Alkane upgrading effected by silica-supported pincer-iridium catalysts: Evidence of a shared active site with solution-phase species

2020 ◽  
Author(s):  
Alan Goldman ◽  
Boris Sheludko ◽  
Fuat Celik ◽  
Cristina Castro
Keyword(s):  
Active Site ◽  
Solution Phase ◽  
Iridium Catalysts

Atomically dispersed iridium catalysts for multifunctional electrocatalysis

2020 ◽  
Vol 8 (37) ◽  
pp. 19665-19673 ◽  
Author(s):  
Qiaoqiao Zhang ◽  
Zhiyao Duan ◽  
Yin Wang ◽  
Lina Li ◽  
Bing Nan ◽  
...  
Keyword(s):  
Active Site ◽  
Iridium Catalysts ◽  
Nitrogen Doped ◽  
Nitrogen Doped Graphene ◽  
Doped Graphene

Atomically dispersed iridium embedded nitrogen-doped graphene shows excellent HER, OER, and ORR performance, where the IrN4–G center is the active site for these reactions.

Another Look at Thrombin-GPIba Interaction in Solution Phaseα

Blood ◽  
2005 ◽  
Vol 106 (11) ◽  
pp. 1646-1646
Author(s):  
Subramanian Yegneswaran ◽  
James R. Roberts ◽  
Richard A. McClintock ◽  
Zaverio M. Ruggeri
Keyword(s):  
Steady State ◽  
Active Site ◽  
Binding Capacity ◽  
Resonance Energy Transfer ◽  
Resonance Energy ◽  
Solution Phase ◽  
Complete Agreement ◽  
Experimental Conditions ◽  
Platelet Surface ◽  
Covalently Linked

Abstract Glycoprotein (GP) Ib in the GPIb-IX-V receptor complex is the most abundant binding site for thrombin on the platelet surface. Virtually the entire thrombin binding capacity of GPIb has been shown to reside on the N-terminal region of the GPIba subunit of GPIb. Recently, Celikel et al and Dumas et al independently solved the structure of the thrombin-GPIba complex. Although comparable N-terminal fragments, comprising residues 1–290 of GPIba, were used for crystallization in both studies, significant differences existed between the two structures. Thus, it is still unclear how GPIb interacts with thrombin. In this study we have examined the interaction of GPIba with thrombin in solution phase. Human a-thrombin was labeled active site-specifically with either dansyl (D) dye via a Glu-Gly-Arg (EGR) linker to yield DEGR-thrombin or with a fluorescein or 5-((((2-iodoacetyl)amino)ethyl)amino)naphthalene-1-sulfonic acid dye (IAEDANS) via a Phe-Pro-Arg tether to yield Fluorescein-thrombin and AEDANS-thrombin, respectively. When DEGR-thrombin (initially 100 nM) was titrated with human glycocalicin, the N-terminal fragment of GPIbα compring ~400 residues, the steady state anisotropy of DEGR-thrombin decreased by ~ 22% before reaching a plateau at ~ 100 nM protein suggesting an interaction between Glycocalicin and DEGR-thrombin. A ~ 10% increase in anisotropy of the dansyl moiety was observed when a recombinant wild-type fragment of GPIba (residues 1–290) containing the three sulfated-tyrosines at positions 276, 277 and 279 was titrated into DEGR-thrombin. However, this change in anisotropy was not observed when either a mutant with tyrosine 276 mutated to phenylalanine (Y276F) or a Y279F mutant (named analogously) were titrated into DEGR-thrombin. To examine if dimerization of GPIba was important for thrombin interaction, a construct was made such that residues 1–288 of GPIba were covalently linked through a C-terminal extended sequence containing 4 Cys residues, and expressed as dimer (C65 +). When C65+ was titrated into DEGR-thrombin, the anisotropy of the dansyl probe increased by ~ 29% before reaching a plateau at 130 nM C65+, suggesting that thrombin can bind dimeric GPIba. To elucidate the stoicheometry of the thrombin-GPIba complex, resonance energy transfer (RET) experiments were performed between AEDANS donor-labeled thrombin and Fluorescein acceptor labeled thrombin. The AEDANS-thrombin and Fl-thrombin were mixed in equimolar ratios and then titrated with increasing amounts of GPIba. No change in donor intensity was observed suggestive of the absence of a AEDANS-thrombin- GPIba- Fl-thrombin complex. In conclusion, our data suggests that the GPIba interaction with thrombin can be observed in solution phase using steady state fluorescence by appropriately active site-labeled thrombin. Tyrosine sulfation at positions 276 and 279 are critical for this interaction. This observation is in complete agreement with both crystal structures where the contact site with exosite II of thrombin seems to be mediated by residues 275–279 of GPIba. However, using RET, we could not find a thrombin-GPIba-thrombin complex in solution under the present experimental conditions.

scholarly journals Allosteric regulation of glycogen phosphorylase solution phase structural dynamics at high spatial resolution

2019 ◽  
Author(s):  
Monika Kish ◽  
Victoria Smith ◽  
Sivaraman Subramanian ◽  
Frank Vollmer ◽  
Natasha Lethbridge ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Structural Dynamics ◽  
Active Site ◽  
Glycogen Phosphorylase ◽  
Direct Evidence ◽  
Solution Phase ◽  
Hydrogen Deuterium Exchange ◽  
Exchange Mass Spectrometry ◽  
Hydrogen Deuterium ◽  
Deuterium Exchange Mass Spectrometry

