Monomeric Model Research Articles

Sustainable design and synthesis of high-performance lignin-based sunscreen ingredients

The active ingredients most commonly employed in sunscreens are compounds containing one or two aromatic rings. Lignin is the most abundant renewable aromatic polymer that has the potential to yield low molecular weight aromatic chemicals when strategically depolymerized. Here, the UV absorbance of a series of monomeric and dimeric lignin model compounds (LMCs) were studied. Specifically, vanillin and ferulic acid demonstrated good absorption in the UVB (280–320 nm) range, while the 5–5 dimer showed efficient absorption in the UVA (320–400 nm) range. Based on this, vanillin, ferulic acid and 5–5 dimer were mixed in pairs and dispersed in the oily isoeugenol to prepare LMC hybrid dispersions. Subsequently, demethylated lignin (DL) was synthesized and used to encapsulate the LMC hybrid dispersions via ultrasonic cavitation to prepare DL-based nano-capsules (DLNCs). The DLNCs were used as the only active ingredient in sunscreens, whose sun protection factor (SPF) value could be up to 55 with a dosage of 10 wt%. Due to anti-photolysis property of DL, the SPF value of DLNCs-based sunscreens increased initially and maintained >8 h under UV irradiation. Additionally, the prepared DLNCs exhibited excellent anti-permeability, antioxidant capacity and biocompatibility, making them a potential substitute for conventional petroleum-based sunscreen agents.

Incorporating Noncovalent Interactions in Transfer Learning Gaussian Process Regression Models for Molecular Simulations.

FFLUX is a quantum chemical topology-based multipolar force field that uses Gaussian process regression machine learning models to predict atomic energies and multipole moments on the fly for fast and accurate molecular dynamics simulations. These models have previously been trained on monomers, meaning that many-body effects, for example, intermolecular charge transfer, are missed in simulations. Moreover, dispersion and repulsion have been modeled using Lennard-Jones potentials, necessitating careful parametrization. In this work, we take an important step toward addressing these shortcomings and show that models trained on clusters, in this case, a dimer, can be used in FFLUX simulations by preparing and benchmarking a formamide dimer model. To mitigate the computational costs associated with training higher-dimensional models, we rely on the transfer of hyperparameters from a smaller source model to a larger target model, enabling an order of magnitude faster training than with a direct learning approach. The dimer model allows for simulations that account for two-body effects, including intermolecular polarization and charge penetration, and that do not require nonbonded potentials. We show that addressing these limitations allows for simulations that are closer to quantum mechanics than previously possible with the monomeric models.

#1838 SGLT2 computational structural studies investigating polypharmacy

Abstract Background and Aims Sodium Glucose Cotransporter 2 (SGLT2) is the main active transport protein involved in sodium and glucose reabsorption in the kidney. SGLT2 inhibitors (SGLT2i) are widely recommended for patients with diabetes, heart failure and chronic kidney disease (CKD). Many multimorbid patients will be prescribed these compounds resulting in polypharmacy. We have performed a computational drug repurposing screen to identify other licensed drugs capable of binding at or near the SGLT2i active site aiming to identify compounds that could either compete with SGLT2i or inhibit sodium and glucose transport. Method The library of BNF listed compounds was obtained from NCBI PubChem. D-I-TASSER was used to generate monomeric structural models and MODELLER was used to incorporate MAP-17 and empaglifozin from a reference structure (PDB 7VSI). CHARM-GUI was used to insert the protein into a membrane. The centroid of a 5 nanosecond GROMACS molecular dynamics (MD) equilibration was used for docking studies using PLANTS. A bespoke tool was used to identify compounds interacting with key protein residues. CHARM-GUI and bespoke software were used to prepare membrane-bound systems to run in GROMACS using GPU's in Google Colab. 10 nanosecond simulations were undertaken (300 Kelvin and 1 bar) to discriminate between binding and non-binding events. Results The SGLT2-MAP17 structure in the inward-open conformation obtained showed good agreement with published structures. Existing SGLT2i (empaglifozin, dapaglifozin, canaglifozin, ertuglifozin) all feature in the top 1% of docked compounds in the repurposing screen. 17 compounds were investigated by MD, with all remaining bound to the protein in simulation. Ceftriaxone, tobramycin, clindamycin, fluvastatin, atorvastatin and ticagrelor were among the compounds with potentially significant interactions. It is not clear whether the stable ligand interactions identified here would result in inhibition of sodium and glucose transport, or if the interactions might provide competitive inhibition for SGLT2i compounds currently used. The compounds identified have no hitherto recognised interactions with SGLT2i; nor do they result in adverse effects suggesting inhibition of the protein. This study is limited by considering only the protein-ligand interaction and not wider pharmacokinetic or pharmacodynamic factors. Conclusion The indication of interactions with several compounds likely to be prescribed alongside SGLT2 inhibitors, such as antibiotics, statins and antiplatelet agents, warrants further investigation of the potential for polypharmacological complications.

