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Related Experiment Videos

Fold and function predictions for Mycoplasma genitalium proteins

L Rychlewski1, B Zhang, A Godzik

  • 1Department of Molecular Biology, Scripps Research Institute, La Jolla, CA 92037, USA.

Folding & Design
|August 26, 1998
PubMed
Summary

A new sequence alignment algorithm predicts protein structures and functions for Mycoplasma genitalium. This method identifies homologous proteins, enabling functional assignments for over 50 uncharacterized proteins.

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Area of Science:

  • Genomics
  • Structural Biology
  • Bioinformatics

Background:

  • Uncharacterized proteins from newly sequenced genomes are valuable targets for predicting protein fold and function.
  • Mycoplasma genitalium is a small bacterium with a relatively compact genome.

Purpose of the Study:

  • To develop and apply a novel sequence alignment algorithm for predicting protein structure and function.
  • To identify homologous proteins and assign functions to uncharacterized proteins within the Mycoplasma genitalium genome.

Main Methods:

  • Utilized a new profile-to-profile alignment algorithm for sequence similarity analysis.
  • Compared the genome of Mycoplasma genitalium against the Escherichia coli proteome.
  • Leveraged known protein structures and functions for comparative analysis.

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Main Results:

  • Recognized sequence similarity to known structures for 38% of Mycoplasma genitalium proteins.
  • Found significant sequence similarity between >80% of Mycoplasma genitalium proteins and proteins in Escherichia coli, including >40 novel examples.
  • Enabled tentative functional assignments for >50 previously uncharacterized proteins based on homology.

Conclusions:

  • The new algorithm can predict the 3D fold for nearly 40% of Mycoplasma genitalium proteins.
  • Tentative functions can be assigned to almost 80% of the entire genome.
  • Predictions offer new insights into known functions and reveal unexpected features of Mycoplasma genitalium.