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Related Concept Videos

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...
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Unraveling Entropic Rate Acceleration Induced by Solvent Dynamics in Membrane Enzymes
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Enzyme-Substrate-Cofactor Dynamical Networks Revealed by High-Resolution Field Cycling Relaxometry.

Masha M Rosenberg1, Tianjiong Yao1, Gregory C Patton1

  • 1Department of Biology, Brandeis University, MS009, 415 South St., Waltham, Massachusetts 02453-9110, United States.

Biochemistry
|June 2, 2020
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Summary
This summary is machine-generated.

Enzyme dynamics are crucial for catalysis. This study uses advanced NMR to reveal how specific amino acids in guanosine-5'-monophosphate reductase (GMPR) control cofactor and substrate movements, essential for distinct reaction steps.

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Area of Science:

  • Biochemistry
  • Enzymology
  • Structural Biology

Background:

  • Enzyme catalysis relies on dynamic interactions between enzymes, substrates, and cofactors.
  • The role of protein dynamics in enzyme function is well-studied, but ligand dynamics are less understood.
  • Guanosine-5 ext-monophosphate reductase (GMPR) provides a model system with catalytically competent complexes mimicking reaction intermediates.

Purpose of the Study:

  • To investigate the dynamics of enzyme-bound substrates and cofactors in GMPR using sub-tesla high-resolution field cycling 31P NMR relaxometry.
  • To identify structural features contributing to distinct dynamic signatures in hydride transfer and deamination complexes.
  • To elucidate the role of specific amino acid residues in modulating cofactor conformation and ammonia binding.

Main Methods:

  • Utilized sub-tesla high-resolution field cycling 31P NMR relaxometry to probe ligand dynamics.
  • Employed site-directed mutagenesis to perturb cofactor conformation and ammonia binding in GMPR.
  • Conducted exchange experiments to assess ammonia/ammonium affinity for different enzyme complexes.

Main Results:

  • Asp129 is integral to dynamic networks for both hydride transfer and deamination.
  • Lys77 modulates substrate and cofactor mobility in a reaction-specific manner.
  • Thr105 and Tyr318 form a deamination-specific network involving the GMP 2 ext-OH, with minimal impact on hydride transfer dynamics.
  • Ammonia/ammonium exhibits high affinity for the deamination complex and low affinity for the hydride transfer complex, potentially gating cofactor conformational changes.

Conclusions:

  • Enzyme, substrates, and cofactors are interconnected in intricate, reaction-specific dynamic networks.
  • Distal regions of substrates and cofactors are critical components of these dynamic networks.
  • High-resolution field cycling NMR relaxometry is a powerful tool for investigating ligand dynamics in enzymatic systems.