Protein topology, altering

All proteins are composed of a limited set of secondary structure elements. Yet, we are just beginning to learn how such building blocks can be combined to yield well-defined tertiary and quaternary structures. Evolutionary strategies that allow simultaneous evaluation of huge numbers of alternatives on the basis of a selectable phenotype, such as catalytic activity, can greatly aid such efforts. 

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Almost all membrane proteins have their own topology that is uniquely determined by its amino acid sequence information. However, some exceptional proteins have dual orientations (Dunlop et al., 1995). In another protein, the orientation is altered in vivo for functional reasons (Bruss et al., 1994 Prange and Streeck, 1995). The molecular mechanisms of the topogenesis of membrane proteins are not fully understood, but some important findings are described next. 

Brass, V., Lu, X., Thomssen, R., and Gerlich, W. (1994). Post-translational alterations in transmembrane topology of the hepatitis B virus large envelope protein. EMBO J. 

Even greater topological changes in GFP have been performed by random circular permutation (Graf and Schachman, 1996) in order to create new N- and C- termini for end-to-end fusion with other genes (Baird et al., 1999). Ten nontrivial fluorescent circular permutations of GFP were found that had altered pIQ values and orientation of the chromophore with respective to its N- and C-termini. The systematic identification of sites for circular permutation in GFP also identifies plausible sites for insertions of other proteins into GFP. This work speaks strongly about the potential of random circular permutation for protein... 

Several aspects of Schwann cell metabolism emerge as potential points of vulnerability to toxicants. The Schwann cell perikaryon (cell body) supports an enormous peripheral structure, the myelin sheath, which, if unwrapped, would dwarf the body of the Schwann cell (see Figure 30.4). Thus, as in the case of axonal transport in neurons, there may be specialized processes involved in supporting the topologically distant myelin. Furthermore, myelin has a specialized lipid and protein composition and a relatively rigid and ordered structure as compared to other membranes. Metabolic perturbations that potentially cause alterations in the composition of lipids and proteins assembled to form this membrane may cause destabilization and collapse of the myelin membrane. In this context, myelin might be much more vulnerable than plasma membranes of other cells. 

Peroxidases are heme-iron proteins involved in oxidative stress control. The mechanisms of this class of enzymes involve rather complex redox and electron transfer processes. These include alterations of spin state and ligands to the active-site heme as well as a novel role for Ca ions in the process as discussed by Moura and colleagues (Chapter 6). The topology and mechanism of the electron transfer process can be studied in detail using dynamic NMR data and molecular modeUng tools as illustrated by Pettigrew and co-workers (Chapter 7). The action of these types of peroxidases can be considered of crucial importance for the redox state regulation of the cell. 

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