Two Sides of Quantum-Based Modeling of Enzyme-Catalyzed Reactions: Mechanistic and Electronic Structure Aspects of the Hydrolysis by Glutamate Carboxypeptidase

We report the results of a computational study of the hydrolysis reaction mechanism of N-acetyl-l-aspartyl-l-glutamate (NAAG) catalyzed by glutamate carboxypeptidase II. Analysis of both mechanistic and electronic structure aspects of this multistep reaction is in the focus of this work. In these simulations, model systems are constructed using the relevant crystal structure of the mutated inactive enzyme. After selection of reaction coordinates, the Gibbs energy profiles of elementary steps of the reaction are computed using molecular dynamics simulations with ab initio type QM/MM potentials (QM/MM MD). Energies and forces in the large QM subsystem are estimated in the DFT(PBE0-D3/6-31G**) approximation. The established mechanism includes four elementary steps with the activation energy barriers not exceeding 7 kcal/mol. The models explain the role of point mutations in the enzyme observed in the experimental kinetic studies; namely, the Tyr552Ile substitution disturbs the “oxyanion hole”, and the Glu424Gln replacement increases the distance of the nucleophilic attack. Both issues diminish the substrate activation in the enzyme active site. To quantify the substrate activation, we apply the QTAIM-based approaches and the NBO analysis of dynamic features of the corresponding enzyme-substrate complexes. Analysis of the 2D Laplacian of electron density maps allows one to define structures with the electron density deconcentration on the substrate carbon atom, i.e., at the electrophilic site of reactants. The similar electronic structure element in the NBO approach is a lone vacancy on the carbonyl carbon atom in the reactive species. The electronic structure patterns revealed in the NBO and QTAIM-based analyses consistently clarify the reactivity issues in this system.

Adsorbed Cobalt Porphyrins Act like Metal Surfaces in Electrocatalysis

Carbon electrodes chemically modified with molecular active sites are potent catalysts for key energy conversion reactions. Generally, it is assumed that these molecularly modified electrodes operate by the same redox mediation mechanisms observed for soluble molecules, in which electron transfer and substrate activation occur in separate elementary steps. Here, we uncover that, depending on the solvent, carbon-bound cobalt porphyrin can carry out electrolysis by the non-mediated mechanisms of metal surfaces in which electron transfer and substrate activation are concerted. We chemically modify glassy carbon electrodes with cobalt tetraphenylporphyrin units that are anchored by flexible aliphatic linkages to form CH-CoTPP. In acetonitrile, CH-CoTPP displays a clear outer-sphere Co(II/I) process which catalyzes the H2 evolution reaction by a step-wise, redox-mediated reaction sequence. In contrast, clear surface redox waves are not observed for CH-CoTPP in aqueous media and H2 evolution proceeds via a non-mediated, concerted proton-electron transfer reaction sequence over a wide pH range. The data suggest that, in aqueous electrolyte, the CoTPP fragments reside inside the electrochemical double layer and are electrostatically coupled to the surface. This coupling allows CH-CoTPP to carry out catalysis without being pinned to the redox potential of the molecular fragment. These studies highlight that the simple adsorption of molecules can lead to reaction mechanisms typically reserved for metal surfaces, ex-posing new principles for the design of molecularly-modified electrodes.

Adsorbed Cobalt Porphyrins Act like Metal Surfaces in Electrocatalysis

Carbon electrodes chemically modified with molecular active sites are potent catalysts for key energy conver-sion reactions. Generally, it is assumed that these molecularly modified electrodes operate by the same redox mediation mechanisms observed for soluble molecules, in which electron transfer and substrate activation occur in separate elementary steps. Here, we uncover that, depending on the solvent, carbon-bound cobalt porphyrin can carry out electrolysis by the non-mediated mechanisms of metal surfaces in which electron transfer and substrate activation are concerted. We chemically modify glassy carbon electrodes with cobalt tetraphenylpor-phyrin units that are anchored by flexible aliphatic linkages to form CH-CoTPP. In acetonitrile, CH-CoTPP dis-plays a clear outer-sphere Co(II/I) process which catalyzes the H2 evolution reaction by a step-wise, redox-mediated reaction sequence. In contrast, clear surface redox waves are not observed for CH-CoTPP in aqueous media and H2 evolution proceeds via a non-mediated, concerted proton-electron transfer reaction sequence over a wide pH range. The data suggest that, in aqueous electrolyte, the CoTPP fragments reside inside the electro-chemical double layer and are electrostatically coupled to the surface. This coupling allows CH-CoTPP to carry out catalysis without being pinned to the redox potential of the molecular fragment. These studies highlight that the simple adsorption of molecules can lead to reaction mechanisms typically reserved for metal surfaces, ex-posing new principles for the design of molecularly-modified electrodes.

