Novel glutathione analogues containing the dithiol and disulfide form of the Cys-Cys dyad

Summary The glutathione analogue -(H-Glu-OH)--OH (5), containing the 8-membered disulfide ring- replacing the native -Cys-Gly fragment, has been synthesized and characterized together with its reduced dithiol form -(H-Glu-OH)-Cys-Cys-OH (6).Abbreviations DBU 1,8-diazabicyclo [5.4.0] undec-7-ene; - DCCI N,N-dicyclohexylcarbodiimide - NMM N-methylmorpholine - THF tetrahydrofuran; (n-Bu)₃P, tri-n-butylphosphine     

Diverse strategies adopted by nature for regulating purine biosynthesis via fine-tuning of purine metabolic enzymes

Purine nucleotides, generated by de novo synthesis and salvage pathways, are essential for metabolism and act as building blocks of genetic material. To avoid an imbalance in the nucleotide pool, nature has devised several strategies to regulate/tune the catalytic performance of key purine metabolic enzymes. Here, we discuss some recent examples, such as stress-regulating alarmones that bind to select pathway enzymes, huge ensembles like dynamic metabolons and self-assembled filaments that highlight the layered fine-control prevalent in the purine metabolic pathway to fulfill requisite purine demands. Examples of enzymes that turn-on only under allosteric control, are regulated via long-distance communication that facilitates transient conduits have additionally been explored.     

Mopane (Colophospermum mopane): A potential winner under climate change in southern Africa

Distribution and abundance under climate change of particularly non-timber forest product tree species is vital since they sustain many livelihoods, especially in rural sub-Saharan Africa. The aim of the study was to determine the current and future natural range of mopane (Colophospermum mopane (J. Kirk ex Benth.) J. Léonard, Fabaceae), a dominant tree species in mopane woodlands of southern Africa. An ensemble model was built in ‘biomod2’ from eight algorithms and used to estimate the current and future distribution. Seven bioclimatic variables and 269 occurrence records were used to calibrate individual models that were later combined into an ensemble model. The ensemble model was projected to two time periods, 2041–2060 and 2081–2100, under two shared socio-economic pathways (SSPs), SSP2-4.5 and SSP5-8.5, and three general circulation models (GCMs). The ensemble model showed high performance (KAPPA = 0.770, ROC = 0.961, TSS = 0.792, ACCURACY = 0.900). A map of the current distribution shows occurrence predominantly in low-lying areas, including the Zambezi, Save and Limpopo valleys, Okavango and Cuvelai basins, and in southern and central Mozambique. Projection maps show expansion under all SSPs, GCMs and time periods. Averaged across GCMs in 2041–2060, the range expanded by 22.37% under SSP2-4.5, and by 19.94% under SSP5-8.5. In 2081–2100, the range expanded by 20.43% under SSP2-4.5, and by 27.62% under SSP5-8.5. Notably, the range expansion was highest under SSP5-8.5, an SSP that envisages unmitigated greenhouse gas release and the largest mean global temperature increase. It is highly likely that mopane is not directly threatened by climate change. Indirect climate change threats, however, remain uncertain.     

Dynamic mechanism of proton transfer in mannitol 2-dehydrogenase from Pseudomonas fluorescens: mobile GLU292 controls proton relay through a water channel that connects the active site with bulk solvent

The active site of mannitol 2-dehydrogenase from Pseudomonas fluorescens (PfM2DH) is connected with bulk solvent through a narrow protein channel that shows structural resemblance to proton channels utilized by redox-driven proton pumps. A key element of the PfM2DH channel is the "mobile" Glu(292), which was seen crystallographically to adopt distinct positions up and down the channel. It was suggested that the "down → up" conformational change of Glu(292) could play a proton relay function in enzymatic catalysis, through direct proton shuttling by the Glu or because the channel is opened for water molecules forming a chain along which the protons flow. We report evidence from site-directed mutagenesis (Glu(292) → Ala) substantiated by data from molecular dynamics simulations that support a role for Glu(292) as a gate in a water chain (von Grotthuss-type) mechanism of proton translocation. Occupancy of the up and down position of Glu(292) is influenced by the bonding and charge state of the catalytic acid base Lys(295), suggesting that channel opening/closing motions of the Glu are synchronized to the reaction progress. Removal of gatekeeper control in the E292A mutant resulted in a selective, up to 120-fold slowing down of microscopic steps immediately preceding catalytic oxidation of mannitol, consistent with the notion that formation of the productive enzyme-NAD(+)-mannitol complex is promoted by a corresponding position change of Glu(292), which at physiological pH is associated with obligatory deprotonation of Lys(295) to solvent. These results underscore the important role of conformational dynamics in the proton transfer steps of alcohol dehydrogenase catalysis.     

