Restricted Intramolecular Energy Flow in Large Molecules. Heterogeneous and Enzyme Catalysis

1997 ◽  
Vol 62 (8) ◽  
pp. 1150-1158 ◽  
Author(s):  
Milan Šolc
Keyword(s):  
Energy Flow ◽  
Enzyme Catalysis ◽  
Reaction Rate ◽  
Vibrational Energy ◽  
Heavy Atom ◽  
Energy Localization ◽  
Large Molecules ◽  
Substrate Complex ◽  
Enzyme Substrate ◽  
Intramolecular Energy Flow

The free intramolecular energy flow can be restricted by the presence of a heavy atom in the molecule. As a result of this restriction, adsorbed molecules bonded on the metal surface and/or substrate molecules in the enzyme-substrate complex with a metal atom near the binding site can have a higher vibrational energy than the surroundings. The reaction rate is then enhanced by this energy localization.

4. Structure for catalysis

2020 ◽  
pp. 49-61
Author(s):  
Paul Engel
Keyword(s):  
Substrate Specificity ◽  
Enzyme Catalysis ◽  
Structural Features ◽  
Enzyme Mechanism ◽  
Substrate Complex ◽  
Enzyme Substrate ◽  
The Right ◽  
Crucial Ingredient

‘Structure for catalysis’ details the various patterns of enzyme mechanism and the various structural features helping to achieve catalysis. One of the striking features of enzyme catalysis is substrate specificity. In the lock-and-key hypothesis, the enzyme is viewed as a precisely shaped lock and only the right key, the substrate, can fit and turn it. The lock-and-key combination is the enzyme–substrate complex. A crucial ingredient of the enzyme’s equipment for achieving outstanding catalysis is the ‘catalytic groups’.

Protein dynamics and enzyme catalysis: the ghost in the machine?

2012 ◽  
Vol 40 (3) ◽  
pp. 515-521 ◽  
Author(s):  
David R. Glowacki ◽  
Jeremy N. Harvey ◽  
Adrian J. Mulholland
Keyword(s):  
Protein Dynamics ◽  
Enzyme Catalysis ◽  
Isotope Effects ◽  
State Theory ◽  
Quantum Tunnelling ◽  
Substrate Complex ◽  
Enzyme Substrate ◽  
Kinetic Isotope ◽  
Temperature Dependences ◽  
Multiple Conformations

One of the most controversial questions in enzymology today is whether protein dynamics are significant in enzyme catalysis. A particular issue in these debates is the unusual temperature-dependence of some kinetic isotope effects for enzyme-catalysed reactions. In the present paper, we review our recent model [Glowacki, Harvey and Mulholland (2012) Nat. Chem. 4, 169–176] that is capable of reproducing intriguing temperature-dependences of enzyme reactions involving significant quantum tunnelling. This model relies on treating multiple conformations of the enzyme–substrate complex. The results show that direct ‘driving’ motions of proteins are not necessary to explain experimental observations, and show that enzyme reactivity can be understood and accounted for in the framework of transition state theory.

Bioorganic Reactions

2016 ◽  
Author(s):  
Gary W. Morrow
Keyword(s):  
Ground State ◽  
Enzyme Catalysis ◽  
Active Sites ◽  
Intermolecular Forces ◽  
Organic Reactions ◽  
Specific Substrate ◽  
Processes And Reactions ◽  
Substrate Complex ◽  
Enzyme Substrate ◽  
Ground State Energies

