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Related Concept Videos

Enzymes02:34

Enzymes

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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...
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Introduction to Mechanisms of Enzyme Catalysis01:13

Introduction to Mechanisms of Enzyme Catalysis

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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...
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Induced-fit Model01:13

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Most chemical reactions in cells require enzymes—biological catalysts that speed up the reaction without being consumed or permanently changed. They reduce the activation energy needed to convert the reactants into products. Enzymes are proteins, that usually work by binding to a substrate—a reactant molecule that they act upon.
Enzymes exhibit substrate specificity, meaning that they can only bind to certain substrates. This is mainly determined by the shape and chemical...
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Enzyme Kinetics01:19

Enzyme Kinetics

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Enzymes speed up reactions by lowering the activation energy of the reactants. The speed at which the enzyme turns reactants into products is called the rate of reaction. Several factors impact the rate of reaction, including the number of available reactants. Enzyme kinetics is the study of how an enzyme changes the rate of a reaction.
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Conserved Binding Sites01:49

Conserved Binding Sites

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Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
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Introduction to Enzyme Kinetics01:19

Introduction to Enzyme Kinetics

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Enzyme kinetics studies the rates of biochemical reactions. Scientists monitor the reaction rates for a particular enzymatic reaction at various substrate concentrations. Additional trials with inhibitors or other molecules that affect the reaction rate may also be performed.
The experimenter can then plot the initial reaction rate or velocity (Vo) of a given trial against the substrate concentration ([S]) to obtain a graph of the reaction properties. For many enzymatic reactions involving a...
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Unraveling Entropic Rate Acceleration Induced by Solvent Dynamics in Membrane Enzymes
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Unraveling Entropic Rate Acceleration Induced by Solvent Dynamics in Membrane Enzymes

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Conserved conformational dynamics determine enzyme activity.

Kristiane R Torgeson1,2, Michael W Clarkson1, Daniele Granata3

  • 1Department of Chemistry and Biochemistry, The University of Arizona, Tucson, AZ, USA.

Science Advances
|August 3, 2022
PubMed
Summary
This summary is machine-generated.

Enzyme function is influenced by conserved dynamics beyond the active site. These dynamics, identified through coevolutionary analysis and NMR, reveal new therapeutic targets for enzyme control.

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The Importance of Correct Protein Concentration for Kinetics and Affinity Determination in Structure-function Analysis
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The Importance of Correct Protein Concentration for Kinetics and Affinity Determination in Structure-function Analysis
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Area of Science:

  • Biochemistry
  • Enzymology
  • Structural Biology

Background:

  • Homologous enzymes can have varying catalytic rates despite conserved active sites.
  • Enzyme function is traditionally linked to sequence and structure, with recent focus on intrinsic protein dynamics.
  • The role of non-active site dynamics in enzyme catalysis remains underexplored.

Purpose of the Study:

  • To investigate the role of protein dynamics, particularly those distant from the active site, in regulating enzyme catalytic rates.
  • To identify novel regulatory mechanisms controlling enzyme activity.
  • To explore potential therapeutic targets based on conserved enzyme dynamics.

Main Methods:

  • Coevolutionary coupling analysis to predict correlated motions.
  • Nuclear Magnetic Resonance (NMR) spectroscopy to detect intermediate time-scale dynamics.
  • Utilizing protein tyrosine phosphatase 1B (PTP1B) as a model enzyme.

Main Results:

  • Residues surrounding the PTP1B active site contribute to dynamically coordinated chemistry.
  • Distinct intermediate time-scale dynamics were detected in residues distant from the active site.
  • These distal dynamics correlate with catalytic activity, explaining rate variations within enzyme families.
  • Conserved dynamics across the PTP family were identified as a key driver of enzymatic activity.

Conclusions:

  • Enzyme activity is significantly influenced by conserved dynamics occurring at various time scales and distances from the active site.
  • These findings challenge the sole focus on active site residues for understanding enzyme function and regulation.
  • Characterizing conserved dynamics can reveal novel allosteric binding pockets for therapeutic intervention in enzyme-controlled pathways.