The reaction with nitrous acid of the "active site" N-terminal isoleucine in chymotrypsin and derivatives

1970 ◽  
Vol 48 (6) ◽  
pp. 671-681 ◽  
Author(s):  
Joan W. Dixon ◽  
T. Hofmann
Keyword(s):  
Active Site ◽  
Rate Constants ◽  
Nitrous Acid ◽  
Amino Group ◽  
Amino Groups ◽  
Guanidinium Chloride ◽  
Third Order ◽  
Potential Activity ◽  
Chymotrypsin B ◽  
Nitrophenyl Ester

Bovine α-chymotrypsin, δ-chymotrypsin, homoarginine-δ-chymotrypsin, and bovine chymotrypsin B were inactivated by nitrous acid at pH 3.8–4.4 and 0°. The potential activity of bovine chymotrypsinogen A was not affected under these conditions. The inactivation rates as measured with the substrates α-N-acetyl-L-tyrosine ethyl ester, carbobenzoxyglycine p-nitrophenyl ester, and p-nitrophenyl acetate, and by 3H-di-isopropyl phosphorofluoridate incorporation were identical with the deamination rates of the amino group of the N-terminal isoleucine-16, but were slower than the deamination rates of the amino groups of the N-terminals half-cystine-1 and alanine-149. It is concluded that the deamination of isoleucine-16 is directly responsible for the inactivation. Third-order deamination rate constants of the N-terminal isoleucine-16 were measured and the following values (in min−1M−2) were obtained: α-chymotrypsin, 0.4–0.6; homoarginine-δ-chymotrypsin, 0.05; di-isopropyl phosphoryl-α-chymotrypsin, [Formula: see text]; tosyl-α-chymotrypsin, 0.05; chymotrypsin B, 0.3; α-chymotrypsin in guanidinium chloride, 30–50; homoarginine-δ-chymotrypsin in guanidinium chloride, > 20. The deamination rate constants for the model dipeptides isoleucylvaline and valylvaline are 40 and 46, respectively (Kurosky, A., and Hofmann, T.: to be published). A comparison shows that the constants for the dipeptides and the two chymotrypsins in guanidinium chloride are very close and are probably those of a fully exposed amino group. The much lower constants for the other enzymes and derivatives represent the varying degrees of accessibility of the amino group and show the usefulness of the reagent as a conformational probe. The results are fully compatible with the proposed structure of α-chymotrypsin (1) and the proposed function of the N-terminal isoleucine (2).

scholarly journals Conformational changes at the active site of creatine kinase at low concentrations of guanidinium chloride

1993 ◽  
Vol 291 (1) ◽  
pp. 103-107 ◽  
Author(s):  
H M Zhou ◽  
X H Zhang ◽  
Y Yin ◽  
C L Tsou
Keyword(s):  
Creatine Kinase ◽  
Fluorescent Probe ◽  
Conformational Change ◽  
Conformational Changes ◽  
Active Site ◽  
Emission Intensity ◽  
Enzyme Inactivation ◽  
Amino Groups ◽  
Guanidinium Chloride ◽  
Low Concentrations

It has been previously reported that, during denaturation of creatine kinase by guanidinium chloride (GdmCl) or urea [Tsou (1986), Trends Biochem. Sci. 11, 427-429], inactivation occurs before noticeable conformational change can be detected, and it is suggested that the conformation at the active site is more easily perturbed and hence more flexible than the molecule as a whole. In this study, the thiol and amino groups at or near the active site of creatine kinase are labelled with o-phthalaldehyde to form a fluorescent probe. Both the emission intensity and anisotropy decrease during denaturation indicating exposure of this probe and increased mobility of the active site. The above conformational changes take place together with enzyme inactivation at lower GdmCl concentrations than required to bring about intrinsic fluorescence changes of the enzyme. At the same GdmCl concentration, the rate of exposure of the probe is comparable with that of inactivation and is several orders of magnitude faster than that for the unfolding of the molecule as a whole.

Kinetics of the Reaction of Nitrous Acid with Model Compounds and Proteins, and the Conformational State of N-terminal Groups in the Chymotrypsin Family

1972 ◽  
Vol 50 (12) ◽  
pp. 1282-1296 ◽  
Author(s):  
A. Kurosky ◽  
T. Hofmann
Keyword(s):  
Nitrous Acid ◽  
Conformational State ◽  
Serine Proteinases ◽  
Amino Groups ◽  
Model Compounds ◽  
Third Order ◽  
Tyrosine Residues ◽  
Reactive Groups ◽  
Primary Amino ◽  
Kinetics Of

