Conformational sequence effect

Where Kunf and Kfiuct are the equilibrium constants for the unfolding transitions and fluctuations respectively. For simplicity, both the unfolded and the fluctuated conformations are assumed to exchange with the rate determined from unstructured dipeptides (Bai et al., 1993 Connelly et al., 1993). This may be a poor assumption, especially for the fluctuated form, but it allows the rates to be normalized for temperature, pH and amino acid sequence effects. Kpp, the equilibrium constant determined from kobs / is then given by... 

Kazmirski SL, Alonso DOV, Cohen FE, Prusiner SB, Daggett V (1995) Theoretical-studies of sequence effects on the conformational properties of a fragment of the prion protein implication for scrapie formation. Chem Biol 2 305... 

L-alanine content (between 20 and 30%), any significant changes in chemical shift change was observed for chemical shift changes may be mainly due to the side-chain effect of the L-valine residue and the neighbouring amino acid sequence effects, but apparently are not due to the main-chain conformation of copolypeptides. 

For a series of [Ala, Asp(OBzl)] , the value of a22 decreases linearly as the L-alanine content increases (5 20% of the L-alanine content). This change of the 022 value may be due mainly to neighbouring amino acid sequence effects, but not to the main-chain conformation of polypeptides. The a[SO, ox, and <733 values, on the other hand, do not change at this L-alanine content (5 20%). 

Figures 27 and 28 show the plots of aiso, au, a22, and o33 values of various [Gly, Ala] and [Gly, Leu] against glycine content. It is interesting that the value of <7iso is nearly constant, but the principal shielding tensor components are displaced over a wide range of glycine content (20 100%). Therefore, these tensor components contain some information about neighbouring amino acid sequence effects as well as conformation. The reason for this is not clear at present.

The determination of the stable conformers by means of molecular mechanics and considering such conformation-dependent effects as the well-known y-gauche effect allowed Li and Hou to achieve independent and complementary support to the chemical shift assignments. The results obtained with an rotational isomeric state (RIS) model of the E-N copolymers suggested for the first time and proved the occurrence of the splitting of the signals of meso and racemic alternating NEN sequences. 

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