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Related Concept Videos

Induced-fit Model01:13

Induced-fit Model

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 characteristics of...
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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...
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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 a mild...
Cooperative Allosteric Transitions01:58

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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

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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...
Introduction to Mechanisms of Enzyme Catalysis01:13

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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 a mild...

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Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
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A model for enzyme-substrate interaction in alanine racemase.

M J Ondrechen1, J M Briggs, J A McCammon

  • 1Department of Chemistry, Northeastern University, Boston, Massachusetts 02115-5000, USA.

Journal of the American Chemical Society
|July 18, 2001
PubMed
Summary

This study models alanine racemase, revealing unusual charge states on key residues like Tyr265' and Lys39. These findings support their roles as catalytic bases in L-alanine and D-alanine conversion, aiding enzyme mechanism understanding.

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Area of Science:

  • Biochemistry
  • Computational Biology
  • Enzyme Kinetics

Background:

  • Alanine racemase (ALR) is crucial for bacterial cell wall synthesis.
  • Understanding ALR's catalytic mechanism is key for developing selective inhibitors.
  • Previous studies suggest specific residues act as catalytic bases, but their ionization states require clarification.

Purpose of the Study:

  • To develop a theoretical model of the alanine racemase complex.
  • To predict the ionization states and electrostatic potentials of key residues.
  • To elucidate the roles of specific residues in ALR's catalytic mechanism.

Main Methods:

  • Theoretical modeling of the enzyme-substrate-cofactor complex.
  • Calculation of electrostatic potentials.
  • Prediction of pKa values and ionization states for ionizable groups.

Main Results:

  • Unusual charge states predicted for Tyr265 (pKa=7.9) and Lys39.
  • Tyr265 predicted to be in phenolate form at physiological pH, supporting its role as a catalytic base.
  • Lys39 predicted to be in unprotonated amine form, enabling its function as a catalytic base.
  • Cys311 (pKa=5.8) shows significant negative charge at pH 7.0.
  • Lys129's low charge supports experimental carbamylation evidence.

Conclusions:

  • The enzyme stabilizes negative charge in the active site.
  • Predicted ionization states align with experimental evidence for catalytic residue functions.
  • Findings provide insights for designing selective ALR inhibitors.