Molecular Mechanics Energy Research Articles

A rotamer library to enable modeling and design of peptoid foldamers.

Peptoids are a family of synthetic oligomers composed of N-substituted glycine units. Along with other “foldamer” systems, peptoid oligomer sequences can be predictably designed to form a variety of stable secondary structures. It is not yet evident if foldamer design can be extended to reliably create tertiary structure features that mimic more complex biomolecular folds and functions. Computational modeling and prediction of peptoid conformations will likely play a critical role in enabling complex biomimetic designs. We introduce a computational approach to provide accurate conformational and energetic parameters for peptoid side chains needed for successful modeling and design. We find that peptoids can be described by a “rotamer” treatment, similar to that established for proteins, in which the peptoid side chains display rotational isomerism to populate discrete regions of the conformational landscape. Because of the insufficient number of solved peptoid structures, we have calculated the relative energies of side-chain conformational states to provide a backbone-dependent (BBD) rotamer library for a set of 54 different peptoid side chains. We evaluated two rotamer library development methods that employ quantum mechanics (QM) and/or molecular mechanics (MM) energy calculations to identify side-chain rotamers. We show by comparison to experimental peptoid structures that both methods provide an accurate prediction of peptoid side chain placements in folded peptoid oligomers and at protein interfaces. We have incorporated our peptoid rotamer libraries into ROSETTA, a molecular design package previously validated in the context of protein design and structure prediction.

Note: charge transfer in a hydrated peptide group is determined mainly by its intrinsic hydrogen-bond energetics.

Charge transfer in a hydrogen-bonded N-methylacetamide(H2O)3 system is obtained from ωB97X-D/6-31++G** and CHelpG atomic charge calculations of individual peptide-water interactions as well as that of the entire complex. In the latter, the electron transfer to water is 0.19 e, influenced primarily by the hydrogen bonds to the C=O group. The values of such charge transfer are paralleled by the corresponding intrinsic hydrogen-bond energies. These results support the desirability of incorporating charge transfer in molecular mechanics energy functions.

Exploring chemical reaction mechanisms through harmonic Fourier beads path optimization

Here, we apply the harmonic Fourier beads (HFB) path optimization method to study chemical reactions involving covalent bond breaking and forming on quantum mechanical (QM) and hybrid QM∕molecular mechanical (QM∕MM) potential energy surfaces. To improve efficiency of the path optimization on such computationally demanding potentials, we combined HFB with conjugate gradient (CG) optimization. The combined CG-HFB method was used to study two biologically relevant reactions, namely, L- to D-alanine amino acid inversion and alcohol acylation by amides. The optimized paths revealed several unexpected reaction steps in the gas phase. For example, on the B3LYP∕6-31G(d,p) potential, we found that alanine inversion proceeded via previously unknown intermediates, 2-iminopropane-1,1-diol and 3-amino-3-methyloxiran-2-ol. The CG-HFB method accurately located transition states, aiding in the interpretation of complex reaction mechanisms. Thus, on the B3LYP∕6-31G(d,p) potential, the gas phase activation barriers for the inversion and acylation reactions were 50.5 and 39.9 kcal∕mol, respectively. These barriers determine the spontaneous loss of amino acid chirality and cleavage of peptide bonds in proteins. We conclude that the combined CG-HFB method further advances QM and QM∕MM studies of reaction mechanisms.

A Hybrid Methacrylate-Sodium Carboxymethylcellulose Interpolyelectrolyte Complex: Rheometry and in Silico Disposition for Controlled Drug Release.

The rheological behavioral changes that occurred during the synthesis of an interpolyelectrolyte complex (IPEC) of methacrylate copolymer and sodium carboxymethylcellulose were assessed. These changes were compared with the rheological behavior of the individual polymers employing basic viscosity, yield stress, stress sweep, frequency sweep, temperature ramp as well as creep and recovery testing. The rheological studies demonstrated that the end-product of the complexation of low viscous methacrylate copolymer and entangled solution of sodium carboxymethylcellulose generated a polymer, which exhibited a solid-like behavior with a three-dimensional network. Additionally, the rheological profile of the sodium carboxymethylcellulose and methacrylate copolymer with respect to the effect of various concentrations of acetic acid on the synthesis of the IPEC was elucidated using molecular mechanics energy relationships (MMER) by exploring the spatial disposition of carboxymethylcellulose and methacrylate copolymer with respect to each other and acetic acid. The computational results corroborated well with the experimental in vitro drug release data. Results have shown that the IPEC may be suitable polymeric material for achieving controlled zero-order drug delivery.

