Helical models

Finally, the acetylation of galacturonic acid in RG-I and HG did not lead to significantly different helical models of these backbones. Integer helices with low-energy conformations could be build in nice agreement with other experimental or theoretical results. 

Information about the putative folding of the H,K-ATPase catalytic subunit through the membrane has been obtained by the combined use of hydropathy analysis according to the criteria of Kyte and Doolittle [51], identification of sites sensitive to chemical modification [46,48,50,52-55], and localization of epitopes of monoclonal antibodies [56]. The model of the H,K-ATPase catalytic subunit (Fig. 1) which has emerged from these studies shows ten transmembrane segments and contains cytosolic N- and C-termini [53]. This secondary structure of the catalytic subunit is probably a common feature of the catalytic subunits of P-type ATPases, since evidence supporting a ten a-helical model with cytosolic N- and C-termini has also been published recently for both Ca-ATPase of the sarcoplasmic reticulum and Na,K-ATPase [57-59]. 

Four helical models have been proposed for the conformation of the gramicidin channel in order to accommodate these and other data (see Fig. 23) ... 

Fig. 23. Possible helical models for the gramicidin A ion channel. The polypeptides are represented as helical strips, one molecule being stippled for clarity. Numbers refer to the substituted terminal amino acid residues. Model (i), proposed originally by Urry, is the one now generally accepted...

X-ray diffraction studies on gramicidin commenced as early as 1949 218-219> and this early work pointed to a helical structure 220). Recent work by Koeppe et al. 221) on gramicidin A crystallised from methanol (/%) and ethanol (.P212121) has shown that the helical channel has a diameter of about 5 A and a length of about 32 A in both cases. The inclusion complexes of gramicidin A with CsSCN and KSCN (P212121) have channels that are wider (6-8 A) and shorter (26 A) than the uncomplexed dimer 221 222). Furthermore there are two cation binding sites per channel situated either 2.5 A from either end of the channel or 2.5 A on each side of its centre 222) Unfortunately these data do not permit a choice to be made from the helical models (i)—(iv) and it is not certain if the helical canals studied are the same as those involved in membrane ion transport. 

Although the dipolar and resonating nature of the interaction of amylose and iodine is well established, Schlamowitz173 regards the iodine in a starch complex as being in a predominantly non-polar form, and Meyer and Bern-feld174 refute the helix theory and consider that adsorption of iodine occurs on colloidal micelles in amylose solutions. Most of the experimental facts which Meyer presents can, however, be satisfactorily explained on the helical model. 

Fig. 4. New structural models for amyloid and prion filaments with the parallel and in-register arrangement of //-strands in the //-sheets. //-Strands are denoted by arrows. The filaments are formed by hydrogen-bonded stacks of repetitive units. Axial projections of single repetitive units corresponding to each model are shown on the top. Lateral views of the overall structures are on the bottom. (A) The core of a //-helical model of the //-amyloid protofilament (Petkova et al., 2002). Two such protofilaments coil around one another to form a //-amyloid fibril. (B) The core of a //-helical model of the HET-s prion fibril (Ritter et al., 2005). The repetitive unit consists of two //-helical coils. (C) The core of a superpleated //-structura l model suggested for yeast prion Ure2p protofilaments and other amyloids (Kajava et al., 2004).

As for /(-helical models in the context of prion variants, we note that /(-helices encompass quite a wide variety of cross-sectional shapes, each reflecting a different configuration of strands and turns in the coil (Hennetin et al., 2006 Kajava and Steven, 2006) thus it seems possible that different parts of the same prion domain could be assigned the role of coil-former and they would have different coil geometries whose distinctions could give rise to variant prions. However, we expect that variability of the /(-helices with more than one coil per subunit—already unlikely on other grounds, except for HET-s (Section VLB)—will be quite limited. 

With the demise of the uniform fiber model in 1974, it became necessary to devise other models to account for the early electron micrographs of chromatin fibers and the X-ray diffraction studies (see Ref. [1], Chapter 1). Two models appeared in 1976, and were the major contenders for consideration in 1978. The superbead model of Franke et al. [36] envisioned the chromatin fiber as a compaction of multi-nucleosome superbeads . The solenoid model of Finch and Klug [37] postulated a regular helical array of nucleosomes, with approximately six nucleosomes per turn and a pitch of 10 nm. Although a number of competing helical models appeared in the 1980s (see Ref. [1], Chapter 7) the solenoid model remains a serious contender to this day. Structural details of this model, such as the precise disposition of linker DNA, are still lacking. 

Garcia de la Torre, J., Navarro, S., and Lopez Martinez, M.C. (1994) Hydrodynamic properties of a double-helical model for DNA. Biophys. J. 66, 1573-1579. 

The Isolated Chain and the Crystalline Form of DeS. The molecular conformation given by Mitra et al. (1 ) for the tetragonal structure of DeS was used as the starting point for building all helical models of the isolated polyanion, assuming the tetrasaccharide I-N-I-N to be... 

From the regularities mentioned here de Rango et al.I45) designed two general models for helicenes, viz. the triple helical model and the stair case model. In the triple helical model all C-atoms are located on one of three helices an inner helix with (n +1) C-atoms (n = number of benzene rings), a medium helix with (n +1) C-atoms and an outer helix with 2n C-atoms. In general, atoms of helicenes coincide very well with the best helices, obtained by computation from crystallographic data. 

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