Proton relay system in the active site of maltodextrinphosphorylase via hydrogen bonds with large proton polarizability: an FT-IR difference spectroscopy study

1999 ◽  
Vol 28 (3) ◽  
pp. 200-207 ◽  
Author(s):  
F. Bartl ◽  
Dieter Palm ◽  
Reinhard Schinzel ◽  
Georg Zundel
Keyword(s):  
Hydrogen Bonds ◽  
Active Site ◽  
Difference Spectroscopy ◽  
Spectroscopy Study ◽  
Relay System ◽  
Proton Relay ◽  
Ft Ir

scholarly journals Interplay of nucleophilic catalysis with proton transfer in the nitrile reductase QueF from Escherichia coli

2019 ◽  
Vol 9 (3) ◽  
pp. 842-853 ◽  
Author(s):  
Jihye Jung ◽  
Jan Braun ◽  
Tibor Czabany ◽  
Bernd Nidetzky
Keyword(s):  
Escherichia Coli ◽  
Hydrogen Bonds ◽  
Proton Transfer ◽  
Active Site ◽  
Nucleophilic Catalysis ◽  
Proton Relay ◽  
Network Of Hydrogen Bonds ◽  
Site Network ◽  
Nitrile Reduction ◽  
Enzyme Intermediate

Proton relay through an active-site network of hydrogen bonds promotes enzymatic nitrile reduction to amine via a covalent thioimidate enzyme intermediate.

WHICH IS THE PROTON-SHUTTLE IN ISOXANTHOPTERIN DEAMINASE? QM/MM MD UNDERSTANDING

2013 ◽  
Vol 12 (08) ◽  
pp. 1341002 ◽  
Author(s):  
XIN ZHANG ◽  
MING LEI
Keyword(s):  
Crystal Structure ◽  
Molecular Dynamics ◽  
Hydrogen Bonds ◽  
Proton Transfer ◽  
Glutamic Acid ◽  
Active Site ◽  
Nucleophilic Attack ◽  
Zinc Ions ◽  
Initial Model ◽  
Dynamics Simulations

The deamination process of isoxanthopterin catalyzed by isoxanthopterin deaminase was determined using the combined QM(PM3)/MM molecular dynamics simulations. In this paper, the updated PM3 parameters were employed for zinc ions and the initial model was built up based on the crystal structure. Proton transfer and following steps have been investigated in two paths: Asp336 and His285 serve as the proton shuttle, respectively. Our simulations showed that His285 is more effective than Aap336 in proton transfer for deamination of isoxanthopterin. As hydrogen bonds between the substrate and surrounding residues play a key role in nucleophilic attack, we suggested mutating Thr195 to glutamic acid, which could enhance the hydrogen bonds and help isoxanthopterin get close to the active site. The simulations which change the substrate to pterin 6-carboxylate also performed for comparison. Our results provide reference for understanding of the mechanism of deaminase and for enhancing the deamination rate of isoxanthopterin deaminase.

Analysis of Noise for Rapid-Scan and Step-Scan Methods of FT-IR Difference Spectroscopy

2001 ◽  
Vol 55 (9) ◽  
pp. 1161-1165 ◽  
Author(s):  
Steven S. Andrews ◽  
Steven G. Boxer
Keyword(s):  
Difference Spectroscopy ◽  
Rapid Scan ◽  
Ft Ir

The catalytic mechanism ofDrosophilaalcohol dehydrogenase: Evidence for a proton relay modulated by the coupled ionization of the active site Lysine/Tyrosine pair and a NAD+ribose OH switch

2003 ◽  
Vol 51 (2) ◽  
pp. 289-298 ◽  
Author(s):  
Assen Koumanov ◽  
Jordi Benach ◽  
Silvia Atrian ◽  
Roser Gonzàlez-Duarte ◽  
Andrey Karshikoff ◽  
...  
Keyword(s):  
Active Site ◽  
Catalytic Mechanism ◽  
Proton Relay

