Helix types

Polymer Melting poiut, °C Crystal type Helix type Crystalline density, g/cm ... 

A few other helical conformations occur occasionally in globular protein structures. The polyproline helix, of the same sort as one strand out of a collagen structure, has been found in pancreatic trypsin inhibitor (Huber et al., 1971) and in cytochrome c551 (Almassy and Dickerson, 1978). An extended e helix has been described as occurring in chymotrypsin (Srinivasan et al., 1976). In view of the usual variability and irregularity seen in local protein conformation it is unclear that either of these last two helix types is reliably distinguishable from simply an isolated extended strand however, the presence of prolines can justify the designation of polyproline helix. 

In order to demonstrate what the various types of turns actually look like, Figs. 31 through 34 show stereo views of turn examples from real structures that have angles very close to the defining values for each type. Type III is illustrated for completeness, but it cannot be distinguished from type I by inspection unless it is part of a continuing 310-helix. Types IV and V are not shown, because type IV is a miscellaneous category and there are no ideal cases of type V (see Fig. 36). The turns are all shown in approximately the same standard orientation with the mean plane of the four a-carbons in the plane of the... 

Balasubramanian et concluded that the Pro ring has two typical puckered conformations (1) conformation A characterized by negative values of %1 (Cq-exo) (found in residues having a-helix-type torsion angles) and (2) conformation B characterized by positive (C7-endo) (found in residues having collagen-type torsion angles). 

Membrane receptors of the 1-helix type with tyrosine kinase activity, which can bind growth factors and hormones (see p. 394). 

Figure 2-24 Tight turns found in polypeptide chains. Two types of 3 turn are shown. A third variant, the type III or 310 turn resembles the type I turn but has the cp, y angles of a 310 helix. Type II P turns containing proline and tighter y turns are thought to be major structural components of elastin. Another P turn, lacking the hydrogen bond has a cz s-proline residue at position 3.

Furthermore it is interesting to notice that connecting monomeric units, the carbon atoms of which are ordered in the conformation with the highest optical activity according to Brewster s rules, one after the other in an isotactic manner, the conformation of the principal chain is of the right- or of the left-handed helix type (100). 

According to the above data and to preliminary determinations of the polymers optical activity in the solid state (112) it was suggested (105) that the principal chain of optically active poly-a-olefins, which in general posses a helix type conformation in the solid state, consists of sections having helix conformation also in the molten state or in dilute solution. Most sections of the principal chain are spiraled in one screw sense only, depending on the absolute configuration of the asymmetric carbon atom of the lateral chains. 

Helix Numbers Helix Types Distance Angle Interaction Type Total Helix 1 Helix 2 ... 

Note The helix types are H for a helix and G for 310 helix. The helical geometry is followed by a measure of the deviation from an ideal helix (this value should be 0 for a perfect helix). For the interacting pairs, the interaction type describes where in each of the helices the distance of closest approach occurs (C, beyond the C terminus of the helix N, beyond the N terminus of the helix I, internal to the helix). 

The above description is a considerable simplification of protein secondary structure possibilities. Thus a number of helix types are possible in addition to the a-helix. Further, particular structured 3-turns exist that are stabilized by hydrogen bonding and link other secondary structure elements. Relatively unstructured coils, loops and random coils can also link a-helical and 3-strand elements. 

In detail The first lobe (residues 1 -39 and 85-129) contains four helices that are close to the Pauling—Corey a-helix type, and one singleturn 310-type helix. There are short stretches (each five to nine residues) of backbone loops and turns connecting the helices. Three a helices (helix A, residues 4—15 helix C, residues 88—99 helix D, residues 108-115) are on the protein surface and are partially exposed to solvent. The a helix (B) consisting of residues 24-36 is totally buried. The 310 helix (residues 119—124) is partially exposed to solvent. The second lobe (residues 40-84) contains a three-stranded antiparallel y3-pleated... 

Helical ( )-)-poly(triphenylmethyl-methacrylate) has been applied successfully as a chromatographic material for the separation of racemates An overview of the helix types exhibited by crystalline macromolecules and some examples are given in Table 3. 

Figure 31. A, Stereo pair plot of the molecular structure of crystalline cyclopentadecapeptide. Reproduced, with permission, from [59]. B, Stereo plots of the molecular structure of the cyclopentadecapeptide in solution. Reproduced, with permission, from [91]. C, -Turn perspective of crystalline cyclopentadecapeptide. Reproduced, with permission, from [59]. D, Solution derived conformation of the cyclopentapeptide which gave the a-helix type of CD spectrum in Figure 30B. Reproduced, with permission, from [92]. In parts A and B, the stereo pairs are plotted for cross-eye viewing.

Osteocalcin (OCN) is one of the most prevalent non-collagenous intraosseous proteins, and it is predominantly localized to osteoblasts. This 9-kD cytoplasmic protein contains abundant gamma carboxyglutamic acid residues. Its expression is down-regulated by helix-loop-helix-type transcription factors and up-regulated by vitamin D analogs such as 1,25 dihydroxyvita-min D2 and 24-epi-l,25 dihydroxyvitamin D2 in the final steps of osteoblastic differentiation and osteoid formation. ... 

The thermobalance is an instrument that permits the continuous weighing of a sample as a function of temperature. The sample may be heated or cooled at some selected rate or it may be isothermally maintained at a fixed temperature. Perhaps the most common mode of operation is heating the sample at furnace heating rates from 5-10°C/min. Almost all modern thermobalances are automatically recording instruments, although manual recording is still used occasionally for long-term isothermal measurements (e.g., with helix-type thermobalances). 

Figure 1.27 Cartoon depiction of the extended Pn-helix. Depiction emphasises the left handed character of this helix type (adapted from Voet, Voet Pratt, 1999 [Wiley], Fig. 6-17).

The similar observations of the sodium hydroxide concentration dependencies of the peak positions, relative peak intensities, and line-widths of schizophyllan revealed that, like lentinan, its molecule adopted single-helical conformation at lower NaOH concentrations (<0.13 N), while the transition to the random-coil state took place at 0.19 N. Grifolan produced soft gel at neutral pH whose NMR spectrum was similar to those of lentinan and schizophyllan [42]. However, different preparations of grifolan possessed two kinds of solid-state structure and formed different gel types that were described as a helix type (similar to that of lentinan) and a native type that had different structure. Both structures were investigated by NMR spectroscopy, the accent being made on the differences in gel-to-sol transitions induced by addition of alkali, DMSO or urea [86]. 

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