In Vitro, In Vivo, and In Silico Evaluation of the Bioresponsive Behavior of an Intelligent Intraocular Implant

An autofeedback complex polymeric platform was used in the design of an intelligent intraocular implant-the I(3)-using stimuli-responsive polymers, producing a smart release system capable of delivering therapeutic levels of an anti-inflammatory agent (indomethacin) and antibiotic (ciprofloxacin) for posterior segment disorders of the eye in response to inflammation. Physicochemical and physicomechanical analysis of the I(3) was undertaken to explicate the highly crosslinked make-up and 'on-off' inflammation-responsive performance of the I(3). In addition, energetic profiles for important complexation reactions were generated using Molecular Mechanics Energy Relationships by exploring the spatial disposition of energy minimized molecular structures. Furthermore, preliminary in vivo determination of the inflammation-responsiveness of the I(3) was ascertained following implantation in the normal and inflamed rabbit eye. In silico modeling simulating a pathological inflammatory intraocular state highlighted the interaction potential of hydroxyl radicals with the selected polysaccharides comprising the I(3). The intricately crosslinked polymeric system forming the I(3) thus responded at an innate level predicted by its molecular make-up to inflammatory conditions as indicated by the results of the drug release studies, rheological analysis, magnetic resonance imaging and scanning electron microscopic imaging. In vivo drug release analysis demonstrated indomethacin levels of 0.749 ± 0.126μg/mL and 1.168 ± 0.186μg/mL, and ciprofloxacin levels of 1.181 ± 0.150μg/mL and 6.653 ± 0.605μg/mL in the normal and inflamed eye, respectively. Extensive in vitro, molecular, and in vivo characterization therefore highlighted successful inflammation-responsiveness of the I(3). The I(3) is a proposed step forward from other described ocular systems owing to its combined bioresponsive, nano-enabled architecture.

Exploration of the biomacromolecular interactions of an interpenetrating proteo‐saccharide hydrogel network at the mucosal interface

The relationship between mucin (MUC) and pectin (PEC) was explored in an attempt to understand the biomacromolecular interactions that occur at mucosal surfaces when mucus membranes are exposed to PEC-based materials. These interactions were explored through techniques, such as attenuated total reflection Fourier transform infrared (ATR-FTIR) spectroscopy, SEM imagery of lyophilized MUC-PEC blends, thermodynamic analysis, rheology investigations, and in silico static lattice atomistic simulations using a molecular mechanics energy relationships (MMER) approach. Three types of PEC that had different degrees of esterification and degrees of amidation were investigated at different MUC-PEC mass ratios (1:0, 1:1, 1:4, 1:9, and 0:1). The effect PEG 400 and Ca(2 +) in the MUC-PEC interactions were also studied. ATR-FTIR spectroscopy revealed broadening and strengthening of FTIR peaks at 3363 cm(-1) and between 3000-3650 cm(-1) due to stretching vibrations of the -OH, -COOH groups on MUC and PEC as well as the -N-H group on MUC. This suggested significant intra- and inter-molecular H-bonding. Morphologically, MUC-rich scaffolds were porous, thin, and multidirectional compared with the smooth, rigid, and unidirectional PEC-rich scaffolds. The Flory-Huggins interaction parameter (χ12 ) for all MUC-PEC mass ratios was negative, thus confirming MUC-PEC miscibility and interactions. UV absorbance increased with increasing relative concentration of PEC in the aqueous MUC-PEC dispersions. Furthermore, rheology investigations demonstrated synergistic enhancement in viscosity (η) and dynamic moduli upon the addition of PEG 400 and Ca(2 +) . MMER analysis revealed several key MUC-PEC interactions that corroborated well with the experimental data. Notably, higher esterification and larger mass ratios of PEC yielded greater MUC-PEC interactions.

Adding diverse noncanonical backbones to rosetta: enabling peptidomimetic design.

