Structured helices

Figure 6.25 Schematic diagram of the structure of one dimer of phosphofructokinase. Each polypeptide chain is folded Into two domains (blue and red, and green and brown), each of which has an oi/p structure. Helices are labeled A to M and p strands 1 to 11 from the amino terminus of one polypeptide chain, and respectively from A to M and 1 to 11 for the second polypeptide chain. The binding sites of substrate and effector molecules are schematically marked In gray. The effector site of one subunit is linked to the active site of the other subunit of the dimer through the 6-F loop between helix F and strand 6. (Adapted from T. Schlrmer and P.R. Evans, Nature 343 140-145, 1990.)...

Armchair structure Zigzag structure Helical structure All other tubes ... 

Define a crude initial structure by either distance geometry algorithms or by model building. The latter starts by defining elements of secundary structure (helices, 3 Sheets) fhom the NMR data. Even starting from an extended structure is feasible (53) ... 

Large portions of most protein structures can be described as stretches of secondary structure (helices or /3 strands) joined by turns, which provide direction change and offset between sequence-adjacent pieces of secondary structure. Tight turns work well as a-a and a-fi joints, but their neatest application is at a hairpin connection... 

Metal chelation has also been applied in studies of the structural-functional basis for seven-trans-membrane receptor activation. Using the (i2-adrenergic receptor as a model system, Filing el al. introduced several point mutations to form a metal binding site between trans-membrane helices III, VI and VII and showed that the receptor could be activated by metal ions alone or metal ions chelated by phenanthroline or bipyridine.1391 Based on a homology model built over the rhodopsin receptor crystal structure, helices III, VI and VII would have to move inwards to form a metal chelation site, suggesting that movement of these helices is critical for receptor activation. 

Materials with the highest values of gabs, IgcppiJ and gCpELl are chirally aggregated molecules or polymers. In many cases, helical supramolecular structures (helically twisted bundles, etc.) or liquid crystalline phases were detected by mi-... 

Fig. 1.6. Photosynthetic bacterial reaction center for Rsp. viridis. The chromophores are indicated but not the protein part of the structure, helices, etc., holding the whole unit...

Fig. 6. Cysteine positions in the HCIIs. The cysteine positions of HCIIs are placed on a schematic diagram of HCII secondary structure. Helices are shown as rectangles and loops as lines. Experimentally determined and predicted disulfide bond linkages are shown.

The structural helicity of benzo[9]annulenone (75, X = C = O) in solution has been evaluated by the chiral shift reagent Eu(dcm)3... 

Bhattacharjya S and Balaram P. Effects of Organic Solvents on Protein Structures Observations of a Structured Helical Core in Hen Egg-white Lysozyme in Dimethyl Sulfoxide. Proteins Structure, Function and Genetics 1997 29 492-507. 

To be successful in these applications, it is important that materials can self-assemble into precisely defined structures. Peptide polymers have many advantages over conventional synthetic polymers since they are able to hierarchically assemble into stable ordered conformations [4]. Depending on the amino acid side chain substituents, polypeptides are able to adopt a multitude of conformationally stable regular secondary structures (helices, sheets, turns), tertiary structures (e.g. the /J-slrand-helix-/J-strand unit found in /1-barrels), and quaternary assembhes (e.g. collagen microfibrils) [4], The synthesis of polypeptides that can assemble into non-natural structures is an attractive challenge for polymer chemists. 

B. Secondary Protein Structure - Helices and Pleated Sheets... 

Application of molecular biological techniques has yielded derived amino acid sequences of intrinsic lightharvesting proteins from all major and some minor groups of algae. These sequences can all accommodate the basic structural pattern determined for higher plants, that is, three fransmembrane structure helices with key... 

At a critical molar mass (M=65,000 g mol"0 the linear [rj]-M-relationships intersect (see Fig. 6.8). In general the curves of log [q]=f log M) intersect only for different polymers in solution. For the same polymer in different solvents the curves do not intersect if the solution structure stays the same. The curves might merge at low molar masses (see The influence of the molar mass below). The intersection shown in Fig. 6.8 is therefore solely caused by changes in the -solution structure. Helical structures of the polymer in solution are stiffer than the polymer chain in a flexible coil and lead to semi-flexible coils or rigid rodlike structures. The exponent a of the [q]-M-relationship shows for these extremely expanded structures values of lpoly(glutamic acid benzyl ester)... 

The structure of the repressor in the complex is similar to that found in the isolated repressor structures (10). ITie overall topology observed in the solution structure of the complex agrees with that of the crystal structure (16). The structure of the hydrophobic core is essentially identical in different forms of the repressor, although the N-terminal segments were found to be highly disordered in both the crystal (16) and NMR (1) structures. Helices D and E were found in a different conformation in the complex than in the isolated apo- or holorepressor, with helix E making contacts with the major groove of the operator DNA. 

Various optoelectronic and related properties of polymers from mono-substituted acetylene monomers have been studied extensively, such as photoconductivity, nonlinear optical properties, photo and electroluminescence, electrochromism, liquid-crystalline structures, helical structures, and stimuli-responsiveness [2, 3, 6, 7]. It is noteworthy that helical structures and stimuli-responsiveness using the change of the helical structure have progressed considerably in this decade [20, 21]. Yashima s induced circular dichroism... 

The next question is whether this initial conformation is itself dependent on the sequence. Or, to put it in another way, can the ribosomes synthesize dilferent sequences with different initial shapes It seems unlikely that the same machinery, using the same code, can produce a variety of shapes according to sequence. The most simple assumption is that all protein sequences are synthesized with the same initial structure. And having come this far, the crucial question is what is this initial structure that all proteins start out with when they have just been synthesized Considering the hierarchical structure of proteins it is reasonable to assume that it will be one of the secondary structures. There are only two secondary structures helices and sheets (turns or random coils correspond essentially to the absence of structure). Of these two, only one can exist in the extended form that is more appropriate to exit the ribosome. It is thus proposed here that the initial conformation of all proteins as they exit the ribosome is that of a helix. More specifically, and considering its stability and ubiquity in protein structure, it is proposed that it is an a-helix. 

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