The kinetics of the reaction of nitrous acid at 4° and pH 4.0 with various amino acids, peptides, and proteins were studied. The reaction with isoleucine methyl ester was found to have a linear dependence on the square of the HONO concentration showing that N2O3 was the reactive species. Third order nitrosation rate constants of primary amino groups showed a correlation with their pK values. They were calculated for the concentration of the unprotonated species to give intrinsic reactivities. The rate of nitrosation of acetyltryptophan to give N-nitrosoacetyltryptophan was found to be a linear function of the nitrous acid concentration. This nitrosation therefore follows a different mechanism. The reaction of nitrous acid with tyrosine residues was examined by spectrophotometry. The reaction was negligible compared to that of other groups. Acetylhistidine and imidazole did not react. Reactivities for α-amino groups, ε-amino groups, and other residues in proteins were compared. The conformational state of the N-terminal residues in serine proteinases, as revealed from their reactivities, is discussed in detail. It is concluded that nitrous acid reacts preferentially with "surface" residues and is a useful tool for exploring conformational states of reactive groups in proteins, especially α-amino groups and indole rings.

The Reactivity of the N-terminal Isoleucine of α-Chymotrypsin as a Function of Ionic Strength

1971 ◽  
Vol 49 (5) ◽  
pp. 529-534 ◽  
Author(s):  
A. Kurosky ◽  
J. E. S. Graham ◽  
Joan W. Dixon ◽  
T. Hofmann
Keyword(s):  
Ionic Strength ◽  
Nitrous Acid ◽  
High Ionic Strength ◽  
Amino Group ◽  
Model Compounds ◽  
Third Order ◽  
X Ray ◽  
A Value ◽  
Group A ◽  
Low Ionic Strength

The reactivity of the α-amino group of isoleucine-16 of α-chymotrypsin towards nitrous acid at pH 4.0 and 0° is strongly dependent on ionic strength. Third-order deamination rate constants at low ionic strength (μ = 0.1 M) are 500–1000 times higher than those at high ionic strength (μ = 5.0 and 6.0 M) and are independent of the nature of the ions and the chymotrypsin concentration. Extrapolation to zero ionic strength of a plot of the logarithms of the constants against ionic strength leads to a value which is the same as that for the exposed α-amino group of the model compounds isoleucylvaline and valylvaline, and of the N-terminal isoleucine of pepsin. The deamination rate constant of the dipeptide valylvaline varies only two- to three-fold between ionic strength of 0.1 M and 6 M. The results suggest that the concept of a "buried" N-terminal as shown by X-ray analysis (carried out at pH 4.2 and ionic strength 9–11 M) requires modification; at low ionic strength (0.1 M) the reactivity of the N-terminal is only little below that of an exposed amino group, a fact which suggests that the amino group is much more available than shown by the X-ray analysis. The results are interpreted in terms of an effect of the ionic strength on the equilibrium between two conformational states of the enzyme.

Investigation of the effect of ring size on the product distribution for the Schiff base reaction of 2-acetylcycloalkanones with diamino alkanes

1995 ◽  
Vol 73 (1) ◽  
pp. 16-21 ◽  
Author(s):  
Raul G. Enriquez ◽  
Juan M. Fernandez-G ◽  
Ismael Leon ◽  
William F. Reynolds ◽  
Ji.-Ping Yang ◽  
...  
Keyword(s):  
Schiff Base ◽  
Condensation Reaction ◽  
2D Nmr ◽  
Product Distribution ◽  
Major Product ◽  
Ring Size ◽  
Amino Group ◽  
Amino Groups ◽  
Similar Product ◽  
Acetyl Group

The Schiff base condensation reaction of 1,2-diaminoethane with a series of 2-acetylcycloalkanones (from cyclopentanone to cyclooctanone) has been investigated and the products characterized by two-dimensional nuclear magnetic resonance. The site of attack of the amino groups, i.e., ring ketone or acetyl ketone, is determined primarily by ring size. 2-Acetylcyclohexanone yields two products in ca. 9:1 ratio, the major product where the two amino groups attack at the ring ketones of two different cyclohexanone molecules, and the minor product where one amino group attacks one ring carbonyl of one cyclohexanone while the second amino group attacks the acetyl group of another. 2-Acetylcyclopentanone yields all three possible products with the major product involving attack at the acetyl groups of two different cyclopentanones. The corresponding reactions for 2-acetylcycloheptanone and 2-acetylcyclooctanone each give a single product corresponding to attack at the acetyl groups of two different cycloalkanones. Similar product distributions are observed for the reactions of the different 2-acetylcycloalkanones with 1,4-diaminobutane. Keywords: Schiff base reactions, diketones, 2D NMR.

scholarly journals Removal of Organic Compounds with an Amino Group during the Nanofiltration Process

