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Related Concept Videos

Ligand Binding Sites02:40

Ligand Binding Sites

Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...
Conserved Binding Sites01:49

Conserved Binding Sites

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.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
Ligand Binding and Linkage00:49

Ligand Binding and Linkage

Allosteric proteins have more than one ligand binding site; the binding of a ligand to any of these sites influences the binding of ligands to the other sites. When a protein is allosteric, its binding sites are called coupled or linked.  In the case of enzymes, the site that binds to the substrate is known as the active site and the other site is known as the regulatory site. When a ligand binds to the regulatory site, this leads to conformational changes in the protein that can influence the...
Cooperative Binding of Transcription Regulators02:13

Cooperative Binding of Transcription Regulators

Transcriptional regulators bind to specific cis-regulatory sequences in the DNA to regulate gene transcription. These cis-regulatory sequences are very short, usually less than ten nucleotide pairs in length. The short length means that there is a high probability of the exact same sequence randomly occurring throughout the genome.  Since regulators can also bind to groups of similar sequences, this further increases the chances of random binding. Transcriptional regulators form dimers that...
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,...
Single-Strand DNA Binding Proteins01:03

Single-Strand DNA Binding Proteins

For successful DNA replication, the unwinding of double-stranded DNA must be accompanied by stabilization and protection of the separated single strands of the DNA. This crucial task is performed by single-strand DNA-binding (SSB) proteins. They bind to the DNA in a sequence-independent manner, which means that the nitrogenous bases of the DNA need not be present in a specific order for binding of SSB proteins to it. The binding of SSB proteins straightens single-stranded DNA (ssDNA) and makes...

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Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins
11:34

Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins

Published on: August 9, 2019

Differences between MyoD DNA binding and activation site requirements revealed by functional random sequence

J Huang1, T K Blackwell, L Kedes

  • 1Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, Washington 98104, USA.

Molecular and Cellular Biology
|July 1, 1996
PubMed
Summary

Researchers identified functional DNA sequences for gene activation by MyoD. Optimal binding sites were not always active, suggesting additional DNA interactions are needed for transcriptional activation by basic helix-loop-helix proteins.

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Area of Science:

  • Molecular Biology
  • Genetics
  • Biochemistry

Background:

  • Basic helix-loop-helix (bHLH) proteins are crucial transcription factors in higher eukaryotes.
  • Understanding the relationship between DNA binding affinity and transcriptional activation is key to gene regulation.

Purpose of the Study:

  • To develop a method for selecting functional enhancer/promoter sites from random DNA sequences.
  • To investigate the correlation between DNA binding characteristics and transcriptional activation mediated by the muscle-specific bHLH protein, MyoD.

Main Methods:

  • Selection of functional enhancer/promoter sequences from random DNA libraries in eukaryotic cells.
  • Analysis of sequence preferences for transcriptional activation by MyoD.
  • Comparison of selected sequences with in vitro binding consensus and naturally occurring muscle-specific promoters.

Main Results:

  • A subset of transcriptionally active sequences showed minimal similarity to the preferred in vitro MyoD binding consensus.
  • An optimal in vitro binding site was found to be inactive in the same promoter context.
  • Sequences with high transcriptional activity exhibited preferences similar to naturally occurring muscle-specific promoters.

Conclusions:

  • DNA binding by MyoD is necessary but not sufficient for transcriptional activation.
  • Additional DNA sequence-dependent interactions or conformational changes are required at the binding site for full transcriptional activation.
  • This study provides insights into the complex mechanisms governing bHLH protein-mediated gene regulation.