MINAREA structural alignment program

John-Marc Chandonia (1), Jonathan Blake (1), and Fred Cohen (1)

(1) Cohen Lab, Department of Cellular and Molecular Pharmacology, UCSF, San Francisco, CA 94143

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Pictures

These are some figures from our poster.

Figure 1: What is the area being minimized?

A graphical representation of a possible triangulation for 2 proteins. Type 1 or 2 triangles contain an edge joining consecutive CA's in Protein 1 or 2. Corresponding regions are represented by triangles with alternating labels, and are circled. Inserted regions (gaps) can be found by locating consecutive triangles with the same labels.

Figure 3: "Soap Film" plots for several structural comparisons:

• A) Globins 2mge and 1babB. Ratio score is 0.05.
• B) Protease inhibitors 3sgbI and 1tgsI. Ratio score is 0.12.
• C) Rossmann fold domains of enzymes 2pgd and 1dih. Ratio score is 0.10.
• D) Beta sandwich domains of enzymes 1aozA and 1nif. Ratio score is 0.18. CATH classifies these in different families at the A (Architecture) level, although they are in the same SCOP family.
• E) Small alpha/beta domains from proteins 9wga (wheat germ agglutinin) and 1cgiI (a protease inhibitor). Ratio score is 0.35, typical for unrelated proteins. In the October 1998 release of CATH, these were considered to be in the same family at the H (Homologous family) level; in the June 1999 release, they have been moved to different families at the H level but remain in the same family at the T (Topology) level.
• F) Beta barrel domains from serine proteases 1sgt and 1sgpE. Ratio score is 0.31. While overall architecture and function are similar, the structures differ significantly in loop conformations. MINAREA correctly aligns the core beta strands, but the long, unaligned loops produce a high ratio score. Both CATH and SCOP classify these proteins in the same family.

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References

Orengo CA, Michie AD, Jones S, Jones DT, Swindells MB, Thornton JM. Orengo CA, Michie AD, Jones S, Jones DT, Swindells MB, Thornton JM. "CATH- A Hierarchic Classification of Protein Domain Structures." Structure 5: 1093-1108 (1997)

Murzin AG, Brenner SE, Hubbard T, Chothia C. "SCOP: a structural classification of proteins database for the investigation of sequences and structures." J Mol Biol 247: 536-540 (1995)

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