scholarly journals Evolution Alters the Enzymatic Reaction Coordinate of Dihydrofolate Reductase

2014 ◽  
Vol 119 (3) ◽  
pp. 989-996 ◽  
Author(s):  
Jean E. Masterson ◽  
Steven D. Schwartz
Keyword(s):  
Dihydrofolate Reductase ◽  
Enzymatic Reaction ◽  
Reaction Coordinate

scholarly journals Substrate binding and turnover modulate the affinity landscape of dihydrofolate reductase to increase its catalytic efficiency

2020 ◽  
Author(s):  
Nicole Stéphanie Galenkamp ◽  
Giovanni Maglia
Keyword(s):  
Free Energy ◽  
Dihydrofolate Reductase ◽  
General Feature ◽  
Enzymatic Reaction ◽  
Catalytic Efficiency ◽  
Excess Energy ◽  
Power Stroke ◽  
High Concentration ◽  
E Coli ◽  
Recovery Stroke

AbstractIt is generally accepted that enzymes structures evolved to stabilize the transition-state of a catalyzed reaction. Here, observing single molecules with a multi-turnover resolution, we provide experimental evidence for a more sophisticated narrative. We found that the binding of the NADPH cofactor to DHFR induces a first allosteric change that increases the affinity of the enzyme for the substrate. Then the enthalpy generated by the chemical step provides a power stroke that switches the enzyme to the product-bound conformations and promotes the release of the oxidized cofactor NADP+. The subsequent binding of NADPH to the vacated site provides the free energy for the recovery stroke, which induces the allosteric release of the product and resets the initial configuration. Intriguingly, the cycle is not perfect. Occasionally, DHFR undergoes second-long catalytic pauses, most likely reflecting the occupancy of an off-path conformation induced by excess energy liberated by the chemical step. This catalytic remodeling of the affinity landscape of DHFR is likely to have evolved to improve the efficiency of the reaction to cope with the high concentration of NADP+ in E. coli. And might be a general feature for complex enzymatic reaction where the binding and release of the products must be tightly controlled.

Snapshots along an Enzymatic Reaction Coordinate:  Analysis of a Retaining β-Glycoside Hydrolase†,‡

Biochemistry ◽  
1998 ◽  
Vol 37 (34) ◽  
pp. 11707-11713 ◽  
Author(s):  
Gideon J. Davies ◽  
Lloyd Mackenzie ◽  
Annabelle Varrot ◽  
Miroslawa Dauter ◽  
A. Marek Brzozowski ◽  
...  
Keyword(s):  
Glycoside Hydrolase ◽  
Enzymatic Reaction ◽  
Reaction Coordinate

High-resolution gold labeling

1993 ◽  
Vol 51 ◽  
pp. 330-331
Author(s):  
James F. Hainfeld ◽  
Frederic R. Furuya ◽  
Kyra Carbone ◽  
Martha Simon ◽  
Beth Lin ◽  
...  
Keyword(s):  
Dihydrofolate Reductase ◽  
Polypeptide Chain ◽  
External Surface ◽  
Gold Cluster ◽  
Macromolecular Complex ◽  
Gold Compound ◽  
Central Cavity ◽  
Chain Folding ◽  
E Coli ◽  
Chaperonin Groel

A recently developed 1.4 nm gold cluster has been found to be useful in labeling macromolecular sites to 1-3 nm resolution. The gold compound is organically derivatized to contain a monofunctional arm for covalent linking to biomolecules. This may be used to mark a specific site on a structure, or to first label a component and then reassemble a multicomponent macromolecular complex. Two examples are given here: the chaperonin groEL and ribosomes.Chaperonins are essential oligomeric complexes that mediate nascent polypeptide chain folding to produce active proteins. The E. coli chaperonin, groEL, has two stacked rings with a central hole ∽6 nm in diameter. The protein dihydrofolate reductase (DHFR) is a small protein that has been used in chain folding experiments, and serves as a model substrate for groEL. By labeling the DHFR with gold, its position with respect to the groEL complex can be followed. In particular, it was sought to determine if DHFR refolds on the external surface of the groEL complex, or whether it interacts in the central cavity.

Computer Simulation of Amperometric Biosensor Response to Mixtures of Compounds

2002 ◽  
Vol 7 (2) ◽  
pp. 3-14 ◽  
Author(s):  
R. Baronas ◽  
J. Christensen ◽  
F. Ivanauskas ◽  
J. Kulys
Keyword(s):  
Computer Simulation ◽  
Enzymatic Reaction ◽  
Diffusion Equations ◽  
Response Data ◽  
Finite Difference Technique ◽  
Stationary Diffusion ◽  
Biosensor Array ◽  
Menten Kinetic ◽  
Biosensor Response

A mathematical model of amperometric biosensors has been developed. The model bases on non-stationary diffusion equations containing a non-linear term related to Michaelis-Menten kinetic of the enzymatic reaction. The model describes the biosensor response to mixtures of multiple compounds in two regimes of analysis: batch and flow injection. Using computer simulation, large amount of biosensor response data were synthesised for calibration of a biosensor array to be used for characterization of wastewater. The computer simulation was carried out using the finite difference technique.

Bacterial Peptidoglycan Stapling with Functionalized D-Amino Acids

2019 ◽  
Author(s):  
Sylvia L. Rivera ◽  
Akbar Espaillat ◽  
Arjun K. Aditham ◽  
Peyton Shieh ◽  
Chris Muriel-Mundo ◽  
...  
Keyword(s):  
Cell Wall ◽  
Clinical Success ◽  
Bacterial Species ◽  
Enzymatic Reaction ◽  
Amino Acid Derivative ◽  
Wall Structure ◽  
Live Bacteria ◽  
Cross Links ◽  
Osmotic Lysis ◽  
Bacterial Peptidoglycan

Transpeptidation reinforces the structure of cell wall peptidoglycan, an extracellular heteropolymer that protects bacteria from osmotic lysis. The clinical success of transpeptidase-inhibiting β-lactam antibiotics illustrates the essentiality of these cross-linkages for cell wall integrity, but the presence of multiple, seemingly redundant transpeptidases in many bacterial species makes it challenging to determine cross-link function precisely. Here we present a technique to covalently link peptide strands by chemical rather than enzymatic reaction. We employ bio-compatible click chemistry to induce triazole formation between azido- and alkynyl-D-alanine residues that are metabolically installed in the cell walls of Gram-positive and Gram-negative bacteria. Synthetic triazole cross-links can be visualized by substituting azido-D-alanine with azidocoumarin-D-alanine, an amino acid derivative that undergoes fluorescent enhancement upon reaction with terminal alkynes. Cell wall stapling protects the model bacterium Escherichia coli from β-lactam treatment. Chemical control of cell wall structure in live bacteria can provide functional insights that are orthogonal to those obtained by genetics.<br>

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