Differential effects of group III metabotropic glutamate receptors on spontaneous inhibitory synaptic currents in spine-innervating double bouquet and parvalbumin-expressing dendrite-targeting GABAergic interneurons in human neocortex.

Diverse neocortical GABAergic neurons specialize in synaptic targeting and their effects are modulated by presynaptic metabotropic glutamate receptors (mGluRs) suppressing neurotransmitter release in rodents, but their effects in human neocortex are unknown. We tested whether activation of group III mGluRs by L-AP4 changes GABAA receptor-mediated spontaneous inhibitory postsynaptic currents (sIPSCs) in 2 distinct dendritic spine-innervating GABAergic interneurons recorded in vitro in human neocortex. Calbindin-positive double bouquet cells (DBCs) had columnar "horsetail" axons descending through layers II-V innervating dendritic spines (48%) and shafts, but not somata of pyramidal and nonpyramidal neurons. Parvalbumin-expressing dendrite-targeting cell (PV-DTC) axons extended in all directions innervating dendritic spines (22%), shafts (65%), and somata (13%). As measured, 20% of GABAergic neuropil synapses innervate spines, hence DBCs, but not PV-DTCs, preferentially select spine targets. Group III mGluR activation paradoxically increased the frequency of sIPSCs in DBCs (to median 137% of baseline) but suppressed it in PV-DTCs (median 92%), leaving the amplitude unchanged. The facilitation of sIPSCs in DBCs may result from their unique GABAergic input being disinhibited via network effect. We conclude that dendritic spines receive specialized, diverse GABAergic inputs, and group III mGluRs differentially regulate GABAergic synaptic transmission to distinct GABAergic cell types in human cortex.

Differences in intimate partner violence exposure across college, crowdsourced, and at-risk samples.

OBJECTIVE: Intimate partner violence (IPV) is a pervasive and common form of violence against women. IPV is multifaceted, with physical, sexual, and/or psychological means of perpetration, and has detrimental effects on women's mental health. IPV generally affects women; however, how IPV differentially affects different groups of women is less clear. Women who are socioeconomically vulnerable are often considered at risk for IPV, although women in college are also often the topic of IPV research due both to high rates of IPV and to ease of study recruitment. There is increasing research on the effects of IPV in a third group of women, those recruited through online platforms (i.e., crowdsourcing). How IPV differs across these three samples has yet to be examined. METHOD: In this study, we examined differences in IPV exposure across three samples of women, at risk (n = 144), college (n = 654), and crowdsourced (n = 168), using a Bayesian approach to general linear modeling. RESULTS: Results indicated that the majority of women in each sample experienced some IPV. Results further suggested that women in the crowdsourced sample had the highest exposure to IPV in general and to physical IPV, sexual IPV, and IPV-related injury in particular, whereas women in the at-risk sample had the highest rates of psychological IPV. CONCLUSION: These findings highlight the importance of sampling in studies of IPV and thus have ramifications for future research. (PsycInfo Database Record (c) 2022 APA, all rights reserved).

pDynamo3 Molecular Modeling and Simulation Program.

pDynamo3 is the first formal version of the Dynamo molecular modeling and simulation library that is written in Python 3. It follows from the previous pDynamo versions written in Python 2, the first of which was released in 2007. Both pDynamo and its predecessor, fDynamo, were designed with the aim of providing easy-to-use and flexible frameworks for performing molecular simulations at an atomistic level with a special emphasis on those employing hybrid quantum chemical and molecular mechanical potential methods. Although the use of pDynamo3 is quite similar to that of pDynamo2, it has added significant new capability and also undergone extensive restructuring that will make it much easier to extend with new functionality. The pDynamo3 code is issued under the GNU general public license at https://github.com/pdynamo/pDynamo3 with additional information on the pDynamo website https:www.pdynamo.org.

Density Fitting for QC/MM Interactions.

