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The Greek key motif: extraction, classification and analysis

E G Hutchinson¹, J M Thornton

¹Department of Biochemistry and Molecular Biology, University College, London, UK.

Protein Engineering

|April 1, 1993

Summary

The common Greek key protein motif has been reclassified into three structural groups based on hydrogen bonding. This protein structure analysis reveals significant variability, suggesting diverse folding pathways.

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Area of Science:

Protein structure and bioinformatics
Structural biology
Computational biophysics

Background:

The Greek key motif is a prevalent structural element in proteins.
Traditionally defined by a '+3,-1,-1' topology of four beta-strands.
This definition includes diverse three-dimensional protein structures.

Purpose of the Study:

To reclassify Greek key motifs based on hydrogen bonding patterns.
To analyze the structural variability within these classified protein motifs.
To investigate the implications for protein folding pathways.

Main Methods:

Classification of Greek key motifs using hydrogen bonding patterns.
Automated extraction of Greek key examples using custom software.
Analysis of secondary structure segment length and amino acid sequences.

Main Results:

Greek key motifs were grouped into three distinct classes with similar 3D structures.
Significant variability in secondary structure segment length was observed within classes.
Sequence variability was also noted even within a single structural class.

Conclusions:

The traditional definition of Greek keys encompasses structurally diverse motifs.
Reclassification based on hydrogen bonding reveals distinct structural classes.
Observed variability suggests that multiple protein folding pathways may exist for Greek keys.

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