Helical conformation, determination

As Fig. 16 shows, the preferential binding of DMSO, DMF and NMF from aqueous solution to (Lys HBr)n at low contents of the organic solvent x increases with its concentration. However, at approximately x3 = 0,2 a maximum is reached and then preferential hydration between x3 = 0,3 and 0,5 occurs. No preferential binding was observed for NMP, EG or 2 PrOH, however increasing hydration occured with x3. Only in 2 PrOH at x3 > 0,3 a-helix formation occured. Furthermore binding parameters for the systems NMP + DMSO, EG + DMSO and DMF + DMSO have been determined. An initial preferential binding of DMSO by (Lys HBr)n, a maximum and a subsequently inversion of the binding parameter was also observed in these mixtures. The order of relative affinity is DMSO > DMF > EG > NMP. In DMF/DMSO-mixtures (Lys HBr) attains an a-helical conformation above 20 vol.- % DMF and in 2-PrOH/water above 70 vol.- % 2 Pr-OH. 

Peptoids based on a-chiral aliphatic side chains can form stable helices as well [43]. A crystal of a pentameric peptoid homooligomer composed of homochiral N-(1-cyclohexylethyl)glycine residues was grown by slow evaporation from methanol solution, and its structure determined by X-ray crystallographic methods. In the crystalline state, this pentamer adopts a helical conformation with repeating cis-... 

What are the physical determinants of the PPII helical conformation Pappu et al. (2000) have shown that the PPII region of (0,0)-space is... 

Once the determinants of PPII helix formation are known in more detail, it will become possible to apply them, along with the known determinants of the cy-helical conformation, to the understanding of protein unfolded states. If, as suggested at the beginning of this article, protein unfolded states are dominated by residues in the PPII and cy-conformal ions, these data will allow for modeling of the unfolded state ensembles of specific proteins with a level of realism that has not been previously anticipated. 

Acridine and its derivatives are also fused nitrogen heterocycles similar to acridones, which display a high fluorescence quantum yield and possess the ability to intercalate tightly, though reversively, to the DNA helical structure [73], with large binding constants [74]. As a result, acridine dyes are recognized in the field of the development of probes for nucleic acid structure and conformational determination [75-77]. 

From the CCR rate one can easily discriminate between an a-helical conformation (y/ -60°) and a yS-sheet (y/ 120°) conformation, as indicated in Fig. 16.6. The curves in the figure are scaled by arc. A more precise determination of the torsion angle is also possible in the case that both CCR rates are measured. By combining the two rates, the term arc as well as the angle i/r can be determined ... 

The reference 28 authors continue to detail experimental observations that place voltage sensor helices in positions within the membrane. Miller and coworkers conducted site-directed mutagenesis for all residues of helices Sl-S3. ° In these experiments, tryptophan (trp) residues were substituted for each amino acid in turn to determine which residues would be trp-tolerant. These experiments confirmed a-helical conformations for SI and S2 and showed that K+ channel function was altered when trp residues were placed in some (labeled non-trp-tolerant), but not all, positions. The same treatment for helix S3 yielded complex results. At S3 s N-terminal end the distribution of trp-tolerant positions were consistent with an a-helical structure, however, this was not the case at S3 s C-terminal end. Other tests indicated that S3 might be helical for its entire length and that the N-terminal end interfaces with both lipid and protein while the C-terminal end interfaces with water. Comparisons of trp-tolerant or trp-intolerant residues over several different Kv channel... 

A 3(— 1.143) helical conformation was proposed. A complete determination of the unit-cell dimensions and the lateral arrangement of the chains was not possible, due to the paucity of the X-ray data. Two intrachain hydrogen-bonds, of the type OH-2-(/3-D-Galp)—0-5-(a-D-Manp) and OH-2-(a-D-GalpA)—0-3-(a-D-Manp), were proposed. No intrachain hydrogen-bond is possible with the a-D-Manp side-group. 

Fig. 13. Structural dynamics of TAR RNA in response to increasing Mg2+ concentrations. (A) The TAR inter-helical conformation as a function of [Mg] [TAR] stoichiometry. Ribbon representation of the relative orientation of stem I (bottom) and II (top) determined by superimposing stem-specific principal axes. The helix axis of stem II is superimposed for all three conformations along the molecular z direction. (B) The generalized degree of order ( ) for stem I (lower line) and II (upper line), as a function of [Mg] [TAR] stoichiometry. Addition of Mg2+ leads to attenuations in the difference between helix-specific values indicating quenching of inter-helical motions.

The use of infrared is not limited to p structure detection, however. The erythrocyte study reported here clearly illustrates the information available when spectra are taken in D20. Optical changes permit one to estimate the extent and rapidity of proton exchange in proteins and hence to estimate the availability of peptide bonds to water protons as well as the contributions from random coil and a-helical conformations. The results with erythrocytes indicate that about two-thirds to three-fourths of the protein amide groups are freely accessible to water and that most of the protein exists in an open, mostly random, conformation. The fraction of non-exchangeable protons agrees reasonably well with the helical content determined by ORD. 

Of all the amino acids, Ala has the highest tendency to adopt an a-helical conformation based on the Chou and Fasman rules for secondary structure prediction181 and host-guest determination of helical propensities/181 This has also been demonstrated in studies by Marqusee et al. on short alanine-based peptides which were found to form stable monomeric peptide helices in water/191... 

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