Synthetic pore proteins

Figure 1.—Continued. Computer-generated molecular model of synthetic pore proteins. (C) Energy-optimized parallel tetramers of T4CaIVS3 (upper) and T4M28 (lower). C is the end view with the N terminus in front (89). Residues are colored according to hydrophobicity see previous page.

Later articles dealt with further elaboration of ideas on the driving forces which would have led to the formation of higher aggregates from RNA and amino acids. As had been suggested 20 years earlier, these processes could have taken place in rock pores and could have been driven by hydration and dehydration phases (Kuhn and Waser, 1994). The tiny pores in rocks act as minute test tubes, so optimal compositions could have been determined and replicated using many millions of systems. According to this model, none of the synthetic processes taking place would have required the presence of protein enzymes (see also Lahav, 1999). Just as other... 

Lashuel, H. A., Petre, B. M., Wall, J., Simon, M., Nowak, R. J., Walz, T., and Lansbury, P. T., Jr. (2002). Alpha-synuclein, especially the Parkinson s disease-associated mutants, forms pore-like annular and tubular protofibrils./. Mol. Biol. 322,1089-1102. LeVine, H. (1993). Thioflavine T interaction with synthetic Alzheimer s disease beta-amyloid peptides Detection of amyloid aggregation in solution. Protein Sci. 2, 404—410. Lin, H., Bhatia, R., and Lai, R. (2001). Amyloid beta protein forms ion channels Implications for Alzheimer s disease pathophysiology. FASEB J. 15, 2433-2444. Lorenzo, A., and Yankner, B. A. (1994). Beta-amyloid neurotoxicity requires fibril formation and is inhibited by Congo red. Proc. Natl. Acad. Sci. USA 91, 12243-12247. Luhrs, T., Ritter, C., Adrian, M., Riek-Loher, D., Bohrmann, B., Dobeli, H., Schubert, D., and Riek, R. (2005). 3D structure of Alzheimer s amyl o id-( be la) (1—12) fibrils. Proc. Natl. Acad. Sci. USA 102, 17342-17347. 

Enzyme membranes can be prepared by adsorbing the enzyme on the surface of a suitable native or synthetic membrane, or, in the case of membranes with large pores, by impregnating the whole membrane with enzyme. The resulting enzyme membrane can be stabilized by covalently cross-linking the adsorbed protein with a suitable bifunctional reagent (8 ). 

This separation is based on the size of the porous, hydrophobic gels. The pore size must be greater than the pore size of the molecules to be separated. Gel-permeation cleanup (GPC) is used for cleaning sample extracts from synthetic macromolecules, polymers, proteins, lipids, steroids, viruses, natural resins, and other high molecular weight compounds. Methylene chloride is used as the solvent for separation. A 5 mL aliquot of the extract is loaded onto the GPC column. Elution is carried out using a suitable solvent, and the eluate is concentrated for analysis. 

The simulation of ion channels and other pore-forming peptides and proteins at atomic detail is nowadays also possible. With the increase in computational power, these complex systems have attracted much more interest, and several simulations have been reported. Very often, only the transmembrane segments of the channel-forming proteins are included in the simulation to reduce the size and complexity of the system. The simulated systems range from synthetic model ion channels to a bacterial porine protein. 

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