Related Experiment Video
Updated: Jun 25, 2026
16:24
Analyzing and Building Nucleic Acid Structures with 3DNA
Published on: April 26, 2013
The TATA-binding protein core domain in solution variably bends TATA sequences via a three-step binding mechanism
Roberto F Delgadillo1, Jodell E Whittington, Laura K Parkhurst
1Department of Chemistry, University of Nebraska, Lincoln, Nebraska 68588-0304, USA.
Biochemistry
|February 10, 2009
Summary
The N-terminal domains (NTDs) of TATA-binding proteins (TBP) influence DNA binding and bending. NTDs destabilize bound DNA, and DNA bending depends on the TATA sequence, differing between solution and crystal states.
Area of Science:
- Molecular Biology
- Biochemistry
- Structural Biology
Background:
- TATA-binding protein (TBP) is crucial for transcription initiation.
- The role of TBP's N-terminal domains (NTDs) in DNA binding and bending is not fully understood.
Purpose of the Study:
- To quantitate the roles of yeast (yTBP) and human (hTBP) NTDs in DNA binding and bending.
- To investigate the mechanism of TBP-DNA interaction and DNA bending.
Main Methods:
- Studied the binding and bending of the AdMLP TATA sequence by yeast TBP core domain.
- Utilized thermodynamic and kinetic analyses to probe protein-DNA interactions.
- Compared solution data with existing crystallographic data.
Main Results:
- All three proteins (yTBP, hTBP, cTBP) bind DNA via a three-step mechanism without initial unbound DNA.
- NTD movement, not DNA bending, drives the energetics of the first binding step for yTBP.
- hTBP's NTD does not initially occupy the DNA binding pocket.
- NTDs destabilize DNA binding for both yTBP and hTBP.
- DNA bend angle depends on TATA sequence, with cTBP and hTBP inducing greater bends than yTBP.
- Solution structures show sequence-dependent bending, contrasting with crystal studies.
Conclusions:
- NTDs play a significant role in modulating DNA binding affinity and DNA bending.
- Differences in NTD structure and dynamics explain variations in DNA binding and bending among TBP proteins.
- Osmolytes in crystals account for discrepancies between solution and crystal structures of TBP-DNA complexes.
More Related Videos
06:02Determining the Thermodynamic and Kinetic Association of a DNA Aptamer and Tetracycline Using Isothermal Titration Calorimetry
Published on: August 23, 2022
12:07Chemical Modification of the Tryptophan Residue in a Recombinant Ca2+-ATPase N-domain for Studying Tryptophan-ANS FRET
Published on: October 9, 2021
Related Concept Videos
01:49Conserved 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...
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...
01:49Conserved 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...
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...
01:03Single-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...
02:13Cooperative 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...
02:13Cooperative 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...
01:19Allosteric 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,...
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,...