A spatial model of YAP/TAZ signaling reveals how stiffness, dimensionality, and shape contribute to emergent outcomes

YAP/TAZ is a master regulator of mechanotransduction whose functions rely on translocation from the cytoplasm to the nucleus in response to diverse physical cues. Substrate stiffness, substrate dimensionality, and cell shape are all input signals for YAP/TAZ, and through this pathway, regulate critical cellular functions and tissue homeostasis. Yet, the relative contributions of each biophysical signal and the mechanisms by which they synergistically regulate YAP/TAZ in realistic tissue microenvironments that provide multiplexed input signals remain unclear. For example, in simple two-dimensional culture, YAP/TAZ nuclear localization correlates strongly with substrate stiffness, while in three-dimensional (3D) environments, YAP/TAZ translocation can increase with stiffness, decrease with stiffness, or remain unchanged. Here, we develop a spatial model of YAP/TAZ translocation to enable quantitative analysis of the relationships between substrate stiffness, substrate dimensionality, and cell shape. Our model couples cytosolic stiffness to nuclear mechanics to replicate existing experimental trends, and extends beyond current data to predict that increasing substrate activation area through changes in culture dimensionality, while conserving cell volume, forces distinct shape changes that result in nonlinear effect on YAP/TAZ nuclear localization. Moreover, differences in substrate activation area versus total membrane area can account for counterintuitive trends in YAP/TAZ nuclear localization in 3D culture. Based on this multiscale investigation of the different system features of YAP/TAZ nuclear translocation, we predict that how a cell reads its environment is a complex information transfer function of multiple mechanical and biochemical factors. These predictions reveal a few design principles of cellular and tissue engineering for YAP/TAZ mechanotransduction.

Cell Behavior of Primary Fibroblasts and Osteoblasts on Plasma-Treated Fluorinated Polymer Coated with Honeycomb Polystyrene

The development of new biocompatible polymer substrates is still of interest to many research teams. We aimed to combine a plasma treatment of fluorinated ethylene propylene (FEP) substrate with a technique of improved phase separation. Plasma exposure served for substrate activation and modification of surface properties, such as roughness, chemistry, and wettability. The treated FEP substrate was applied for the growth of a honeycomb-like pattern from polystyrene solution. The properties of the pattern strongly depended on the primary plasma exposure of the FEP substrate. The physico-chemical properties such as changes of the surface chemistry, wettability, and morphology of the prepared pattern were determined. The cell response of primary fibroblasts and osteoblasts was studied on a honeycomb pattern. The prepared honeycomb-like pattern from polystyrene showed an increase in cell viability and a positive effect on cell adhesion and proliferation for both primary fibroblasts and osteoblasts.

Dye-loaded metal-organic helical capsules applied to the combination of photocatalytic H2S splitting and nitroaromatic hydrogenation

Two dye-loaded metal-organic capsules that were constructed with different spatial sizes and functional groups simulated the enzymatic substrate activation for hydrogenation of nitroarenes with the kinetics obeying the Michaelis-Menten mechanism.

Simple isolation for two forms of malic enzyme from crustacean abdomen muscle

Two forms of NADP-dependent malic enzyme (ME, EC 1.1.1.40) were purified from the abdomen muscle of the crayfish Orconectes limosus (Rafinesque, 1817) and the shrimp Crangon crangon L., 1758 by affinity chromatography on 2′,5′-ADP-Sepharose 4B, with good qualitative recovery in a single step, using a substrate activation method with a malate–manganese chloride pair. The enzymes were identified by native polyacrylamide gel electrophoresis stained for protein and enzyme activity. The faster migrating mitochondrial enzyme from crayfish is inhibited by sulfhydryl reagent and loses its activity. Ellman’s Reagent, 5,5′-Dithiobis-(2-nitrobenzoic acid) (DTNB), can be used for the differentiation and measurement of cytoplasmic and mitochondrial malic enzyme in decapod crustacean tissue.

Transfer function for YAP/TAZ nuclear translocation revealed through spatial systems modeling

ABSTRACTYAP/TAZ is a master regulator of mechanotransduction whose functions rely on translocation from the cytoplasm to the nucleus in response to diverse physical cues. Substrate stiffness, substrate dimensionality, and cell shape are all input signals for YAP/TAZ, and through this pathway, regulate critical cellular functions and tissue homeostasis. Yet, the relative contributions of each biophysical signal and the mechanisms by which they synergistically regulate YAP/TAZ in realistic tissue microenvironments that provide multiplexed input signals remains unclear. For example, in simple 2D culture, YAP/TAZ nuclear localization correlates strongly with substrate stiffness, while in 3D environments, YAP/TAZ translocation can increase with stiffness, decrease with stiffness, or remain unchanged. Here, we develop a spatial model of YAP/TAZ translocation to enable quantitative analysis of the relationships between substrate stiffness, substrate dimensionality, and cell shape. Our model couples cytosolic stiffness to nuclear mechanics to replicate existing experimental trends, and extends beyond current data to predict that increasing substrate activation area through changes in culture dimensionality, while conserving cell volume, forces distinct shape changes that result in nonlinear effect on YAP/TAZ nuclear localization. Moreover, differences in substrate activation area versus total membrane area can account for counterintuitive trends in YAP/TAZ nuclear localization in 3D culture. Based on this multiscale investigation of the different system features of YAP/TAZ nuclear translocation, we predict that how a cell reads its environment is a complex information transfer function of multiple mechanical and biochemical factors. These predictions reveal design principles of cellular and tissue engineering for YAP/TAZ mechanotransduction.STATEMENT OF SIGNIFICANCEIn chemical engineering, a transfer function is a mathematical function that models the output of a reactor for all possible inputs, and enables the reliable design and operation of complex reaction systems. Here, we apply this principle to cells to derive the transfer function by which substrate stiffness is converted into YAP/TAZ nuclear localization. This function is defined by a spatial model of the YAP/TAZ mechano-chemical sensing network, wherein key spatial and physical inputs to the system, namely cell and nuclear shape, surface area to volume ratios of cytoplasmic and nuclear compartments, substrate dimensionality, substrate activation area, and substrate stiffness, are all integrated. The resulting model accounts for seemingly contradictory experimental trends and lends new insight into controlling YAP/TAZ signalling.