Helix propagation

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. 

In the case of cooperative processes, the formation of a nucleus, already discussed from the kinetical point of view, plays a crucial role. The steady state described by Eq. (1) depicts the formation of a triple helix as the simplest model by the formation of a nucleus Hx through fast pre-equilibria and subsequent propagation steps, Hx in this case is a triple-helical intermediate with x tripeptide units (that means x hydrogen bonds) in the helical state. The final product H3n 2 possesses two hydrogen bonds less than tripeptide units because the three single chains are staggered at one amino add residue each. 

The parameters indexed with a are connected with the nucleation step or other effects occurring only once per triple helix. Parameters denoted by s are related with the equilibrium constants of the propagation steps and are ordered to be independent of the position of the reacting chain segment. This implies that end effects are neglected. Since the same dependences are valid for AH° and AS, with the help of their chain length dependence we can determine AG by extrapolation up to 3 n - 2 = 0, and thus, a can be estimated it depends neither on temperature nor on the chain length. 

For most collagens, the folding of the triple helical domain proceeds from the carboxyl end toward the amino end of the trimeric molecule in a zipper-like fashion with a rate that is limited by cis—trans isomerization of peptidyl prolyl bonds." The fast propagation of the triple helix formation is followed by a slower folding... 

Fig. 38 General mechanism of the nucleation and elongation stages of polymerization generating a helical structure (the arrows represent the interactions among repeating units). Secondary interactions light arrows), absent in the first turn of the helix, are the molecular origins of a less favorable nucleation event (i.e.,the critical chain length) beyond which propagation becomes more favorable...

The statistical weight for amino acid residue / is unity if it is not in a helical state. Its statistical weight is os if it initiates a sequence of helical amino residues and s if it propagates an existing helix. 

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

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