Related Experiment Video
Updated: May 21, 2026
13:00
Hot Biological Catalysis: Isothermal Titration Calorimetry to Characterize Enzymatic Reactions
Published on: April 4, 2014
Wide-open flaps are key to urease activity
Benjamin P Roberts1, Bill R Miller, Adrian E Roitberg
1Quantum Theory Project, University of Florida, P.O. Box 118435, Gainesville, Florida 32611-8435, USA.
Journal of the American Chemical Society
|June 8, 2012
Summary
Researchers discovered a new, wide-open state of the urease enzyme flap. This finding reveals more of the active site, offering new possibilities for drug discovery targeting urease.
Area of Science:
- Biochemistry
- Enzymology
- Structural Biology
Background:
- Urease enzyme activity is regulated by an active-site flap controlling substrate and product movement.
- Understanding urease's conformational dynamics is crucial for enzyme inhibition and drug development.
Purpose of the Study:
- To investigate the conformational states of the urease active-site flap using molecular dynamics simulations.
- To identify novel states of the urease active-site flap that could be exploited for drug discovery.
Main Methods:
- Utilized molecular dynamics (MD) simulations to explore the conformational landscape of the urease active-site flap.
- Analyzed simulation trajectories to identify distinct flap states and their associated energy barriers.
Main Results:
- Identified a previously unobserved, wide-open flap state of urease, distinct from known closed and open states.
- Demonstrated that the wide-open state provides ready access to the urease active site's metal cluster.
- Observed a solvent-exposed region in the binding pocket even when the flap is closed, suggesting a potential substrate/product reservoir.
Conclusions:
- The newly identified wide-open flap state significantly expands the accessible active-site pocket of urease.
- This expanded pocket presents new opportunities for designing small-molecule inhibitors and drugs targeting urease.
- The potential substrate/product reservoir warrants further investigation for its role in enzyme function.
Related Concept Videos
02:34Enzymes
Inside living organisms, enzymes act as catalysts for many biochemical reactions involved in cellular metabolism. The role of enzymes is to reduce the activation energies of biochemical reactions by forming complexes with its substrates. The lowering of activation energies favor an increase in the rates of biochemical reactions.
Enzyme deficiencies can often translate into life-threatening diseases. For example, a genetic abnormality resulting in the deficiency of the enzyme G6PD...
Enzyme deficiencies can often translate into life-threatening diseases. For example, a genetic abnormality resulting in the deficiency of the enzyme G6PD...
01:13Introduction to Mechanisms of Enzyme Catalysis
For many years, scientists thought that enzyme-substrate binding took place in a simple "lock-and-key" fashion. This model stated that the enzyme and substrate fit together perfectly in one instantaneous step. However, current research supports a more refined view scientists call induced fit. The induced-fit model expands upon the lock-and-key model by describing a more dynamic interaction between enzyme and substrate. As the enzyme and substrate come together, their interaction causes a mild...
01:13Introduction to Mechanisms of Enzyme Catalysis
For many years, scientists thought that enzyme-substrate binding took place in a simple "lock-and-key" fashion. This model stated that the enzyme and substrate fit together perfectly in one instantaneous step. However, current research supports a more refined view scientists call induced fit. The induced-fit model expands upon the lock-and-key model by describing a more dynamic interaction between enzyme and substrate. As the enzyme and substrate come together, their interaction causes a mild...
01:22Introduction to Enzymes
The use of enzymes by humans dates to 7000 BCE. Humans first used enzymes to ferment sugars and produce alcohol without knowing that this was an enzyme-catalyzed reaction. Wilhelm Kuhne coined the term 'enzyme' in 1877 from the Greek words ‘en’ meaning ‘in’ or ‘within’ and ‘zyme’ meaning ‘yeast.’
Most enzymes are proteins that speed up biochemical reactions without being consumed. Enzymes contain one or more active sites that bind the substrates and convert them into products. Many enzymes also...
Most enzymes are proteins that speed up biochemical reactions without being consumed. Enzymes contain one or more active sites that bind the substrates and convert them into products. Many enzymes also...
01:22Introduction To Enzymes
The use of enzymes by humans dates to 7000 BCE. Humans first used enzymes to ferment sugars and produce alcohol without knowing that this was an enzyme-catalyzed reaction. Wilhelm Kuhne coined the term 'enzyme' in 1877 from the Greek words ‘en’ meaning ‘in’ or ‘within’ and ‘zyme’ meaning ‘yeast.’
Most enzymes are proteins that speed up biochemical reactions without being consumed. Enzymes contain one or more active sites that bind the substrates and convert them into products. Many enzymes also...
Most enzymes are proteins that speed up biochemical reactions without being consumed. Enzymes contain one or more active sites that bind the substrates and convert them into products. Many enzymes also...
01:07Catalytically Perfect Enzymes
The theory of catalytically perfect enzymes was first proposed by W.J. Albery and J. R. Knowles in 1976. These enzymes catalyze biochemical reactions at high-speed. Their catalytic efficiency values range from 108-109 M-1s-1. These enzymes are also called 'diffusion-controlled' as the only rate-limiting step in the catalysis is that of the substrate diffusion into the active site. Examples include triose phosphate isomerase, fumarase, and superoxide dismutase.