A-Helix formation

Several years ago Makino et al. 86) studied the influence of anions on the conformation of poly-[L-methionine-S-methylsulfonium] salts in solution. They found that especially perchlorate will induce a-helix formation whereas Cl- and Br do not. Since then several authors 87 92) have found a similar a-helix inducing effect in the case of poly-L-lysine (Lys) and other BPAA at low pH-values where the polymer molecules usually attain an extended conformation due to the electrostatic repulsion of the ammonium groups. Therefore, the a-helix inducing effect is obviously an... 

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. 

In comparison to the constant of propagation of the a-helix formation (kp — 1010s 1) and the double-helix formation (kp — 107s-1), a comparatively small parameter concerning the formation of triple helix has been found (fcp = 8 x 10 3s1). A higher entropy of activation is assumed as the main cause of this occurrence which means a lower frequence factor in the Arrhenius equation. 

The amino acid sequence of our first aPNA (which we termed backbone 1 or bl) was designed based on this amphipathic hehx sequence (Fig. 5.3 B). Specifically, this aPNA backbone included hydrophobic amino acids (Ala and Aib), internal salt bridges (Glu-(aa)3-Lys-(aa)3-Glu), a macrodipole (Asp-(aa)i5-Lys), and an N-ace-tyl cap to favor a-helix formation. The C-termini of these aPNA modules end in a carboxamide function to preclude any potential intramolecular end effects. Each aPNA module incorporates five nucleobases for Watson-Crick base pairing to a target nucleic acid sequence. 

Further evidence for these a-helix ROA band assignments in the extended amide III region comes from the ROA spectrum of poly-L-alanine dissolved in a mixture of chloroform (70%) and dichloracetic acid (30%), known to promote a-helix formation (Fasman, 1987), which shows strong positive ROA bands at 1305 and 1341 cm-1 (unpublished results), and of the cv-helix forming alanine-rich peptide AK21 (sequence Ac-AAKAAAAKAAAAKAAAAKAGY-NHg) in aqueous solution which shows strong positive ROA bands at 1309 and 1344 cm-1 (Blanch et al., 2000). 

The validity of this model for unfolded proteins rests on elucidation of the physical determinants of the two types of helix and the determination of the energetic favorability of these conformations relative to all other possible conformations in unfolded proteins. The determinants of a-helix formation have received significant attention over the past 15 years, and are thought to be mostly understood (reviewed in part by Aurora et al., 1997). The determinants of PPII helix formation have received far less attention and are only now beginning to be understood. 

Studies of synthetic polypeptides as well as examination of known protein structures reveal that some amino acids, e.g., Glu, Ala, Leu, tend to promote a helix formation. Others, such as Tyr, Val, and lie, are more often present in (3 structure, while Gly, Pro, and Asn are likely to be found in bends 270 270a 270b The frequencies with which particular amino acids appear in helices, (3 structure, or turns were first compiled by... 

Signal sequences vary in structure but usually have a net positive charge within the first 5-8 residues at the N terminus. This region is followed by a "hydro-phobic core" made up of 8-10 residues with a strong tendency toward a helix formation. This sequence is often followed by one or a few proline, glycine, or serine residues and then a sequence AXA that immediately precedes the cleavage site. Here, A is usually alanine in prokaryotes but may also be glycine, serine, or threonine in eukaryotes. Residue X is any amino... 

Early studies of peptides from helical regions of proteins failed to detect any helicity in experiments conducted at 25 °C. 95,96 Despite the ensuing expectation that short peptides cannot form stable helices in water, Brown and Klee197 in 1971 first noted that the C-peptide and S-peptide of RNase A form a partial helix in water at 1 °C. Bierzynski et al. 81 also studied the S-peptide and found a-helix formation at 10 °C. It is now known that helices are more stable at lower temperatures, undergoing thermal unfolding to the unordered coil form as the temperature is raised. 

Interaction of bivalent metal cations with poly(glutamic acid) has been extensively investigated 6-17), including the induction of a-helix formation by transition metal ions. Nevertheless, available data are not sufficient to explain the wide variety of metal-ion-induced conformational changes. 

France LL, Piatti PG, Newman JFE, Toth I, Gibbons WA, Brown F (1994) Circular dichro-ism, molecular modeling, and serology indicate that the structural basis of antigenic variation in foot-and-mouth disease virus is a-helix formation. Proc Natl Acad Sci U S A 91(18) 8442-8446... 

Although a helices are abundant in proteins, the average length is fairly short, that is, 17 A long containing about 11 amino acids or three turns. Therefore, a helices are typically found in short domains within proteins and not as continuous stretches. Keratins that make up hair and the most superficial layer of skin contain a central domain with an a helical component of 310 amino acids or about 46.5 nm in length. Keratin is an example of a protein with a fairly long a helix. The amino acid composition that favors a helix formation is fairly broad with the exception of proline and serine. 

Elastin is a macromolecule synthesized as a 70,000 single peptide chain, termed tropoelastin and secreted into the extracellular matrix where it is rapidly crosslinked to form mature elastin. The carboxy-terminal end of elastin is highly conserved with the sequence Gly-Gly-Ala-Cys-Leu-Gly-Leu-Ala-Cys-Gly-Arg-Lys-Arg-Lys. The two Cys residues that form disulfide crosslinks are found in this region as well as a positively charged pocket of residues that is believed to be the site of interaction with microfibrillar protein residues. Hydrophobic alanine-rich sequences are known to form a helices in elastin these sequences are found near lysine residues that form crosslinks between two or more chains. Alanine residues not adjacent to lysine residues found near proline and other bulky hydrophobic amino acids inhibit a helix formation. Additional evidence exists for (3 structures and 3 turns within elastin thereby giving an overall model of the molecule that contains helical stiff segments connected by flexible segments. 

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