Density fitting is a standard technique in quantum chemistry as it helps to accelerate certain parts of a calculation, such as the computation of the electron repulsion energy, without significant loss of accuracy. This paper explores the effectiveness of this technique when it is extended to treat interactions with external electrostatic potentials, in particular those that arise from the environment in hybrid quantum chemical/molecular mechanical calculations. It is found that fitted densities are able to well reproduce the energies, forces, and properties obtained using unfitted densities, as long as a suitable operator is employed for the fitting. It is expected that this precision would be improved by the development of basis sets specifically designed to treat these types of interactions and that the use of this approximation could lead to substantial speed-ups in large hybrid potential simulations.

Tonic GABAA Receptor-Mediated Currents of Human Cortical GABAergic Interneurons Vary Amongst Cell Types.

Persistent anion conductances through GABAA receptors (GABAARs) are important modulators of neuronal excitability. However, it is currently unknown how the amplitudes of these currents vary among different cell types in the human neocortex, particularly among diverse GABAergic interneurons. We have recorded 101 interneurons in and near layer 1 from cortical tissue surgically resected from both male and female patients, visualized 84 of them and measured tonic GABAAR currents in 48 cells with an intracellular [Cl-] of 65 mm and in the presence of 5 µm GABA. We compare these tonic currents among five groups of interneurons divided by firing properties and four types of interneuron defined by axonal distributions; rosehip, neurogliaform, stalked-bouton, layer 2-3 innervating and a pool of other cells. Interestingly, the rosehip cell, a type of interneuron only described thus far in human tissue, and layer 2-3 innervating cells exhibit larger tonic currents than other layer 1 interneurons, such as neurogliaform and stalked-bouton cells; the latter two groups showing no difference. The positive allosteric modulators of GABAARs allopregnanolone and DS2 also induced larger current shifts in the rosehip and layer 2-3 innervating cells, consistent with higher expression of the δ subunit of the GABAAR in these neurons. We have also examined how patient parameters, such as age, seizures, type of cancer and anticonvulsant treatment may alter tonic inhibitory currents in human neurons. The cell type-specific differences in tonic inhibitory currents could potentially be used to selectively modulate cortical circuitry.SIGNIFICANCE STATEMENT Tonic currents through GABAA receptors (GABAARs) are a potential therapeutic target for a number of neurologic and psychiatric conditions. Here, we show that these currents in human cerebral cortical GABAergic neurons display cell type-specific differences in their amplitudes which implies differential modulation of their excitability. Additionally, we examine whether the amplitudes of the tonic currents measured in our study show any differences between patient populations, finding some evidence that age, seizures, type of cancer, and anticonvulsant treatment may alter tonic inhibition in human tissue. These results advance our understanding of how pathology affects neuronal excitability and could potentially be used to selectively modulate cortical circuitry.

Physiological role for GABAA receptor desensitization in the induction of long-term potentiation at inhibitory synapses.

GABAA receptors (GABAARs) are pentameric ligand-gated ion channels distributed throughout the brain where they mediate synaptic and tonic inhibition. Following activation, these receptors undergo desensitization which involves entry into long-lived agonist-bound closed states. Although the kinetic effects of this state are recognised and its structural basis has been uncovered, the physiological impact of desensitization on inhibitory neurotransmission remains unknown. Here we describe an enduring form of long-term potentiation at inhibitory synapses that elevates synaptic current amplitude for 24 h following desensitization of GABAARs in response to agonist exposure or allosteric modulation. Using receptor mutants and allosteric modulators we demonstrate that desensitization of GABAARs facilitates their phosphorylation by PKC, which increases the number of receptors at inhibitory synapses. These observations provide a physiological relevance to the desensitized state of GABAARs, acting as a signal to regulate the efficacy of inhibitory synapses during prolonged periods of inhibitory neurotransmission.

Theoretical characterization of the shikimate 5-dehydrogenase reaction from Mycobacterium tuberculosis by hybrid QC/MM simulations and quantum chemical descriptors.