Peptidomimetics are classes of molecules that mimic structural and functional attributes of polypeptides. Peptidomimetic oligomers can frequently be synthesized using efficient solid phase synthesis procedures similar to peptide synthesis. Conformationally ordered peptidomimetic oligomers are finding broad applications for molecular recognition and for inhibiting protein-protein interactions. One critical limitation is the limited set of design tools for identifying oligomer sequences that can adopt desired conformations. Here, we present expansions to the ROSETTA platform that enable structure prediction and design of five non-peptidic oligomer scaffolds (noncanonical backbones), oligooxopiperazines, oligo-peptoids, -peptides, hydrogen bond surrogate helices and oligosaccharides. This work is complementary to prior additions to model noncanonical protein side chains in ROSETTA. The main purpose of our manuscript is to give a detailed description to current and future developers of how each of these noncanonical backbones was implemented. Furthermore, we provide a general outline for implementation of new backbone types not discussed here. To illustrate the utility of this approach, we describe the first tests of the ROSETTA molecular mechanics energy function in the context of oligooxopiperazines, using quantum mechanical calculations as comparison points, scanning through backbone and side chain torsion angles for a model peptidomimetic. Finally, as an example of a novel design application, we describe the automated design of an oligooxopiperazine that inhibits the p53-MDM2 protein-protein interaction. For the general biological and bioengineering community, several noncanonical backbones have been incorporated into web applications that allow users to freely and rapidly test the presented protocols (http://rosie.rosettacommons.org). This work helps address the peptidomimetic community's need for an automated and expandable modeling tool for noncanonical backbones.

Modulation of the nano-tensile mechanical properties of co-blended amphiphilic alginate fibers as oradurable biomaterials for specialized biomedical application

The modulation of the mechanical properties of monolithic fibers by plasticizing and crosslinking enables the dynamic control of the nano-tensile forces, thereby obtaining optimized Young's modulus and ultimate strain for specialized application in the treatment of periodontal disease. In this work, drug-loaded crosslinked and plasticized alginate fibers (cl-PAFs) were prepared by extrusion-gelification with the aim of designing oradurable biomaterials for placement within the periodontal pocket and provide prolonged drug delivery. Mechanical properties of drug-free cl-PAFs were determined using a nanoTensile™ 5000 instrument and subsequently optimized versus the quantity of plasticizer and crosslinker as formulation variables employing a Box–Behnken experimental design strategy. Mechanically optimized fibers obtained (Young's Modulus=314.04MPa, yield stress=5.80MPa, ultimate strength=10.05MPa, ultimate strain=0.29MPa and toughness=2.39Jcm−3) were loaded with the model drugs ciprofloxacin and diclofenac both individually and simultaneously. The Young's modulus of cl-PAFs loaded with either drug individually exhibited a steep decline. However, in the case of cl-PAFs loaded with both drugs simultaneously, Young’s modulus regained the original value which may be attributed to the cohesive energy density, porosity and space filling. The effect of various formulation variables on the drug entrapment and release characteristics of the alginate fibers was elucidated at pH 4.0 and pH 6.8. Furthermore, a previously established atomistic computational model based on energy refinements was employed to mechanistically describe the fiber performance. The effect of varying the plasticizer and crosslinking ion concentration on Young’s modulus and ultimate strain of the linear elastic polymer matrix and the performance of the ciprofloxacin and/or diclofenac loaded optimized fiber was elucidated and conceptualized using molecular mechanics energy relationships (MMER) via the geometrical conformation and positioning of the molecular architectures.

In silico elucidation of the inclusion phenomenon and permeation behavior of a zidovudine–cyclodextrin complex via static lattice atomistic simulation