AbstractGlycogen phosphorylase (GlyP) was the first allosteric enzyme to be described. Yet, the precise dynamic changes in solution phase structure and stability that underpin functional regulation have remained elusive. We have developed a new fully-automated and highly flexible implementation of hydrogen/deuterium-exchange mass spectrometry, operating in the millisecond regime. This enabled measurements of the solution phase local structural dynamics involved in allosteric regulation of GlyP. Here, we quantify GlyP structural dynamics in solution, describing correlated changes in structure in the activated (pSer14) and inhibited (glucose-6-phosphate bound) forms of the enzyme. The sensitivity of these measurements discerned that the 250s’ loop is natively disordered in the apo T-state, adopting a more ordered conformation in the active state. The quantitative change in stability of the 280s loop is identified, providing the first direct evidence of the entropic switch that sterically regulates substrate access to the active site.Significance StatementWe have developed a new fully-automated and highly flexible implementation of hydrogen/deuterium-exchange mass spectrometry, operating in the millisecond regime. Measurements of glycogen phosphorylase quantify the solution phase stability of local structure at near-amino acid structural resolution and with no appreciable lower limit of stability. This uncovered the highly-resolved local alterations in stability which provides direct evidence of the entropic mechanism by which access to the active site is gated by the 280s loop.FootnotesAuthor contributions: M.K., V.S., S.S., N.L., F.V., N.B., L.C. and J.J.P. designed research; M.K., V.S., S.S., L.C. and J.J.P. performed research; M.K., V.S., S.S., L.C. and J.J.P. analyzed data; and M.K. and J.J.P. wrote the manuscript.

Transition alpha structure in beta-isomorphous Nb-Hf alloys

1987 ◽  
Vol 45 ◽  
pp. 232-233
Author(s):  
R.W. Carpenter ◽  
Changhai Li ◽  
David J. Smith
Keyword(s):  
Solid Solution ◽  
Solution Phase ◽  
Miscibility Gap ◽  
Large Strains ◽  
Solid Solution Phase ◽  
Two Phase ◽  
Diffuse Intensity ◽  
Metastable Form ◽  
The Matrix ◽  
Equilibrium Morphology

Binary Nb-Hf alloys exhibit a wide bcc solid solution phase field at temperatures above the Hfα→ß transition (2023K) and a two phase bcc+hcp field at lower temperatures. The β solvus exhibits a small slope above about 1500K, suggesting the possible existence of a miscibility gap. An earlier investigation showed that two morphological forms of precipitate occur during the bcc→hcp transformation. The equilibrium morphology is rod-type with axes along <113> bcc. The crystallographic habit of the rod precipitate follows the Burgers relations: {110}||{0001}, <112> || <1010>. The earlier metastable form, transition α, occurs as thin discs with {100} habit. The {100} discs induce large strains in the matrix. Selected area diffraction examination of regions ∼2 microns in diameter containing many disc precipitates showed that, a diffuse intensity distribution whose symmetry resembled the distribution of equilibrium α Bragg spots was associated with the disc precipitate.

Locating Al in the DABCO catalyst before and after Al extraction

1990 ◽  
Vol 48 (4) ◽  
pp. 265-267
Author(s):  
Kathleen B. Reuter
Keyword(s):  
Active Site ◽  
Inverse Relationship ◽  
Transverse Direction ◽  
Reaction Rate ◽  
Acid Phosphate ◽  
Fracture Surfaces ◽  
Al Content ◽  
Before And After ◽  
Relationship Of

The reaction rate and efficiency of piperazine to 1,4-diazabicyclo-octane (DABCO) depends on the Si/Al ratio of the MFI topology catalysts. The Al was shown to be the active site, however, in the Si/Al range of 30-200 the reaction rate increases as the Si/Al ratio increases. The objective of this work was to determine the location and concentration of Al to explain this inverse relationship of Al content with reaction rate.Two silicalite catalysts in the form of 1/16 inch SiO2/Al2O3 bonded extrudates were examined: catalyst A with a Si/Al of 83; and catalyst B, the acid/phosphate Al extracted form of catalyst A, with a Si/Al of 175. Five extrudates from each catalyst were fractured in the transverse direction and particles were obtained from the fracture surfaces near the center of the extrudate diameter. Particles were also obtained from the outside surfaces of five extrudates.

A High Resolution Study of Alumina Supported Iridium Catalysts

1980 ◽  
Vol 38 ◽  
pp. 202-203
Author(s):  
C. Stoeckert ◽  
B. Etherton ◽  
M. Beer ◽  
J. Gryder
Keyword(s):  
Electron Microscope ◽  
High Resolution ◽  
Metal Particles ◽  
Optical Transfer Function ◽  
Particle Sizes ◽  
Iridium Catalysts ◽  
Transmission Electron ◽  
Optical Transfer ◽  
Conventional Transmission Electron Microscope ◽  
Resolution Study

The interpretation of the activity of catalysts requires information about the sizes of the metal particles, since this has implications for the number of surface atoms available for reaction. To determine the particle dimensions we used a high resolution STEM1. Such an instrument with its simple optical transfer function is far more suitable than a conventional transmission electron microscope for the establishment of particle sizes. We report here our study on the size and number distribution of Ir particles supported on Al2O3 and also examine simple geometric models for the shape of Ir particles.

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.

Contributions of the substrate-binding arginine residues to maleate-induced closure of the active site of Escherichia coli aspartate aminotransferase

2001 ◽  
Vol 268 (6) ◽  
pp. 1640-1645
Author(s):  
Annelise Matharu ◽  
Hideyuki Hayashi ◽  
Hiroyuki Kagamiyama ◽  
Bruno Maras ◽  
Robert A. John
Keyword(s):  
Escherichia Coli ◽  
Active Site ◽  
Aspartate Aminotransferase ◽  
Substrate Binding ◽  
Arginine Residues
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