scholarly journals Kinetic trapping of intermediates of the scallop heavy meromyosin adenosine triphosphatase reaction revealed by formycin nucleotides

1988 ◽  
Vol 251 (2) ◽  
pp. 527-540 ◽  
Author(s):  
A P Jackson ◽  
C R Bagshaw
Keyword(s):  
Conformational Changes ◽  
Rate Constants ◽  
Tryptophan Fluorescence ◽  
Fluorescence Decay ◽  
Fluorescence Signal ◽  
Heavy Meromyosin ◽  
Protein Fluorescence ◽  
Association Rate Constants ◽  
Kinetic Trapping ◽  
Kinetics Of

The kinetics of interaction of formycin nucleotides with scallop myosin subfragments were investigated by exploiting the fluorescence signal of the ligand. Formycin triphosphate gives a 5-fold enhancement of the emission intensity on binding to heavy meromyosin, and the profile indicates that the kinetics of binding are Ca2+-insensitive. In contrast, the subsequent product-release steps show a marked degree of regulation by Ca2+. In the absence of Ca2+ formycin triphosphate turnover by the unregulated and the regulated heavy meromyosin fractions are clearly resolved, the latter showing a fluorescence decay rate of 0.002 s-1, corresponding to the Pi-release step. In the presence of Ca2+ this step is activated 50-fold. Formycin diphosphate release is also regulated by Ca2+, being activated from 0.008 s-1 to 5 s-1. In contrast with protein tryptophan fluorescence [Jackson & Bagshaw (1988) Biochem. J. 251, 515-526], formycin fluorescence is sensitive to conformational changes that occur subsequent to the binding step and demonstrate, directly, an effect of Ca2+ on both forward and reverse rate constants. Apart from a decrease in the apparent second-order association rate constants, formycin derivatives appear to mimic adenosine nucleotides closely in their interaction with scallop heavy meromyosin and provide a spectroscopic handle on steps that are optically silent with respect to protein fluorescence. A novel mechanism is discussed in which regulation of the formycin triphosphate activity by Ca2+ involves kinetic trapping of product complexes.

scholarly journals Positive co-operative binding at two weak lysine-binding sites governs the Glu-plasminogen conformational change

1992 ◽  
Vol 285 (2) ◽  
pp. 419-425 ◽  
Author(s):  
U Christensen ◽  
L Mølgaard
Keyword(s):  
Ligand Binding ◽  
Binding Site ◽  
Conformational Change ◽  
Conformational Changes ◽  
Binding Sites ◽  
High Specificity ◽  
Stopped Flow ◽  
Protein Fluorescence ◽  
Lysine Residues ◽  
Kinetics Of

The kinetics of a series of Glu-plasminogen ligand-binding processes were investigated at pH 7.8 and 25 degrees C (in 0.1 M-NaCl). The ligands include compounds analogous to C-terminal lysine residues and to normal lysine residues. Changes of the Glu-plasminogen protein fluorescence were measured in a stopped-flow instrument as a function of time after rapid mixing of Glu-plasminogen and ligand at various concentrations. Large positive fluorescence changes (approximately 10%) accompany the ligand-induced conformational changes of Glu-plasminogen resulting from binding at weak lysine-binding sites. Detailed studies of the concentration-dependencies of the equilibrium signals and the rate constants of the process induced by various ligands showed the conformational change to involve two sites in a concerted positive co-operative process with three steps: (i) binding of a ligand at a very weak lysine-binding site that preferentially, but not exclusively, binds C-terminal-type lysine ligands, (ii) the rate-determining actual-conformational-change step and (iii) binding of one more lysine ligand at a second weak lysine-binding site that then binds the ligand more tightly. Further, totally independent initial small negative fluorescence changes (approximately 2-4%) corresponding to binding at the strong lysine-binding site of kringle 1 [Sottrup-Jensen, Claeys, Zajdel, Petersen & Magnusson (1978) Prog. Chem. Fibrinolysis Thrombolysis 3, 191-209] were observed for the C-terminal-type ligands. The finding that the conformational change in Glu-plasminogen involves two weak lysine-binding sites indicates that the effect cannot be assigned to any single kringle and that the problem of whether kringle 4 or kringle 5 is responsible for the process resolves itself. Probably kringle 4 and 5 are both participating. The involvement of two lysine binding-sites further makes the high specificity of Glu-plasminogen effectors more conceivable.

