scholarly journals Properties of the histidine residues of indole-chymotrypsin. Implications for the activation process and catalytic mechanism.

1975 ◽  
Vol 147 (3) ◽  
pp. 411-416 ◽  
Author(s):  
W H Cruickshank ◽  
H Kaplan
Keyword(s):  
Charge Transfer ◽  
Aspartic Acid ◽  
Catalytic Mechanism ◽  
Enzymic Activity ◽  
Activation Process ◽  
Linear Free Energy Relationship ◽  
Relay System ◽  
X Ray ◽  
Histidine Residues ◽  
Linear Free Energy

The use of a linear free-energy relationship shows that both histidine residues of alpha-chymotrypsin and chymotrypsinogen are super-reactive toward 1-fluoro-2,4-dinitrobenzene. The binding of indole to the specificity site of alpha-chymotrypsin causes both histidine residues to become less reactive. On the basis of these results and those from X-ray-crystallographic studies, the following conclusions are made. (1) The super-reactivity of the catalytic-site histidine-57 is due to charge transfer from aspartic acid-102 by means of hydrogen bonding. (2) The aspartic acid-102-histidine-57-serine-195 ‘charge-relay’ system is not complete in the zymogen or native enzyme and only on binding of a suitable substrate or ligand to the specificity site of the enzyme is the charge transfer to serine-195 completed. (3) The lack of substantial enzymic activity in the zymogen is due to the absence of a completed specificity site, and therefore it cannot bind suitable substrates or ligands to induce completion of the charge-relay system.

Triplet Charge Transfer Complex between Excited Electron Acceptor and Ground State Electron Donor

1972 ◽  
Vol 50 (24) ◽  
pp. 4052-4056 ◽  
Author(s):  
Rafik O. Loutfy ◽  
Raouf O. Loutfy
Keyword(s):  
Free Energy ◽  
Charge Transfer ◽  
Linear Free Energy Relationship ◽  
Quenching Rate ◽  
Linear Free Energy ◽  
Oxidation Potentials ◽  
Half Wave ◽  
Ct Complex ◽  
Quenching Rate Constant ◽  
Ground State Electron

The half-wave reduction and oxidation potentials, E1/2's, of carbonyl compounds and amines, respectively, are used to estimate the location of triplet charge transfer states (CT). A linear free-energy relationship between the calculated CT triplet energies and the corresponding carbonyl molecules triplet energies was obtained. It has also been found that the free energy change (ΔF) for CT complex formation correlate with the triplet carbonyl quenching rate constant kq.

scholarly journals Catalytic mechanism of α-retaining glucosyl transfer by Corynebacterium callunae starch phosphorylase: the role of histidine-334 examined through kinetic characterization of site-directed mutants

2005 ◽  
Vol 387 (2) ◽  
pp. 437-445 ◽  
Author(s):  
Alexandra SCHWARZ ◽  
Francesco Maria PIERFEDERICI ◽  
Bernd NIDETZKY
Keyword(s):  
Steady State ◽  
Transition State ◽  
Catalytic Mechanism ◽  
Single Step ◽  
Free Enzyme ◽  
Linear Free Energy Relationship ◽  
Wild Type ◽  
Starch Phosphorylase ◽  
Linear Free Energy ◽  
Corynebacterium Callunae

