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Related Concept Videos

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...
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...
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...
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...
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...

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Related Experiment Video

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Analyzing and Building Nucleic Acid Structures with 3DNA
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Published on: April 26, 2013

DBD2BS: connecting a DNA-binding protein with its binding sites.

Ting-Ying Chien1, Chih-Kang Lin, Chih-Wei Lin

  • 1Department of Computer Science and Information Engineering, National Taiwan University, Taipei 106, Taiwan.

Nucleic Acids Research
|June 14, 2012
PubMed
Summary

This study introduces DBD2BS, a web server that predicts DNA-binding sequences (PWMs) from protein structures, even unbound ones. This advances understanding of gene regulation by enabling analysis of more protein structures.

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Area of Science:

  • Structural Biology
  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • DNA-binding proteins (DBDs) regulate biological processes by binding to specific DNA sequences.
  • Identifying these DNA-binding sites, often represented as position weight matrices (PWMs), is crucial for understanding cellular control mechanisms.
  • Current methods for PWM inference often rely on experimental data like chromatin immunoprecipitation, which is not always available.

Purpose of the Study:

  • To present DBD2BS, a novel web server for predicting PWMs of DBDs.
  • To enable PWM prediction from both bound and unbound protein structures, expanding the utility of existing structural data.
  • To provide an effective alternative for PWM inference when experimental data is limited.

Main Methods:

  • Utilizes an atom-level knowledge-based potential function to predict PWMs from query DBD structures.
  • For unbound structures, synthesizes bound structures using a template library of 1066 DBD-DNA complexes.
  • Offers an intuitive interface for visualizing predicted PWMs and spatial relationships between protein, DBD, and DNA.

Main Results:

  • DBD2BS successfully predicts PWMs characterizing DNA sequences bound by DBDs.
  • The approach allows the prediction of PWMs from unbound protein structures, a first in the field.
  • Predicted PWMs demonstrate consistency with experimentally derived data, validating the method's accuracy.

Conclusions:

  • DBD2BS significantly expands the range of protein structures usable for analyzing protein-DNA interactions.
  • The web server provides a valuable tool for researchers studying gene regulation and protein-DNA binding.
  • Integration with sequence-based methods can facilitate genome-wide binding site discovery.