scholarly journals The kinetics of effector binding to phosphofructokinase. The allosteric conformational transition induced by 1,N6-ethenoadenosine triphosphate

1979 ◽  
Vol 183 (2) ◽  
pp. 349-360 ◽  
Author(s):  
D Roberts ◽  
G L Kellett
Keyword(s):  
Conformational Transition ◽  
Catalytic Site ◽  
Slow Phase ◽  
Fluorescence Signal ◽  
Regulatory Site ◽  
Protein Fluorescence ◽  
Binding Reaction ◽  
T State ◽  
Intrinsic Protein Fluorescence ◽  
Kinetics Of

1. The fluorescent ATP analogue 1,N6-etheno-ATP is a good substrate and an efficient allosteric inhibitor of rabbit skeletal-muscle phosphofructokinase. 2. Fluorescence energy transfer occurs between bound 1,N6-etheno-ATP and phosphofructokinase. 1,N6-Etheno-ATP fluorescence is enhanced, intrinsic protein fluorescence is quenched, and the excitation spectrum of 1,N6-etheno-ATP fluorescence is characteristic of protein absorption. 3. The binding reaction of 1,N6-etheno-ATP observed by stopped-flow fluorimetry is biphasic. The fast phase results from binding to the catalytic site alone. The slow phase results from the allosteric transition of the R conformation into the T conformation induced by the binding of 1,N6-etheno-ATP to the regulatory site. 4. The fluorescence signal that allows the transition of the R conformation into the T conformation to be observed does not arise from 1,N6-etheno-ATP bound to the regulatory site. It arises instead from 1,N6-etheno-ATP bound to the catalytic site as a consequence of changes at the catalytic site caused by the transition of the R conformation into the T conformation. 5. In the presence of excess of Mg2+, the affinity of 1,N6-etheno-ATP for the regulatory site is very much greater in the T state than in the R state.

scholarly journals Transient-kinetic studies of the adenosine triphosphatase activity of scallop heavy meromyosin

1988 ◽  
Vol 251 (2) ◽  
pp. 515-526 ◽  
Author(s):  
A P Jackson ◽  
C R Bagshaw
Keyword(s):  
Conformational Changes ◽  
Active Site ◽  
Kinetic Studies ◽  
Tryptophan Fluorescence ◽  
Adductor Muscle ◽  
Reverse Direction ◽  
Heavy Meromyosin ◽  
Thin Filaments ◽  
Adp Release ◽  
Atp Binding And Hydrolysis

Fluorescence stopped-flow experiments were performed to elucidate the elementary steps of the ATPase mechanism of scallop heavy meromyosin in the presence and in the absence of Ca2+. ATP binding and hydrolysis, as monitored by the change in tryptophan fluorescence, appear to be Ca2+-insensitive, whereas both Pi release and ADP release are markedly suppressed in the absence of Ca2+. Rate constants for Pi release are 0.2 s-1 and 0.002 s-1 and for ADP release are 6 s-1 and 0.01 s-1 in the presence and in the absence of Ca2+ respectively. Ca2+ binding to the specific site of the regulatory domain is rapid and its release occurs at 25 s-1, consistent with the time scale of a twitch of the striated adductor muscle. Nucleotide binding is a multi-step process requiring a minimum of three states. In such a model Ca2+ controls the rate of conformational changes at the active site in both the forward and the reverse direction, leading to a large dependence of the rate of nucleotide release, but a lesser effect on the overall equilibrium position. The kinetic trapping of nucleotides and Pi at the active site, in the absence of Ca2+, appears to be a fundamental step in suppressing the interaction of the myosin head with the thin filaments in relaxed molluscan muscle.

scholarly journals Conformational kinetics reveals affinities of protein conformational states

