scholarly journals Atomic design and fine-tuning of sub-nanometric Pt catalysts to tame hydrogen generation

2020 ◽  
Author(s):  
Jie Yang ◽  
Wenzhao Fu ◽  
Chaoqiu Chen ◽  
Wenyao Chen ◽  
Wugen Huang ◽  
...  
Keyword(s):  
Active Site ◽  
Catalytic Mechanism ◽  
Hydrogen Generation ◽  
Atomic Layer ◽  
Fine Tuning ◽  
Superior Performance ◽  
Single Atom ◽  
Intrinsic Activity ◽  
Atomic Structures ◽  
Metal Metal

Abstract Rational synthesis of sub-nanocatalysts with controllable electronic and atomic structures remains a challenge to break the limits of traditional catalysts for superior performance. Here we report the atomic-level precise synthesis of Pt/graphene sub-nanocatalysts (from single atom, dimer, and to cluster) by atomic layer deposition, achieved by a novel high temperature pulsed ozone strategy to controllably pre-create abundant in-plane epoxy groups on graphene as anchoring sites. The specific in-plane epoxy structure endows the deposited Pt species with outstanding uniformity, controllability and stability. Their size-depended electronic and geometric effects have been observed for ammonia borane hydrolysis, revealing a volcano-type dependence of intrinsic activity on their sizes. Their active site structures have been identified based on extensive characterizations, dynamic compensation effect, kinetic isotope experiments and density function theory simulation. The Pt dimers show the highest catalytic activity and good durability than Pt single atoms and nanoparticles, ascribed to the unique C-Pt-Pt-O (C5Pt2O, metal-metal bond dimer) active site structure. Our work provides new insights into the precise tailoring and catalytic mechanism in sub-nanometer level.

Quasiperiodic interfaces: HREM observations of grain and phase boundaries

1990 ◽  
Vol 48 (4) ◽  
pp. 332-333
Author(s):  
K. L. Merkle
Keyword(s):  
Atomic Structure ◽  
Direct Determination ◽  
Lattice Parameter ◽  
Atomic Scale ◽  
Misfit Dislocations ◽  
Oxide Systems ◽  
Atomic Structures ◽  
Periodic Arrays ◽  
Parameter Ratio ◽  
Metal Metal

The atomic structures of internal interfaces have recently received considerable attention, not only because of their importance in determining many materials properties, but also because the atomic structure of many interfaces has become accessible to direct atomic-scale observation by modem HREM instruments. In this communication, several interface structures are examined by HREM in terms of their structural periodicities along the interface.It is well known that heterophase boundaries are generally formed by two low-index planes. Often, as is the case in many fcc metal/metal and metal/metal-oxide systems, low energy boundaries form in the cube-on-cube orientation on (111). Since the lattice parameter ratio between the two materials generally is not a rational number, such boundaries are incommensurate. Therefore, even though periodic arrays of misfit dislocations have been observed by TEM techniques for numerous heterophase systems, such interfaces are quasiperiodic on an atomic scale. Interfaces with misfit dislocations are semicoherent, where atomically well-matched regions alternate with regions of misfit. When the misfit is large, misfit localization is often difficult to detect, and direct determination of the atomic structure of the interface from HREM alone, may not be possible.

Structures of c-di-GMP/cGAMP degrading phosphodiesterase VcEAL: identification of a novel conformational switch and its implication

2019 ◽  
Vol 476 (21) ◽  
pp. 3333-3353 ◽  
Author(s):  
Malti Yadav ◽  
Kamalendu Pal ◽  
Udayaditya Sen
Keyword(s):  
Active Site ◽  
Metal Binding ◽  
Metal Ion ◽  
Triosephosphate Isomerase ◽  
Catalytic Mechanism ◽  
Degradation Mechanism ◽  
Structural Basis ◽  
Conserved Residues ◽  
Phosphodiester Bond ◽  
Cyclic Dinucleotides