The white rot basidiomycete Gelatoporia subvermispora produces fatty aldehydes that enable fungal manganese peroxidases to degrade recalcitrant lignin structures.

The ability of some white rot basidiomycetes to remove lignin selectively from wood indicates that low molecular weight oxidants have a role in ligninolysis. These oxidants are likely free radicals generated by fungal peroxidases from compounds in the biodegrading wood. Past work supports a role for manganese peroxidases (MnPs) in the production of ligninolytic oxidants from fungal membrane lipids. However, the fatty acid alkylperoxyl radicals initially formed during this process are not reactive enough to attack the major structures in lignin. Here, we evaluate the hypothesis that the peroxidation of fatty aldehydes might provide a source of more reactive acylperoxyl radicals. We found that Gelatoporia subvermispora produced trans-2-nonenal, trans-2-octenal, and n-hexanal (a likely metabolite of trans-2,4-decadienal) during the incipient decay of aspen wood. Fungal fatty aldehydes supported the in vitro oxidation by MnPs of a nonphenolic lignin model dimer, and also of the monomeric model veratryl alcohol. Experiments with the latter compound showed that the reactions were partially inhibited by oxalate, the chelator that white rot fungi employ to detach Mn3+ from the MnP active site, but nevertheless proceeded at its physiological concentration of 1 mM. The addition of catalase was inhibitory, which suggests that the standard MnP catalytic cycle is involved in the oxidation of aldehydes. MnP oxidized trans-2-nonenal quantitatively to trans-2-nonenoic acid with the consumption of one O2 equivalent. The data suggest that when Mn3+ remains associated with MnP, it can oxidize aldehydes to their acyl radicals, and the latter subsequently add O2 to become ligninolytic acylperoxyl radicals.IMPORTANCEThe biodegradation of lignin by white rot fungi is essential for the natural recycling of plant biomass and has useful applications in lignocellulose bioprocessing. Although fungal peroxidases have a key role in ligninolysis, past work indicates that biodegradation is initiated by smaller, as yet unidentified oxidants that can infiltrate the substrate. Here, we present evidence that the peroxidase-catalyzed oxidation of naturally occurring fungal aldehydes may provide a source of ligninolytic free radical oxidants.

Enhancing Fluorescence in Both Solution and Solid States Induced by Imine Cage Formation.

Developing luminescent materials that exhibit strong emissions in both solution and solid phases is highly desirable and challenging. Herein, we report imine-bond directed formation of a rigid organic cage (TPE-cage) that was synthesized by [2+4] imine condensation of a TPE-cored tetra-aldehyde (TPE-TA) with a clip-like diamine (XA) to illustrate confinement-induced fluorescence enhancement. Compared to the non-emissive TPE-TA (ϕF =0.26 %) in the dichloromethane (DCM) solution, the TPE-cage achieved a remarkable (~520-fold) emission enhancement (ϕF =70.38 %). In contrast, a monomeric tetra-imine model compound (TPE-model) showed only a minor enhancement (ϕF =0.56 %) in emission compared to the parent tetra-aldehyde TPE-TA. The emission of TPE-cage was further enhanced by ~1.5-fold (ϕF =80.96 %) in the aggregated state owing to aggregation-induced emission enhancement (AIEE). This approach establishes the potential for synthesizing luminescent materials with high emission in both solution and solid-state by employing a single-step imine condensation reaction.

Stochastic nucleosome disassembly mediated by remodelers and histone fragmentation.

