Related Experiment Video
Updated: May 23, 2026
07:09
Förster Resonance Energy Transfer Mapping: A New Methodology to Elucidate Global Structural Features
Published on: March 16, 2022
A structural model of the E. coli PhoB dimer in the transcription initiation complex
Chang-Shung Tung1, Benjamin H McMahon
1Theoretical Biology & Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA. ct@lanl.gov
BMC Structural Biology
|March 22, 2012
Summary
A new Motif Binding Geometries (MBG) approach models protein complexes by inferring interactions from homologous proteins. This method successfully predicted the PhoB/RNAP/σ-factor/DNA complex structure, advancing our understanding of cellular regulation.
Area of Science:
- Structural Biology
- Computational Biology
- Biochemistry
Background:
- Over 78,000 experimentally determined protein and nucleic acid structures exist, yet few represent protein complexes.
- Current homology modeling techniques for individual proteins do not extend to predicting protein complex structures.
- A gap exists in methods for understanding and predicting protein-protein interactions within complexes.
Purpose of the Study:
- To develop a novel computational method for inferring protein complex structures.
- To demonstrate the utility of the Motif Binding Geometries (MBG) approach for modeling biological complexes.
- To apply the MBG method to a significant regulatory complex involved in transcription.
Main Methods:
- Utilized a Motif Binding Geometries (MBG) approach.
- Inferred complex structures from databases of homologous protein complexes in different contexts.
- Applied the method to model the PhoB/RNAP/σ-factor/DNA transcription initiation complex.
Main Results:
- The modeled PhoB/RNAP/σ-factor/DNA complex exhibited stereo-chemical reasonableness.
- The complex demonstrated sufficient interfacial Solvent Excluded Surface Areas (SESAs) for adequate binding.
- The predicted structure was physically meaningful for transcription regulation and consistent with experimental data.
Conclusions:
- A structural model for the PhoB dimer in the transcription initiation complex was developed based on the principle that similar folding implies similar interactions.
- The MBG approach offers a scalable method for structural modeling and prediction of diverse biomolecular complexes.
- Models of protein complexes will enhance understanding of cellular regulation and signaling, complementing insights from individual protein models.
More Related Videos
Related Concept Videos
01:53Bacterial Transcription
RNA polymerase (RNAP) carries out DNA-dependent RNA synthesis in both bacteria and eukaryotes. Bacteria do not have a membrane-bound nucleus. So, transcription and translation occur simultaneously, on the same DNA template.
Transcription can be divided into three main stages, each involving distinct DNA sequences to guide the polymerase. These are:
Transcription can be divided into three main stages, each involving distinct DNA sequences to guide the polymerase. These are:
01:28Transcription in Prokaryotes
Transcription is a highly regulated process that converts genetic information into RNA molecules. The transcription cycle is divided into three key stages: initiation, elongation, and termination, each driven by specific molecular mechanisms.Initiation of TranscriptionIn bacteria, transcription begins when the RNA polymerase core enzyme associates with a sigma factor to form a holoenzyme. For example, the E. coli sigma factor called σ70 forms a holoenzyme, which recognizes the -10 (Pribnow box)...
01:30General Transcription Factors
Tissue-specific transcription factors contribute to diverse cellular functions in mammals. For example, the gene for beta globin, a major component of hemoglobin, is present in all cells of the body. However, it is only expressed in red blood cells because the transcription factors that can bind to the promoter sequences of the beta globin gene are only expressed in these cells. Tissue-specific transcription factors also ensure that mutations in these factors may impair only the function of...
01:47Transcription Initiation
Initiation is the first step of transcription in eukaryotes. Prokaryotic RNA Polymerase (RNAP) can bind to the template DNA and start transcribing. On the other hand, transcription in eukaryotes requires additional proteins, called transcription factors, to first bind to the promoter region in the DNA template. This binding helps recruit the specific RNAP that can assemble on the DNA and start transcription.
The promoters and enhancers and their accessory proteins allow tight regulation of...
The promoters and enhancers and their accessory proteins allow tight regulation of...
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...