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A limited universe of membrane protein families and folds

¹ Department of Chemistry and Biochemistry, UCLA-DOE Institute for Genomics and Proteomics, Molecular Biology Institute, Los Angeles, California 90095-1570, USA
² Department of Life Science POSTECH, Pohang, Kyungbuk 790-784, Korea

(RECEIVED January 23, 2006; FINAL REVISION March 27, 2006; ACCEPTED March 27, 2006)

One of the goals of structural genomics is to obtain a structural representative of almost every fold in nature. A recent estimate suggests that 70%–80% of soluble protein domains identified in the first 1000 genome sequences should be covered by about 25,000 structures—a reasonably achievable goal. As no current estimates exist for the number of membrane protein families, however, it is not possible to know whether family coverage is a realistic goal for membrane proteins. Here we find that virtually all polytopic helical membrane protein families are present in the already known sequences so we can make an estimate of the total number of families. We find that only 700 polytopic membrane protein families account for 80% of structured residues and 1700 cover 90% of structured residues. While apparently a finite and reachable goal, we estimate that it will likely take more than three decades to obtain the structures needed for 90% residue coverage, if current trends continue.

Keywords: structural genomics; protein structure; Pfam; SCOP

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