How proteins adapt to a membrane-water interface.

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Published in Trends Biochem Sci on September 01, 2000

Authors

J A Killian1, G von Heijne

Author Affiliations

1: Dept of Biochemistry of Membranes, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands. j.a.killian@chem.uu.nl

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Molecular mechanism of membrane protein integration into the endoplasmic reticulum. Cell (1997) 1.70

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Trans-membrane translocation of proteins. A detailed physico-chemical analysis. Eur J Biochem (1980) 1.00

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A de novo designed signal peptide cleavage cassette functions in vivo. J Biol Chem (1991) 0.91

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