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Related Concept Videos

Allosteric Proteins-ATCase01:19

Allosteric Proteins-ATCase

Binding sites linkages can regulate a protein's function.  For example, enzyme activity is often regulated through a feedback mechanism where the end product of the biochemical process serves as an inhibitor.
Aspartate transcarbamoylase (ATCase) is a cytosolic enzyme that catalyzes the condensation of L-aspartate and carbamoyl phosphate to  N-carbamoyl-L-aspartate. This reaction is the first step in pyrimidine biosynthesis. UTP and CTP, the end products of the pyrimidine synthesis pathway,...
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Ribosome Profiling

Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
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The technique helps...
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Labeling DNA Probes

DNA probes are fragments of DNA labeled with a reporter tag to enable their detection or purification. The resulting labeled DNA probes can then hybridize to target nucleic acid sequences through complementary base-pairing, and may be used to recover or identify these regions.
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Allosteric Regulation01:08

Allosteric Regulation

Allosteric regulation of enzymes occurs when the binding of an effector molecule to a site that is different from the active site causes a change in the enzymatic activity. This alternate site is called an allosteric site, and an enzyme can contain more than one of these sites. Allosteric regulation can either be positive or negative, resulting in an increase or decrease in enzyme activity. Most enzymes that display allosteric regulation are metabolic enzymes involved in the degradation or...
Allosteric Regulation01:08

Allosteric Regulation

Allosteric regulation of enzymes occurs when the binding of an effector molecule to a site that is different from the active site causes a change in the enzymatic activity. This alternate site is called an allosteric site, and an enzyme can contain more than one of these sites. Allosteric regulation can either be positive or negative, resulting in an increase or decrease in enzyme activity. Most enzymes that display allosteric regulation are metabolic enzymes involved in the degradation or...
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The flow of genetic information in cells from DNA to mRNA to protein is described by the central dogma, which states that genes specify the sequence of mRNAs, which in turn specify the sequence of amino acids making up all proteins. The decoding of one molecule to another is performed by specific proteins and RNAs. Because the information stored in DNA is so central to cellular function, it makes intuitive sense that the cell would make mRNA copies of this information for protein synthesis...

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Optimizing the Genetic Incorporation of Chemical Probes into GPCRs for Photo-crosslinking Mapping and Bioorthogonal Chemistry in Live Mammalian Cells
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Probing allostery through DNA.

Sangjin Kim1, Erik Broströmer, Dong Xing

  • 1Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA.

Science (New York, N.Y.)
|February 16, 2013
PubMed
Summary
This summary is machine-generated.

Researchers discovered DNA allostery, where nearby proteins alter DNA-protein binding. This interaction

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Area of Science:

  • Molecular Biology
  • Biophysics
  • Genetics

Background:

  • Allostery, the modulation of protein function by distant binding events, is well-established for proteins.
  • Allosteric effects in DNA-protein interactions remain less understood, representing a significant knowledge gap.
  • Understanding DNA-protein interactions is crucial for gene regulation and cellular processes.

Purpose of the Study:

  • To investigate and characterize the phenomenon of allostery in DNA-protein interactions.
  • To determine the physical basis and periodicity of DNA allosteric effects.
  • To explore the physiological implications of DNA allostery in biological systems.

Main Methods:

  • Experimental determination of protein-DNA binding affinities under varying protein-protein separations.
  • Analysis of ternary complex free energy as a function of inter-protein distance.
  • Molecular dynamics simulations to elucidate the structural basis of DNA allostery.
  • In vivo studies in bacteria to assess effects on gene expression.

Main Results:

  • Specific binding of proteins to DNA is significantly stabilized or destabilized by the presence of nearby proteins.
  • The free energy of ternary complexes oscillates with a periodicity of approximately 10 base pairs (B-DNA helical pitch).
  • DNA allostery originates from the deformation of the DNA double-helical structure, as supported by simulations.
  • This phenomenon impacts gene expression in bacteria and influences transcription factor binding near nucleosomes.

Conclusions:

  • DNA allostery is a newly recognized mechanism modulating DNA-protein interactions.
  • The helical structure of DNA plays a critical role in mediating these allosteric effects.
  • DNA allostery has significant physiological relevance in regulating gene expression and protein binding in vivo.