We construct and analyze monomeric and multimeric models of the stochastic disassembly of a single nucleosome. Our monomeric model predicts the time needed for a number of histone-DNA contacts to spontaneously break, leading to dissociation of a non-fragmented histone from DNA. The dissociation process can be facilitated by DNA binding proteins or processing molecular motors that compete with histones for histone-DNA contact sites. Eigenvalue analysis of the corresponding master equation allows us to evaluate histone detachment times under both spontaneous detachment and protein-facilitated processes. We find that competitive DNA binding of remodeling proteins can significantly reduce the typical detachment time but only if these remodelers have DNA-binding affinities comparable to those of histone-DNA contact sites. In the presence of processive motors, the histone detachment rate is shown to be proportional to the product of the histone single-bond dissociation constant and the speed of motor protein procession. Our simple intact-histone model is then extended to allow for multimeric nucleosome kinetics that reveal additional pathways of disassembly. In addition to a dependence of complete disassembly times on subunit-DNA contact energies, we show how histone subunit concentrations in bulk solutions can mediate the disassembly process by rescuing partially disassembled nucleosomes. Moreover, our kinetic model predicts that remodeler binding can also bias certain pathways of nucleosome disassembly, with higher remodeler binding rates favoring intact-histone detachment.

Crystal structure simulation of cationic cholesteric Liquid-Crystal polyesters. Non-Viral vectors

The crystal structure of six cationic cholesteric liquid crystal polyesters with choline, ammonium, and amide end groups are reported: PTOBEE-Choline [(C26H20O8)n-C5H13N]; PTOBDME-Choline [(C34H36O8)n-C5H13N]; PTOBEE-Ammonium [(C26H20O8)n-C5H13N]; PTOBDME-Ammonium [(C34H36O8)n-C5H13N]; PTOBEE-Amide (C26H19O9N)n and PTOBUME-Amide (C33H33O9N)n, have demonstrated non-viral vector properties in gene therapy by delivering DNA to the cell nucleus. They were synthesized by functionalization of precursor racemic polyesters via a condensation reaction between 4,4′-(terephthaloyl-di-oxydibenzoic chloride) (TOBC) and the racemic mixture of glycol (R-S-1,2-butanediol) or (R-S-1,2-dodecanediol), respectively. The resulting helical macromolecular structures exhibit unexpected optical activity and chiral morphology, previously attributed to the kinetic resolution of one preferable helical conformer of the possible four observed by NMR. Conformational analysis and energy minimization are performed on the four helical conformer monomeric models which are then polymerized to obtain helical chains. Three levels of chirality were observed in these polymer structures. Crystal models are built in triclinic primitive P1cells, with their molecular chains oriented parallel to the Z-axis (c lattice parameter equal to the helical pitch length), the cell parameters are obtained by performing geometry optimization tasks. A raw estimation of the relative weight of the four possible helical conformers on each synthetic cationic polymer has been performed on ideal mixtures considering their approximate known crystal structure with their experimental X-ray powder diffraction by Powder Quantitative Phase Analysis. The results would confirm the theory of the preferable recrystallization of a diastereoisomer, among the four possible, during the synthetic procedures. These findings shed light on the observed optical activity and provide insights into the crystal structure of these cationic polymers. The morphology of the cationic polymers is studied by ESEM in wet samples and crystals after drying the solvent.

Construction Method for a Three-Dimensional Tunnel General Monomer Model Based on Parallel Pathfinding

Existing approaches for the 3D modeling of tunnels suffer from several problems, such as highly difficult data acquisition, redundancy of model data, large computational burden, and the inability of the resulting models to be monolithic. Therefore, solutions to the tunnel network modeling problem for complex structures need to be proposed and elaborated in detail. In this paper, a construction method for a three-dimensional tunnel general monomer model based on parallel pathfinding is proposed. Widely used tunnel CAD drawings are analyzed and read, a disordered arc ensemble intersection trend decision method is developed, and an automatic path extraction solution algorithm for unidirectional modeling of tunnel centerlines is constructed. By constructing and splicing the surface elements of the 3D model, a monomeric 3D tunnel model representing the complex network structure is finally obtained. Moreover, the modeling of shafts is realized based on the monomer model, allowing for the three-dimensional topological relationships between different sub-levels of the tunnel and the ground to be established. The automatic modeling method proposed in this paper is applied to the digital twin platform of a filling project in a mining area in Gansu province, China. The experimental results demonstrate that the 3D tunnel models constructed in this way have a smaller data volume, higher modeling accuracy, and more stable growth of modeling speed.

