Simulation of Biochemical Reactions with ANN-Dependent Kinetic Parameter Extraction Method

The measurement of thermodynamic properties of chemical or biological reactions were often confined to experimental means, which produced overall measurements of properties being investigated, but were usually susceptible to pitfalls of being too general. Among the thermodynamic properties that are of interest, reaction rates hold the greatest significance, as they play a critical role in reaction processes where speed is of essence, especially when fast association may enhance binding affinity of reaction molecules. Association reactions with high affinities often involve the formation of a intermediate state, which can be demonstrated by a hyperbolic reaction curve, but whose low abundance in reaction mixture often preclude the possibility of experimental measurement. Therefore, we resorted to computational methods using predefined reaction models that model the intermediate state as the reaction progresses. Here, we present a novel method called AKPE (ANN-Dependent Kinetic Parameter Extraction), our goal is to investigate the association/dissociation rate constants and the concentration dynamics of lowly-populated states (intermediate states) in the reaction landscape. To reach our goal, we simulated the chemical or biological reactions as system of differential equations, employed artificial neural networks (ANN) to model experimentally measured data, and utilized Particle Swarm Optimization (PSO) algorithm to obtain the globally optimum parameters in both the simulation and data fitting. In the Results section, we have successfully modeled a protein association reaction using AKPE, obtained the kinetic rate constants of the reaction, and constructed a full concentration versus reaction time curve of the intermediate state during the reaction. Furthermore, judging from the various validation methods that the method proposed in this paper has strong robustness and accuracy.

Phospholipid polymer hydrogels with rapid dissociation for reversible cell immobilization

Reversible and cytocompatible cell immobilization polymer matrix with rapid dissociation rate was prepared by using with a zwitterionic phospholipid polymer bearing phenylboronic acid and poly(vinyl alcohol)(PVA). A reversible and spontaneously...

Bipolar Membrane and Water Splitting in Electrodialysis

The traditional view of the conductivity of electrolytes is based on the mobility of ions in an electric field. A new concept of water conductivity introduces an electron–hole mechanism known from semiconductor theory. The electrolyte ions in the hydrogen bond network of water imitate the structure of a doped silicon lattice. The source of the current carriers is the electrode reaction generating H+ and OH− ions. The continuity of current flow is provided through the electron–hole mechanism, and the movement of electrolyte ions is only a side process. Bipolar membrane in the semiconductor approach is an electrochemical diode forward biased. Generation of large amounts of H+ and OH− has to be considered as a result of current flow and does not require any increase in the water dissociation rate. Bipolar membranes are essential in electrodialysis stacks for the recovery of acids and bases by salt splitting. Graphic Abstract

The Effect of Acute Oral Galactose Administration on the Redox System of the Rat Small Intestine

Galactose is a ubiquitous monosaccharide with important yet incompletely understood nutritive and physiological roles. Chronic parenteral d-galactose administration is used for modeling aging-related pathophysiological processes in rodents due to its ability to induce oxidative stress (OS). Conversely, chronic oral d-galactose administration prevents and alleviates cognitive decline in a rat model of sporadic Alzheimer’s disease, indicating that galactose may exert beneficial health effects by acting in the gut. The present aim was to explore the acute time-response of intestinal redox homeostasis following oral administration of d-galactose. Male Wistar rats were euthanized at baseline (n = 6), 30 (n = 6), 60 (n = 6), and 120 (n = 6) minutes following orogastric administration of d-galactose (200 mg/kg). The overall reductive capacity, lipid peroxidation, the concentration of low-molecular-weight thiols (LMWT) and protein sulfhydryls (SH), the activity of Mn and Cu/Zn superoxide dismutases (SOD), reduced and oxidized fractions of nicotinamide adenine dinucleotide phosphates (NADPH/NADP), and the hydrogen peroxide dissociation rate were analyzed in duodenum and ileum. Acute oral administration of d-galactose increased the activity of SODs and decreased intestinal lipid peroxidation and nucleophilic substrates (LMWT, SH, NADPH), indicating activation of peroxidative damage defense pathways. The redox system of the small intestine can acutely tolerate even high luminal concentrations of galactose (0.55 M), and oral galactose treatment is associated with a reduction rather than the increment of the intestinal OS. The ability of oral d-galactose to modulate intestinal OS should be further explored in the context of intestinal barrier maintenance, and beneficial cognitive effects associated with long-term administration of low doses of d-galactose.