2015 ◽  
Vol 112 (30) ◽  
pp. 9352-9357 ◽  
Author(s):  
Kyle G. Daniels ◽  
Yang Suo ◽  
Terrence G. Oas
Keyword(s):  
Ligand Binding ◽  
Conformational Change ◽  
Conformational Changes ◽  
Rate Constants ◽  
Conformational Dynamics ◽  
Forward Rate ◽  
Binding Affinities ◽  
Conformational States ◽  
Kinetics Of

Most biological reactions rely on interplay between binding and changes in both macromolecular structure and dynamics. Practical understanding of this interplay requires detection of critical intermediates and determination of their binding and conformational characteristics. However, many of these species are only transiently present and they have often been overlooked in mechanistic studies of reactions that couple binding to conformational change. We monitored the kinetics of ligand-induced conformational changes in a small protein using six different ligands. We analyzed the kinetic data to simultaneously determine both binding affinities for the conformational states and the rate constants of conformational change. The approach we used is sufficiently robust to determine the affinities of three conformational states and detect even modest differences in the protein’s affinities for relatively similar ligands. Ligand binding favors higher-affinity conformational states by increasing forward conformational rate constants and/or decreasing reverse conformational rate constants. The amounts by which forward rate constants increase and reverse rate constants decrease are proportional to the ratio of affinities of the conformational states. We also show that both the affinity ratio and another parameter, which quantifies the changes in conformational rate constants upon ligand binding, are strong determinants of the mechanism (conformational selection and/or induced fit) of molecular recognition. Our results highlight the utility of analyzing the kinetics of conformational changes to determine affinities that cannot be determined from equilibrium experiments. Most importantly, they demonstrate an inextricable link between conformational dynamics and the binding affinities of conformational states.

scholarly journals The magnesium ion-dependent adenosine triphosphatase of myosin. Two-step processes of adenosine triphosphate association and adenosine diphosphate dissociation

1974 ◽  
Vol 141 (2) ◽  
pp. 351-364 ◽  
Author(s):  
Clive R. Bagshaw ◽  
John F. Eccleston ◽  
Fritz Eckstein ◽  
Roger S. Goody ◽  
Herbert Gutfreund ◽  
...  
Keyword(s):  
Adenosine Diphosphate ◽  
Conformation Change ◽  
Protein Fluorescence ◽  
Association Rate ◽  
Myosin Subfragment ◽  
Fluorescence Change ◽  
Skeletal Myosin ◽  
Myosin Subfragment 1 ◽  
Association Rate Constants ◽  
Kinetics Of

The kinetics of protein-fluorescence change when rabbit skeletal myosin subfragment 1 is mixed with ATP or adenosine 5′-(3-thiotriphosphate) in the presence of Mg2+ are incompatible with a simple bimolecular association process. A substrate-induced conformation change with ΔG0<-24kJ·mol-1 (i.e. ΔG0 could be more negative) at pH8 and 21°C is proposed as the additional step in the binding of ATP. The postulated binding mechanism is M+ATP⇌M·ATP⇌M*·ATP, where the association constant for the first step, K1, is 4.5×103m-1 at I 0.14m and the rate of isomerization is 400s-1. In the presence of Mg2+, ADP binds in a similar fashion to ATP, the rate of the conformation change also being 400s-1, but with ΔG0 for that process being -14kJ·mol-1. The effect of increasing ionic strength is to decrease K1, the kinetics of the conformation change being essentially unaltered. Alternative schemes involving a two-step binding process for ATP to subfragment 1 are possible. These are not excluded by the experimental results, although they are perhaps less likely because they imply uncharacteristically slow bimolecular association rate constants.

