First-Principles-Based Microkinetic Modeling of Methane Steam Reforming with Improved Description of Product Desorption

The method combining density functional theory (DFT) calculations with microkinetic modeling has attracted increasing attention in obtaining a deeper understanding of catalytic reactions. While product desorption is conventionally regarded as an equilibrated process in the microkinetic modeling, it might be influential to product selectivity when competing reactions should be considered. In this work, a complex reaction network is established first for the methane steam reforming reaction using the equilibrium and immobile models over Ni, Pd, and Pt surfaces. This provides a basis to further investigate the reaction mechanism and kinetic modeling results. The results show that when different desorption models are considered, the total activity regarding methane conversion and the coverage and DRC value of the main species at the steady state are the same on each surface. In contrast, the mechanism of CO2 formation is varied based on different desorption models. Consequently, the rate and selectivity of CO2 generation on each metal catalyst are significantly improved when the barrier of CO desorption is considered in the microkinetic modeling compared with the modeling only with barrierless CO desorption

Hydrogen–Deuterium Exchange Mass Spectrometry Identifies Local and Long-Distance Interactions within the Multicomponent Radical SAM Enzyme, PqqE

Interactions among proteins and peptides are essential for many biological activities including the tailoring of peptide substrates to produce natural products. The first step in the production of the bacterial redox cofactor pyrroloquinoline quinone (PQQ) from its peptide precursor is catalyzed by a radical SAM (rSAM) enzyme, PqqE. We describe the use of hydrogen–deuterium exchange mass spectrometry (HDX-MS) to characterize the structure and conformational dynamics in the protein–protein and protein–peptide complexes necessary for PqqE function. HDX-MS-identified hotspots can be discerned in binary and ternary complex structures composed of the peptide PqqA, the peptide-binding chaperone PqqD, and PqqE. Structural conclusions are supported by size-exclusion chromatography coupled to small-angle X-ray scattering (SEC-SAXS). HDX-MS further identifies reciprocal changes upon the binding of substrate peptide and S-adenosyl­methionine (SAM) to the PqqE/PqqD complex: long-range conformational alterations have been detected upon the formation of a quaternary complex composed of PqqA/PqqD/PqqE and SAM, spanning nearly 40 Å, from the PqqA binding site in PqqD to the PqqE active site Fe4S4. Interactions among the various regions are concluded to arise from both direct contact and distal communication. The described experimental approach can be readily applied to the investigation of protein conformational communication among a large family of peptide-modifying rSAM enzymes

Synthesis of Cylindrical Polymer Brushes with Umbrella-Like Side Chains via a Combination of Grafting-from and Grafting-onto Methods

Cylindrical polymer brushes with umbrella-like side chains have been synthesized by a combination of grafting-from and grafting-onto methods. First, the polymer brushes with azido end-functionalized poly­(<i>tert</i>-butyl acrylate) (P<i>t</i>BA-N₃) side chains, PBIEM-<i>g</i>-(P<i>t</i>BA-N₃), were prepared by atom transfer radical polymerization (ATRP) of <i>t</i>BA monomers using polyinitiator PBIEM followed by a substitution of bromo-side terminals with sodium azide. Subsequently, polyamidoamino dendrons of three generations with a propargyl focal point (G<i>n</i>) were introduced onto the brush-shaped P<i>t</i>BA-N₃ by copper-catalyzed azide–alkyne cycloaddition (CuAAC) coupling reaction. The efficiency of CuAAC between P<i>t</i>BA-N₃ side chains and G<i>n</i> has showed a dependence on generation number <i>n</i> of the dendrons. At the feed ratio of [G<i>n</i>]:[N₃] = 1:1, the grafting efficiency of the first generation dendron (G1) reached above 95%, whereas that of G2 and G3 was at least 84% and 73%, respectively. AFM images indicated that diameter of the brushes hybridized with G3 increased obviously than that of the brushes without dendrons

Hydrogen–Deuterium Exchange Mass Spectrometry Identifies Local and Long-Distance Interactions within the Multicomponent Radical SAM Enzyme, PqqE

Interactions among proteins and peptides are essential for many biological activities including the tailoring of peptide substrates to produce natural products. The first step in the production of the bacterial redox cofactor pyrroloquinoline quinone (PQQ) from its peptide precursor is catalyzed by a radical SAM (rSAM) enzyme, PqqE. We describe the use of hydrogen–deuterium exchange mass spectrometry (HDX-MS) to characterize the structure and conformational dynamics in the protein–protein and protein–peptide complexes necessary for PqqE function. HDX-MS-identified hotspots can be discerned in binary and ternary complex structures composed of the peptide PqqA, the peptide-binding chaperone PqqD, and PqqE. Structural conclusions are supported by size-exclusion chromatography coupled to small-angle X-ray scattering (SEC-SAXS). HDX-MS further identifies reciprocal changes upon the binding of substrate peptide and S-adenosyl­methionine (SAM) to the PqqE/PqqD complex: long-range conformational alterations have been detected upon the formation of a quaternary complex composed of PqqA/PqqD/PqqE and SAM, spanning nearly 40 Å, from the PqqA binding site in PqqD to the PqqE active site Fe4S4. Interactions among the various regions are concluded to arise from both direct contact and distal communication. The described experimental approach can be readily applied to the investigation of protein conformational communication among a large family of peptide-modifying rSAM enzymes

