scholarly journals Evidence for a two-state transition in papain that may have no close analogue in ficin. Differences in the disposition of cationic sites and hydrophobic binding areas in the active centres of papain and ficin

1980 ◽  
Vol 191 (3) ◽  
pp. 707-718 ◽  
Author(s):  
K Brocklehurst ◽  
J P G Malthouse
Keyword(s):  
Aspartic Acid ◽  
Catalytic Mechanism ◽  
Striking Difference ◽  
Compound I ◽  
Active Centre ◽  
Aspartic Acid Residue ◽  
Wide Range ◽  
Cationic Site ◽  
Hydrophobic Binding ◽  
Kinetics Of

The kinetics of the reactions of the active-centre thiol groups of papain (EC 3.4.22.2) and ficin (EC 3.4.22.3) with the two-protonic-state reactivity probes 2,2′-dipyridyl disulphide, n-propyl 2-pyridyl disulphide and 4-(N-aminoethyl 2′-pyridyl disulphide)- 7-nitrobenzo-2-oxa-1,3-diazole (compound I) were studied over a wide range of pH. Differences between the reactivities of ficin and papain towards the cationic forms of the alkyl 2-pyridyl disulphide probes suggest that ficin contains a cationic site without exact analogue in papain, and the striking difference in the shapes of the pH-rate profiles for the reactions of the two enzymes with compound (1) suggests differences in the mobilities or dispositions of the active-centre histidine imidazole groups with respect to relevant hydrophobic binding areas. The evidence from reactivity-probe studies that the papain catalytic mechanism involves substantial repositioning of the active-centre imidazole group during the catalytic act does not apply also to ficin. If ficin contains an aspartic acid residue analogous to aspartic acid-158 in papain, the pKa of its carboxy group is probably significantly lower than the pKa of the analogous group in papain.

scholarly journals Evidence for a close similarity in the catalytic sites of papain and ficin in near-neutral media despite differences in acidic and alkaline media. Kinetics of the reactions of papain and ficin with chloroacetate

1982 ◽  
Vol 201 (1) ◽  
pp. 101-104 ◽  
Author(s):  
K Brocklehurst ◽  
S M Mushiri ◽  
G Patel ◽  
F Willenbrock
Keyword(s):  
Catalytic Triad ◽  
Interactive Systems ◽  
Alkaline Media ◽  
Active Centre ◽  
Wide Range ◽  
Catalytic Sites ◽  
Rate Maximum ◽  
Neutral Media ◽  
Acidic And Alkaline Media ◽  
Kinetics Of

1. The pH-dependences of the second-order rate constants (k) for the alkylation by chloroacetate of the active-centre thiol groups of papain (EC 3.4.22.2) and ficin (EC 3.4.22.3) were determined over a wide range of pH at 25 degrees C at I 0.1. 2. The main feature of both pH-k profiles is a striking rate maximum at pH6 (characterizing parameters in both cases pKI approx. 3.5, pKII approx. 8.4 and pH-independent rate constant approximately kXH 2.5-3.0 M-1 . s-1). 3. The profile for the ficin reaction contains a plateau at high pH, with approximately kX 0.10 M-1 . s-1; if an analogous plateau exists in the papain reaction, approximately kX ix much lower, less than 0.02 M-1 . s-1. 4. Both enzymes appear to contain closely similar thiolate-imidazolium interactive systems at pH6, but differences in their behaviour in more-acidic media and in alkaline media suggest differences in interaction with the postulated carboxylate component of the putative catalytic triad.

The catalytic mechanism of dye-decolorizing peroxidase DyP may require the swinging movement of an aspartic acid residue

FEBS Journal ◽  
2011 ◽  
Vol 278 (13) ◽  
pp. 2387-2394 ◽  
Author(s):  
Toru Yoshida ◽  
Hideaki Tsuge ◽  
Hiroki Konno ◽  
Toru Hisabori ◽  
Yasushi Sugano
Keyword(s):  
Aspartic Acid ◽  
Catalytic Mechanism ◽  
Aspartic Acid Residue

scholarly journals Evidence that binding to the S2-subsite of papain may be coupled with catalytically relevant structural change involving the cysteine-25–histidine-159 diad. Kinetics of the reaction of papain with a two-protonic-state reactivity probe containing a hydrophobic side chain

1979 ◽  
Vol 183 (2) ◽  
pp. 223-231 ◽  
Author(s):  
Keith Brocklehurst ◽  
J. Paul G. Malthouse ◽  
Michael Shipton
Keyword(s):  
Hydrogen Bonding ◽  
Thiol Group ◽  
Side Chain ◽  
Striking Difference ◽  
Pyridyl Nitrogen ◽  
Active Centre ◽  
Specific Reactivity ◽  
Kinetics Of ◽  
Imidazolium Ion ◽  
S2 Subsite