Membranes ◽  
2021 ◽  
Vol 12 (1) ◽  
pp. 58
Author(s):  
Renata Żyłła ◽  
Magdalena Foszpańczyk ◽  
Magdalena Olak-Kucharczyk ◽  
Joanna Marszałek ◽  
Stanisław Ledakowicz
Keyword(s):  
Organic Compounds ◽  
Natural Organic Matter ◽  
Oxidation Product ◽  
Membrane Filtration ◽  
Separation Efficiency ◽  
Ph Value ◽  
Oxidation Products ◽  
Low Molecular Weight ◽  
Amino Group ◽  
Amino Groups

The research covered the process of nanofiltration of low molecular weight organic compounds in aqueous solution. The article presents the results of experiments on membrane filtration of compounds containing amino groups in the aromatic ring and comparing them with the results for compounds without amino groups. The research was carried out for several commercial polymer membranes: HL, TS40, TS80, DL from various manufacturers. It has been shown that the presence of the amino group and its position in relation to the carboxyl group in the molecule affects the retention in the nanofiltration process. The research also included the oxidation products of selected pharmaceuticals. It has been shown that 4-Amino-3,5-dichlorophenol—a oxidation product of diclofenac and 4-ethylbenzaldehyde—a oxidation product of IBU, show poor separation efficiency on the selected commercial membranes, regardless of the pH value and the presence of natural organic matter (NOM). It has been shown that pre-ozonation of natural river water can improve the retention of pollutants removed.

scholarly journals Breaking the Carboxyl Rule

2013 ◽  
Vol 288 (29) ◽  
pp. 21254-21265 ◽  
Author(s):  
Sergei P. Balashov ◽  
Lada E. Petrovskaya ◽  
Eleonora S. Imasheva ◽  
Evgeniy P. Lukashev ◽  
Andrei K. Dioumaev ◽  
...  
Keyword(s):  
Schiff Base ◽  
Water Molecule ◽  
Proton Pump ◽  
Rate Constants ◽  
Proton Donor ◽  
Carboxyl Group ◽  
Amino Group ◽  
Wild Type ◽  
Fast Phase ◽  
Proton Uptake

A lysine instead of the usual carboxyl group is in place of the internal proton donor to the retinal Schiff base in the light-driven proton pump of Exiguobacterium sibiricum (ESR). The involvement of this lysine in proton transfer is indicated by the finding that its substitution with alanine or other residues slows reprotonation of the Schiff base (decay of the M intermediate) by more than 2 orders of magnitude. In these mutants, the rate constant of the M decay linearly decreases with a decrease in proton concentration, as expected if reprotonation is limited by the uptake of a proton from the bulk. In wild type ESR, M decay is biphasic, and the rate constants are nearly pH-independent between pH 6 and 9. Proton uptake occurs after M formation but before M decay, which is especially evident in D2O and at high pH. Proton uptake is biphasic; the amplitude of the fast phase decreases with a pKa of 8.5 ± 0.3, which reflects the pKa of the donor during proton uptake. Similarly, the fraction of the faster component of M decay decreases and the slower one increases, with a pKa of 8.1 ± 0.2. The data therefore suggest that the reprotonation of the Schiff base in ESR is preceded by transient protonation of an initially unprotonated donor, which is probably the ϵ-amino group of Lys-96 or a water molecule in its vicinity, and it facilitates proton delivery from the bulk to the reaction center of the protein.

scholarly journals Comparison of the activity and conformation changes of lactate dehydrogenase H4 during denaturation by guanidinium chloride

1991 ◽  
Vol 277 (1) ◽  
pp. 207-211 ◽  
Author(s):  
Y Z Ma ◽  
C L Tsou
Keyword(s):  
Lactate Dehydrogenase ◽  
Active Site ◽  
Cross Linking ◽  
Native Conformation ◽  
Guanidinium Chloride ◽  
Original Activity ◽  
Limited Region ◽  
Low Concentrations ◽  
Two Stages ◽  
Inhibited Enzyme

