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Related Concept Videos

Protein Networks02:26

Protein Networks

4.6K
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,...
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Protein-protein Interfaces02:04

Protein-protein Interfaces

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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...
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Protein and Protein Structure02:15

Protein and Protein Structure

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Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. Proteins may be structural, regulatory, contractile, or protective. They may serve in transport, storage, or membranes; or they may be toxins or enzymes. Their structures, like their functions, vary greatly. They are all, however, amino acid polymers arranged in a linear sequence.
A protein's shape is critical to its function. For example, an enzyme...
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Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

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Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to...
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What are Proteins?01:55

What are Proteins?

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Overview
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Protein Families02:47

Protein Families

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Protein families are groups of homologous proteins; that is, they have similarities in amino acid sequences and three-dimensional structures. Protein families usually occur because of gene duplication, where an additional copy of a gene is inserted into the genome of an organism.   Mutations that change the amino acids but still allow the protein to be properly synthesized, will lead to new protein family members.   If these new proteins contain similar amino acids in key...
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Related Experiment Video

Updated: Feb 11, 2026

Generation of Comprehensive Thoracic Oncology Database - Tool for Translational Research
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Generation of Comprehensive Thoracic Oncology Database - Tool for Translational Research

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PDZscape: a comprehensive PDZ-protein database.

Jitesh Doshi1, Raja Reddy Kuppili1,2, Siddharth Gurdasani1,3

  • 1Integrated Biophysics and Structural Biology Lab, Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Centre, Kharghar, Navi Mumbai, 410210, India.

BMC Bioinformatics
|April 28, 2018
PubMed
Summary
This summary is machine-generated.

PDZscape is a new database detailing 58,648 PDZ-containing proteins and their interactions. It integrates multiple databases and includes disease-associated mutations, offering a comprehensive resource for cell signaling research.

Keywords:
DatabasePDZ-domainPDZ-proteinsProtein-protein interactions

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In Vitro Analysis of PDZ-dependent CFTR Macromolecular Signaling Complexes
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In Vitro Analysis of PDZ-dependent CFTR Macromolecular Signaling Complexes

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In Vitro Analysis of PDZ-dependent CFTR Macromolecular Signaling Complexes
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In Vitro Analysis of PDZ-dependent CFTR Macromolecular Signaling Complexes

Published on: August 13, 2012

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Area of Science:

  • Molecular Biology
  • Bioinformatics
  • Cellular Signaling

Background:

  • PDZ-containing proteins are crucial for cell localization, membrane receptor clustering, and signal transduction.
  • The existing PDZBase database is outdated and limited, containing only 339 proteins.
  • A comprehensive, up-to-date resource for PDZ-containing proteins is needed.

Purpose of the Study:

  • To develop PDZscape, a comprehensive database for PDZ-containing proteins and their interactomes.
  • To integrate diverse biological databases for a unified view of PDZ protein information.
  • To provide tools for querying and analyzing PDZ protein data, including mutations and diseases.

Main Methods:

  • Development of a user-friendly web interface for PDZscape.
  • Integration of data from NCBI, UniProtKB, Swiss-Prot, Pubmed, PDB, STRING, IntAct, KEGG, Pfam, and Protein Mutant Database.
  • Manual curation of mutations and diseases associated with PDZ-containing proteins.

Main Results:

  • PDZscape contains information on 58,648 PDZ-containing proteins and their known/putative binding partners.
  • The database offers a user-friendly interface with a customized BLAST option (PDZ-Blast).
  • Detailed information on the PDZ interactome, including mutations and associated diseases, is provided.

Conclusions:

  • PDZscape is a comprehensive and freely available resource for studying PDZ-containing proteins.
  • The database facilitates research on cell signaling pathways and related diseases.
  • PDZscape enhances the understanding of PDZ protein functions and interactions.