In this study, we have investigated the enzyme shikimate 5-dehydrogenase from the causative agent of tuberculosis, Mycobacterium tuberculosis. We have employed a mixture of computational techniques, including molecular dynamics, hybrid quantum chemical/molecular mechanical potentials, relaxed surface scans, quantum chemical descriptors and free-energy simulations, to elucidate the enzyme's reaction pathway. Overall, we find a two-step mechanism, with a single transition state, that proceeds by an energetically uphill hydride transfer, followed by an energetically downhill proton transfer. Our mechanism and calculated free energy barrier for the reaction, 64.9 kJ mol- 1, are in good agreement with those predicted from experiment. An analysis of quantum chemical descriptors along the reaction pathway indicated a possibly important, yet currently unreported, role of the active site threonine residue, Thr65.

Hydrogen evolution reaction mediated by an all-sulfur trinuclear nickel complex.

We report the synthesis and the characterization of a trinuclear nickel complex. Solid state and solution studies using X-ray diffraction, NMR and UV-vis spectroscopy highlight the square planar geometries around the metal centers and an all-sulfur coordination sphere. It exhibits significant electrocatalytic activity for hydrogen evolution in DMF using Et3NHCl as the proton source. DFT studies suggest that sulfur atoms act as proton relay, as proposed in [NiFe] hydrogenases.

Photoswitching mechanism of a fluorescent protein revealed by time-resolved crystallography and transient absorption spectroscopy.

Reversibly switchable fluorescent proteins (RSFPs) serve as markers in advanced fluorescence imaging. Photoswitching from a non-fluorescent off-state to a fluorescent on-state involves trans-to-cis chromophore isomerization and proton transfer. Whereas excited-state events on the ps timescale have been structurally characterized, conformational changes on slower timescales remain elusive. Here we describe the off-to-on photoswitching mechanism in the RSFP rsEGFP2 by using a combination of time-resolved serial crystallography at an X-ray free-electron laser and ns-resolved pump-probe UV-visible spectroscopy. Ten ns after photoexcitation, the crystal structure features a chromophore that isomerized from trans to cis but the surrounding pocket features conformational differences compared to the final on-state. Spectroscopy identifies the chromophore in this ground-state photo-intermediate as being protonated. Deprotonation then occurs on the µs timescale and correlates with a conformational change of the conserved neighbouring histidine. Together with a previous excited-state study, our data allow establishing a detailed mechanism of off-to-on photoswitching in rsEGFP2.

Modeling the Hydrolysis of Iron-Sulfur Clusters.

Iron-sulfur (FeS) clusters are essential metal cofactors involved in a wide variety of biological functions. Their catalytic efficiency, biosynthesis, and regulation depend on FeS stability in aqueous solution. Here, molecular modeling is used to investigate the hydrolysis of an oxidized (ferric) mononuclear FeS cluster by bare dissociation and water substitution mechanisms in neutral and acidic solution. First, approximate electronic structure descriptions of FeS reactions by density functional theory are validated against high-level wave function CCSD(T) calculations. Solvation contributions are included by an all-atom model with hybrid quantum chemical/molecular mechanical (QM/MM) potentials and enhanced sampling molecular dynamics simulations. The free energy profile obtained for FeS cluster hydrolysis indicates that the hybrid functional M06 together with an implicit solvent correction capture the most important aspects of FeS cluster reactivity in aqueous solution. Then, 20 reaction channels leading to two consecutive Fe-S bond ruptures were explored with this calibrated model. For all protonation states, nucleophilic substitution with concerted bond breaking and forming to iron is the preferred mechanism, both kinetic and thermodynamically. In neutral solution, proton transfer from water to the sulfur leaving group is also concerted. Dissociative reactions show higher barriers and will not be relevant for FeS reactivity when exposed to solvent. These hydrolysis mechanisms may help to explain the stability and catalytic mechanisms of FeS clusters of multiple sizes and proteins.

Electrocatalytic Hydrogen Evolution with a Cobalt Complex Bearing Pendant Proton Relays: Acid Strength and Applied Potential Govern Mechanism and Stability.

