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Related Experiment Videos

Linking enzyme sequence to function using Conserved Property Difference Locator to identify and annotate positions

Kimberly M Mayer1, Sean R McCorkle, John Shanklin

  • 1Biology Department, Brookhaven National Laboratory, Upton, NY 11973, USA. mayerk@uncw.edu

BMC Bioinformatics
|December 2, 2005
PubMed
Summary
This summary is machine-generated.

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A new method, the Conserved Property Difference Locator (CPDL), identifies key enzyme residues. This tool analyzes homologous enzyme sequences to predict functional differences, aiding in protein engineering and structure-function studies.

Area of Science:

  • Biochemistry
  • Bioinformatics
  • Structural Biology

Background:

  • Homologous enzyme families share common evolutionary origins.
  • Analyzing multiple enzyme sequences can reveal functional determinants.
  • The Conserved Property Difference Locator (CPDL) program offers a novel approach.

Purpose of the Study:

  • To develop a method for identifying residues critical for class-specific enzyme function.
  • To leverage multiple sequence alignments for functional inference.
  • To create an annotated graphical representation of sequence data.

Main Methods:

  • Utilizing the Conserved Property Difference Locator (CPDL) program.
  • Converting multiple sequence alignments into an annotated graphical format.

Related Experiment Videos

  • Testing the algorithm on desaturase/hydroxylase, ATP/GTP cyclase, and MurD/MurE synthase families.

    • Main Results:

    • CPDL identified small groups of residues (8, 4, and 10) of interest in the tested enzyme families.
    • These identified residues contain empirically defined specificity-determining positions.
    • The method was validated using well-characterized enzyme families.

    Conclusions:

    • CPDL accurately identifies residues near active sites important for enzyme specificity and function.
    • The program has broad utility for predicting class-determining residues from sequence data.
    • Its sequence-based nature makes it suitable for both membrane and soluble proteins.