Neuron-Recognizable Characteristics of Peptides Recombined Using A Neuronal Binding Domain of Botulinum Neurotoxin

Recombinant peptides were designed using the C-terminal domain (receptor binding domain, RBD) and its subdomain (peptide A2) of a heavy chain of botulinum neurotoxin A-type 1 (BoNT/A1), which can bind to the luminal domain of synaptic vesicle glycoprotein 2C (SV2C-LD). Peptide A2- or RBD-containing recombinant peptides linked to an enhanced green fluorescence protein (EGFP) were prepared by expression in Escherichia coli. A pull-down assay using SV2C-LD-covered resins showed that the recombinant peptides for CDC5328 BoNT/A1, referred to EGFP-A2ʹ and EGFP-RBDʹ, exhibited ≥ 2.0-times stronger binding affinity to SV2C-LD than those for the wild-type BoNT/A1. Using bio-layer interferometry, an equilibrium dissociation rate constant (KD) of EGFP-RBDʹ to SV2C-LD was determined to be 5.45 mM, which is 33.87- and 15.67-times smaller than the KD values for EGFP and EGFP-A2ʹ, respectively. Based on confocal laser fluorescence micrometric analysis, the adsorption/absorption of EGFP-RBDʹ to/in differentiated PC-12 cells was 2.49- and 1.29-times faster than those of EGFP and EGFP-A2ʹ, respectively. Consequently, the recombinant peptides acquired reasonable neuron-specific binding/internalizing ability through the recruitment of RBDʹ. In conclusion, RBDs of BoNTs are versatile protein domains that can be used to mark neural systems and treat a range of disorders in neural systems.

Mechanochemistry of phosphate esters confined between sliding iron surfaces

The molecular structure of lubricant additives controls not only their adsorption and dissociation behaviour at the nanoscale, but also their ability to reduce friction and wear at the macroscale. Here, we show using nonequilibrium molecular dynamics simulations with a reactive force field that tri(s-butyl)phosphate dissociates much faster than tri(n-butyl)phosphate when heated and compressed between sliding iron surfaces. For both molecules, dissociative chemisorption proceeds through cleavage of carbon−oxygen bonds. The dissociation rate increases exponentially with temperature and stress. When the rate−temperature−stress data are fitted with the Bell model, both molecules have similar activation energies and activation volumes and the higher reactivity of tri(s-butyl)phosphate is due to a larger pre-exponential factor. These observations are consistent with experiments using the antiwear additive zinc dialkyldithiophosphate. This study represents a crucial step towards the virtual screening of lubricant additives with different substituents to optimise tribological performance.

Generation of a Novel High-Affinity Antibody Binding to PCSK9 Catalytic Domain with Slow Dissociation Rate by CDR-Grafting, Alanine Scanning and Saturated Site-Directed Mutagenesis for Favorably Treating Hypercholesterolemia

Inhibition of proprotein convertase subtilisin/kexin type 9 (PCSK9) has become an attractive therapeutic strategy for lowering low-density lipoprotein cholesterol (LDL-C). In this study, a novel high affinity humanized IgG1 mAb (named h5E12-L230G) targeting the catalytic domain of human PCSK9 (hPCSK9) was generated by using CDR-grafting, alanine-scanning mutagenesis, and saturated site-directed mutagenesis. The heavy-chain constant region of h5E12-L230G was modified to eliminate the cytotoxic effector functions and mitigate the heterogeneity. The biolayer interferometry (BLI) binding assay and molecular docking study revealed that h5E12-L230G binds to the catalytic domain of hPCSK9 with nanomolar affinity (KD = 1.72 nM) and an extremely slow dissociation rate (koff, 4.84 × 10−5 s−1), which interprets its quite low binding energy (−54.97 kcal/mol) with hPCSK9. Additionally, h5E12-L230G elevated the levels of LDLR and enhanced the LDL-C uptake in HepG2 cells, as well as reducing the serum LDL-C and total cholesterol (TC) levels in hyperlipidemic mouse model with high potency comparable to the positive control alirocumab. Our data indicate that h5E12-L230G is a high-affinity anti-PCSK9 antibody candidate with an extremely slow dissociation rate for favorably treating hypercholesterolemia and relevant cardiovascular diseases.

Measurements and simulations of microtubule growth imply strong longitudinal interactions and reveal a role for GDP on the elongating end

Microtubule polymerization dynamics result from the biochemical interactions of αβ-tubulin with the polymer end, but a quantitative understanding has been challenging to establish. We used interference reflection microscopy to make improved measurements of microtubule growth rates and growth fluctuations in the presence and absence of GTP hydrolysis. In the absence of GTP hydrolysis, microtubules grew steadily with very low fluctuations. These data were best described by a computational model implementing slow assembly kinetics, such that the rate of microtubule elongation is primarily limited by the rate of αβ-tubulin associations. With GTPase present, microtubules displayed substantially larger growth fluctuations than expected based on the no GTPase measurements. Our modeling showed that these larger fluctuations occurred because exposure of GDP-tubulin on the microtubule end transiently "poisoned" growth, yielding a wider range of growth rate compared to GTP only conditions. Our experiments and modeling point to slow association kinetics (strong longitudinal interactions), such that drugs and regulatory proteins that alter microtubule dynamics could do so by modulating either the association or dissociation rate of tubulin from the microtubule tip. By causing slower growth, exposure of GDP tubulin at the growing microtubule end may be an important early event determining catastrophe.