[Co(bapbpy)Cl]+ (bapbpy: 6,6'-bis(2-aminopyridyl)-2,2'-bipyridine) is a polypyridyl cobalt(II) complex bearing both a redox-active bipyridine ligand and pendant proton relays. This compound catalyzes electro-assisted H2 evolution in DMF with distinct mechanisms depending on the strength of the acid used as the proton source (pKa values ranging from 3.4 to 13.5 in DMF) and the applied potential. Electrochemical studies combining cyclic voltammetry and bulk electrolysis measurements enabled one to bring out four distinct catalytic processes. Where applicable, relevant kinetic information were obtained using either foot-of-the-wave analysis (FOWA) or analytical treatment of bulk electrolysis experiments. Among the different catalytic pathways identified in this study, a clear relationship between the catalyst performances and stability was evidenced. These results draw attention to a number of interesting considerations and may help in the development of future adequately designed catalysts.

Negative Impact of Carbapenem Methylation on the Reactivity of ß-Lactams for Cysteine Acylation as Revealed by Quantum Calculations and Kinetic Analyses.

The Enterococcus faecium l,d-transpeptidase (Ldtfm) mediates resistance to most ß-lactam antibiotics in this bacterium by replacing classical peptidoglycan polymerases. The catalytic Cys of Ldtfm is rapidly acylated by ß-lactams belonging to the carbapenem class but not by penams or cephems. We previously reported quantum calculations and kinetic analyses for Ldtfm and showed that the inactivation profile is not determined by differences in drug binding (KD [equilibrium dissociation constant] values in the 50 to 80 mM range). In this study, we analyzed the reaction of a Cys sulfhydryl with various ß-lactams in the absence of the enzyme environment in order to compare the intrinsic reactivity of drugs belonging to the penam, cephem, and carbapenem classes. For this purpose, we synthesized cyclic Cys-Asn (cCys-Asn) to generate a soluble molecule with a sulfhydryl closely mimicking a cysteine in a polypeptide chain, thereby avoiding free reactive amino and carboxyl groups. Computational studies identified a thermodynamically favored pathway involving a concerted rupture of the ß-lactam amide bond and formation of an amine anion. Energy barriers indicated that the drug reactivity was the highest for nonmethylated carbapenems, intermediate for methylated carbapenems and cephems, and the lowest for penams. Electron-withdrawing groups were key reactivity determinants by enabling delocalization of the negative charge of the amine anion. Acylation rates of cCys-Asn determined by spectrophotometry revealed the same order in the reactivity of ß-lactams. We concluded that the rate of Ldtfm acylation is largely determined by the ß-lactam reactivity with one exception, as the enzyme catalytic pocket fully compensated for the detrimental effect of carbapenem methylation.

Chromophore twisting in the excited state of a photoswitchable fluorescent protein captured by time-resolved serial femtosecond crystallography.

Chromophores absorb light in photosensitive proteins and thereby initiate fundamental biological processes such as photosynthesis, vision and biofluorescence. An important goal in their understanding is the provision of detailed structural descriptions of the ultrafast photochemical events that they undergo, in particular of the excited states that connect chemistry to biological function. Here we report on the structures of two excited states in the reversibly photoswitchable fluorescent protein rsEGFP2. We populated the states through femtosecond illumination of rsEGFP2 in its non-fluorescent off state and observed their build-up (within less than one picosecond) and decay (on the several picosecond timescale). Using an X-ray free-electron laser, we performed picosecond time-resolved crystallography and show that the hydroxybenzylidene imidazolinone chromophore in one of the excited states assumes a near-canonical twisted configuration halfway between the trans and cis isomers. This is in line with excited-state quantum mechanics/molecular mechanics and classical molecular dynamics simulations. Our new understanding of the structure around the twisted chromophore enabled the design of a mutant that displays a twofold increase in its off-to-on photoswitching quantum yield.

Crystal structures of a GABAA-receptor chimera reveal new endogenous neurosteroid-binding sites.