Mono- and dinuclear CuII complexes of the benzyldipicolylamine (BDPA) ligand: crystal structure, synthesis and characterization

2017 ◽  
Vol 73 (11) ◽  
pp. 1024-1029
Author(s):  
Dharmalingam Sivanesan ◽  
Min Hye Youn ◽  
Ki Tae Park ◽  
Hak Joo Kim ◽  
Andrews Nirmala Grace ◽  
...  
Keyword(s):  
Hydrogen Bonds ◽  
Reaction Medium ◽  
Bound Water ◽  
Dinuclear Complex ◽  
Residual Moisture ◽  
Structure Synthesis ◽  
Distorted Octahedral ◽  
Vis Spectroscopy ◽  
Ft Ir ◽  
Solvent Molecules

The crystal structures of mono- and dinuclear CuII trifluoromethanesulfonate (triflate) complexes with benzyldipicolylamine (BDPA) are described. From equimolar amounts of Cu(triflate)2 and BDPA, a water-bound CuII mononuclear complex, aqua(benzyldipicolylamine-κ3 N,N′,N′′)bis(trifluoromethanesulfonato-κO)copper(II) tetrahydrofuran monosolvate, [Cu(CF3SO3)2(C19H19N3)(H2O)]·C4H8O, (I), and a triflate-bridged CuII dinuclear complex, bis(μ-trifluoromethanesulfonato-κ2 O:O′)bis[(benzyldipicolylamine-κ3 N,N′,N′′)(trifluoromethanesulfonato-κO)copper(II)], [Cu2(CF3SO3)4(C19H19N3)2], were synthesized. The presence of residual moisture in the reaction medium afforded water-bound complex (I), whereas dinuclear complex (II) was synthesized from an anhydrous reaction medium. Single-crystal X-ray structure analysis reveals that the CuII centres adopt slightly distorted octahedral geometries in both complexes. The metal-bound water molecule in (I) is involved in intermolecular O—H...O hydrogen bonds with triflate ligands and tetrahydrofuran solvent molecules. In (II), weak intermolecular C—H...F(triflate) and C—H...O(triflate) hydrogen bonds stabilize the crystal lattice. Complexes (I) and (II) were also characterized fully using FT–IR and UV–Vis spectroscopy, cyclic voltammetry and elemental analysis.

scholarly journals How [FeFe]-Hydrogenase Facilitates Bidirectional Proton Transfer

2019 ◽  
Author(s):  
Moritz Senger ◽  
Viktor Eichmann ◽  
Konstantin Laun ◽  
Jifu Duan ◽  
Florian Wittkamp ◽  
...  
Keyword(s):  
Amino Acid ◽  
Proton Transfer ◽  
Active Site ◽  
Molecular Hydrogen ◽  
H2 Production ◽  
Amino Acid Residues ◽  
Difference Spectroscopy ◽  
Dynamic Changes ◽  
In Situ Ir

Hydrogenases are metalloenzymes that catalyse the interconversion of protons and molecular hydrogen, H2. [FeFe]-hydrogenases show particularly high rates of hydrogen turnover and have inspired numerous compounds for biomimetic H2 production. Two decades of research on the active site cofactor of [FeFe]-hydrogenases have put forward multiple models of the catalytic proceedings. In comparison, understanding of the catalytic proton transfer is poor. We were able to identify the amino acid residues forming a proton transfer pathway between active site cofactor and bulk solvent; however, the exact mechanism of catalytic proton transfer remained inconclusive. Here, we employ in situ IR difference spectroscopy on the [FeFe]-hydrogenase from Chlamydomonas reinhardtii evaluating dynamic changes in the hydrogen-bonding network upon catalytic proton transfer. Our analysis allows for a direct, molecular unique assignment to individual amino acid residues. We found that transient protonation changes of arginine and glutamic acid residues facilitate bidirectional proton transfer in [FeFe]-hydrogenases.<br>

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