Deca-L-alanine

ABF was probed through the reversible unfolding of a short peptide, deca-L-alanine, in vacuo [52] (see Fig. 4.10). The reaction coordinate, , is the distance separating the first and the last Ca carbon atom of the peptide chain. was varied between 12 and 32 A, thereby allowing the peptide to sample the full range of conformations between the native a-helical structure and the extended structures. The force acting along was accrued in bins 0.1 A wide. 

It is interesting to note that the free energy profiles obtained with ABF are essentially identical to those derived by Park et al. [53] from a reversible, 200-ns steered molecular dynamics simulation and from a set of 100 shorter runs, pulling very 

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Fig. 4.11. Free energy profile for Deca-L-alanine calculated using the ABF. The inset shows the number of samples as a function of ...

Casella L, Gullotti M, Monzani E, De Gioia L, Chillemi F (1991) Biomimetic oxidation catalysis by iron (III) deuteroporpbyrin carrying a deca-L-alanine peptide chain. Rend Fis Acc Lincei 2 201-212... 

K. D. Gibson and H. A. Scheraga, Proc. Natl. Acad. Sci. USA, 63,9 (1969). Minimization of Polypeptide Energy. VI. Systematic Searches for Low-Energy Conformations of Deca-L-alanine and the Octapeptide Loop of Ribonudease. 

Figure 7 compares the shape fluctuations in deca(L-alanine) and deca(L-... 

Figure 7 Monitoring structural stability in terms of shap fluctuations Comparison of the fluctuations in the mean number of overcrossings N(f) along molecular dynamics trajectories of deca(L-alanine) and deca(L-glycine). The computations correspond to isolated peptides immersed in a thermal bath at 500 K. The initial conformations were a-helices. See text for further details.

Four cyclic heptapeptide toxins (extracted fixim Microceptis auruginosd) consisting of D-alanine, eryfAro-yJ-methylaspartic acid, glutamic acid, L-leucine, L-alanine, A -methyldehydroadenosine, and 3-amino-9-methoxy-2,6,8-trimethyl-10-phenyl-deca-4,6-dioenoic acid were baseline resolved in 20 min using a C g column (A = 238 nm) and a 58/42 methanol/water (50 mM phosphate buffer at pH 3) mobile phase [472]. Excellent peak shapes were obtained. 

Figure 1. Structure of the blue-green algal toxin microcystin-LR. Besides the two variable L-amino acids, leucine and arginine, the microcystin contains three D-amino acids (glutamic acid, alanine and methylaspartic acid) and two unusual amino acids, N-methyl-dehydroalanine (Mdha) and 3-amino-9-methoxy-2,6,8-trimethyl-10-phenyl-deca-4,6-dienoic acid (Adda) (see Ref. 4).

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