Purified site-directed mutants of Corynebacterium callunae starch phosphorylase in which His-334 was replaced by an alanine, glutamine or asparagine residue were characterized by steady-state kinetic analysis of enzymic glycosyl transfer to and from phosphate and studies of ligand binding to the active site. Compared with wild-type, the catalytic efficiencies for phosphorolysis of starch at 30 °C and pH 7.0 decreased approx. 150- and 50-fold in H334Q (His334→Gln) and H334N mutants, and that of H334A was unchanged. In the direction of α-glucan synthesis, selectivity for the reaction with G1P (α-D-glucose 1-phosphate) compared with the selectivity for reaction with α-D-xylose 1-phosphate decreased from a wild-type value of ∼20000 to 2600 and 100 in H334N and H334Q respectively. Binding of G1P to the free enzyme was weakened between 10-fold (H334N, H334Q) and 50-fold (H334A) in the mutants, whereas binding to the complex of enzyme and α-glucan was not affected. Quenching of fluorescence of the pyridoxal 5′-phosphate cofactor was used to examine interactions of the inhibitor GL (D-gluconic acid 1,5-lactone) with wild-type and mutant enzymes in transient and steady-state experiments. GL binding to the free enzyme and the enzyme–phosphate complex occurred in a single step. The 50-fold higher constant (Kd) for GL dissociation from H334Q bound to phosphate resulted from an increased off-rate for the ligand in the mutant, compared with wild-type. A log-log correlation of catalytic-centre activity for phosphorolysis of starch with a reciprocal Kd value established a linear free-energy relationship (slope=1.19±0.07; r2=0.991) across the series of wild-type and mutant enzymes. It reveals that GL in combination with phosphate has properties of a transition state analogue and that the His-334 side chain has a role in selectively stabilizing the transition state of the reaction.

scholarly journals Substrate analogues as probes of the catalytic mechanism of l-mandelate dehydrogenase from Rhodotorula graminis

1994 ◽  
Vol 297 (3) ◽  
pp. 647-652 ◽  
Author(s):  
O Smékal ◽  
G A Reid ◽  
S K Chapman
Keyword(s):  
Transition State ◽  
Catalytic Mechanism ◽  
Activation Parameters ◽  
Linear Free Energy Relationship ◽  
Free Energies ◽  
Linear Free Energy ◽  
Kinetic Isotope ◽  
Substrate Analogues ◽  
Reaction Constant ◽  
Delta G

A detailed kinetic analysis of the oxidation of mono-substituted mandelates catalysed by L-(+)-mandelate dehydrogenase (L-MDH) from Rhodotorula graminis has been carried out to elucidate the role of the substrate in the catalytic mechanism. Values of Km and kcat. (25 degrees C, pH 7.5) were determined for mandelate and eight substrate analogues. Values of the activation parameters, delta H++ and delta S++ (determined over the range 5-37 degrees C), for mandelate and all substrate analogues were compensatory resulting in similar low values for free energies of activation delta G++ (approx. 60 kJ.mol-1 at 298.15 K) in all cases. A kinetic-isotope-effect value of 1.1 +/- 0.1 was observed using D,L-[2-2H]mandelate as substrate and was invariant over the temperature range studied. The logarithm of kcat. values for the enzymic oxidation of mandelate and all substrate analogues (except 4-hydroxymandelate) showed good correlation with Taft's dual substituent constant omega (where omega = omega I + 0.64 omega +R) and gave a positive reaction constant value, rho, of 0.36 +/- 0.07. This linear free-energy relationship was verified by analysing the data using isokinetic methods. These findings support the hypothesis that the enzyme-catalysed reaction proceeds via the same transition state for each substrate and indicates that this transition state is relatively nonpolar but has an electron-rich centre at the alpha-carbon position.

Copper–oxygen Dynamics in Tyrosinase

2019 ◽  
Author(s):  
Nobutaka Fujieda ◽  
Sachiko Yanagisawa ◽  
Minoru Kubo ◽  
Genji Kurisu ◽  
Shinobu Itoh
Keyword(s):  
Catalytic Mechanism ◽  
Substrate Binding ◽  
Active Form ◽  
Copper Ion ◽  
Atomic Resolution ◽  
Oxygen Species ◽  
X Ray ◽  
Oxygen Dynamics ◽  
Insight Into ◽  
Copper Centre

To unveil the activation of dioxygen on the copper centre (Cu<sub>2</sub>O<sub>2</sub>core) of tyrosinase, we performed X-ray crystallograpy with active-form tyrosinase at near atomic resolution. This study provided a novel insight into the catalytic mechanism of the tyrosinase, including the rearrangement of copper-oxygen species as well as the intramolecular migration of copper ion induced by substrate-binding.<br>

