Penta-alanine

We will first explain the background of these two approaches and comment on their relation. In the second part of this contribution we will discuss the identification of the most persistent conformations of penta-alanine as a numerical example. Other examples can be found in [13,14]. 

As penta-alanine is a short peptide it will not have a stable / -sheet conformation, but as we will see in our analysis it exhibits a stable a-helix conformation and several other conformations which can be characterized by certain flexibility patterns. 

Fig. 2. Left The Penta-alanine peptide in baU-and-stick representation. The ten peptide angles determining the secondary structure are marked by Right Ramachandran plot, showing the energetically preferred regions of a L> [ pair with the associated secondary structures (simplefied plot due to [32])...

We are indebted to G. Stock for the courtesy of making the simulation data of penta-alanine available to us. 

The dynamics of hydration water was investigated by quasi-elastic neutronscattering (QENS) experiments in a completely deuterated penta-alanine peptide at different levels of hydration (7, 30, 50, and 90%) and of dried powder. The last... 

The absence of slow dynamics in this system can be attributed to the fact that the penta-alanine peptide does not have any polar side-chain atom which can form a strong HB with water. With a higher level of hydration, the rotational dynamics of water approached that of bulk water, again as expected. A QENS study of protein dynamics was also carried out on the picosecond timescale of a protein, lysozyme solvated in glycerol at different water contents, h (g water/g lysozyme). For all h, a well-visible low-frequeney vibrational bump was observed. The quasi-elastic scattering can be decomposed into two Lorentzian components, corresponding to motions with charaeteristic time constants of 15 ps and 0.8 ps. The 15 ps component is the slow component, which is in the same range observed in many other experimental studies. 

Tropoelastin is the soluble precursor of elastin and consists of alternating hydrophobic and hydrophilic peptide domains. The most common amino acids in the hydrophobic domains are Gly, Val, Ala, and Pro, which are often present in repeats of tetra-, penta-, and hexapeptides, such as Gly-Gly-Val-Pro, Gly-Val-Gly-Val-Pro, Gly-Val-Pro-Gly-Val, and Gly-Val-Gly-Val-Ala-Pro, respectively [3, 4]. The hydrophilic domains are mainly composed of lysines interspersed by alanines. 

Initially, some linear libraries of penta-, hexa-, octa and decamers with structure (A )ra-/J- -/J- -TentaGelS (where ft = /1-alanine and s = e-aminocaproic acid) were tested. For each position 19 natural amino acids (cysteine was avoided) were used, and the active ligand structures are shown in Figure 8.13. Some recurrent motifs emerged, such as FDW and QDPR, especially for 5- and 6-mers, and WXXGF for 8- and 10-mers. 

A well-defined monodisperse penta(L-alanine)- -butylamide H-[Ala]5-NHBu was synthesized by an activated ester method " and other natural abundant polypeptides, [Ala]n-5, [Leu]n-1 and [Leu]n-2, were synthesized by the N-carboxy a-amino-acid anhydride (NCA) method.Fully N-labelled homopolypeptides, [Ala ]n (99 at.% of N purity MASSTRACE, Inc.) and [Leu ]n (99 at.% of N purity MASSTRACE, Inc.), which show characteristic differences in conformation such as the a-helix and /3-sheet forms, were prepared by the heterogeneous polymerization of the corresponding NCAs in acetonitrile with -butylamine as an initiator. Conformational characterization of these samples was made on the basis of the conformation-dependent C and chemical shifts determined from the CP-MAS NMR method and from the characteristic bands in the IR and far-IR spectra. Figs. 38 and 39 show the 75.5 MHz C and 30.4 MHz N CP-MAS NMR spectra respectively of these fully N-labelled (99 at.% purity of N) homopolypeptides adopting the a-helical and /3-sheet forms (A) [Ala ]n-2 (a-helix), (B) [Ala ]n-1 (/3-sheet), (C) [Leu ]n-2 (a-helix), (D) [Leu ]n-1 (/3-sheet) in the solid state. Synthetic conditions and conformational characteristics of these samples are summarized... 

In an investigation of the peptide of the cell wall of a strain of S.faecalis, 1V -(l-alanyl-D-isoglutaminyl)-Af -(D-isoasparaginyl)-L-lysyl-D-alanine, the location of the D-isoasparaginyl residue as a substituent of the Af -lysine in the disaccharide penta-peptide monomer has emerged from several lines of investigation (Ghuysen et al.. 

DD-transpeptidases-catalyse the cross linking of adjacent NAM penta-peptides with loss of the terminal D-alanine residue (Scheme I). 

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