A method is proposed by which site-specific reactivity probes that exhibit different reactivities in two ionization states can be used to detect association–activation phenomena that involve repositioning of acid/base groups in enzyme active centres. The pH-dependences of the apparent second-order rate constants (k) for the reactions of the thiol group of papain (EC 3.4.22.2) with a series of two-protonic-state reactivity probes are compared. The short-chain probes, 2,2′-dipyridyl disulphide and n-propyl 2-pyridyl disulphide, react at pH6 in adsorptive complexes and/or transition states with geometries that do not permit hydrogen-bonding of the pyridyl nitrogen atom with the active-centre imidazolium ion, as evidenced by the rate minima at pH6 and the rate maxima at pH4 provided by reagent protonation. Only when the probe molecule, e.g. 4-(N-aminoethyl 2′-pyridyl disulphide)-7-nitrobenzo-2-oxa-1,3-diazole [compound(III)], contains a long hydrophobic side chain is the reaction characterized by maximal rates at about pH6, as in the acylation step of the catalytic act (at pH6, kcompound III/k2,2′-dipyridyl disulphide ≃ 100). It is proposed that this striking difference in profile shape may result from binding of the hydrophobic side chain of compound (III) possibly in the S2-subsite of papain, which promotes a change in catalytic-site geometry involving repositioning of the imidazolium ion of histidine-159 and hydrogen-bonding with the N atom of the leaving group, as has been postulated to occur in the acylation step of substate hydrolysis.

scholarly journals Bovine pepsinogens and pepsins. The sequence around a reactive aspartyl residue

1971 ◽  
Vol 124 (4) ◽  
pp. 673-676 ◽  
Author(s):  
Patricia A. Meitner
Keyword(s):  
Methyl Ester ◽  
Aspartic Acid ◽  
Specific Inhibitor ◽  
Enzymic Activity ◽  
Active Centre ◽  
Aspartic Acid Residue ◽  
Porcine Pepsin ◽  
Simultaneous Loss ◽  
Aspartyl Residue

The specific inhibitor, N-diazoacetylnorleucine methyl ester reacts stoicheiometrically with bovine pepsin resulting in a simultaneous loss of all enzymic activity. A peptide containing a modified aspartyl group was isolated from bovine pepsin labelled with 14C-labelled inhibitor. The aspartic acid residue is presumed to be part of the active centre and is in the same heptapeptide sequence as in porcine pepsin: Ile-Val-Asp-Thr-Gly-Thr-Ser.

Scintigraphic studies in rats. Kinetics of insulin analogues covering wide range of receptor affinities

Diabetes ◽  
1991 ◽  
Vol 40 (5) ◽  
pp. 628-632 ◽  
Author(s):  
I. Jensen ◽  
V. Kruse ◽  
U. D. Larsen
Keyword(s):  
Insulin Analogues ◽  
Wide Range ◽  
Kinetics Of

Kinetics of the Thermal Disappearance of Radicals Formed During the Radiolysis of Aspartic Acid

2009 ◽  
Vol 59 (12) ◽  
Author(s):  
Mihai Contineanu ◽  
iulia Contineanu ◽  
Ana Neacsu ◽  
Stefan Perisanu
Keyword(s):  
Thermal Resistance ◽  
Aspartic Acid ◽  
Room Temperature ◽  
Esr Spectra ◽  
Complex Mechanism ◽  
Radical Species ◽  
Mechanisms Of Formation ◽  
Kinetics Of

The radiolysis of the isomers L-, D- and DL- of the aspartic acid, in solid polycrystalline state, was investigated at room temperature. The analysis of their ESR spectra indicated the formation of at least two radicalic entities. The radical, identified as R3, resulting from the deamination of the acid, exhibits the highest concentration and thermal resistance. Possible mechanisms of formation of three radical species are suggested, based also on literature data. The kinetics of the disappearance of radical R3 indicated a complex mechanism. Three possible variants were suggested for this mechanism.

scholarly journals Capsid assembly in a family of animal viruses primes an autoproteolytic maturation that depends on a single aspartic acid residue.