The inactivation and unfolding of lactate dehydrogenase (LDH) during denaturation by guanidinium chloride (GuHCl) under diverse conditions have been compared. Unfolding of the native conformation, as monitored by fluorescence and c.d. measurements, occurs in two stages with increasing GuHCl concentrations, and the inactivation approximately coincides with, but slightly precedes, the first stage of unfolding. The enzyme is inhibited to about 60-70% of its original activity by cross-linking with glutaraldehyde or in the presence of 1 M-(NH4)2SO4, with its conformation stabilized as shown by the requirement for higher GuHCl concentrations to bring about both inactivation and unfolding. Low concentrations of GuHCl (0.2-0.4 M) activate the cross-linked and the (NH4)2SO4-inhibited enzyme back to the level of the native enzyme. For the enzyme stabilized by (NH4)2SO4 or by cross-linking with glutaraldehyde, inactivation occurs at a markedly lower GuHCl concentration than that required to bring about its first stage of unfolding. It is concluded that the active site of LDH is situated in a limited region relatively fragile in conformation as compared with the molecule as a whole. The GuHCl activation of LDH stabilized in (NH4)2SO4 or by cross-linking with glutaraldehyde suggests that this fragility and consequently flexibility of the active site is required for its catalytic activity.

scholarly journals Beyond the Active Site: Mechanistic Investigations of the Role of the Secondary Coordination Sphere and Beyond on Multi-Electron Electrocatalytic Reactions and Their Relations Between Kinetics and Thermodynamics

2020 ◽  
Author(s):  
Vincent Wang
Keyword(s):  
Thermodynamic Parameters ◽  
Coordination Sphere ◽  
Active Site ◽  
Rate Constants ◽  
Reduction Reaction ◽  
Rate Limiting Step ◽  
Limiting Step ◽  
Secondary Coordination Sphere ◽  
Catalytic Rate ◽  
Rate Limiting

<p>The development of an electrocatalyst with a rapid turnover frequency, low overpotential and long-term stability is highly desired for fuel-forming reactions, such as water splitting and CO<sub>2</sub> reduction. The findings of the scaling relationships between the catalytic rate and thermodynamic parameters over a wide range of electrocatalysts in homogeneous and heterogeneous systems provide useful guidelines and predictions for designing better catalysts for those redox reactions. However, such relationships also suggest that a catalyst with a high catalytic rate is typically associated with a high overpotential for a given reaction. Inspired by enzymes, the introduction of additional interactions through the secondary coordination sphere beyond the active site, such as hydrogen-bonding or electrostatic interactions, have been shown to offer a promising avenue to disrupt these unfavorable relationships. Herein, we further investigate the influence of these cooperative interactions on the faster chemical steps, in addition to the rate-limiting step widely examined before, for molecular electrocatalysts with the structural and electronic modifications designed to facilitate the dioxygen reduction reaction, CO<sub>2</sub> reduction reaction and hydrogen evolving reaction. Based on the electrocatalytic kinetic analysis, the rate constants for faster chemical steps and their correlation with the corresponding thermodynamic parameters are evaluated. The results suggest that the effects of the secondary coordination sphere and beyond on these fuel-forming reactions are not necessarily beneficial for promoting all chemical steps and no apparent relation between rate constants and thermodynamic parameters are found in some cases studied here, which may implicate the design of electrocatalysts in the future. Finally, these analyses demonstrate that the characteristic features for voltammograms and foot-of-the-wave-analysis plots are associated with the specific kinetic phenomenon among these multi-electron electrocatalytic reactions, which provides a useful framework to probe the insights of chemical and electronic modifications on the catalytic steps quantitatively (i.e. kinetic rate constants) and to optimize some of critical steps beyond the rate-limiting step.</p>

scholarly journals Bacterial pseudokinase catalyzes protein polyglutamylation to inhibit the SidE-family ubiquitin ligases

Science ◽  
2019 ◽  
Vol 364 (6442) ◽  
pp. 787-792 ◽  
Author(s):  
Miles H. Black ◽  
Adam Osinski ◽  
Marcin Gradowski ◽  
Kelly A. Servage ◽  
Krzysztof Pawłowski ◽  
...  
Keyword(s):  
Protein Kinase ◽  
Host Cell ◽  
Crystal Structures ◽  
Active Site ◽  
Bond Formation ◽  
Ubiquitin Ligases ◽  
Carboxyl Group ◽  
Amino Group ◽  
Isopeptide Bond

Enzymes with a protein kinase fold transfer phosphate from adenosine 5′-triphosphate (ATP) to substrates in a process known as phosphorylation. Here, we show that the Legionella meta-effector SidJ adopts a protein kinase fold, yet unexpectedly catalyzes protein polyglutamylation. SidJ is activated by host-cell calmodulin to polyglutamylate the SidE family of ubiquitin (Ub) ligases. Crystal structures of the SidJ-calmodulin complex reveal a protein kinase fold that catalyzes ATP-dependent isopeptide bond formation between the amino group of free glutamate and the γ-carboxyl group of an active-site glutamate in SidE. We show that SidJ polyglutamylation of SidE, and the consequent inactivation of Ub ligase activity, is required for successful Legionella replication in a viable eukaryotic host cell.

Sign in / Sign up

Export Citation Format

Share Document