Related Experiment Video
Updated: May 5, 2026
06:48
CD Spectroscopy to Study DNA-Protein Interactions
Published on: February 10, 2022
6.5K
Conformational changes in DNA-binding proteins: relationships with precomplex features and contributions to
Munazah Andrabi, Kenji Mizuguchi1, Shandar Ahmad
1Bioinformatics project, National Institute of Biomedical Innovation, 7-6-8 Saito-Asagi, Ibaraki City, Osaka 567-0085, Japan.
Proteins
|November 23, 2013
Summary
Conformational changes in DNA-binding proteins are crucial for stable, specific interactions. Most changes occur when proteins bind specific DNA targets, enhancing complex stability and recognition.
Area of Science:
- Structural Biology
- Biochemistry
- Genetics
Background:
- Proteins and DNA undergo conformational changes to form functional complexes and interact with other molecules.
- These dynamic alterations impact complex stability, specificity, and interaction cooperativity.
Purpose of the Study:
- To extensively analyze conformational changes in DNA-binding proteins.
- To investigate the relationship between these changes and protein function, binding, and stability.
Main Methods:
- Superimposed DNA-bound and unbound protein structures from a curated database of 90 proteins.
- Manually examined protein pairs, unified annotations, and classified conformational changes into six categories.
- Explored correlations with functional classes, binding motifs, target specificity, biophysical features, and complex stability.
Main Results:
- Conformational changes significantly enhance the stability of protein-DNA complexes.
- These changes are critical for the specificity of DNA target recognition by proteins.
- Most conformational changes are observed in proteins binding specific DNA targets.
Conclusions:
- Conformational flexibility in DNA-binding proteins is a key determinant of complex stability and target specificity.
- While unbound proteins may possess inherent nonspecific binding capabilities, specific interactions drive significant conformational adaptations.
Keywords:
DNA-binding proteinsDNA-target specificityclassification of proteinsconformational changesintrinsic flexibility of proteinsprotein-DNA interactionsstabilityMore Related Videos
Related Concept Videos
01:49Conserved Binding Sites
4.1K
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...
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...
4.1K
01:49Conserved Binding Sites
1.1K
1.1K
01:03Single-Strand DNA Binding Proteins
12.9K
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...
12.9K
01:57Protein Complexes with Interchangeable Parts
2.1K
Groups of proteins may form a complex where each protein in this complex has a different role in the overall execution of the complex’s function. Often some of the proteins in the complex can be replaced by a closely related variant to give a complex that contains many of the same components yet is functionally distinct.
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order...
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order...
2.1K
02:13Cooperative Binding of Transcription Regulators
6.0K
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...
6.0K
02:04Covalently Linked Protein Regulators
8.2K
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....
These groups modify specific amino acids in a protein....
8.2K