and percentage of CS were slightly affected by the RGEO incorporation. Interesting saturation phenomena were observed for mechanical and water permeability tests when RGEO was incorporated at higher than 0.5% (v/v). The results of subdermal implantation after 30 days in Wistar rats showed that increasing the amount of RGEO resulted in greater resorption of the material, but also more significant inflammation of the tissue surrounding the materials. On the other hand, the thermal analysis showed that the RGEO incorporation almost did not affect thermal degradation. However, mechanical properties demonstrated an understandable loss of tensile strength and Young's modulus for F3 and F4. However, given the volatility of the RGEO, it was possible to generate a slightly porous structure, as can be seen in the microstructure analysis of the surface and the cross-section of the films. The cytotoxicity analysis of the CS+RGEO compositions by the hemolysis technique agreed with in vivo results of the low toxicity observed. All these results demonstrate that films including crude essential oil have great application potential in the biomedical field.


Subject(s)
Chitosan/chemistry , Oils, Volatile/chemistry , Ruta/chemistry , Adult , Animals , Biocompatible Materials/chemistry , Calorimetry, Differential Scanning/methods , Elastic Modulus , Humans , Male , Permeability , Porosity , Rats , Rats, Wistar , Spectroscopy, Fourier Transform Infrared/methods , Tensile Strength , Tissue Engineering/methods , Tissue Scaffolds/chemistry , X-Ray Diffraction/methods , Young Adult
14.
Biochim Biophys Acta Biomembr ; 1860(6): 1292-1300, 2018 Jun.
Article in English | MEDLINE | ID: mdl-29501607

ABSTRACT

Pex11p plays a crucial role in peroxisome fission. Previously, it was shown that a conserved N-terminal amphipathic helix in Pex11p, termed Pex11-Amph, was necessary for peroxisomal fission in vivo while in vitro studies revealed that this region alone was sufficient to bring about tubulation of liposomes with a lipid consistency resembling the peroxisomal membrane. However, molecular details of how Pex11-Amph remodels the peroxisomal membrane remain unknown. Here we have combined in silico, in vitro and in vivo approaches to gain insights into the molecular mechanisms underlying Pex11-Amph activity. Using molecular dynamics simulations, we observe that Pex11-Amph peptides form linear aggregates on a model membrane. Furthermore, we identify mutations that disrupted this aggregation in silico, which also abolished the peptide's ability to remodel liposomes in vitro, establishing that Pex11p oligomerisation plays a direct role in membrane remodelling. In vivo studies revealed that these mutations resulted in a strong reduction in Pex11 protein levels, indicating that these residues are important for Pex11p function. Taken together, our data demonstrate the power of combining in silico techniques with experimental approaches to investigate the molecular mechanisms underlying Pex11p-dependent membrane remodelling.


Subject(s)
Cell Membrane/chemistry , Fungal Proteins/chemistry , Membrane Proteins/chemistry , Penicillium chrysogenum/enzymology , Peroxins/chemistry , Amino Acid Substitution , Fungal Proteins/genetics , Fungal Proteins/physiology , Membrane Proteins/genetics , Membrane Proteins/physiology , Models, Molecular , Molecular Dynamics Simulation , Mutation, Missense , Penicillium chrysogenum/genetics , Peptide Fragments/chemistry , Peroxins/genetics , Peroxins/physiology , Peroxisomes/chemistry , Protein Aggregates , Protein Conformation
15.
Hum Mol Genet ; 25(13): 2728-2737, 2016 07 01.
Article in English | MEDLINE | ID: mdl-27260403

ABSTRACT

Spinocerebellar ataxia type 23 (SCA23) is caused by missense mutations in prodynorphin, encoding the precursor protein for the opioid neuropeptides α-neoendorphin, Dynorphin (Dyn) A and Dyn B, leading to neurotoxic elevated mutant Dyn A levels. Dyn A acts on opioid receptors to reduce pain in the spinal cord, but its cerebellar function remains largely unknown. Increased concentration of or prolonged exposure to Dyn A is neurotoxic and these deleterious effects are very likely caused by an N-methyl-d-aspartate-mediated non-opioid mechanism as Dyn A peptides were shown to bind NMDA receptors and potentiate their glutamate-evoked currents. In the present study, we investigated the cellular mechanisms underlying SCA23-mutant Dyn A neurotoxicity. We show that SCA23 mutations in the Dyn A-coding region disrupted peptide secondary structure leading to a loss of the N-terminal α-helix associated with decreased κ-opioid receptor affinity. Additionally, the altered secondary structure led to increased peptide stability of R6W and R9C Dyn A, as these peptides showed marked degradation resistance, which coincided with decreased peptide solubility. Notably, L5S Dyn A displayed increased degradation and no aggregation. R6W and wt Dyn A peptides were most toxic to primary cerebellar neurons. For R6W Dyn A, this is likely because of a switch from opioid to NMDA- receptor signalling, while for wt Dyn A, this switch was not observed. We propose that the pathology of SCA23 results from converging mechanisms of loss of opioid-mediated neuroprotection and NMDA-mediated excitotoxicity.


