Dipeptide, alanine

In principle, energy landscapes are characterized by their local minima, which correspond to locally stable confonnations, and by the transition regions (barriers) that connect the minima. In small systems, which have only a few minima, it is possible to use a direct approach to identify all the local minima and thus to describe the entire potential energy surface. Such is the case for small reactive systems [9] and for the alanine dipeptide, which has only two significant degrees of freedom [50,51]. The direct approach becomes impractical, however, for larger systems with many degrees of freedom that are characterized by a multitude of local minima. 

BM Pettitt, M Karplus. The potential of mean force surface for the alanine dipeptide in aqueous solution A theoretical approach. Chem Phys Lett 121 194-201, 1985. 

AG Anderson, J Hermans. Microfoldmg Conformational probability map for the alanine dipeptide in water from molecular dynamics simulations. Proteins 3 262-265, 1988. 

Fig. 8.1 Biosynthesis of peptidoglycan. The large circles represent A -acetylglucosamine orN-acetylmuramic acid to the latter is linked initially a pentapeptide chain comprising L-alanine, D-glutamic acid and meso-diaminopiraelic acid (small circles) terminating in two D-alanine residues (small, darker circles). The lipid molecule is undecaprenyl phosphate. In the initial (cytoplasm) stage where inhibition by the antibiotic D-cycloserine is shown, two molecules of Dalanine (small circles) are converted by an isomerase to the D-forms (small, darker circles), alter which a ligase joins the two D-alanines together to produce a D-alanyl-D-alanine dipeptide.

Fig. 1. Conformational energy diagram for the alanine dipeptide (adapted from Ramachandran et al., 1963). Energy contours are drawn at intervals of 1 kcal mol-1. The potential energy minima for p, ofR, and aL are labeled. The dependence of the sequential d (i, i + 1) distance (in A) on the 0 and 0 dihedral angles (Billeter etal., 1982) is shown as a set of contours labeled according to interproton distance at the right of the figure. The da (i, i + 1) distance depends only on 0 for trans peptide bonds (Wright et al., 1988) and is represented as a series of contours parallel to the 0 axis. Reproduced from Dyson and Wright (1991). Ann. Rev. Biophys. Chem. 20, 519-538, with permission from Annual Reviews.

Cheam, T. C. 1993. Normal Mode Analysis of Alanine Dipeptide in the Crystal Conformation Using a Scaled Ab Initio Force Field. J. Mol. Struct. 295,259-271. 

Gould, I. R., and I. H. Hillier. 1993. Solvation of Alanine Dipeptide a Quantum Mechanical Treatment. J. Chem. Soc., Chem. Commun. 951-952. 

Head-Gordon, T., M. Head-Gordon, M. J. Frisch, C. Brooks HI, and J. A. Pople. 1989. A Theoretical Study of Alanine Dipeptide and Analogs. Int. J. Quantum Chem. Quantum Biol. Symp. 16, 311-322. 

Peters, D., and J. Peters. 1981c. Quantum Theory of the Structure and Bonding in Proteins Part 8. The alanine dipeptide. J. Mol. Struct. (Theochem) 85,107-123. 

Shang, H. S., and T. Head-Gordon. 1994. Stabilization of Helices in Glycine and Alanine Dipeptides in a Reaction Field Model of Solvent. J. Am. Chem. Soc. 116, 1528-1532. 

Fig. 4.5. Free energy profile of alanine dipeptide as a function of

As an example, this approach was applied to the calculation of the PMF for alanine dipeptide as a function of the two torsion angles

resulting free energy surface is shown in Fig. 4.5. Bilinear Qi elements were used to approximate the free energy. Control points were chosen such that there are four of them around each data point. This was done in order to increase the smoothness and quality of the reconstructed free energy. The position of the Q i nodes and control points is shown in Fig. 4.6. 

Several problems have been studied with this technique, including the dissociation of NaCl [34], alanine dipeptide [34], C4H6 [32], and phase transitions in silicon [33]. 

D-Alanine is found in bacterial cell wall peptidogly-can. l-Alanine is converted to D-alanine by a racemase that contains pyridoxal phosphate as a cofactor. The racemiza-tion is followed by the formation of a D-alanyl-D-alanine dipeptide, which is accompanied by the conversion of ATP to ADP. The dipeptide is subsequently incorporated into the glycopeptide (see fig. 16.16). 

So far, we have investigated higher-order structure of polypeptides by solid-state high-resolution NMR not only using experimental but also theoretical methods[2-4]. The chem cal shifts can be characterized by variations in the electronic states of the local conformation as defined by the dihedral angles(4>,W). Ando et al. have calculated contour map for the Cp carbons of an alanine dipeptide by using the FPT INDO method within the semi-empirical MO framework. The calculated map reasonably predicts the experimental version. This shows that the chemical shift behavior of the L-alanine residue Cp-carbonyl carbons in the... 

The impact of solvation on conformation becomes stronger as the size of the flexible system increases and is specially great for biological molecules as seen in Figure 4.7, which represents the Ramachandran map in the gas phase and water of an alanine dipeptide as determined by LMP2/6-31G/(d) and MST/6-31G(d) calculations. Because of the polymeric nature of proteins the marked effect of solvation in the [Pg.505]

Figure 4.7 Ramachandran s map of alanine dipeptide in the gas phase and aqueous solution (see Colour Plate section). Energy contours are in kcal/mol.

M. Pellegrini et al., Potentials of mean force for biomolecular simulations Theory and test on alanine dipeptide. J. Chem. Phys. 104, 8639-8648 (1996)... 

Figure 14-1. The lowest energy conformation C f of the alanine dipeptide model in gas phase...

Figure 14-2. The alanine dipeptide model surrounded by four water molecules from the first solvation shell...

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