This study explored the molecular arrangement of the drug molecule zidovudine (AZT) within an inclusion complex of β-cyclodextrin (βCD). The intrinsic mechanistic profiling of the AZT–βCD inclusion complex was investigated using molecular modeling and structurally designed docking studies via molecular mechanics Force-Field simulations. The energetically and geometrically optimized molecular conformations revealed that the AZT molecule was preferentially oriented toward the primary rim of the βCD cavity with the azido group positioned within the cyclodextrin ring. In the second phase of this study, the mechanism of AZT permeability across the transmucosal membrane after inclusion into βCD was elucidated via interaction between βCD and the transmucosal lipid, glycosylceramide (GLC). Interestingly, βCD formed H-bonds with the lipid head groups of GLC via the secondary rim. A systematic merge of these findings elucidated a novel “tunnel model” designated to the trimolecular complex: AZT-1°ring–βCD-2°ring–GLC. The energetic parameters, grid surface area, molecular volume, surface-to-volume-ratio, Log-P, refractivity, and polarizability were computed for the molecular complexes. Computationally, the Molecular Mechanics Assisted Model Building and Energy Refinements (AMBER) algorithm was used to develop a molecular mechanics energy relationship (MMER). The MMER elucidated the role of destabilized bond stretching, angle modification and torsional strain in ionic stabilization of the geometrical complexes through hydrophobic H-bonding and electrostatic interactions. These results provided a novel bonding and non-bonding correlation for the formation and performance of βCD in terms of its role in the prospective permeation modification of the AZT molecule through the transmucosal membrane with an optimum hydrophilic–lipophilic-permeation balance.

Structural mimicry between SLA/LP and Rickettsia surface antigens as a driver of autoimmune hepatitis: insights from an in silico study.

BackgroundAutoimmune hepatitis (AIH) is a chronic, progressive liver disease, characterized by continuing hepatocellular inflammation and necrosis. A subgroup of AIH patients presents specific autoantibodies to soluble liver antigen/liver-pancreas (SLA/LP) protein, which is regarded as a highly specific diagnostic marker. Autoantigenic SLA/LP peptides are targeted by CD4+ T cells, and restricted by the allele HLA-DRB1*03:01, which confers disease susceptibility in Europeans and Americans. A positively charged residue at position 71 has been indicated as critical for AIH susceptibility in all of the HLA alleles identified to date. Though the exact molecular mechanisms underlying pathogenesis of AIH are not clear, molecular mimicry between SLA/LP and viral/bacterial antigens has been invoked.MethodsThe immunodominant region of SLA/LP was used as query in databank searches to identify statistically significant similarities with viral/bacterial peptides. Homology modeling and docking was used to investigate the potential interaction of HLA-DRB1*03:01 with the identified peptides. By molecular mechanics means, the interactions and energy of binding at the HLA binding site was also scrutinized.ResultsA statistically significant structural similarity between the immunodominant regions of SLA/LP and a region of the surface antigen PS 120 from Rickettsia spp. has been detected. The interaction of the SLA/LP autoepitope and the corresponding Rickettsia sequence with the allele HLA-DRB1*03:01 has been simulated. The obtained results predict for both peptides a similar binding mode and affinity to HLA-DRB1*03:01. A “hot spot” of interaction between HLA-DRB1*03:01 and PS 120 is located at the P4 binding pocket, and is represented by a salt bridge involving Lys at position 71 of the HLA protein, and Glu 795 of PS120 peptide.ConclusionsThese findings strongly support the notion that a molecular mimicry mechanism can trigger AIH onset. CD4+ T cells recognizing peptides of SLA/LP could indeed cross-react with foreign Rickettsia spp. antigens. Finally, the same analysis suggests a molecular explanation for the importance of position 71 in conferring the susceptibility of the allele HLA-DRB1*03:01 to AIH. The lack of a positive charge at such position could prevent HLA alleles from binding the foreign peptides and triggering the molecular mimicry event.