Synthesis and characterization of a series of 1-methyl-4-[2-aryl-1-diazenyl]piperazines and a series of ethyl 4-[2-aryl-1-diazenyl]-1-piperazinecarboxylates

2004 ◽  
Vol 82 (8) ◽  
pp. 1294-1303 ◽  
Author(s):  
Vanessa Renée Little ◽  
Keith Vaughan
Keyword(s):  
Free Energy ◽  
Chemical Shifts ◽  
Linear Free Energy Relationship ◽  
Piperazine Ring ◽  
Linear Free Energy ◽  
In Series ◽  
Methylene Groups ◽  
Diazonium Coupling ◽  
The Difference

1-Methylpiperazine was coupled with a series of diazonium salts to afford the 1-methyl-4-[2-aryl-1-diazenyl]piperazines (2), a new series of triazenes, which have been characterized by 1H and 13C NMR spectroscopy, IR spectroscopy, and elemental analysis. Assignment of the chemical shifts to specific protons and carbons in the piperazine ring was facilitated by comparison with the chemical shifts in the model compounds piperazine and 1-methylpiperazine and by a HETCOR experiment with the p-tolyl derivative (2i). A DEPT experiment with 1-methylpiperazine (6) was necessary to distinguish the methyl and methylene groups in 6, and a HETCOR spectrum of 6 enabled the correlation of proton and carbon chemical shifts. Line broadening of the signals from the ring methylene protons is attributed to restricted rotation around the N2-N3 bond of the triazene moiety in 2. The second series of triazenes, the ethyl 4-[2-phenyl-1-diazenyl]-1-piperazinecarboxylates (3), have been prepared by similar diazonium coupling to ethyl 1-piperazinecarboxylate and were similarly characterized. The chemical shifts of the piperazine ring protons are much closer together in series 3 than in series 2, resulting in distortion of the multiplets for these methylenes. It was noticed that the difference between these chemical shifts in 3 exhibited a linear free energy relationship with the Hammett substituent constants for the substituents in the aryl ring. Key words: triazene, piperazine, diazonium coupling, NMR, HETCOR, linear free energy relationship.

scholarly journals Congener-specific partition properties of chlorinated paraffins evaluated with COSMOtherm and gas chromatographic retention indices

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Jort Hammer ◽  
Hidenori Matsukami ◽  
Satoshi Endo
Keyword(s):  
Chemical Properties ◽  
High Volume ◽  
Retention Indices ◽  
Chromatographic Retention ◽  
Linear Free Energy Relationship ◽  
Linear Free Energy ◽  
Chlorinated Paraffins ◽  
Gas Chromatographic Retention Indices ◽  
High Volume Production ◽  
Volume Production

AbstractChlorinated Paraffins (CPs) are high volume production chemicals and have been found in various organisms including humans and in environmental samples from remote regions. It is thus of great importance to understand the physical–chemical properties of CPs. In this study, gas chromatographic (GC) retention indexes (RIs) of 25 CP congeners were measured on various polar and nonpolar columns to investigate the relationships between the molecular structure and the partition properties. Retention measurements show that analytical standards of individual CPs often contain several stereoisomers. RI values show that chlorination pattern have a large influence on the polarity of CPs. Single Cl substitutions (–CHCl–, –CH2Cl) generally increase polarity of CPs. However, many consecutive –CHCl– units (e.g., 1,2,3,4,5,6-C11Cl6) increase polarity less than expected from the total number of –CHCl– units. Polyparameter linear free energy relationship descriptors show that polarity difference between CP congeners can be explained by the H-bond donating properties of CPs. RI values of CP congeners were predicted using the quantum chemically based prediction tool COSMOthermX. Predicted RI values correlate well with the experimental data (R2, 0.975–0.995), indicating that COSMOthermX can be used to accurately predict the retention of CP congeners on GC columns.

