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Related Concept Videos

Membrane Domains01:18

Membrane Domains

The membrane domains concentrate specific lipids and proteins at one place within the membrane, which helps in cell signaling, adhesion, and other critical cellular processes. These domains can differ in size, composition, function, and lifespan.
Protein Domains
The membrane comprises a group of distinct proteins responsible for carrying out a cell's specific function. For example, the plasma membrane of the human sperm, or a single germ cell, contains a unique set of proteins in the anterior...
pV-Diagrams01:18

pV-Diagrams

The pV diagram, which is a graph of pressure versus volume of the gas under study, is helpful in describing certain aspects of the substance. When the substance behaves like an ideal gas, the ideal gas equation describes the relationship between its pressure and volume. On a pV diagram, it is common to plot an isotherm, which is a curve showing p as a function of V with the number of molecules and the temperature fixed. Then, for an ideal gas, the product of the pressure of the gas and its...
Mechanisms of Membrane Domain Formation00:59

Mechanisms of Membrane Domain Formation

Different physical properties of lipids and proteins allow them to localize and form distinct islands or domains in the membrane. Some membrane domains are formed due to protein-protein interactions, whereas others are formed due to the presence of specific lipids such as sphingolipids and sterols—for example, large proteins, such as bacteriorhodopsin, aggregate and create distinct domains.
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IP3/DAG Signaling Pathway01:11

IP3/DAG Signaling Pathway

Membrane lipids such as phosphatidylinositol (PI) are precursors for several membrane-bound and soluble second messengers. Specific kinases phosphorylate PI and produce phosphorylated inositol phospholipids. One such inositol phospholipids are the  phosphatidylinositol-4,5 bisphosphate [PI(4,5)P2], present in the inner half of the lipid bilayer. Upon ligand binding, GPCR stimulates Gq proteins to turn on phospholipase Cꞵ. Activated phospholipase Cꞵ cleaves PI(4,5)P2 and produces two-second...
Three Developmental Domains01:29

Three Developmental Domains

Human development is typically examined across three main domains: physical, cognitive, and socio-emotional. These domains represent the significant areas of change and continuity throughout the lifespan, from infancy to late adulthood.
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Three-Domain System of Life

Ribosomal RNA (rRNA) sequence analysis revealed three distinct groups of cells: eukaryotes, bacteria, and archaea. In 1978, Carl R. Woese proposed the concept of domains, a taxonomic level above kingdoms, to differentiate these groups. He suggested that archaea and bacteria, despite their similar appearance, represent separate domains. Domains differ in rRNA, membrane lipid structure, transfer RNA, and antibiotic sensitivity.In this classification, animals, plants, and fungi belong to the...

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Picometer-Precision Atomic Position Tracking through Electron Microscopy
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DIMA 3.0: Domain Interaction Map.

Qibin Luo1, Philipp Pagel, Baiba Vilne

  • 1Department of Genome Oriented Bioinformatics, Technische Universität München, Wissenschaftszentrum Weihenstephan, 85350 Freising, Germany.

Nucleic Acids Research
|November 25, 2010
PubMed
Summary
This summary is machine-generated.

The Domain Interaction MAp (DIMA) database integrates known and predicted protein domain interactions. It offers tools to visualize domain interaction networks for specific domains or whole organisms.

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Area of Science:

  • Bioinformatics
  • Structural Biology
  • Computational Biology

Background:

  • Protein domain interactions are crucial for understanding cellular functions.
  • Existing databases offer limited coverage of known and predicted domain interactions.
  • Computational methods can predict novel domain interactions.

Purpose of the Study:

  • To create a comprehensive database of protein domain interactions.
  • To integrate known and computationally predicted interactions.
  • To provide a web-based tool for exploring domain interaction networks.

Main Methods:

  • Integrated 5807 known domain interactions from iPfam and 3did.
  • Incorporated 46,900 predicted domain interactions using four computational methods.
  • Filtered predictions against the Negatome database to remove non-interacting pairs.

Main Results:

  • The Domain Interaction MAp (DIMA) database contains a large collection of domain interactions.
  • DIMA integrates both structurally validated and computationally predicted interactions.
  • The database provides interactive visualization of domain interaction networks.

Conclusions:

  • DIMA serves as a valuable resource for studying protein domain interactions.
  • The integrated data and visualization tools facilitate network analysis.
  • This resource aids in understanding protein function and biological pathways.