Ligand-functionalized nanoliposomes for targeted delivery of galantamine

The purpose of this study was to design ligand-functionalized nanoliposomes that are proficient in providing effective intracellular delivery of an alkaloid drug (galantamine) into PC12 neuronal cells in response to managing Alzheimer's disease (AD). Ligand-functionalized nanoliposomes were produced and validated for their physicochemical properties, in silico molecular mechanics energy relationships, ex vivo cytotoxicity, peptide coupling efficiency (PCE), drug entrapment efficiency (DEE), drug release, fluorometry and confocal microscopy. Particle sizes of the nanoliposomes ranged from 127 nm to 165 nm (PdI=0.39-0.03), zeta potential values of -18 mV to -36 mV, PCE from 40% to 78% while DEE ranged from 42% to 79%. The surface morphology of the nanoliposomes was stable, spherically and uniform in shape. Thermal behavior and Fourier transform infrared (FTIR) analyses confirmed that galantamine and the peptide-ligand were incorporated into the inner core and surface of the nanoliposomes, respectively. The optimized formulation showed sustained drug release (30% of drug released within 48 h). Fluorometry and confocal microscopy revealed that the ligand-functionalized nanoliposomes facilitated galantamine uptake into PC12 neuronal cells via the Serpin Enzyme Complex Receptor in a mediated manner. CytoTox-Glo™ cytotoxicity assay established the low cytotoxicity on PC12 neuronal cells when exposed to native nanoliposomes and the ligand-functionalized nanoliposomes. Response surface analysis demonstrated there was a high degree of correlation between the experimental and fitted values. Furthermore, ex vivo studies showed that the high galantamine accumulation into PC12 neuronal cells was influenced by the post-engineering of peptides on the surface of the galantamine-loaded nanoliposomes. MMER analysis aptly corroborated the experimental findings.

Multiscale Modeling Techniques Based on Molecular Structure and Elastic Properties

Based on the principle of using atomistic force field, and the use of ultra-flexible multi-scale modeling techniques to predict the polycarbonate and polyimide polymer molecular structure and the elastic properties of the system. The model combines molecular modeling and nonlinear continuum mechanics basic principles, to simulate and predict the behavior of the material properties of the polymer molecular structure. For the polymer structure and properties, using a plurality of force field simulation to predict the contrast, and binding experiments measured polymer performance value, using static and dynamic molecular simulation technology for molecular mechanics energy minimization to solve.

Structure-Guided Deimmunization of Therapeutic Proteins

Therapeutic proteins continue to yield revolutionary new treatments for a growing spectrum of human disease, but the development of these powerful drugs requires solving a unique set of challenges. For instance, it is increasingly apparent that mitigating potential anti-therapeutic immune responses, driven by molecular recognition of a therapeutic protein's peptide fragments, may be best accomplished early in the drug development process. One may eliminate immunogenic peptide fragments by mutating the cognate amino acid sequences, but deimmunizing mutations are constrained by the need for a folded, stable, and functional protein structure. These two concerns may be competing, as the mutations that are best at reducing immunogenicity often involve amino acids that are substantially different physicochemically. We develop a novel approach, called EpiSweep, that simultaneously optimizes both concerns. Our algorithm identifies sets of mutations making such Pareto optimal trade-offs between structure and immunogenicity, embodied by a molecular mechanics energy function and a T-cell epitope predictor, respectively. EpiSweep integrates structure-based protein design, sequence-based protein deimmunization, and algorithms for finding the Pareto frontier of a design space. While structure-based protein design is NP-hard, we employ integer programming techniques that are efficient in practice. Furthermore, EpiSweep only invokes the optimizer once per identified Pareto optimal design. We show that EpiSweep designs of regions of the therapeutics erythropoietin and staphylokinase are predicted to outperform previous experimental efforts. We also demonstrate EpiSweep's capacity for deimmunization of the entire proteins, case analyses involving dozens of predicted epitopes, and tens of thousands of unique side-chain interactions. Ultimately, Epi-Sweep is a powerful protein design tool that guides the protein engineer toward the most promising immunotolerant biotherapeutic candidates.

Variational Implicit Solvation with Solute Molecular Mechanics: From Diffuse-Interface to Sharp-Interface Models

Central in a variational implicit-solvent description of biomolecular solvation is an effective free-energy functional of the solute atomic positions and the solute-solvent interface (i.e., the dielectric boundary). The free-energy functional couples together the solute molecular mechanical interaction energy, the solute-solvent interfacial energy, the solute-solvent van der Waals interaction energy, and the electrostatic energy. In recent years, the sharp-interface version of the variational implicit-solvent model has been developed and used for numerical computations of molecular solvation. In this work, we propose a diffuse-interface version of the variational implicit-solvent model with solute molecular mechanics. We also analyze both the sharp-interface and diffuse-interface models. We prove the existence of free-energy minimizers and obtain their bounds. We also prove the convergence of the diffuse-interface model to the sharp-interface model in the sense of Γ-convergence. We further discuss properties of sharp-interface free-energy minimizers, the boundary conditions and the coupling of the Poisson-Boltzmann equation in the diffuse-interface model, and the convergence of forces from diffuse-interface to sharp-interface descriptions. Our analysis relies on the previous works on the problem of minimizing surface areas and on our observations on the coupling between solute molecular mechanical interactions with the continuum solvent. Our studies justify rigorously the self consistency of the proposed diffuse-interface variational models of implicit solvation.

