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Related Concept Videos

Protein-protein Interfaces02:04

Protein-protein Interfaces

Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a polypeptide...
Protein-Protein Interfaces02:04

Protein-Protein Interfaces

Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a polypeptide...
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,...
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...
DNA as a Genetic Template02:05

DNA as a Genetic Template

Two structural features of the DNA molecule provide a basis for the mechanisms of heredity: the four nucleotide bases and its double-stranded nature. The Watson-Crick model of double-helical DNA structure, proposed in 1952, drew heavily upon the X-ray crystallography work of researchers Rosalind Franklin and Maurice Wilkins. Watson, Crick, and Wilkins jointly received the Nobel Prize in Physiology or Medicine for their work in 1962. Franklin was, controversially, excluded from the prize for...
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.

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Related Experiment Video

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

Analyzing and Building Nucleic Acid Structures with 3DNA

Published on: April 26, 2013

A feature-based approach to modeling protein-DNA interactions.

Eilon Sharon1, Shai Lubliner, Eran Segal

  • 1Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel.

Plos Computational Biology
|August 30, 2008
PubMed
Summary
This summary is machine-generated.

Feature motif models (FMMs) offer a novel way to understand transcription factor (TF) DNA binding. These models better explain TF binding specificities than traditional position specific scoring matrices (PSSMs).

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Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
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Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Transcription factor (TF) binding to DNA is crucial for gene regulation.
  • Position specific scoring matrices (PSSMs) are common but assume independent binding positions, which is often inaccurate.
  • A more sophisticated model is needed to capture complex TF-DNA interactions.

Purpose of the Study:

  • To introduce Feature Motif Models (FMMs), a novel probabilistic approach for modeling TF-DNA interactions.
  • To develop algorithms for learning FMMs and a motif finder for discovering new models.
  • To evaluate FMMs against PSSMs using synthetic and experimental TF binding data.

Main Methods:

  • Developed a log-linear model framework for FMMs, utilizing sequence features that can span multiple positions.
  • Created an algorithm for learning FMM structures from TF binding site data.
  • Implemented a discriminative motif finder to identify de novo FMMs enriched in target sequences.

Main Results:

  • FMMs were evaluated on synthetic data and a TF chromatin immunoprecipitation (ChIP) dataset.
  • Applied FMMs to high-throughput ChIP data from mouse and human, identifying novel sequence features.
  • Demonstrated that FMMs significantly outperform PSSMs in explaining TF binding specificities.

Conclusions:

  • FMMs provide a more accurate and comprehensive representation of TF-DNA binding interactions compared to PSSMs.
  • The developed methods and software enable better understanding of TF binding specificity in various organisms.
  • This advancement has implications for gene regulation studies and disease research.