It is not essential to have a background in enzymology or biochemistry to gain at least an introductory-level understanding of many biosynthetic processes, so this book does not deal with enzymology or enzyme structure or function in any significant way, even though much of the chemistry we will be examining depends almost entirely on enzyme catalysis. Nevertheless, we will refer to enzyme catalysis and the names of specific enzymes throughout the text as we examine biosynthetic processes and reactions in significant detail. So what exactly are enzymes? Simply put, enzymes are naturally occurring proteins that catalyze various biochemical reactions in living systems. As we will see, many of the reactions they catalyze are familiar organic reactions, but have specific purposes and target structures. Generally speaking, enzymes catalyze organic reactions by lowering transition state energies or raising ground state energies of reactants in much the same way as nonenzymatic catalysts in laboratory chemical reactions, though in the case of enzyme catalysis, rate enhancements of as much as 1023 have been reported, far exceeding rate enhancements currently achievable by conventional chemical means. Understanding the interaction of enzymes and substrates (reactants) to form an enzyme–substrate complex (E–S complex) is fundamental to having some appreciation for how enzymes carry out their work. While overly simplistic, the “lock-and-key” model of enzyme–substrate interaction provides an intuitive context for understanding the remarkable substrate specificity of enzyme-mediated reactions. Thus, so-called enzyme active sites or binding sites (the “lock”) will only accept certain specific substrate structures (the “key”), with shape, conformation, intermolecular forces, and other factors determining the lock-and-key fit. Enzymes not only catalyze specific kinds of reactions, they can act specifically on certain compounds or classes of compounds or functional groups, often showing remarkable selectivity and stereospecificity, especially in the recognition and/or introduction of chirality centers in organic molecules. In terms of nomenclature, enzyme names always end with an ase suffix and are typically named in accordance with the substrate they act upon and/or the kind of reaction process they catalyze.

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 An alternative view of enzyme catalysis

2005 ◽  
Vol 77 (11) ◽  
pp. 1873-1886 ◽  
Author(s):  
Fredric M. Menger
Keyword(s):  
Transition State ◽  
Enzyme Catalysis ◽  
Alternative View ◽  
Spatiotemporal Model ◽  
Substrate Complex ◽  
Site Model ◽  
Enzyme Substrate ◽  
Transition State Stabilization ◽  
Computational Data ◽  
The Many

This paper begins with a brief review of theories and concepts that have influenced today's view of enzyme catalysis: transition-state stabilization, entropy, orbital steering, proximity, and intramolecularity. The discussion then launches into the "spatiotemporal" model of enzyme catalysis in which fast intramolecular and enzymatic rates are ascribed to short distances that are imposed rigidly upon the reacting entities. An equation relating rate and distance is set forth, as are experimental and computational data supporting this relationship. Finally, enzyme systems themselves are analyzed in terms of the distance parameter and the so-called "split-site" model in which ground-state geometries play a crucial role. Among the many surprising conclusions is a transition-state stabilization by noncovalent forces (e.g., hydrogen-bonding) that are positioned far away from the actual transition-state chemistry. The model also confronts and dismisses the claim in classical enzymology that the ubiquitous enzyme-substrate complex is either inconsequential or inhibitory to the overall reaction rate.

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 Spontaneous Cleavages of a Heterologous Protein, the CenA Endoglucanase of Cellulomonas fimi, in Escherichia coli

2021 ◽  
Vol 14 ◽  
pp. 117863612110246
Author(s):  
Cheuk Yin Lai ◽  
Ka Lun Ng ◽  
Hao Wang ◽  
Chui Chi Lam ◽  
Wan Keung Raymond Wong
Keyword(s):  
Escherichia Coli ◽  
Cellulolytic Bacterium ◽  
Systematic Screening ◽  
Cellulomonas Fimi ◽  
E Coli ◽  
Substrate Complex ◽  
Enzyme Substrate ◽  
Glycosylation Sites ◽  
Endogenous Proteins ◽  
Cellulose Binding

CenA is an endoglucanase secreted by the Gram-positive cellulolytic bacterium, Cellulomonas fimi, to the environment as a glycosylated protein. The role of glycosylation in CenA is unclear. However, it seems not crucial for functional activity and secretion since the unglycosylated counterpart, recombinant CenA (rCenA), is both bioactive and secretable in Escherichia coli. Using a systematic screening approach, we have demonstrated that rCenA is subjected to spontaneous cleavages (SC) in both the cytoplasm and culture medium of E. coli, under the influence of different environmental factors. The cleavages were found to occur in both the cellulose-binding (CellBD) and catalytic domains, with a notably higher occurring rate detected in the former than the latter. In CellBD, the cleavages were shown to occur close to potential N-linked glycosylation sites, suggesting that these sites might serve as ‘attributive tags’ for differentiating rCenA from endogenous proteins and the points of initiation of SC. It is hypothesized that glycosylation plays a crucial role in protecting CenA from SC when interacting with cellulose in the environment. Subsequent to hydrolysis, SC would ensure the dissociation of CenA from the enzyme-substrate complex. Thus, our findings may help elucidate the mechanisms of protein turnover and enzymatic cellulolysis.

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