Alanine relative hydrophobicity

Monera, O. D., Zhou, N. E., Lavigne, P., Kay, C. M., and Hodges, R.S. (1996). Formation of parallel and antiparallel coiled-coils controlled by the relative positions of alanine residues in the hydrophobic core./. Biol. Chem. 271, 3995—4001. 

Polymers of the naturally occurring amino acids alanine, leucine, and methionine all show interactions which depend on the relative directions of the backbones. In contrast, poly(L-norleucine) shows less specific interactions clearly for the hydrophobic regions of proteins to function in a precise manner the natural amino acids are most suitable. 

A well-studied system is alanine dipeptide (AcAlaNHMe). The relative stability of different conformational states in vacuum - and in water were obtained from PMF calculations, °> and again different models and simulation parameters were applied. In a recent study Marrone, Gilson, and McCammon calculated the PMF of alanine dipeptide by using the Pois-son-Boltzmann method with a hydrophobic term and by using explicit water and found comparable results. Fraternali and van Gunsteren studied PMFs of glycine dipeptide in water for two reaction coordinates. Tobias and Brooks used their own technique to calculate the PMF of the central torsional angle... 

By means of calorimetric measurements reflecting the dependence of the stability constants of metal complexes on the composition of the solvent mixture, Gergely and Kiss have shown that the stability increase resulting from a decrease in the relative permittivity shows up primarily in an increase in the — dff values, whereas the dS values decrease or remain unchanged compared with those measured in aqueous medium. A comparison of the AH values for aliphatic and aromatic amino acid complexes of copper(II) has revealed that the change in the medium acts to a lesser extent on the AH values of the aromatic amino acid complexes. This is probably due to the presence of the hydrophobic phenyl group in the aromatic ligands, as a consequence of which the extent of hydration even in aqueous medium is lower than in the case of alanine. 

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