Blind assessment of monomeric AlphaFold2 protein structure models with experimental NMR data

Recent advances in molecular modeling of protein structures are changing the field of structural biology. AlphaFold-2 (AF2), an AI system developed by DeepMind, Inc., utilizes attention-based deep learning to predict models of protein structures with high accuracy relative to structures determined by X-ray crystallography and cryo-electron microscopy (cryoEM). Comparing AF2 models to structures determined using solution NMR data, both high similarities and distinct differences have been observed. Since AF2 was trained on X-ray crystal and cryoEM structures, we assessed how accurately AF2 can model small, monomeric, solution protein NMR structures which (i) were not used in the AF2 training data set, and (ii) did not have homologous structures in the Protein Data Bank at the time of AF2 training. We identified nine open-source protein NMR data sets for such “blind” targets, including chemical shift, raw NMR FID data, NOESY peak lists, and (for 1 case) 15N-1H residual dipolar coupling data. For these nine small (70–108 residues) monomeric proteins, we generated AF2 prediction models and assessed how well these models fit to these experimental NMR data, using several well-established NMR structure validation tools. In most of these cases, the AF2 models fit the NMR data nearly as well, or sometimes better than, the corresponding NMR structure models previously deposited in the Protein Data Bank. These results provide benchmark NMR data for assessing new NMR data analysis and protein structure prediction methods. They also document the potential for using AF2 as a guiding tool in protein NMR data analysis, and more generally for hypothesis generation in structural biology research.

Molecular Structure, Hydrogen Bonding Interactions and Docking Simulations of Nicotinamide (Monomeric and Trimeric Models) by Using Spectroscopy and Theoretical Approach

The present work focuses on the structural properties, spectroscopic signatures, intermolecular hydrogen bonding interactions, chemical and biological activity of nicotinamide (NIC) based on its monomeric and trimeric models using density functional theory and vibrational spectroscopy. FT-IR and FT-Raman spectra were obtained using the double-side forward-backward acquisition mode under vacuum. UV-Vis absorption spectra were recorded in methanol and compared with the calculated values. Geometry optimization and vibrational wavenumbers were obtained with the aid of Gaussian 09 program packages. The structural analysis of NIC revealed that the trimeric model was in better agreement with the experimental values than the monomer due to the incorporation of nearest hydrogen bond interactions. Spectroscopic results showed that NH2 and C = O groups of NIC were involved in intermolecular interactions in the trimeric model. The natural bond orbital (NBO) and quantum theory of atoms in molecules (QTAIM) analyses determined the presence, strength as well as nature of the hydrogen bonds were partially covalent. The lesser value of the HOMO-LUMO energy gap for the trimeric model indicated higher reactivity than monomer. Moreover, chemical reactivity was calculated using molecular electrostatic potential surface (MESP) and reactivity descriptors. The docking studies for NIC with several targets explored its biological activity.

Heterologous Expression and Structural Elucidation of a Highly Thermostable Alkaline Serine Protease from Haloalkaliphilic Actinobacterium, Nocardiopsis sp. Mit-7.

A highly thermostable alkaline serine protease gene (SPSPro, MN429015) obtained from haloalkaliphilic actinobacteria, Nocardiopsis sp. Mit-7 (NCIM-5746), was successfully cloned and overexpressed in Escherichia coli BL21 under the control of the T7 promoter in the pET Blue1 vector leading to a 20-kDa gene product. The molecular weight of the recombinant alkaline protease, as determined by SDS-PAGE and the Mass Spectrometer (MALDI-TOF), was 34kDa. The structural and functional attributes of the recombinant thermostable alkaline serine protease were analyzed by Bioinformatic tools. 3D Monomeric Model and Molecular Docking established the role of the amino acid residues, aspartate, serine, and tryptophan, in the active site of thealkaline protease.The activity of the recombinant alkaline protease was optimal at 65°C, 5°C higher than its native protease. The recombinant protease was also active over a wide range of pH 7.0-13.0, with a maximal activity of 6050.47 U/mg at pH 9. Furthermore, the thermodynamic parameters of the immobilized recombinant alkaline protease suggested its reduced vulnerability against adverse conditions under which the enzyme has to undergo varied applications.