Subject(s)
Dynorphins/metabolism , Spinocerebellar Degenerations/metabolism , Amino Acid Sequence , Animals , Cell Culture Techniques , Computer Simulation , Dynorphins/physiology , Endorphins/metabolism , Enkephalins/genetics , Enkephalins/metabolism , Mice , Mice, Inbred C57BL , N-Methylaspartate/metabolism , Neurons/metabolism , Neurotoxins , Protein Precursors/genetics , Protein Precursors/metabolism , Protein Structure, Secondary , Receptors, N-Methyl-D-Aspartate/metabolism , Signal Transduction , Spinal Cord/metabolism , Spinocerebellar Degenerations/genetics
16.
J Exp Biol ; 221(Pt 8)2018 04 19.
Article in English | MEDLINE | ID: mdl-29530973

ABSTRACT

Tegu lizards (Salvator merianae) aestivate for up to 5 months during Brazil's winter, when they retreat to burrows and halt most activities. Dormant tegus reduce their gastrointestinal (GI) mass, which allows a substantial energy economy. This strategy, however, implies that the first post-dormancy digestion would be more costly than subsequent feeding episodes as a result of GI atrophy. To address this, we determined the postprandial metabolic response (SDA) of the first (M1), second (M2) and several (RM) feeding episodes after tegus' dormancy. Another group of tegus (PF) was subjected to an extra 50 day fasting period after arousal. Glucose, triglycerides and uric acid levels were checked before and after feeding. M1 digestion lasted twice as long and cost twofold more when compared with M2 or RM, in agreement with the idea that GI atrophy inflates digestion cost at the first post-dormancy meal. The SDA response was similar in M2 and RM, suggesting that the GI tract was fully reorganized after the first feeding. The SDA cost was equal in PF and RM, implying that the change in state per se (dormant to arousal) triggers the regrowth of GI, independently of feeding. Fasting tegus at M1 presented higher triglyceride and lower uric acid levels than fed tegus, indicating that fasting is mainly sustained by fat storage. Our results show that seasonal fasting imposes an extra digestion cost to tegus following their next feeding, which is fully paid during their first digestion. This surplus cost, however, is negligible compared with the overall energetic savings from GI tract atrophy during the dormancy period.


Subject(s)
Fasting/physiology , Lizards/metabolism , Lizards/physiology , Animals , Blood Glucose , Digestion/physiology , Gastrointestinal Tract/growth & development , Gastrointestinal Tract/physiology , Hibernation/physiology , Postprandial Period/physiology , Seasons , Triglycerides/blood , Uric Acid/blood
17.
Biophys J ; 113(12): 2669-2681, 2017 Dec 19.
Article in English | MEDLINE | ID: mdl-29262360

ABSTRACT

The thylakoid membrane has a unique lipid composition, consisting mostly of galactolipids. These thylakoid lipids have important roles in photosynthesis. Here, we investigate to what extent these lipids bind specifically to the Photosystem II complex. To this end, we performed coarse-grain MD simulations of the Photosystem II complex embedded in a thylakoid membrane with realistic composition. Based on >85 µs simulation time, we find that monogalactosyldiacylglycerol and sulfoquinovosyldiacylglycerol lipids are enriched in the annular shell around the protein, and form distinct binding sites. From the analysis of residue contacts, we conclude that electrostatic interactions play an important role in stabilizing these binding sites. Furthermore, we find that chlorophyll a has a prevalent role in the coordination of the lipids. In addition, we observe lipids to diffuse in and out of the plastoquinone exchange cavities, allowing exchange of cocrystallized lipids with the bulk membrane and suggesting a more open nature of the plastoquinone exchange cavity. Together, our data provide a wealth of information on protein-lipid interactions for a key protein in photosynthesis.