Cyclic dinucleotides (CDNs) have emerged as the central molecules that aid bacteria to adapt and thrive in changing environmental conditions. Therefore, tight regulation of intracellular CDN concentration by counteracting the action of dinucleotide cyclases and phosphodiesterases (PDEs) is critical. Here, we demonstrate that a putative stand-alone EAL domain PDE from Vibrio cholerae (VcEAL) is capable to degrade both the second messenger c-di-GMP and hybrid 3′3′-cyclic GMP–AMP (cGAMP). To unveil their degradation mechanism, we have determined high-resolution crystal structures of VcEAL with Ca2+, c-di-GMP-Ca2+, 5′-pGpG-Ca2+ and cGAMP-Ca2+, the latter provides the first structural basis of cGAMP hydrolysis. Structural studies reveal a typical triosephosphate isomerase barrel-fold with substrate c-di-GMP/cGAMP bound in an extended conformation. Highly conserved residues specifically bind the guanine base of c-di-GMP/cGAMP in the G2 site while the semi-conserved nature of residues at the G1 site could act as a specificity determinant. Two metal ions, co-ordinated with six stubbornly conserved residues and two non-bridging scissile phosphate oxygens of c-di-GMP/cGAMP, activate a water molecule for an in-line attack on the phosphodiester bond, supporting two-metal ion-based catalytic mechanism. PDE activity and biofilm assays of several prudently designed mutants collectively demonstrate that VcEAL active site is charge and size optimized. Intriguingly, in VcEAL-5′-pGpG-Ca2+ structure, β5–α5 loop adopts a novel conformation that along with conserved E131 creates a new metal-binding site. This novel conformation along with several subtle changes in the active site designate VcEAL-5′-pGpG-Ca2+ structure quite different from other 5′-pGpG bound structures reported earlier.

Engineering Ru atomic structures toward enhanced kinetics of hydrogen generation

2021 ◽  
Vol 235 ◽  
pp. 116507
Author(s):  
Wenzhao Fu ◽  
Qianhong Wang ◽  
Wenyao Chen ◽  
Gang Qian ◽  
Jing Zhang ◽  
...  
Keyword(s):  
Hydrogen Generation ◽  
Atomic Structures ◽  
Kinetics Of

scholarly journals Serine protease dynamics revealed by NMR analysis of the thrombin-thrombomodulin complex

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Riley B. Peacock ◽  
Taylor McGrann ◽  
Marco Tonelli ◽  
Elizabeth A. Komives
Keyword(s):  
Active Site ◽  
Serine Proteases ◽  
Protein C ◽  
Catalytic Mechanism ◽  
Bond Cleavage ◽  
Peptide Bond ◽  
Peptide Bond Cleavage ◽  
Exchange Mass Spectrometry ◽  
Catalytically Active ◽  
Hydrogen Deuterium

AbstractSerine proteases catalyze a multi-step covalent catalytic mechanism of peptide bond cleavage. It has long been assumed that serine proteases including thrombin carry-out catalysis without significant conformational rearrangement of their stable two-β-barrel structure. We present nuclear magnetic resonance (NMR) and hydrogen deuterium exchange mass spectrometry (HDX-MS) experiments on the thrombin-thrombomodulin (TM) complex. Thrombin promotes procoagulative fibrinogen cleavage when fibrinogen engages both the anion binding exosite 1 (ABE1) and the active site. It is thought that TM promotes cleavage of protein C by engaging ABE1 in a similar manner as fibrinogen. Thus, the thrombin-TM complex may represent the catalytically active, ABE1-engaged thrombin. Compared to apo- and active site inhibited-thrombin, we show that thrombin-TM has reduced μs-ms dynamics in the substrate binding (S1) pocket consistent with its known acceleration of protein C binding. Thrombin-TM has increased μs-ms dynamics in a β-strand connecting the TM binding site to the catalytic aspartate. Finally, thrombin-TM had doublet peaks indicative of dynamics that are slow on the NMR timescale in residues along the interface between the two β-barrels. Such dynamics may be responsible for facilitating the N-terminal product release and water molecule entry that are required for hydrolysis of the acyl-enzyme intermediate.