Improvement of protein tertiary and quaternary structure predictions using the ReFOLD refinement method and the AlphaFold2 recycling process.

The accuracy gap between predicted and experimental structures has been significantly reduced following the development of AlphaFold2 (AF2). However, for many targets, AF2 models still have room for improvement. In previous CASP experiments, highly computationally intensive MD simulation-based methods have been widely used to improve the accuracy of single 3D models. Here, our ReFOLD pipeline was adapted to refine AF2 predictions while maintaining high model accuracy at a modest computational cost. Furthermore, the AF2 recycling process was utilized to improve 3D models by using them as custom template inputs for tertiary and quaternary structure predictions. According to the Molprobity score, 94% of the generated 3D models by ReFOLD were improved. AF2 recycling showed an improvement rate of 87.5% (using MSAs) and 81.25% (using single sequences) for monomeric AF2 models and 100% (MSA) and 97.8% (single sequence) for monomeric non-AF2 models, as measured by the average change in lDDT. By the same measure, the recycling of multimeric models showed an improvement rate of as much as 80% for AF2-Multimer (AF2M) models and 94% for non-AF2M models. Refinement using AlphaFold2-Multimer recycling is available as part of the MultiFOLD docker package (https://hub.docker.com/r/mcguffin/multifold). The ReFOLD server is available at https://www.reading.ac.uk/bioinf/ReFOLD/ and the modified scripts can be downloaded from https://www.reading.ac.uk/bioinf/downloads/. Supplementary data are available at Bioinformatics Advances online.

Photoluminescent supramolecular gels derived from phenylenediamine hydrochlorides.

Supramolecular gels are promising as chemosensors, drug delivery systems and oil gelators. The present paper deals with photoluminescent supramolecular gels derived from phenylenediamine hydrochlorides. N-(3,5-Diaminobenzoyl)-L-alanine dodecyl ester dihydrochlorides (1L) underwent gelation in tetrahydrofuran (THF) and CHCl3, but not in C1-C4 alcohols, dimethyl sulfoxide (DMSO) and N,N-dimethylformamide (DMF). Compound 1L emitted blue fluorescence in the sol state and green fluorescence in the gel state. A THF solution of 1L exhibited absorption and emission maxima at wavelengths 94-104 nm and 92-110 nm longer than those in other solvents, such as methanol and ethanol, that cause no gelation of 1L. Particles with hydrodynamic diameters around 13 nm were detected in a THF solution (c = 1.0 mM) of 1L. The gelation of 1L in THF and CHCl3, and the lack of gelation in MeOH were supported by molecular dynamics simulations and dynamic light scattering measurements. N-(3,5-Diaminobenzoyl)-L-alanine dodecyl ester (1L'), an HCl-free analogous compound of 1L, underwent no gelation in THF and CHCl3, indicating the necessity of the ammonium salt structure for gelation. The UV-vis absorption and photoluminescence spectroscopic peaks of 1L red-shifted upon aggregation, which was supported by TD-DFT calculations of monomeric and dimeric models of 1L.

Conformational characteristics of poly(3-hydroxyvalerate) (P3HV) and structure-property relationships of P3HV and poly(3-hydroxybutyrate).

Conformational analysis of biosynthetic and biodegradable poly(3-hydroxyvalerate) (P3HV), an analog of poly(3-hydroxybutyrate) (P3HB), was performed. The only structural difference between the two polymers consists in the side chain, which is either methyl (P3HB) or ethyl (P3HV). Molecular orbital calculations and NMR experiments were conducted on a monomeric model compound to determine the bond conformations of the main and side chains of P3HV. The refined rotational isomeric state (RIS) scheme was applied to derive configurational properties of P3HV. The characteristic ratio of P3HV (2.1-3.0) is smaller than that of P3HB (5.4-5.6), indicating greater conformational flexibility of the P3HV chain. The increased flexibility due to the internal rotation of the ethyl side group of P3HV results in a lower equilibrium melting point (130 °C) compared with P3HB (203 °C). The RIS calculations on P3HV also suggested its potential for rubber-like properties. Periodic density functional theory calculations were used to optimize the crystal structures of P3HB and P3HV and obtain their elastic moduli. Three-dimensional Young's modulus distributions of both crystals are closer to isotropic than anisotropic. In conclusion, the material design and usage of poly(3-hydroxybutyrate-co-3-hydroxyvalerate) are discussed.