scholarly journals Zeolite NaP1 Functionalization for the Sorption of Metal Complexes with Biodegradable N-(1,2-dicarboxyethyl)-D,L-aspartic Acid

Materials ◽  
2021 ◽  
Vol 14 (10) ◽  
pp. 2518
Author(s):  
Dorota Kołodyńska ◽  
Yongming Ju ◽  
Małgorzata Franus ◽  
Wojciech Franus
Keyword(s):  
Experimental Data ◽  
Aspartic Acid ◽  
Ph Value ◽  
Complexing Agents ◽  
X Ray Diffraction ◽  
Experimental Conditions ◽  
Modified Zeolite ◽  
X Ray ◽  
Slow Release Fertilizers ◽  
Pseudo Second Order

The possibility of application of chitosan-modified zeolite as sorbent for Cu(II), Zn(II), Mn(II), and Fe(III) ions and their mixtures in the presence of N-(1,2-dicarboxyethyl)-D,L-aspartic acid, IDHA) under different experimental conditions were investigated. Chitosan-modified zeolite belongs to the group of biodegradable complexing agents used in fertilizer production. NaP1CS as a carrier forms a barrier to the spontaneous release of the fertilizer into soil. The obtained materials were characterized by Fourier transform infrared spectroscopy (FTIR); surface area determination (ASAP); scanning electron microscopy (SEM-EDS); X-ray fluorescence (XRF); X-ray diffraction (XRD); and carbon, hydrogen, and nitrogen (CHN), as well as thermogravimetric (TGA) methods. The concentrations of Cu(II), Zn(II), Mn(II), and Fe(III) complexes with IDHA varied from 5–20 mg/dm3 for Cu(II), 10–40 mg/dm3 for Fe(III), 20–80 mg/dm3 for Mn(II), and 10–40 mg/dm3 for Zn(II), respectively; pH value (3–6), time (1–120 min), and temperature (293–333 K) on the sorption efficiency were tested. The Langmuir, Freundlich, Dubinin–Radushkevich, and Temkin adsorption models were applied to describe experimental data. The pH 5 proved to be appropriate for adsorption. The pseudo-second order and Langmuir models were consistent with the experimental data. The thermodynamic parameters indicate that adsorption is spontaneous and endothermic. The highest desorption percentage was achieved using the HCl solution, therefore, proving that method can be used to design slow-release fertilizers.

scholarly journals Discovery of fungal surface NADases predominantly present in pathogenic species

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Øyvind Strømland ◽  
Juha P. Kallio ◽  
Annica Pschibul ◽  
Renate H. Skoge ◽  
Hulda M. Harðardóttir ◽  
...  
Keyword(s):  
Cell Death ◽  
Aspergillus Fumigatus ◽  
Neurospora Crassa ◽  
Binding Site ◽  
Host Cell ◽  
Nicotinamide Adenine Dinucleotide ◽  
Catalytic Mechanism ◽  
Pathogenic Species ◽  
X Ray ◽  
Cellular Bioenergetics

AbstractNicotinamide adenine dinucleotide (NAD) is a key molecule in cellular bioenergetics and signalling. Various bacterial pathogens release NADase enzymes into the host cell that deplete the host’s NAD+ pool, thereby causing rapid cell death. Here, we report the identification of NADases on the surface of fungi such as the pathogen Aspergillus fumigatus and the saprophyte Neurospora crassa. The enzymes harbour a tuberculosis necrotizing toxin (TNT) domain and are predominately present in pathogenic species. The 1.6 Å X-ray structure of the homodimeric A. fumigatus protein reveals unique properties including N-linked glycosylation and a Ca2+-binding site whose occupancy regulates activity. The structure in complex with a substrate analogue suggests a catalytic mechanism that is distinct from those of known NADases, ADP-ribosyl cyclases and transferases. We propose that fungal NADases may convey advantages during interaction with the host or competing microorganisms.

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