1994 ◽  
Vol 269 (18) ◽  
pp. 13680-13684
Author(s):  
A. Zlotnick ◽  
V.S. Reddy ◽  
R. Dasgupta ◽  
A. Schneemann ◽  
W.J. Ray ◽  
...  
Keyword(s):  
Aspartic Acid ◽  
Capsid Assembly ◽  
Aspartic Acid Residue

scholarly journals Conversion of secretory proteins into membrane proteins by fusing with a glycosylphosphatidylinositol anchor signal of alkaline phosphatase

1994 ◽  
Vol 301 (2) ◽  
pp. 577-583 ◽  
Author(s):  
K Oda ◽  
J Cheng ◽  
T Saku ◽  
N Takami ◽  
M Sohda ◽  
...  
Keyword(s):  
Alkaline Phosphatase ◽  
Endoplasmic Reticulum ◽  
Aspartic Acid ◽  
Chimeric Protein ◽  
Attachment Site ◽  
In Vitro Translation ◽  
Placental Alkaline Phosphatase ◽  
Wild Type ◽  
Aspartic Acid Residue

Placental alkaline phosphatase (PLAP) is initially synthesized as a precursor (proPLAP) with a C-terminal extension. We constructed a recombinant cDNA which encodes a chimeric protein (alpha GL-PLAP) comprising rat alpha 2u-globulin (alpha GL) and the C-terminal extension of PLAP. Two molecular species (25 kDa and 22 kDa) were expressed in the COS-1 cell transfected with the cDNA for alpha GL-PLAP. Only the 22 kDa form was labelled with both [3H]stearic acid and [3H]ethanolamine. Upon digestion with phosphatidylinositol-specific phospholipase C the 22 kDa form was released into the medium, indicating that this form is anchored on the cell surface via glycosylphosphatidylinositol (GPI). A specific IgG raised against a C-terminal nonapeptide of proPLAP precipitated the 25 kDa form but not the 22 kDa form, suggesting that the 25 kDa form is a precursor retaining the C-terminal propeptide. When a mutant alpha GL-PLAP, in which the aspartic acid residue is replaced with tryptophan at a putative cleavage/attachment site, was expressed in COS-1 cells, the 25 kDa precursor was the only form found inside the cell and retained in the endoplasmic reticulum, as judged by immunofluorescence microscopy. In vitro translation programmed with mRNAs coding for the wild-type and mutant forms of alpha GL-PLAP demonstrated that the C-terminal propeptide was cleaved from the wild-type chimeric protein, but not from the mutant one. This gave rise to the 22 kDa form attached with a GPI anchor, suggesting that GPI is covalently linked to the aspartic acid residue (Asp159) of alpha GL-PLAP. Taken together, these results indicate that the C-terminal propeptide of PLAP functions as a signal to render alpha GL a GPI-linked membrane protein in vitro and in vivo in cultured cells, and that the chimeric protein constructed in this study may be useful for elucidating the mechanism underlying the cleavage of the propeptide and attachment of GPI, which occur in the endoplasmic reticulum.

scholarly journals Combining experimental and simulation data of molecular processes via augmented Markov models

2017 ◽  
Vol 114 (31) ◽  
pp. 8265-8270 ◽  
Author(s):  
Simon Olsson ◽  
Hao Wu ◽  
Fabian Paul ◽  
Cecilia Clementi ◽  
Frank Noé
Keyword(s):  
Force Field ◽  
Structural Changes ◽  
Markov Models ◽  
Force Fields ◽  
Divide And Conquer ◽  
Simulation Data ◽  
Wide Range ◽  
Simulation And Experiment ◽  
Kinetics Of

Accurate mechanistic description of structural changes in biomolecules is an increasingly important topic in structural and chemical biology. Markov models have emerged as a powerful way to approximate the molecular kinetics of large biomolecules while keeping full structural resolution in a divide-and-conquer fashion. However, the accuracy of these models is limited by that of the force fields used to generate the underlying molecular dynamics (MD) simulation data. Whereas the quality of classical MD force fields has improved significantly in recent years, remaining errors in the Boltzmann weights are still on the order of a few kT, which may lead to significant discrepancies when comparing to experimentally measured rates or state populations. Here we take the view that simulations using a sufficiently good force-field sample conformations that are valid but have inaccurate weights, yet these weights may be made accurate by incorporating experimental data a posteriori. To do so, we propose augmented Markov models (AMMs), an approach that combines concepts from probability theory and information theory to consistently treat systematic force-field error and statistical errors in simulation and experiment. Our results demonstrate that AMMs can reconcile conflicting results for protein mechanisms obtained by different force fields and correct for a wide range of stationary and dynamical observables even when only equilibrium measurements are incorporated into the estimation process. This approach constitutes a unique avenue to combine experiment and computation into integrative models of biomolecular structure and dynamics.

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