Atomic Design and Fine-Tuning of Subnanometric Pt Catalysts to Tame Hydrogen Generation

ACS Catalysis ◽  
2021 ◽  
pp. 4146-4156
Author(s):  
Jie Yang ◽  
Wenzhao Fu ◽  
Chaoqiu Chen ◽  
Wenyao Chen ◽  
Wugen Huang ◽  
...  
Keyword(s):  
Hydrogen Generation ◽  
Fine Tuning ◽  
Pt Catalysts

scholarly journals Crystal Structure of Escherichia coli Agmatinase: Catalytic Mechanism and Residues Relevant for Substrate Specificity

2021 ◽  
Vol 22 (9) ◽  
pp. 4769
Author(s):  
Pablo Maturana ◽  
María S. Orellana ◽  
Sixto M. Herrera ◽  
Ignacio Martínez ◽  
Maximiliano Figueroa ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Active Site ◽  
Catalytic Mechanism ◽  
Conformational Dynamics ◽  
High Specificity ◽  
Arginine Decarboxylase ◽  
Space Groups ◽  
X Ray Crystallography ◽  
High Dynamics ◽  
Dynamics Simulations

Agmatine is the product of the decarboxylation of L-arginine by the enzyme arginine decarboxylase. This amine has been attributed to neurotransmitter functions, anticonvulsant, anti-neurotoxic, and antidepressant in mammals and is a potential therapeutic agent for diseases such as Alzheimer’s, Parkinson’s, and cancer. Agmatinase enzyme hydrolyze agmatine into urea and putrescine, which belong to one of the pathways producing polyamines, essential for cell proliferation. Agmatinase from Escherichia coli (EcAGM) has been widely studied and kinetically characterized, described as highly specific for agmatine. In this study, we analyze the amino acids involved in the high specificity of EcAGM, performing a series of mutations in two loops critical to the active-site entrance. Two structures in different space groups were solved by X-ray crystallography, one at low resolution (3.2 Å), including a guanidine group; and other at high resolution (1.8 Å) which presents urea and agmatine in the active site. These structures made it possible to understand the interface interactions between subunits that allow the hexameric state and postulate a catalytic mechanism according to the Mn2+ and urea/guanidine binding site. Molecular dynamics simulations evaluated the conformational dynamics of EcAGM and residues participating in non-binding interactions. Simulations showed the high dynamics of loops of the active site entrance and evidenced the relevance of Trp68, located in the adjacent subunit, to stabilize the amino group of agmatine by cation-pi interaction. These results allow to have a structural view of the best-kinetic characterized agmatinase in literature up to now.

scholarly journals Structural and functional insights into esterase-mediated macrolide resistance

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Michał Zieliński ◽  
Jaeok Park ◽  
Barry Sleno ◽  
Albert M. Berghuis
Keyword(s):  
Active Site ◽  
Pathogenic Bacteria ◽  
Catalytic Mechanism ◽  
Three Dimensional ◽  
Resistance Mechanisms ◽  
Docking Studies ◽  
Macrolide Resistance ◽  
Flexible Docking ◽  
Sequence Identity ◽  
Substrate Spectrum

AbstractMacrolides are a class of antibiotics widely used in both medicine and agriculture. Unsurprisingly, as a consequence of their exensive usage a plethora of resistance mechanisms have been encountered in pathogenic bacteria. One of these resistance mechanisms entails the enzymatic cleavage of the macrolides’ macrolactone ring by erythromycin esterases (Eres). The most frequently identified Ere enzyme is EreA, which confers resistance to the majority of clinically used macrolides. Despite the role Eres play in macrolide resistance, research into this family enzymes has been sparse. Here, we report the first three-dimensional structures of an erythromycin esterase, EreC. EreC is an extremely close homologue of EreA, displaying more than 90% sequence identity. Two structures of this enzyme, in conjunction with in silico flexible docking studies and previously reported mutagenesis data allowed for the proposal of a detailed catalytic mechanism for the Ere family of enzymes, labeling them as metal-independent hydrolases. Also presented are substrate spectrum assays for different members of the Ere family. The results from these assays together with an examination of residue conservation for the macrolide binding site in Eres, suggests two distinct active site archetypes within the Ere enzyme family.

Active site engineering of atomically dispersed transition metal-heteroatom-carbon catalysts for oxygen reduction

2021 ◽  
Author(s):  
Jiawei Zhu ◽  
Shichun Mu
Keyword(s):  
Transition Metal ◽  
Oxygen Reduction ◽  
Active Site ◽  
Catalytic Reactions ◽  
Single Atom ◽  
Carbon Catalysts

Owing to the advantage of atomic utilization, the single-atom catalyst has attracted much attention and been employed in multifarious catalytic reactions. Their definite site configuration is favorable for exploring the...

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