Catalysis, binding and enzyme-substrate complementarity

1974 ◽  
Vol 187 (1089) ◽  
pp. 397-407 ◽  
Keyword(s):  
Transition State ◽  
Reaction Rate ◽  
Reaction Rates ◽  
Special Role ◽  
Simple Derivation ◽  
Maximum Reaction Rate ◽  
Substrate Complex ◽  
Enzyme Substrate ◽  
Maximum Reaction

A simple derivation is given that the catalytic term k cat / K S is at a maximum when the structure of the enzyme is complementary to the structure of the substrate in the transition state. In addition, at a constant substrate concentration, [S], the maximum reaction rate is obtained when k cat and K S are individually high so that K S is greater than [S]; the overall reaction rate decreases with decreasing k cat and K S for K S less than [S]. Two corollaries of this are that intermediates accumulating after the initial Michaelis complex are undesirable and also enzymes whose function is to optimize reaction rates should have evolved to exhibit K M values above those of accessible substrate concentrations. This could be achieved by an often ‘distortionless’ strain which consists either of unfavourable interactions in the enzyme substrate complex which are relieved in the transition state or increasingly favourable interactions in the transition state. A possible special role of the backbone NH groups in this context is discussed. The enzyme need not be complementary to the transition state of the substrate for catalysis to occur.

scholarly journals The Role of Evolving Interfacial Substrate Properties on Heterogeneous Cellulose Hydrolysis Kinetics

2019 ◽  
Author(s):  
Jennifer Nill ◽  
Tina Jeoh
Keyword(s):  
Binding Sites ◽  
Binding Capacity ◽  
Cellulose Hydrolysis ◽  
Reaction Rates ◽  
Hydrolysis Kinetics ◽  
Substrate Complex ◽  
Enzyme Substrate ◽  
Substrate Properties ◽  
Hydrolysis Of

AbstractInterfacial enzyme reactions require formation of an enzyme-substrate complex at the surface of a heterogeneous substrate, but often multiple modes of enzyme binding and types of binding sites complicate analysis of their kinetics. Excess of heterogeneous substrate is often used as a justification to model the substrate as unchanging; but using the study of the enzymatic hydrolysis of insoluble cellulose as an example, we argue that reaction rates are dependent on evolving substrate interfacial properties. We hypothesize that the relative abundance of binding sites on cellulose where hydrolysis can occur (productive binding sites) and binding sites where hydrolysis cannot be initiated or is inhibited (non-productive binding sites) contribute to rate limitations. We show that the initial total number of productive binding sites (the productive binding capacity) determines the magnitude of the initial burst phase of cellulose hydrolysis, while productive binding site depletion explains overall hydrolysis kinetics. Furthermore, we show that irreversibly bound surface enzymes contribute to the depletion of productive binding sites. Our model shows that increasing the ratio of productive- to non-productive binding sites promotes hydrolysis, while maintaining an elevated productive binding capacity throughout conversion is key to preventing hydrolysis slowdown.

Some features of the gas phase oxidation of n -butenes

1963 ◽  
Vol 272 (1349) ◽  
pp. 164-191 ◽  
Keyword(s):  
Gas Phase ◽  
Reaction Rate ◽  
Reaction Rates ◽  
Maximum Reaction Rate ◽  
Oxygen System ◽  
Maximum Reaction ◽  
Phase Oxidation ◽  
Gas Phase Oxidation ◽  
Analytical System ◽  
The Individual

Conventional kinetic techniques (static and flow systems) have been used in conjunction with an integral gas chromatographic analytical system in a study of the oxidation behaviour of butene-1, cis butene-2 and trans butene-2. The cis and trans isomers of butene-2 behaved indistinguishably. All three olefins gave qualitatively the same products, but butene-1 differed in the proportions of the individual products formed, and also in oxidation rate. A mechanism, based on that previously proposed for the ethylene + oxygen system, has been found to account for these differences. The ethylene mechanism is only possible, however, because of the slow rate of oxidation of the allylic type radicals easily formed in the reactions. The relative stability of these radicals provides a natural explanation of the phenomenon of self-inhibition observed in olefin + oxygen reactions. The discontinuous production of intermediate substances noted during the oxidation of butene-2 at high reaction rates, provides further evidence for a thermal theory of cool-fiame formation. Acetaldehyde has been found to be the degenerate branching agent and the maximum reaction rate of these systems was found to be identically related to the concentration of this substance.

The role of secondary alcoholic groups of D-galacturonan in its degradation with exo-D-galacturonanase

1980 ◽  
Vol 45 (2) ◽  
pp. 427-434 ◽  
Author(s):  
Kveta Heinrichová ◽  
Rudolf Kohn
Keyword(s):  
Acetyl Derivative ◽  
Competitive Inhibitor ◽  
Hydroxyl Groups ◽  
Pectic Acid ◽  
Substrate Complex ◽  
Enzyme Substrate ◽  
The Individual ◽  
Degradation Degree ◽  
Derivatives Of

The effect of exo-D-galacturonanase from carrot on O-acetyl derivatives of pectic acid of variousacetylation degree was studied. Substitution of hydroxyl groups at C(2) and C(3) of D-galactopyranuronic acid units influences the initial rate of degradation, degree of degradation and its maximum rate, the differences being found also in the time of limit degradations of the individual O-acetyl derivatives. Value of the apparent Michaelis constant increases with increase of substitution and value of Vmax changes. O-Acetyl derivatives act as a competitive inhibitor of degradation of D-galacturonan. The extent of the inhibition effect depends on the degree of substitution. The only product of enzymic reaction is D-galactopyranuronic acid, what indicates that no degradation of the terminal substituted unit of O-acetyl derivative of pectic acid takes place. Substitution of hydroxyl groups influences the affinity of the enzyme towards the modified substrate. The results let us presume that hydroxyl groups at C(2) and C(3) of galacturonic unit of pectic acid are essential for formation of the enzyme-substrate complex.

