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Related Concept Videos

Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

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 form...
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...
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...
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,...
Assembly of Signaling Complexes01:30

Assembly of Signaling Complexes

Multiprotein signaling complexes are formed in a dynamic process involving protein-protein interactions at the cytoplasmic domain of transmembrane receptors or enzymatic and non-enzymatic proteins associated with the receptor. These complexes ensure the activation and propagation of intracellular signals that regulate cell functions.
Interaction domains in cell signaling
Interaction domains recognize exposed features of their binding partners containing post-translationally modified sequences,...
Conservation of Protein Domains02:26

Conservation of Protein Domains

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 form...

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A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

PSCL: predicting protein subcellular localization based on optimal functional domains.

Kai Wang1, Le-Le Hu, Xiao-He Shi

  • 1Laboratory of Molecular Neurobiology, School of Life Sciences, Shanghai University, Shanghai, PR China.

Protein and Peptide Letters
|September 17, 2011
PubMed
Summary
This summary is machine-generated.

Predicting plant protein subcellular localization is crucial for understanding protein function. A new web server, PSCL, uses optimized functional domains to achieve 75.7% accuracy in predicting plant protein locations.

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Enriching Subcellular Proteins in Leptospira Using a Triton X-114-Based Fractionation Approach
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A Protocol for Computer-Based Protein Structure and Function Prediction
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Area of Science:

  • Plant biology
  • Computational biology
  • Bioinformatics

Background:

  • Protein subcellular localization is intrinsically linked to protein function.
  • Existing computational tools for predicting protein localization require improvement for better understanding of plant systems.
  • Developing novel algorithms is essential for advancing the field of plant subcellular localization prediction.

Purpose of the Study:

  • To develop a new computational tool, PSCL, for predicting plant protein subcellular localization.
  • To improve the accuracy of subcellular localization prediction by utilizing optimized functional domains.

Main Methods:

  • Feature optimization using InterPro functional domains to identify 848 optimal domains.
  • Development of the PSCL web server for plant protein subcellular localization prediction.
  • Performance evaluation using a jackknife test on a dedicated dataset.

Main Results:

  • PSCL achieved a first-order prediction accuracy of 75.7% on the test dataset.
  • Gene Ontology enrichment analysis revealed strong correlations between catalytic activity, cellular processes, metabolic processes, and plant protein localization.
  • A user-friendly web interface for PSCL was developed and made publicly accessible.

Conclusions:

  • PSCL provides an accurate and accessible method for predicting plant protein subcellular localization.
  • The study highlights the importance of specific functional domains and biological processes in determining protein location.
  • The developed tool can aid researchers in understanding plant protein functions and biological mechanisms.