γ-Aminobutyric acid receptors (GABAARs) are vital for controlling excitability in the brain. This is emphasized by the numerous neuropsychiatric disorders that result from receptor dysfunction. A critical component of most native GABAARs is the α subunit. Its transmembrane domain is the target for many modulators, including endogenous brain neurosteroids that impact anxiety, stress and depression, and for therapeutic drugs, such as general anesthetics. Understanding the basis for the modulation of GABAAR function requires high-resolution structures. Here we present the first atomic structures of a GABAAR chimera at 2.8-Å resolution, including those bound with potentiating and inhibitory neurosteroids. These structures define new allosteric binding sites for these modulators that are associated with the α-subunit transmembrane domain. Our findings will enable the exploitation of neurosteroids for therapeutic drug design to regulate GABAARs in neurological disorders.

Proton reduction reaction catalyzed by homoleptic nickel bis-1,2-dithiolate complexes: Experimental and theoretical mechanistic investigations.

A series of homoleptic monoanionic nickel dithiolene complexes [Ni(bdt)2](NBu4), [Ni(tdt)2](NBu4), and [Ni(mnt)2](NBu4) containing the ligands benzene-1,2-dithiolate (bdt2-), toluene-3,4-dithiolate (tdt2-) and maleonitriledithiolate (mnt2-), respectively, have been employed as electrocatalysts in the hydrogen evolution reaction with trifluoroacetic acid as proton source in acetonitrile. All complexes were active catalysts with TONs reaching 113, 158 and 6 for [Ni(bdt)2](NBu4), [Ni(tdt)2](NBu4), and [Ni(mnt)2](NBu4), respectively. Faradaic yield for hydrogen evolution reaction reaches 88 % for 2- , which also displays the minimal overpotential requirement value (467 mV) within the series. Two pathways for H2 evolution can be hypothesized that differ on on the sequence of protonation and reduction steps. DFT calculations are in agreement with experimental data and indicate that protonation at sulfur follows reduction to the dianion. Hydrogen evolves from the direduced-diprotonated form via a highly distorted nickel hydride intermediate. The effects of acid strength and concentration in the hydrogen-evolving mechanism are also discussed.

Norovirus RNA-dependent RNA polymerase: A computational study of metal-binding preferences.

Norovirus (NV) RNA-dependent RNA polymerase (RdRP) is essential for replicating the genome of the virus, which makes this enzyme a key target for the development of antiviral agents against NV gastroenteritis. In this work, a complex of NV RdRP bound to manganese ions and an RNA primer-template duplex was investigated using X-ray crystallography and hybrid quantum chemical/molecular mechanical simulations. Experimentally, the complex crystallized in a tetragonal crystal form. The nature of the primer/template duplex binding in the resulting structure indicates that the complex is a closed back-tracked state of the enzyme, in which the 3'-end of the primer occupies the position expected for the post-incorporated nucleotide before translocation. Computationally, it is found that the complex can accept a range of divalent metal cations without marked distortions in the active site structure. The highest binding energy is for copper, followed closely by manganese and iron, and then by zinc, nickel, and cobalt. Proteins 2017; 85:1435-1445. © 2017 Wiley Periodicals, Inc.

An Algorithm for Adaptive QC/MM Simulations.

An algorithm is proposed for the simulation of molecular systems with hybrid quantum chemical (QC) and molecular mechanical (MM) potentials that permits the adaptive partitioning of the atoms in the system between QC and MM regions. In contrast to existing methods, the algorithm requires only a single QC calculation of the QC/MM system per energy calculation and yet has consistent energy and forces, which makes it suitable for geometry optimizations and molecular dynamics calculations within the microcanonical ensemble, in addition to other types of simulation. This article describes the algorithm and its implementation, presents some simple test cases with both semiempirical and density functional theory QC/MM potentials, and discusses perspectives for future work.

Catalytic Mechanism of Peptidoglycan Deacetylase: A Computational Study.

