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Related Concept Videos

Inducible Operons: lac Operon01:25

Inducible Operons: lac Operon

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The lac operon in Escherichia coli is a model for understanding inducible gene regulation and metabolic flexibility. It integrates local control by lactose and global regulation through catabolite repression, enabling E. coli to preferentially metabolize glucose when available and switch to lactose utilization when glucose is scarce.Structure and Function of the lac OperonThe lac operon contains three structural genes: lacZ (β-galactosidase), lacY (lactose permease), and lacA...
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Operons02:09

Operons

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Prokaryotes can control gene expression through operons—DNA sequences consisting of regulatory elements and clustered, functionally related protein-coding genes. Operons use a single promoter sequence to initiate transcription of a gene cluster (i.e., a group of structural genes) into a single mRNA molecule. The terminator sequence ends transcription. An operator sequence, located between the promoter and structural genes, prohibits the operon’s transcriptional activity if bound by...
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Combining Single-molecule Manipulation and Imaging for the Study of Protein-DNA Interactions
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Simulated pressure changes in LacI suggest a link between hydration and functional conformational changes.

Nilusha L Kariyawasam1, Elizabeth A Ploetz1, Liskin Swint-Kruse2

  • 1Department of Chemistry, 213 CBC Building, 1212 Mid-Campus Dr. North, Kansas State University, Manhattan, KS 66506, USA.

Biophysical Chemistry
|November 4, 2023
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Summary

Pressure perturbations reveal hydration

Keywords:
Hydrostatic pressureLacI proteinMolecular dynamics simulationsProtein conformationProtein volumeSolvation changes

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Area of Science:

  • Biochemistry
  • Structural Biology
  • Computational Biology

Background:

  • Protein functions often involve dynamic conformational changes between substates.
  • Experimentally measuring these substates and isolating hydration effects is challenging.
  • The Escherichia coli lactose repressor protein (LacI) undergoes conformational changes upon DNA binding.

Purpose of the Study:

  • To investigate the utility of pressure perturbations for sampling protein conformational substates.
  • To assess the role of hydration in modulating LacI conformational states.
  • To understand how pressure affects LacI conformation.

Main Methods:

  • Utilized molecular dynamics simulations with applied pressure perturbations.
  • Examined the conformational landscape of the lactose repressor protein (LacI).
  • Compared pressure effects to ligand binding (DNA, ONPF).

Main Results:

  • Increased simulation pressure inhibited the transition from an Open to a Closed conformation in LacI.
  • Pressure effects mimicked the conformational stabilization observed with DNA and anti-inducer binding.
  • Hydration of specific residues was implicated in controlling LacI substate populations.

Conclusions:

  • Simulating pressure perturbations is a viable method for probing protein substates.
  • Hydration changes significantly influence functionally relevant protein conformational dynamics.
  • This approach can aid in understanding the impact of hydration on protein function and mutations.