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Related Experiment Videos

Natively disordered proteins: functions and predictions.

Pedro Romero1, Zoran Obradovic, A Keith Dunker

  • 1Center for Computational Biology and Bioinformatics, Indiana University-Purdue University Indianapolis, 714 North Senate Avenue, Indianapolis, IN 46202, USA. promero@compbio.iupui.edu

Applied Bioinformatics
|February 8, 2005
PubMed
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Proteins exist in ordered, partially folded, or extended forms. This study used bioinformatics to predict disordered protein regions, finding eukaryotes have more disorder, likely for complex signaling and regulation.

Area of Science:

  • * Molecular biology and bioinformatics.
  • * Protein structure and function.
  • * Intrinsically disordered proteins (IDPs).

Background:

  • * Proteins exhibit three forms: ordered, partially folded (liquid-like), and extended (gas-like).
  • * The protein trinity hypothesis posits that native proteins can adopt any form based on sequence and environment, with function arising from these forms or transitions.
  • * Intrinsic protein disorder is crucial for biological processes.

Purpose of the Study:

  • * To investigate intrinsic disorder in proteins using bioinformatics and data mining.
  • * To develop neural network-based predictors for natural disordered regions (PONDR).
  • * To analyze the distribution and implications of protein disorder across different life kingdoms and biological processes.

Main Methods:

Related Experiment Videos

  • * Employed bioinformatics and data mining techniques.
  • * Developed and utilized neural network-based predictors of natural disordered regions (PONDR).
  • * Applied PONDR to analyze protein disorder in eubacteria, archaebacteria, and eukaryotes, including signaling, cancer-associated, and control protein databases.

Main Results:

  • * Developed PONDR predictors achieving up to 84% accuracy in discriminating ordered and disordered residues.
  • * Revealed a disorder ranking: eubacteria < archaebacteria << eukaryotes.
  • * Approximately half of eukaryotic proteins predicted to have substantial intrinsically disordered regions, particularly in signaling and regulation.
  • * Identified disordered regions acting as molecular recognition elements that become structured upon binding.

Conclusions:

  • * Intrinsic protein disorder is widespread, especially in eukaryotes, correlating with increased complexity in signaling and regulation.
  • * PONDR is an effective tool for predicting disordered regions and identifying molecular recognition elements.
  • * The study supports the protein trinity hypothesis and highlights the functional significance of protein disorder in diverse biological contexts.