A good introduction into membrane proteins and their structural organization can be found in the course "Principles of Protein Structure Using the Internet" at the Birkbeck University of London.
In contrast to outer membrane proteins whose membrane-embedded domain is formed by β sheets (Koebnik et al., 2000), the polypeptide chain of cytoplasmic membrane proteins traverses the membrane in the form of α helices.
The following websites allow to predict the membrane topology of cytyplasmic membrane proteins.
The lab of Gunnar von Heijne developed several algoriths to predict the topology of cytoplasmic membrane proteins and tested the corresponding rules experimentally. All algorithms are based on the observation that the amino acid compositions of the extra-membraneous loops differ significantly depending on whether they are located in the cytoplasm or outside of the cytoplasm. In particular, positively charges amino acids (arginine and lysine) act as discriminators, as expressed by the "positive-inside rule" (von Heijne and Gavel, 1988).
The folding process of cytoplasmic membrane proteins can be described by the two-step model which was proposed by Popot and Engelman (Popot and Engelman, 1990): In the first step, membrane-spanning α helices are formed which then pack against each other within the plane of the membrane in the second step. This concept was extensively studied by experiments and simulations in the lab of Donald M. Engelman. As model peptides served the transmembrane helices of glycophorin A and of phospholamban. Similar studies were performed in the lab of Dieter Langosch. An overview about these studies can be found in:
Latest update: October 14, 2009
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