Prolonged Delivery of Ciprofloxacin and Diclofenac Sodium from a Polymeric Fibre Device for the Treatment of Peridontal Disease

In vitro analysis of drug release and antimicrobial activity of the coblended crosslinked polymeric fibre device (PFD) were investigated. The fibre loaded with ciprofloxacin and diclofenac sodium was comprised of alginate and glycerol crosslinked with barium cations. The pH dependent drug release was evident with ciprofloxacin and diclofenac sodium diffusing from the fibre at pH 4.0 compared to pH 6.8, where the fibre swelled and eroded resulting in zero-order drug release. Agar diffusion studies followed by minimum inhibitory assays were conducted to determine the antimicrobial activity of the device against Escherichia coli, Enterococcus faecalis, and Streptococcus mutans. The antimicrobial activity of the PFD was confirmed in both test assays against all test pathogens. The MIC ranges at pH 4.0 for E. coli, E. faecalis, and S. mutans were 0.5–0.8, 0.4–1.1, and 0.7–2.1 μg/mL, respectively. At pH 6.8, similar efficacies (0.3–0.5 μg/mL for E. coli and E. faecalis and 0.6–1.0 μg/mL for S. mutans) were observed. The effect of varying the plasticizer and crosslinking ion concentration on drug release profile of the fibers was further elucidated and conceptualized using molecular mechanics energy relationships (MMER) and by exploring the spatial disposition of geometrically minimized molecular conformations.

In vivo evaluation of a conjugated poly(lactide-ethylene glycol) nanoparticle depot formulation for prolonged insulin delivery in the diabetic rabbit model.

Poly(ethylene glycol) (PEG) and polylactic acid (PLA)-based copolymeric nanoparticles were synthesized and investigated as a carrier for prolonged delivery of insulin via the parenteral route. Insulin loading was simultaneously achieved with particle synthesis using a double emulsion solvent evaporation technique, and the effect of varied PEG chain lengths on particle size and insulin loading efficiency was determined. The synthesized copolymer and nanoparticles were analyzed by standard polymer characterization techniques of gel permeation chromatography, dynamic light scattering, nuclear magnetic resonance, and transmission electron microscopy. In vitro insulin release studies performed under simulated conditions provided a near zero-order release pattern up to 10 days. In vivo animal studies were undertaken with varied insulin loads of nanoparticles administered subcutaneously to fed diabetic rabbits and, of all doses administered, nanoparticles containing 50 IU of insulin load per kg body weight controlled the blood glucose level within the physiologically normal range of 90–140 mg/dL, and had a prolonged effect for more than 7 days. Histopathological evaluation of tissue samples from the site of injection showed no signs of inflammation or aggregation, and established the nontoxic nature of the prepared copolymeric nanoparticles. Further, the reaction profiles for PLA-COOH and NH2-PEGDA-NH2 were elucidated using molecular mechanics energy relationships in vacuum and in a solvated system by exploring the spatial disposition of various concentrations of polymers with respect to each other. Incorporation of insulin within the polymeric matrix was modeled using Connolly molecular surfaces. The computational results corroborated the experimental and analytical data. The ability to control blood glucose levels effectively coupled with the nontoxic behavior of the nanoparticles indicates that these nanoparticles are a potential candidate for insulin delivery.

