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Related Concept Videos

Protein Networks02:26

Protein Networks

An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
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...
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...
Protein Organization01:24

Protein Organization

Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
The primary structure of a protein is its amino acid sequence.
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...
Covalently Linked Protein Regulators02:04

Covalently Linked Protein Regulators

Proteins can undergo many types of post-translational modifications, often in response to changes in their environment. These modifications play an important role in the function and stability of these proteins. Covalently linked molecules include functional groups, such as methyl, acetyl, and phosphate groups, and also small proteins, such as ubiquitin. There are around 200 different types of covalent regulators that have been identified.
These groups modify specific amino acids in a protein.

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Related Experiment Video

Updated: Jun 30, 2026

Analyzing and Building Nucleic Acid Structures with 3DNA
16:24

Analyzing and Building Nucleic Acid Structures with 3DNA

Published on: April 26, 2013

Computational structural analysis: multiple proteins bound to DNA.

Andrija Tomovic1, Edward J Oakeley

  • 1Friedrich Miescher Institute for Biomedical Research, Novartis Research Foundation, Basel, Switzerland. andrija.tomovic@fmi.ch

Plos One
|September 20, 2008
PubMed
Summary
This summary is machine-generated.

Multiple proteins binding to DNA form more stable and specific complexes than single proteins. DNA shape changes enhance ternary complex stability by reducing protein off-rates, unlike protein-protein interactions without DNA.

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Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion

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Area of Science:

  • Structural biology
  • Computational biophysics
  • Molecular interactions

Background:

  • Increasing availability of protein-DNA and protein-protein-DNA complex structures allows for detailed analysis of macromolecular interactions.
  • Properties of multi-protein DNA-binding assemblies remain underexplored despite advances in structural data.

Purpose of the Study:

  • To computationally analyze macromolecular assemblies of multiple proteins bound to DNA.
  • To compare interface properties, DNA conformational changes, and thermodynamic stability of multi-protein-DNA complexes with binary complexes.

Main Methods:

  • Utilized computational tools including PISA, PROMOTIF, X3DNA, ReadOut, DDNA, and DCOMPLEX.
  • Developed and applied an algorithm for approximate collision detection and overlapping volume estimation between macromolecules.
  • Compared structural, physical-chemical, and thermodynamic parameters of ternary complexes with binary protein-DNA and protein-protein complexes.

Main Results:

  • Interface properties of multi-protein-DNA complexes are similar to binary complexes, but DNA undergoes greater conformational changes.
  • Water-mediated contacts are less significant in ternary complexes compared to binary ones.
  • Ternary complexes exhibit higher thermodynamic stability, specificity, and affinity than binary protein-DNA interactions, though protein-protein affinities are stronger without DNA.

Conclusions:

  • Interface characteristics (area, residues, bonds, etc.) are consistent across binary and ternary protein-DNA complexes.
  • DNA shape modulation upon multi-protein binding significantly reduces protein off-rates, enhancing ternary complex stability and specificity.
  • These findings highlight distinct stabilization mechanisms in multi-protein-DNA assemblies compared to simpler binary interactions.