Subject(s)
Membrane Lipids/metabolism , Molecular Dynamics Simulation , Photosystem II Protein Complex/metabolism , Thylakoids/metabolism , Binding Sites , Glycerol/metabolism , Photosystem II Protein Complex/chemistry , Protein Binding , Protein Conformation
18.
J Am Chem Soc ; 139(7): 2664-2671, 2017 02 22.
Article in English | MEDLINE | ID: mdl-28122455

ABSTRACT

The mechanosensitive channels of large conductance (MscL) are bacterial membrane proteins that serve as last resort emergency release valves in case of severe osmotic downshock. Sensing bilayer tension, MscL channels are sensitive to changes in the bilayer environment and are, therefore, an ideal test case for exploring membrane protein coupling. Here, we use high-throughput coarse-grained molecular dynamics simulations to characterize MscL gating kinetics in different bilayer environments under the influence of alcohols. We performed over five hundred simulations to obtain sufficient statistics to reveal the subtle effects of changes in the membrane environment on MscL gating. MscL opening times were found to increase with the addition of the straight-chain alcohols ethanol, octanol, and to some extent dodecanol but not with hexadecanol. Increasing concentration of octanol increased the impeding effect, but only up to 10-20 mol %. Our in silico predictions were experimentally confirmed using reconstituted MscL in a liposomal fluorescent efflux assay. Our combined data reveal that the effect of alcohols on MscL gating arises not through specific binding sites but through a combination of the alcohol-induced changes to a number of bilayer properties and their alteration of the MscL-bilayer interface. Our work provides a key example of how extensive molecular simulations can be used to predict the functional modification of membrane proteins by subtle changes in their bilayer environment.


Subject(s)
Bacterial Proteins/chemistry , Cell Membrane/chemistry , Ion Channels/physiology , Molecular Dynamics Simulation , Bacterial Proteins/physiology , Cell Membrane/physiology , Ethanol , Ion Channel Gating/physiology , Mechanical Phenomena , Octanols
19.
Chemistry ; 23(46): 11108-11118, 2017 Aug 16.
Article in English | MEDLINE | ID: mdl-28628248

ABSTRACT

The kinetic and thermodynamic selectivities of imine formation have been investigated for several dynamic covalent libraries of aldehydes and amines. Two systems were examined, involving the reaction of different types of primary amino groups (aliphatic amines, alkoxy-amines, hydrazides and hydrazines) with two types of aldehydes, sulfobenzaldehyde and pyridoxal phosphate in aqueous solution at different pD (5.0, 8.5, 11.4) on one hand, 2-pyridinecarboxaldehyde and salicylaldehyde in organic solvents on the other hand. The reactions were performed separately for given amine/aldehyde pairs as well as in competitive conditions between an aldehyde and a mixture of amines. In the latter case, the time evolution of the dynamic covalent libraries generated was followed, taking into consideration the operation of both kinetic and thermodynamic selectivities. The results showed that, in aqueous solution, the imine of the aliphatic amine was not stable, but oxime and hydrazone formed well in a pH dependent way. On the other hand, in organic solvents, the kinetic product was the imine derived from an aliphatic amine and the thermodynamic products were oxime and hydrazone. The insights gained from these experiments provide a basis for the implementation of imine formation in selective derivatization of mono-amines in mixtures as well as of polyfunctional compounds presenting different types of amino groups. They may in principle be extended to other dynamic covalent chemistry systems.

20.
Chemistry ; 23(59): 14872-14882, 2017 Oct 20.
Article in English | MEDLINE | ID: mdl-28815776

ABSTRACT

Herein, we report the synthesis of a double hydrazone capable of undergoing photochemical E/Z isomerization through the imine double bonds. The bis(hydrazone) 1-E,E can be considered as a "two-arm" system in which the controlled movement of each arm is obtained by photo-modulation, making possible the appearance of two isolable metastable isomeric states 1-E,Z and 1-Z,Z. Such states are characterized by very specific structural, optical, and electrochemical properties. The latter allows the reversible return from either 1-E,Z or 1-Z,Z to the 1-E,E state. Our results are of great importance in the further development of molecular machines and photochemically controlled reactions by introducing for the first time double hydrazones as tunable photochemical switches.

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