Peptides clustering

FIGURE 10.35 The amino acid sequences of several amphipathic peptide antibiotics, a-Helices formed from these peptides cluster polar residues on one face of the helix, with nonpolar residues at other positions. 

Keywords. Molecular geometry, Polymer, Protein, Peptide, Cluster... 

These procedures have been used to create a number of peptide clusters with over 65 amino acid residues. A common motif for forming these clusters is the ferredoxin consensus sequence (6) (Figure 7) incorporated into a longer chain or even peptide sequences with additional secondary structure. 

In a preliminary study, we compared the reproducibility and peptide distribution across eight salt fractions (0 to 2M ammonium acetate, pH = 3.5) for a protein extract of control U937 cells. Figure 8.3a compares the distribution of peptide clusters for individual salt fractions to that observed for the injection of the same sample on a one-dimensional nanoLC-chip-MS system. A total of 2028 unique peptide clusters were obtained for the injection of 100 ng of protein digest for the Cig-only separation whereas 13 848 peptide clusters (a 6-fold increase) were detected for 1.5 pg injection on the combined SCX/Cig separation. In addition to the increased sample loading capacity of SCX, its... 

Figure 8.4 Distribution of peptide cluster intensities for control and PMA-treated U937 cells (w = 3). (a) Scatter plot of ion intensity for peptide clusters reproducibly detected in at least 2 replicates. The dotted lines show the 3-fold change in abundance, (b) Expression plot showing the number of down-regulated (30.0%), up-regulated (24.6%) and unaffected (45.6%) peptide clusters from a total of 9756 peptide clusters. Conditions as for Figure 8.3 for SCX/C18 separation. Replicate injections of 1.5 pg of protein digest from control and PMA-treated U937 cells were injected on two-dimensional nanoLC-chip-MS systems.

Figure 4. Depiction of ligand substitution reactions of [Fe4S4(S-t-Bu)4] with cysteinyl peptides to yield peptide clusters 11-14 and their conversion to [Fe4S4(SPh)4] , in MejSO solution (78).

Clusters (6b) with L = halide have been obtained from (6a) by reaction (4) , and are useful starting materials for the preparation of clusters (6b) with L = ArO and C4H4N , as in ligand substitution reaction (5) . This reaction has also been used with NaSR to prepare thiolate clusters (6, including those containing short cysteinyl peptides as closer models of protein site (1). Peptide clusters are also accessible by reaction (3). Bis(pentasulfide) cluster (6c) is obtained by the reaction of [Fe(SPh)4] with five equivalents of (PhCFl2S)2S. ... 

We are planning to study these transitions in the composition-protein concentration phase plane. Another interesting issue is the possibility that peptide clustering can affect the lifetime of ion channels, a study which is already under way. 

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