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The topological analysis of integral cytoplasmic membrane proteins

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Summary

We review three general approaches to determining the topology of integral cytoplasmic membrane proteins. (i) Inspection of the amino acid sequence and use of algorithms to predict membrane spanning segments allows the construction of topological models. For many proteins, the mere identification of such segments and an analysis of the distribution of basic amino acids in hydrophilic domains leads to correct structure predictions. For others, additional factors must come into play in determining topology, (ii) Gene fusion analysis of membrane proteins, in many cases, leads to complete topological models. Such analyses have been carried out in both bacteria and in the yeast Saccharomyces cerevisiae. Conflicts between results from gene fusion analysis and other approaches can be used to explore details of the process of membrane protein assembly. For instance, anomalies in gene fusion studies contributed evidence for the important role of basic amino acids in determining topolog. (iii) Biochemical probes and the site of natural biochemical modifications of membrane proteins give information on their topology. Chemical modifiers, proteases and antibodies made to different domains of a membrane protein can identify which segments of the protein are in the cytoplasm and which are on the extracytoplasmic side of the membrane. Sites of such modifications as glycosylation and phosphorylation help to specify the location of particular hydrophilic domains. The advantages and limitations of these methods are discussed.

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Author notes

  1. Beth Traxler

    Present address: Department of Microbiology, University of Washington, 98195, Seattle, Washington

Authors and Affiliations

  1. Department of Microbiology and Molecular Genetics, Harvard Medical School, 02115, Boston, Massachusetts

    Beth Traxler, Dana Boyd & Jon Beckwith

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  1. Beth Traxler
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Additional information

This work was supported by a fellowship from the National Institute of General Medical Sciences to B.T., by a grant from the National Science Foundation to D.B. and by a grant from the National Institutes of Health to J.B.. J.B. is an American Cancer Society Research Professor.

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Traxler, B., Boyd, D. & Beckwith, J. The topological analysis of integral cytoplasmic membrane proteins. J. Membarin Biol. 132, 1–11 (1993). https://doi.org/10.1007/BF00233047

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