P-sheet model system

Fisk. J.D. Gellman. S.H. A parallel P-sheet model system that folds in water. J. Am. Chein. Soc. 2001.123. 343-344. Das, C. Raghothama, S. Balaram. P. A designed three stranded p-sheet peptide as a multiple P-hairpin model. J. Am. Chem. Soc. 1998, 120. 5812-5813. and references cited therein. 

Gerhards M, Unterberg C (2002) Structures of the protected amino acid Ac-Phe-OMe and its dimer a p-sheet model system in the gas phase. Phys Chem Chem Phys 4 1760... 

Unterberg C, Gerlach A, Schrader T, Gerhards M (2002) Clusters of a protected amino acid with pyrazole derivatives p-sheet model systems in the gas phase. Eur Phys J D 20 543... 

Gerhards M, Unterberg C, Gerlach A, Jansen A (2004) p-Sheet model systems in the gas phase structures and vibrations of Ac-Phe-NHMe and its dimer (Ac-Phe-NHMe)2. Phys Chem Chem Phys. 6 2682... 

Fricke H, Funk A, Schrader T, Gerhards M (2008) Investigation of secondary structure elements by IRAJV double resonance spectroscopy analysis of an isolated p-sheet model system. J Am Chem Soc 130 4692... 

Given the limitations of the above systems, it is apparent that the optimal peptide model of a p-sheet (and a p-turn) should be as analagous to the monomeric helix models as possible. In particular, the ideal p-sheet model should be small (< 20 residues), monomeric, water-soluble, pure (composed of only p-sheets and p-turns), amphipathic (to investigate sidedness), reversibly denaturable, composed of only natural amino acids, easily synthesized and easily characterized by standard spectroscopic techniques. We believe that we have developed such a peptide model. It is based on the naturally occurring cyclic peptide gramicidin S, an antibiotic produced by the bacterium bacillus brevis (12). The schematic structure of gramicidin S as determined by X-ray and NMR studies (13, 14) is shown in Figure 1. 

Clusters of three or more positive chemical shift index (CSI) values are indicative of a p-sheet. Overall, these results suggest that it is possible to greatly increase the solubility of this p-sheet model without significantly disrupting the structure. They also suggest that some residues (His in particular) can disrupt the type 11 p-tum and eliminate most of the p-sheet structure. This result also implies that it may be possible to use host-guest techniques (17) to study type IF P-tum propensities with this system. 

A key feature of our simulations is the use of a model that is as similar as possible to the experimental sample. We have seen that a way to do so is to intercalate between the clay sheets the same amount of water and monomers molecules as ob rved by TGA measurements. As to the clay itself, we are using an idealised model, that is a 3D p odic model system that cannot account for isolated particules or grain junctions. A vay to comi rc this model, idealised clay to a real sample is then to calculate the volume accessible by the oligpmers in both systems. 

These results indicate that is it possible to change the fold of a protein by changing a restricted set of residues. They also confirm the validity of the rules for stability of helical folds that have been obtained by analysis of experimentally determined protein structures. One obvious impliction of this work is that it might be possible, by just changing a few residues in Janus, to design a mutant that flip-flops between a helical and p sheet structures. Such a polypeptide would be a very interesting model system for prions and other amyloid proteins. 

Fuhs et al.m investigated P p0 Aj in multilayers of Synechocystis PCC 6803 oriented on mylar sheets by transient W-band EPR. They could show an enhanced resolution of structural parameters of the RP in this model system. A problem is the uncertainty of the orientation distribution (width 30 10°). Limitations and possibilities of the method are discussed in this work. The technique is interesting for all systems for which no single crystals are available. 

The result of the interactions of some copolymer mimics of AMP with model bacterial membranes has been studied via atomistic molecular dynamics simulation (Figure 3.2). The model bacterial membrane expands homogeneously in a lateral manner in the membrane thickness profile compared with the polymer-free system. The individual polymers taken together are released into the bacterial membrane in a phased manner and the simulations propose that the most possible location of the partitioned polymers is near the l-palmitoyl-2-oleoyl-phosphatidylglycerol clusters. The partitioned polymers preferentially adopt facially amphiphilic conformations at the lipid-water interface, although lack intrinsic secondary structures, such as an a-helix or P-sheet, found in naturally occurring AMP [23]. 

Gelhnan SH (1998) Minimal models systems for p-sheet secondary structure in proteins. Curr Opin Chem Biol 2 717-725... 

Electron transfer in biological systems where the electron donor and acceptor are separated by a long molecular distance is encountered in very important processes such as photosynthesis and respiration [54]. As natural systems are not appropriate for such studies. Gray et al. have employed proteins chemically labeled with transition metal complexes to measure ET rates in metaUoproteins. In particular, they have shown that long-lived luminescent probes enabled a wider range of ET measurements than is possible with non-luminescent complexes [55]. The blue copper protein azurin is a convenient model for the study of ET in p-sheet proteins. 

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