Impact of Mutations on the Allosteric Conformational Equilibrium

Allostery in a protein involves effector binding at an allosteric site that changes the structure and/or dynamics at a distant, functional site. In addition to the chemical equilibrium of ligand binding, allostery involves a conformational equilibrium between one protein substate that binds the effector and a second substate that less strongly binds the effector. We run molecular dynamics simulations using simple, smooth energy landscapes to sample specific ligand-induced conformational transitions, as defined by the effector-bound and effector-unbound protein structures. These simulations can be performed using our web server (http://salilab.org/allosmod/). We then develop a set of features to analyze the simulations and capture the relevant thermodynamic properties of the allosteric conformational equilibrium. These features are based on molecular mechanics energy functions, stereochemical effects, and structural/dynamic coupling between sites. Using a machine-learning algorithm on a data set of 10 proteins and 179 mutations, we predict both the magnitude and the sign of the allosteric conformational equilibrium shift by the mutation; the impact of a large identifiable fraction of the mutations can be predicted with an average unsigned error of 1kBT. With similar accuracy, we predict the mutation effects for an 11th protein that was omitted from the initial training and testing of the machine-learning algorithm. We also assess which calculated thermodynamic properties contribute most to the accuracy of the prediction.

Initial Events in the Degradation of Hyaluronan Catalyzed by Hyaluronate Lyase from Spectrococcus pneumoniae: QM/MM Simulation

Hyaluronate lyase from Spectrococcus pneumonia can degrade hyaluronic acid, which is one of the major components in the extracellular matrix. The major functions of hyaluronan are to regulate water balance and osmotic pressure and act as an ion-exchange resin. In this work, we focus on the prerequisite issue of the enzymatic reaction, i.e., the initial reactive conformer. Based on the quantum mechanical and molecular mechanical molecular dynamic simulations and free energy profiles, a near attack conformer was obtained for the degradation of hyaluronan catalyzed by the hyaluronate lyase. Along with the substrate binding, the phenylhydroxyl hydrogen atom of Tyr408 will transfer to nearby His399 via a near barrierless transition state, which results in a negatively charged Tyr408 and positively charged His399. The Tyr408, rather than the previously proposed His399, was suggested to act as the general base for the subsequent β-elimination reaction. The His399 was suggested to have the function of neutralizing the C5-carboxyl group.

Stabilization of Silicon Islands in Silicoaluminophosphates by Proton Redistribution

The relative stabilities of different proton distributions around a five-atom silicon island in silicoaluminophosphate-34 (SAPO-34) have been investigated by periodic molecular mechanics (MM) energy minimization calculations, and the MM calculations were validated using density functional theory (DFT). SAPO-34 has chabazite topology with only one symmetrically independent tetrahedral site (T-site) and four unique oxygen sites. The preferred position of the proton at isolated acid sites has been the subject of both experimental and computational studies. In previous computational studies of silicon islands, it was assumed that the protons, necessary to keep the silicon island neutral, would occupy the same positions as those preferred for solitary silicon atoms. We have studied all 108 possible proton distributions around a five-atom silicon island in SAPO-34. The results indicate that the proton placement is critical for stability, as the limit deviation in our data set is as high as 90 kJ/mol. Careful an...

Crosslinked electrospun PVA nanofibrous membranes: elucidation of their physicochemical, physicomechanical and molecular disposition

The effects of modifying electrospun poly(vinyl alcohol) (PVA) nanofibers through crosslinking using glutaraldehyde (GA) are explored in this paper. Various concentrations of PVA solutions containing model drugs rifampicin (RIF) and isoniazid (INH) were electrospun and thereafter crosslinked using GA vapors. PVA nanofibers demonstrated high drug entrapment efficiency of 98.77% ± 1.384% and 95.07% ± 1.988% for the INH- and RIF-loaded PVA nanofibers, respectively. The surface morphology, molecular vibrational transitions, tensile attributes and in vitro drug release were characterized and supported by in silico molecular mechanics simulations. Results indicated that crosslinking caused a significant reduction in the rate of drug release where 81.11% ± 2.35% of INH and 59.31% ± 2.57% of RIF were released after 12 h. Tensile properties such as the ultimate strength and Young's modulus increased after crosslinking, caused by crosslinks forming between PVA nanofibers as was revealed through scanning electron microscopy analysis. Fourier Transform infrared analysis was conducted to further support the mode of crosslinking. Additionally, image processing analysis was carried out to quantify the effect of formulation variables on the morphology of nanofibers. Furthermore, the effect of GA-induced crosslinking and addition of drugs on the performance of electrospun fibers was further elucidated and conceptualized using a molecular mechanics assisted model building and energy refinement approach via molecular mechanics energy relationships by exploring the spatial disposition of energy-minimized molecular structures of the polymer, crosslinker and the drugs.