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Multiple Motif Scanning to identify methyltransferases from the yeast proteome.

Tanya C Petrossian¹, Steven G Clarke

¹Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, USA.

Molecular & Cellular Proteomics : MCP

|April 9, 2009

Summary

A new program, Multiple Motif Scanning, identifies S-adenosylmethionine-dependent methyltransferases in yeast proteomes. This tool aids in discovering novel enzymes and refining classifications of known ones.

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Area of Science:

Biochemistry
Bioinformatics
Structural Biology

Background:

S-adenosylmethionine-dependent methyltransferases are crucial enzymes.
Identifying these enzymes in proteomes is essential for understanding cellular functions.
Existing methods may not fully capture the diversity and conserved motifs within this enzyme class.

Purpose of the Study:

To develop and validate a computational program for identifying Class I S-adenosylmethionine-dependent methyltransferases.
To expand the definition of conserved motifs within methyltransferases.
To subgroup methyltransferases based on substrate specificity.

Main Methods:

Development of the Multiple Motif Scanning program.
Utilizing hidden Markov model profiling on yeast and methyltransferase databases.
Analysis of conserved amino acids within identified motifs (I, Post I, II, III).
Application of Fisher-based negative log statistical matrices.
Clustering analysis of methyltransferase subgroups.

Main Results:

The Multiple Motif Scanning program successfully scanned the Saccharomyces cerevisiae proteome.
Conserved motifs were identified and expanded based on sequence and structural analysis.
The program generated a ranked list of potential methyltransferases.
Class I methyltransferases were subgrouped according to substrate specificity.

Conclusions:

Multiple Motif Scanning is an effective tool for identifying and classifying methyltransferases.
The program facilitates the discovery of novel enzymes and reassessment of putative ones.
This approach aids in understanding methyltransferase diversity and substrate specificity.