scholarly journals Role of Sulfated Tyrosines of Thyroglobulin in Thyroid Hormonosynthesis

Endocrinology ◽  
2005 ◽  
Vol 146 (11) ◽  
pp. 4834-4843 ◽  
Author(s):  
Marie-Christine Nlend ◽  
David M. Cauvi ◽  
Nicole Venot ◽  
Odile Chabaud
Keyword(s):  
Amino Acid ◽  
Coupling Reaction ◽  
Short Life ◽  
Hormone Synthesis ◽  
Amino Acid Peptide ◽  
Substrate Complex ◽  
Enzyme Substrate ◽  
Saturation Binding ◽  
Hydrolysis Of

Our previous studies showed that sulfated tyrosines (Tyr-S) are involved in thyroid hormone synthesis and that Tyr5, the main hormonogenic site of thyroglobulin (Tg), is sulfated. In the present paper, we studied the role of Tyr-S in the formation and activity of the peroxidase-Tg complex. Results show that noniodinated 35SO3-Tg specifically binds (Kd = 1.758 μm) to immobilized lactoperoxidase (LPO) via Tyr-S linkage by using saturation binding and competition experiments. We found that NIFEY-S, a 15-amino acid peptide corresponding to the NH2-end sequence of Tg and containing the hormonogenic acceptor Tyr5-S, was a better competitor than cholecystokinin and Tyr-S. 35SO3-Tg, iodinated without peroxidase, bound to LPO with a Kd (1.668 μm) similar to that of noniodinated Tg, suggesting that 1) its binding occurs via Tyr-S linkage and 2) Tyr-S requires peroxidase to be iodinated, whereas nonsulfated Tyr does not. Iodination of NIFEY-S with [125I]iodide showed that Tyr5-S iodination increased with LPO concentration, whereas iodination of a nonsulfated peptide containing the donor Tyr130 was barely dependent on LPO concentration. Enzymatic hydrolysis of iodinated Tg or NIFEY-S showed that the amounts of sulfated iodotyrosines also depended on LPO amount. Sulfated iodotyrosines were detectable in the enzyme-substrate complex, suggesting they have a short life before the coupling reaction occurs. Our data suggest that after Tyr-S binding to peroxidase where it is iodinated, the sulfate group is removed, releasing an iodophenoxy anion available for coupling with an iodotyrosine donor.

Biodegradation of 2,4-dichlorophenol in a fluidized bed reactor with immobilized Phanerochaete chrysosporium

2010 ◽  
Vol 62 (4) ◽  
pp. 947-955 ◽  
Author(s):  
Xiao-ming Li ◽  
Qi Yang ◽  
Ying Zhang ◽  
Wei Zheng ◽  
Xiu Yue ◽  
...  
Keyword(s):  
Fluidized Bed ◽  
Phanerochaete Chrysosporium ◽  
Reaction Rate ◽  
Immobilized Cells ◽  
Fluidized Bed Reactor ◽  
Degradation Process ◽  
Maximum Reaction Rate ◽  
Monod Equation ◽  
Continuous Bioreactor ◽  
Maximum Reaction

The performance of a fluidized bed reactor using immobilized Phanerochaete chrysosporium to remove 2,4-dichlorophenol (2,4-DCP) from aqueous solution was investigated. The contribution of lignin peroxidase (LiP) and manganese peroxidase (MnP) secreted by Phanerochaete chrysosporium to the 2,4-DCP degradation was examined. Results showed that Lip and Mnp were not essential to 2,4-DCP degradation while their presence enhanced the degradation process and reaction rate. In sequential batch experiment, the bioactivity of immobilized cells was recovered and improved during the culture and the maximum degradation rate constant of 13.95 mg (Ld)−1 could be reached. In continuous bioreactor test, the kinetic behavior of the Phanerochaete chrysosporium immobilized on loofa sponge was found to follow the Monod equation. The maximum reaction rate was 7.002 mg (Lh)−1, and the saturation constant was 26.045 mg L−1.

scholarly journals Proofreading through spatial gradients

2020 ◽  
Author(s):  
Vahe Galstyan ◽  
Kabir Husain ◽  
Fangzhou Xiao ◽  
Arvind Murugan ◽  
Rob Phillips
Keyword(s):  
Error Correction ◽  
Reaction Rates ◽  
Structural Features ◽  
Product Formation ◽  
Concentration Gradients ◽  
Nucleotide Hydrolysis ◽  
Substrate Complex ◽  
Spatial Gradients ◽  
Enzyme Substrate ◽  
Kinetic Proofreading

Key enzymatic processes in biology use the nonequilibrium error correction mechanism called kinetic proofreading to enhance their specificity. Kinetic proofreading typically requires several dedicated structural features in the enzyme, such as a nucleotide hydrolysis site and multiple enzyme–substrate conformations that delay product formation. Such requirements limit the applicability and the adaptability of traditional proofreading schemes. Here, we explore an alternative conceptual mechanism of error correction that achieves delays between substrate binding and subsequent product formation by having these events occur at distinct physical locations. The time taken by the enzyme–substrate complex to diffuse from one location to another is leveraged to discard wrong substrates. This mechanism does not require dedicated structural elements on the enzyme, making it easier to overlook in experiments but also making proofreading tunable on the fly. We discuss how tuning the length scales of enzyme or substrate concentration gradients changes the fidelity, speed and energy dissipation, and quantify the performance limitations imposed by realistic diffusion and reaction rates in the cell. Our work broadens the applicability of kinetic proofreading and sets the stage for the study of spatial gradients as a possible route to specificity.

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