DFT Study on the Adsorption of Monomeric Hydroxyl Aluminum on Fe(II)/Mg Replacement Kaolinite (001) Surfaces.

In the natural environment, Al and Si in the kaolinite crystal structure are likely to form lattice defects or be replaced by low-valence positive ions so that the base surfaces have permanent negatively charged sites. It is therefore very important to investigate the adsorption process and adsorption mechanism of adsorbates on the replaced surfaces. In this paper, two types of surface models formed by replacing Al atoms in the alumina octahedron of kaolinite (001) surface with Fe(II) and Mg were selected as the adsorption surfaces, these being the kaolinite Fe(II)Al-(001) and MgAl-(001) surfaces, respectively. Then, we used density functional theory (DFT) to simulate the adsorption of three monomeric hydroxy aluminum models (i.e., Al(OH)2 +, Al(OH)3, and Al(OH)4 -) on the two replaced surfaces. Results show that, when compared to the adsorption on the ideal kaolinite (001) surface, the adsorption energies of the three adsorbates adsorbed on the replaced surfaces are lower and the adsorption is more stable. When the three adsorbates are adsorbed on the kaolinite Fe(II)Al-(001) surface, adsorption stability increases with the number of hydroxyl groups, and hydrogen bonding and electrostatic adsorption play a major role. Conversely, when they were adsorbed on the kaolinite MgAl-(001) surface, the stability of the adsorption deteriorated as the number of hydroxyl groups increased. Moreover, the decisive roles are the interaction between the aluminum atoms in the adsorbates and the oxygen atoms on the replaced surface and the electrostatic adsorption.

Spectroscopic and quantum chemical investigations to explore the effect of intermolecular interactions in a diuretic drug: Hydrochlorothiazide

Hydrochlorothiazide (HCTZ) being a diuretic drug widely used in anti-hypertensive therapy as it lowers the blood pressure by reducing the reabsorption of electrolytes in kidney resulting an increment of urine output and lowering the blood pressure. The purpose of the present work is to study the structural, vibrational and chemical properties of HCTZ based on its monomeric, dimeric and trimeric models by utilizing computational methods and experimental techniques. Density functional theory (DFT) with functional B3LYP and 6-311++G (d, p) basis set was used for a detailed computational study. Monomeric, dimeric and trimeric models of HCTZ have been studied for a better understanding of inter- and intramolecular hydrogen bonding. FT-IR (400–3800 cm−1) and FT-Raman (100–3600 cm−1) spectroscopy have been utilized for the characterization of HCTZ. The shifting in wavenumber of NH2 and OSO group were observed in dimer and trimer due to the formation of intermolecular hydrogen bonding. Quantum theory of atoms in molecules (QTAIM) along with natural bond orbital (NBO) analysis were performed to examine the nature and strength of hydrogen bonding which showed that all the interactions were medium and partially covalent in nature; transition from LP(3)O15 → σ*(H46 → N32) and LP(3)O39 → σ*(H74 → N51) were responsible for the formation of O15•••H46 and O39•••H74 H-bonds, respectively. HOMO-LUMO energies predicted the chemical reactivity and stability of the molecule and the energy gap for dimer (4.6240 eV) and trimer (4.0493 eV) was found to be lesser than the monomer (5.0888 eV) which showed that the dimer and trimer have predicted more chemical reactivity in comparison to monomer. The most electronegative electrostatic potential was observed around the OSO group and the most electropositive potential around the amide group from MEPS analysis. Global as well as local reactivity descriptors have predicted the reactivity and hence, stability of the title molecule.

Rethinking the MtInhA tertiary and quaternary structure flexibility: a molecular dynamics view.