Bacterial peptidoglycan deacetylase enzymes are potentially important targets for the design of new drugs. In pathogenic bacteria, they modify cell-wall peptidoglycan by removing the acetyl group, which makes the bacteria more resistant to the host's immune response and other forms of attack, such as degradation by lysozyme. In this study, we have investigated the mechanism of reaction of acetyl removal from a model substrate, the N-acetylglucosamine/N-acetylmuramic acid dimer, by peptidogylcan deacetylase from Helicobacter pylori. For this, we employed a range of computational approaches, including molecular docking, Poisson-Boltzmann electrostatic pKa calculations, molecular dynamics simulations, and hybrid quantum chemical/molecular mechanical potential calculations, in conjunction with reaction-path-finding algorithms. The active site of this enzyme is in a region of highly negative electrostatic potential and contains a zinc dication with a bound water molecule. In the docked enzyme-substrate complex, our pKa calculations indicate that in the most stable protonation states of the active site the zinc-bound water molecule is in its hydroxide form and that the adjacent histidine residue, His247, is doubly protonated. In addition, there are one or two excess protons, with the neighboring aspartate residues, Asp12 and/or Asp199, being protonated. Overall, we find five classes of feasible reaction mechanisms, with the favored mechanism depending heavily on the protonation state of the active site. In the major one-excess-proton form, the mechanism with the lowest barrier (84 kJ mol-1) involves an initial protonation of the substrate nitrogen, followed by nucleophilic attack of the zinc-bound hydroxide and rupture of the substrate's carbon-nitrogen bond. However, in the minor two-excess-proton form, four mechanisms are almost equienergetic (83-86 kJ mol-1), comprising both those that start with nitrogen protonation and those in which nucleophilic attack by hydroxide occurs first.

Structural Determinants of Improved Fluorescence in a Family of Bacteriophytochrome-Based Infrared Fluorescent Proteins: Insights from Continuum Electrostatic Calculations and Molecular Dynamics Simulations.

Using X-ray crystallography, continuum electrostatic calculations, and molecular dynamics simulations, we have studied the structure, protonation behavior, and dynamics of the biliverdin chromophore and its molecular environment in a series of genetically engineered infrared fluorescent proteins (IFPs) based on the chromophore-binding domain of the Deinococcus radiodurans bacteriophytochrome. Our study suggests that the experimentally observed enhancement of fluorescent properties results from the improved rigidity and planarity of the biliverdin chromophore, in particular of the first two pyrrole rings neighboring the covalent linkage to the protein. We propose that the increases in the levels of both motion and bending of the chromophore out of planarity favor the decrease in fluorescence. The chromophore-binding pocket in some of the studied proteins, in particular the weakly fluorescent parent protein, is shown to be readily accessible to water molecules from the solvent. These waters entering the chromophore region form hydrogen bond networks that affect the otherwise planar conformation of the first three rings of the chromophore. On the basis of our simulations, the enhancement of fluorescence in IFPs can be achieved either by reducing the mobility of water molecules in the vicinity of the chromophore or by limiting the interactions of the nearby protein residues with the chromophore. Finally, simulations performed at both low and neutral pH values highlight differences in the dynamics of the chromophore and shed light on the mechanism of fluorescence loss at low pH.

Hybrid Potential Simulation of the Acylation of Enterococcus faecium l,d-Transpeptidase by Carbapenems.

The l,d-transpeptidases, Ldts, catalyze peptidoglycan cross-linking in ß-lactam-resistant mutant strains of several bacteria, including Enterococcus faecium and Mycobacterium tuberculosis. Although unrelated to the essential d,d-transpeptidases, which are inactivated by the ß-lactam antibiotics, they are nevertheless inhibited by the carbapenem antibiotics, making them potentially useful targets in the treatment of some important diseases. In this work, we have investigated the acylation mechanism of the Ldt from E. faecium by the carbapenem, ertapenem, using computational techniques. We have employed molecular dynamics simulations in conjunction with QC/MM hybrid potential calculations to map out possible reaction paths. We have focused on determining the following: (i) the protonation state of the nucleophilic cysteine of the enzyme when it attacks; (ii) whether nucleophilic attack and ß-lactam ring-opening are concerted or stepwise, the latter occurring via an oxyanion intermediate; and (iii) the identities of the proton acceptors at the beginning and end of the reaction. Overall, we note that there is considerable plasticity in the mechanisms, owing to the significant flexibility of the enzyme, but find that the preferred pathways are ones in which nucleophilic attack of cysteine thiolate is concerted with ß-lactam ring-opening.