Biological and physicochemical evaluation of the conformational stability of tumor necrosis factor-related apoptosis-inducing ligand (TRAIL)

Tumor necrosis factor (TNF)-related, apoptosis-inducing ligand (Apo2L/TRAIL) has a unique homotrimeric structure, and its conformational stability is essential for its apoptotic activity. The conformational stability of a modified version of TRAIL(114–281) with two additional domains of histidine tag and isoleucine zipper [His-ILZ-TRAIL(114–281)] was evaluated in various pH environments according to three different biological or physicochemical considerations: cytotoxicity, antibody-binding affinity, and tertiary structure. The biological properties of His-ILZ-TRAIL(114–281) were the most stably maintained at pH 6.0. The physicochemical analyses (circular dichroism and fluorescence spectroscopy) demonstrate that its bioactivity loss by pH challenge was originated from its structural collapse as a homotrimer.     

A Neural Basis for Categorizing Sensory Stimuli to Enhance Decision Accuracy

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Metal and substrate binding to an Fe(II) dioxygenase resolved by UV spectroscopy with global regression analysis

The addition of divalent metal ions or substrate taurine to TauD, an α-ketoglutarate-dependent dioxygenase, alters its UV absorption, as clearly observed by monitoring the protein’s difference spectra. Binding of metal ions leads to a decrease in absorption at ∼297 nm and modulation of other features. A separate signature with enhanced absorption at ∼295 nm is identified for binding of taurine. These narrow (∼700 cm⁻¹) and intense (∼0.5 mM⁻¹ cm⁻¹) spectral changes are attributed to ligand-induced protein conformational changes affecting the environment of aromatic residues. The changes in the UV difference spectra were exploited to assess directly the thermodynamics and kinetics of ligand interactions in wild-type TauD and selected variants. This approach holds promise as a new tool to probe ligand-induced conformational changes in a wide range of other proteins. Experimental and quantification approaches for a reliable analysis of protein absorption below 320 nm are presented.     

Analysis of binding modes of ligands to multiple conformations of CYP3A4

Cytochromes P450 (CYPs) are extremely versatile enzymes capable of catalyzing a vast number of compounds, and CYP3A4 is no exception metabolizing approximately half of the currently marketed drugs, besides endogenous compounds. To metabolize such a variety of compounds, CYP3A4 has to be extremely flexible, which makes interaction studies difficult. We employ a multi-conformational docking setup where conformations are generated by several molecular dynamics simulations to analyze the binding modes of various ligands, and the docking is considered successful if the ligand site of catalysis (SOC) is within 6.0 Å of the haem Fe. While docking with the X-ray structure proved unsuccessful with all ligands, the multi-conformational docking achieved successful binding of each ligand to at least one protein conformation. Analysis of the docked solutions highlights residues in the active site cavity that may have an important role in access, binding and stabilization of the ligand.     

EDock‐ML: A web server for using ensemble docking with machine learning to aid drug discovery

EDock‐ML is a web server that facilitates the use of ensemble docking with machine learning to help decide whether a compound is worthwhile to be considered further in a drug discovery process. Ensemble docking provides an economical way to account for receptor flexibility in molecular docking. Machine learning improves the use of the resulting docking scores to evaluate whether a compound is likely to be useful. EDock‐ML takes a bottom‐up approach in which machine‐learning models are developed one protein at a time to improve predictions for the proteins included in its database. Because the machine‐learning models are intended to be used without changing the docking and model parameters with which the models were trained, novice users can use it directly without worrying about what parameters to choose. A user simply submits a compound specified by an ID from the ZINC database (Sterling, T.; Irwin, J. J., J Chem Inf Model 2015, 55[11], 2,324–2,337.) or upload a file prepared by a chemical drawing program and receives an output helping the user decide the likelihood of the compound to be active or inactive for a drug target. EDock‐ML can be accessed freely at edock‐ml.umsl.edu     

A Modified Gibbs Ensemble Method for Calculating Fluid Phase Equilibria

Abstract

A modification of the Gibbs ensemble Monte Carlo computer simulation method for fluid phase equilibrium is described. The modification, which is based on the assumption of a thermodynamic model for the vapor phase, reduces the computational time for the simulation as compared to the original Gibbs ensemble methods. Since the computational time is largely proportional to the number of particle-particle interactions, avoiding the direct simulation of the vapor phase typically leads to a thirty to forty percent reduction in computational time. For a pure Leonard-Jones-(12,6) fluid the results obtained at moderate reduced temperatures, T/T_c < 0.8, are in good agreement with the full Gibbs ensemble method.