Flexibility and function are related properties in the study of protein dynamics. Flexibility reflects in the conformational potential of proteins and thus in their functionalities. The presence of interactions between protein-ligands and protein-protein complexes, substrates, and environmental changes can alter protein plasticity, acting from the rearrangement of the side chains of amino acids to the folding/unfolding of large structural motifs. To evaluate the effects of the flexibility in protein systems, we defined the enzyme 2-trans-enoyl-ACP (CoA) reductase from Mycobacterium tuberculosis, or MtInhA, as our target system. MtInhA is biologically active as a tetramer in solution; however, computational studies commonly use the monomer justifying the independence of its active sites due to their distances. However, differences in flexibility between tertiary and quaternary structures could present impact on the size of the active site, influencing the drug discovery process. In this study, we investigated the influence of flexibility restrictions in A- and B-loops of the MtInhA in order to suggest a monomeric structure that describes the conformational behavior of the tetrameric system. Overall, we observed that simulations where restrictions were applied to the A- and B-loops present a more similar behavior to the native structure when compared to unrestricted simulations. Therefore, our work presents a monomeric model of MtInhA, which has conformational characteristics of the biologically active structure. Thus, the data obtained in this work can be applied to the MtInhA system for the generation of more reliable flexible models for molecular docking experiments, and also for the performance of longer simulations by molecular dynamics and with a lower computational cost.

Implementation of Water-Soluble Cyclodextrin-Based Polymers in Biomedical Applications: How Far Are We?

Cyclodextrin-based polymers can be prepared starting from the naturally occurring monomers following green and low-cost procedures. They can be selectively derivatized pre- or post-polymerization allowing to fine-tune functionalities of ad hoc customized polymers. Preparation nowadays has reached the 100g scale thanks also to the interest of industries in these extremely versatile compounds. During the last 15 years, these macromolecules have been the object of intense investigations in view of possible biomedical applications as the ultimate goal and large amounts of scientific data are now available. Compared to their monomeric models, already used in the formulation of various therapeutic agents, they display superior behavior in terms of their solubility in water and solubilizing power toward drugs incompatible with biological fluids. Moreover, they allow the combination of more than one type of therapeutic agent in the polymeric system. In this review, a complete state of the art on the knowledge and potentialities of water-soluble cyclodextrin-based polymers as therapeutic agents as well as carrier systems for different types of therapeutics to implement combination therapy is provided. Finally, a perspective on their assets for innovation in disease treatment as well as their limits that still need to be addressed is given.

Thermodynamic and biophysical study of fatty acid effector binding to soybean lipoxygenase: implications for allostery driven by helix α2 dynamics.

Previous comparative kinetic isotope effects have inferred an allosteric site for fatty acids and their derivatives that modulates substrate selectivity in 15-lipoxygenases. Hydrogen-deuterium exchange also previously revealed regionally defined enhanced protein flexibility, centred at helix α2 - a gate to the substrate entrance. Direct evidence for allosteric binding and a complete understanding of its mechanism remains elusive. In this study, we examine the binding thermodynamics of the fatty acid mimic, oleyl sulfate (OS), with the monomeric model plant 15-LOX, soybean lipoxygenase (SLO), using isothermal titration calorimetry. Dynamic light scattering and differential scanning calorimetry rule out OS-induced oligomerization or structural changes. These data provide evidence that the fatty acid allosteric regulation of SLO is controlled by the dynamics of helix α2.

Effects of residual phenolic compounds on xylanase-assisted ClO2 bleaching of hardwood kraft pulp

In both pulping and bleaching processes, lignin in the pulp fiber is degraded into smaller molecules that need to be rinsed away. However, despite the installation of automatic washing equipment, the small phenolic compounds among other lignin degradation products can hardly be completely removed from the brownstock. Among the myriad of small phenolic compounds degrading from lignin, some are water-soluble and highly reactive with bleaching reagents. To understand the impact of residual phenolic compounds from black liquor on pulp bleaching, six monomeric phenolic model compounds were tested in this study. Catechol and vanillin showed inhibitory effects on xylanase activity, while catechol, vanillin, and guaiacol interfered with the delignification reaction in the chlorine dioxide (D) and alkaline extraction (E) stages of the bleaching sequence, thereby preserving the integrity of cellulose in the pulp. Because the efficiency of xylanase and bleaching reagents is hindered by the presence of these phenolic compounds, higher operational cost and more bleaching reagents are needed, which are incompatible with modern environmental policies in the world. Nonetheless, the presence of remaining soluble phenolic compounds in the brownstock can improve the bleaching selectivity important for the production of high-quality pulp with less-degraded cellulose chains.