Helix internal parameters

CO) makes a H-bond with a third amide group away from it. There are 3.6 residues in each turn of the right-handed helix (thus 3.6-fold), and the rise of the helix per turn, the pitch, is —5.4 A. The diameter of the helix backbone is 6 A. Certain amino acids have helix-forming propensities (measured by s values, the helix propagation parameter). They are in the order Ala > Leu > Phe > He > Val > Thr > Gly at internal positions, where Pro is a helix destahilizer (62,63). At N- and C-terminal positions of an a helix, however, Gly shows a substantially increased helix-stabilizing tendency which may be greater than that of Ala (125). 

The considerations of the preceding section are illustrated in more detail here by describing a procedure that has been implemented for studying polymer crystal packing [2]. It allows the simultaneous optimization of the internal atom coordinates of the chain unit and the helix parameters along with the cell packing parameters. 

In 1975 a review on the kinetics of helix-coil equilibrium (19) concluded that polyglutamic acid (PGA) was probably the only polypeptide where the excess absorption is due to the helix-coil equilibrium. However, subsequent measurements on PGA (20) revealed that the excess absorption was time dependent and, moreover, that the equilibrium value of this absorption did not go through a maximum at the pH corresponding to mid-transition, in contradiction with previous observations (references (3) and (9) and references therein 17a, 21). Moreover, theoretical calculations were reported (22) where it was shown that internal proton transfers between helical and coiled regions of PGA in the transition range can quantitatively account for the excess absorption of PGA in the 10 kHz-1 MHz range, previously attributed to the helix-coil equilibrium (21). It should however be kept in mind that several adjustable parameters are involved in these calculations and render a critical evaluation of this work very difficult. 

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