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Related Concept Videos

Introduction to Mechanisms of Enzyme Catalysis01:13

Introduction 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...
Introduction to Mechanisms of Enzyme Catalysis01:13

Introduction 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...
Cooperative Allosteric Transitions01:58

Cooperative Allosteric Transitions

Cooperative allosteric transitions can occur in multimeric proteins, where each subunit of the protein has its own ligand-binding site. When a ligand binds to any of these subunits, it triggers a conformational change that affects the binding sites in the other subunits; this can change the affinity of the other sites for their respective ligands. The ability of the protein to change the shape of its binding site is attributed to the presence of a mix of flexible and stable segments in the...
Cooperative Allosteric Transitions01:58

Cooperative Allosteric Transitions

Cooperative allosteric transitions can occur in multimeric proteins, where each subunit of the protein has its own ligand-binding site. When a ligand binds to any of these subunits, it triggers a conformational change that affects the binding sites in the other subunits; this can change the affinity of the other sites for their respective ligands. The ability of the protein to change the shape of its binding site is attributed to the presence of a mix of flexible and stable segments in the...
Cooperative Allosteric Transitions01:58

Cooperative Allosteric Transitions

Cooperative allosteric transitions can occur in multimeric proteins, where each subunit of the protein has its own ligand-binding site. When a ligand binds to any of these subunits, it triggers a conformational change that affects the binding sites in the other subunits; this can change the affinity of the other sites for their respective ligands. The ability of the protein to change the shape of its binding site is attributed to the presence of a mix of flexible and stable segments in the...
Catalytically Perfect Enzymes01:07

Catalytically 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.

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Related Experiment Video

Updated: May 18, 2026

Unraveling Entropic Rate Acceleration Induced by Solvent Dynamics in Membrane Enzymes
09:42

Unraveling Entropic Rate Acceleration Induced by Solvent Dynamics in Membrane Enzymes

Published on: January 16, 2016

Coupling between catalytic loop motions and enzyme global dynamics.

Zeynep Kurkcuoglu1, Ahmet Bakan, Duygu Kocaman

  • 1Department of Chemical Engineering and Polymer Research Center, Bogazici University, Bebek, Istanbul, Turkey.

Plos Computational Biology
|October 3, 2012
PubMed
Summary
This summary is machine-generated.

Enzyme catalytic loops utilize inherent global dynamics for substrate binding. Elastic network models reveal that collective enzyme motions guide functional loop movements, optimizing active site closure.

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Last Updated: May 18, 2026

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Published on: January 16, 2016

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Area of Science:

  • Biochemistry
  • Structural Biology
  • Computational Biology

Background:

  • Enzyme catalytic loops undergo flexible motions crucial for substrate recognition and binding.
  • The functional significance of these motions implies underlying structure-encoded preferences guiding their mechanisms.

Purpose of the Study:

  • To investigate if collective enzyme dynamics, predicted by elastic network models (ENMs), influence or dictate the local motions of functional loops.
  • To correlate global enzyme architecture with specific loop movements essential for catalysis.

Main Methods:

  • Analysis of 117 crystal structures from ten diverse enzymes (varying sizes and oligomerization states).
  • Application of Principal Component Analysis (PCA) to study conformational changes in functional loops (10-21 residues) upon substrate binding.
  • Utilized elastic network models (ENMs) to predict enzyme collective dynamics.

Main Results:

  • Experimentally observed loop reconfigurations upon substrate binding are primarily driven by energetically favorable intrinsic enzyme motions.
  • These intrinsic motions are accessible to the enzyme even without a substrate.
  • Dominant global modes of motion, dictated by overall enzyme architecture, include local components that facilitate catalytic loop opening/closure.

Conclusions:

  • Enzyme global dynamics play a critical role in directing functional loop movements for substrate binding.
  • The inherent conformational landscape of an enzyme pre-favors motions required for catalysis.
  • Understanding these structure-dynamics-function relationships can inform enzyme engineering and drug design.