Submerged upflow biotower operation and computer simulation

1994 ◽  
Vol 30 (11) ◽  
pp. 143-146
Author(s):  
Ronald D. Neufeld ◽  
Christopher A. Badali ◽  
Dennis Powers ◽  
Christopher Carson
Keyword(s):  
Computer Simulation ◽  
Benzoic Acid ◽  
Computer Model ◽  
Rate Constants ◽  
Batch Mode ◽  
Operational Conditions ◽  
First Order ◽  
Low Concentrations ◽  
Biological Transformation ◽  
Kinetics Of

A two step operation is proposed for the biodegradation of low concentrations (&lt; 10 mg/L) of BETX substances in an up flow submerged biotower configuration. Step 1 involves growth of a lush biofilm using benzoic acid in a batch mode. Step 2 involves a longer term biological transformation of BETX. Kinetics of biotransformations are modeled using first order assumptions, with rate constants being a function of benzoic acid dosages used in Step 1. A calibrated computer model is developed and presented to predict the degree of transformation and biomass level throughout the tower under a variety of inlet and design operational conditions.

Kinetics of hydrolysis of peroxodisulphate ions in acidic medium to peroxomonosulphuric acid

1981 ◽  
Vol 46 (5) ◽  
pp. 1229-1236 ◽  
Author(s):  
Jan Balej ◽  
Milada Thumová
Keyword(s):  
Ionic Strength ◽  
Rate Constants ◽  
Acidic Medium ◽  
Measured Data ◽  
Molar Ratios ◽  
Starting Solution ◽  
Kinetics Of Hydrolysis ◽  
Rate Of Hydrolysis ◽  
Kinetics Of ◽  
Hydrolysis Of

The rate of hydrolysis of S2O82- ions in acidic medium to peroxomonosulphuric acid was measured at 20 and 30 °C. The composition of the starting solution corresponded to the anolyte flowing out from an electrolyser for production of this acid or its ammonium salt at various degrees of conversion and starting molar ratios of sulphuric acid to ammonium sulphate. The measured data served to calculate the rate constants at both temperatures on the basis of the earlier proposed mechanism of the hydrolysis, and their dependence on the ionic strength was studied.

Kinetics of the reaction between hexamethylenediisocyanate and 1-pentanol

1983 ◽  
Vol 48 (11) ◽  
pp. 3279-3286
Author(s):  
Slavko Hudeček ◽  
Miloslav Bohdanecký ◽  
Ivana Hudečková ◽  
Pavel Špaček ◽  
Pavel Čefelín
Keyword(s):  
Liquid Chromatography ◽  
Rate Constants ◽  
Reversed Phase ◽  
Order Reaction ◽  
Second Order ◽  
Second Order Reaction ◽  
Reversed Phase Liquid Chromatography ◽  
Consecutive Reactions ◽  
Phase Liquid ◽  
Kinetics Of

The reaction between hexamethylenediisocyanate and 1-pentanol in toluene was studied by means of reversed-phase liquid chromatography. By employing this method, it was possible to determine all components of the reaction mixture including both products, i.e. N-(6-isocyanate hexyl)pentylcarbamate and N,N'-bis(pentyloxycarbonyl)hexamethylenediamine. Relations for the calculation of kinetic constants were derived assuming a competitive consecutive second-order reaction. It was demonstrated that the reaction involved in this case is indeed a second-order reaction, and the rate constants of the first and second consecutive reactions were determined.

Kinetics of esterification of monoisopropylphenols with phosphoryl trichloride

1989 ◽  
Vol 54 (5) ◽  
pp. 1311-1317
Author(s):  
Miroslav Magura ◽  
Ján Vojtko ◽  
Ján Ilavský
Keyword(s):  
Liquid Phase ◽  
Rate Constants ◽  
Reaction Rates ◽  
Activation Energies ◽  
The Individual ◽  
Kinetics Of

The kinetics of liquid-phase isothermal esterification of POCl3 with 2-isopropylphenol and 4-isopropylphenol have been studied within the temperature intervals of 110 to 130 and 90 to 110 °C, respectively. The rate constants and activation energies of the individual steps of this three-step reaction have been calculated from the values measured. The reaction rates of the two isomers markedly differ: at 110 °C 4-isopropylphenol reacts faster by the factors of about 7 and 20 for k1 and k3, respectively. This finding can be utilized in preparation of mixed triaryl phosphates, since the alkylation mixture after reaction of phenol with propene contains an excess of 2-isopropylphenol over 4-isopropylphenol.

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