Gene Regulatory Network Inferences Using a Maximum-Relevance and Maximum-Significance Strategy

<div><p>Recovering gene regulatory networks from expression data is a challenging problem in systems biology that provides valuable information on the regulatory mechanisms of cells. A number of algorithms based on computational models are currently used to recover network topology. However, most of these algorithms have limitations. For example, many models tend to be complicated because of the “large p, small n” problem. In this paper, we propose a novel regulatory network inference method called the maximum-relevance and maximum-significance network (MRMSn) method, which converts the problem of recovering networks into a problem of how to select the regulator genes for each gene. To solve the latter problem, we present an algorithm that is based on information theory and selects the regulator genes for a specific gene by maximizing the relevance and significance. A first-order incremental search algorithm is used to search for regulator genes. Eventually, a strict constraint is adopted to adjust all of the regulatory relationships according to the obtained regulator genes and thus obtain the complete network structure. We performed our method on five different datasets and compared our method to five state-of-the-art methods for network inference based on information theory. The results confirm the effectiveness of our method.</p></div

Hydrogen–Deuterium Exchange Mass Spectrometry Identifies Local and Long-Distance Interactions within the Multicomponent Radical SAM Enzyme, PqqE

Interactions among proteins and peptides are essential for many biological activities including the tailoring of peptide substrates to produce natural products. The first step in the production of the bacterial redox cofactor pyrroloquinoline quinone (PQQ) from its peptide precursor is catalyzed by a radical SAM (rSAM) enzyme, PqqE. We describe the use of hydrogen–deuterium exchange mass spectrometry (HDX-MS) to characterize the structure and conformational dynamics in the protein–protein and protein–peptide complexes necessary for PqqE function. HDX-MS-identified hotspots can be discerned in binary and ternary complex structures composed of the peptide PqqA, the peptide-binding chaperone PqqD, and PqqE. Structural conclusions are supported by size-exclusion chromatography coupled to small-angle X-ray scattering (SEC-SAXS). HDX-MS further identifies reciprocal changes upon the binding of substrate peptide and S-adenosyl­methionine (SAM) to the PqqE/PqqD complex: long-range conformational alterations have been detected upon the formation of a quaternary complex composed of PqqA/PqqD/PqqE and SAM, spanning nearly 40 Å, from the PqqA binding site in PqqD to the PqqE active site Fe4S4. Interactions among the various regions are concluded to arise from both direct contact and distal communication. The described experimental approach can be readily applied to the investigation of protein conformational communication among a large family of peptide-modifying rSAM enzymes

Comparison of different methods on reaction chain with 4 species dataset.

<p>Comparison of different methods on reaction chain with 4 species dataset.</p

MRMSn for network inference.

<p>MRMSn for network inference.</p

Simple, Clean Preparation Method for Cross-Linked α‑Cyclodextrin Nanoparticles via Inclusion Complexation

A simple, clean method was presented in this letter to prepare cross-linked α-cyclodextrin (α-CD) nanoparticles with a low dispersion. The nanoparticles were synthesized in water by cross-linking the inclusion complex of α-CDs and poly­(ethylene glycol) (PEG). The structure of the nanoparticles was characterized by ¹H NMR, nuclear overhauser enhancement spectroscopy (NOESY), and wide-angle X-ray diffraction (XRD). Spherical morphology was observed by scanning electron microscopy (SEM) for these nanoparticles. Their average hydrodynamic radius was determined to be 67 nm by dynamic light scattering (DLS). Small guest molecules could be included in the cross-linked α-CD nanoparticles, and anticancer drug cisplatin was used to evaluate the drug release behavior

Simple, Clean Preparation Method for Cross-Linked α‑Cyclodextrin Nanoparticles via Inclusion Complexation

A simple, clean method was presented in this letter to prepare cross-linked α-cyclodextrin (α-CD) nanoparticles with a low dispersion. The nanoparticles were synthesized in water by cross-linking the inclusion complex of α-CDs and poly­(ethylene glycol) (PEG). The structure of the nanoparticles was characterized by ¹H NMR, nuclear overhauser enhancement spectroscopy (NOESY), and wide-angle X-ray diffraction (XRD). Spherical morphology was observed by scanning electron microscopy (SEM) for these nanoparticles. Their average hydrodynamic radius was determined to be 67 nm by dynamic light scattering (DLS). Small guest molecules could be included in the cross-linked α-CD nanoparticles, and anticancer drug cisplatin was used to evaluate the drug release behavior