Helix initiator

The shortest helical sequence that can be created in an a-helix-forming polypeptide is hhh, and its statistical weight is as. Since s is of the order of unity in the helix-coil transition region, the probability that such a nucleus for the growth of a helical sequence will be produced is essentially equal to a. For this reason, a is also called the helix-initiation parameter. 

N 086 "Helix Initiation and Propagation by (Hydroxyethyl)-L-glutaminyl Residues in Water"... 

The (TV-aminoamide) link 4 is a convenient intermediate to cyclization of the peptide chain as in the cyclic initiators 81 (n=l, 2) of an a-helix (Scheme 24)J981 Replacement of the N—H O=C hydrogen bond by the N-N=CH-C hydrazone moiety gives another a-helix initiator 82, synthesized by coupling the TV-amino group with an aldehyde carbonyl/99 ... 

Helix initiation (represented by the helix nucleation parameter a) in a random coil conformation is the slowest and energetically least favored step, whereas subsequent growth of the helix nucleus (represented by the helix propagation factor, s) is rapid and relatively favored. 83 ... 

Noting that Pro often plays the role of helix initiator and is often found at the beginning of helices, Kemp and co-workers have designed a series of helix-nucleating templates based on constrained di-[122 124 or triprolines 125-128 8-10 (Scheme 3). These templates can be easily incorporated at the N-terminus of any sequence. 

Figure 4.10. PDB file (partial) for 3D structure of hen s egg-white lysozyme (ILYZ.pdb). The abbreviated file shows partial atomic coordinates for residues 34-36. Informational lines such as AUTHOR (contributing authors of the 3D structure), REVDAT, JRNL (primary bibliographic citation), REMARK (other references, corrections, refinements, resolution and missing residues in the structure), SEQRES (amino acid sequence), FTNOTE (list of possible hydrogen bonds), HELIX (initial and final residues of a-helices), SHEET (initial and final residues of / -sheets), TURN (initial and final residues of turns, types of turns), and SSBOND (disulfide linkages) are deleted here for brevity. Atomic coordinates for amino acid residues are listed sequentially on ATOM lines. The following HETATM lines list atomic coordinates of water and/or ligand molecules.

Side-chain-main-chain interactions involving mostly serine, threonine, aspartate, and asparagine help to satisfy the hydrogen bond potential of free N—H groups in turns and at the ends of a helices. The authors speculate that these residues may have a role in a helix initiation. 

Lee, M.C., Orci, L., Hamamoto, S., Futal, E., Ravazzola, M., Schekman, R. Sarlp N-terminal helix initiates membrane curvature and completes the fission of a COPII vesicle. Cell 2005,122,605-17. 

D. J. Tobias and C. L. Brooks III, Biochemistry, 30, 6059 (1991). Thermodynamics and Mechanism of a-Helix Initiation in Alanine and Valine Peptides. 

The proportionality constant between theoretical helix content and optical rotation is found by fitting the data at the highest concentration of 5.66% measured. Then, theoretical results at other concentrations automatically fit the experimental data with high accuracy. It turned out that, for (n) = 50, the helix initiation parameter cf2 should be as small as 0.001 to obtain good fit. One of the main reasons why t-carrageenan does not form gels is the smallness of this helix initiation probability. The coil-helix transition temperature at dilute limit is fixed at To = 65°C. 

---