P-sheet preferences

Figure 4 Score profiles for porin from Rhodobacter capsulatus are obtained by subtraction of turn preferences from helical preferences (full line) and as sum of P-sheet preferences and hydrophobic moment scores for assumed p-sheet conformation (dotted line). Kyte-Doolittle scale [17] is used to calculate preferences, while PRIFT scale [50] is used to calculate hydrophobic moments. Observed transmembrane strands are shown as bold horizontal bars at the score level 2.0.

The anticipated lamellar structure is shown in schematic form in Fig. 1. Exclusion of the Glu residues from interior sites confines them to the surfaces of the lamella, while the number of AlaGly dyads in the periodic repeating unit determines the lamellar thickness. We expected that the chain conformation in the crystal stems, and the unit cell structure, would be dictated by the strong p-sheet preference and the packing requirements of the AlaGly dyads. Reversal of the chain direction at the lamellar surfaces leads to an antiparallel arrangement of the p-sheets. 

Similar EG modifications to the p-sheet preferring amino acids L-serine and L-cysteine were also studied by Deming to allow facile aqueous processing of their corresponding p-forming polymers. The EG side chains should provide good water solubility to the polymers, which could then form P-sheet... 

Murzin, A.G. Structural principles for the propeller assembly of p sheets the preference for seven-fold symmetry. Trotei/is 14 191-201, 1992. 

The amino acids are grouped according to their preference for a helices (top group), P sheets (second group), or turns (third group). Arginine shows no significant preference for any of the structures. 

Studies on host-guest peptides have shown that incorporation of a proline residue into peptides which have a high tendency to fold into ordered secondary structures disrupts the onset of helical as well as P-sheet conformations and increases solubility and coupling rates.f Based on this observation, serine- and threonine-derived oxazolidine, and cysteine-derived thiazolidine derivatives (pseudoprolines) were proposed as valuable tools for combining protection of their side-chain functions with the simultaneous solubilization of the peptide chain. Due to the induction of kink conformations in the peptide backbone, originating from the preference of these pseudoproline residues to adopt the cis-imide bond configuration, insertion of such derivatives into peptides prevents self-association and P-structure formation. 

Fabiola, G.G., Bobde, V., Damodharan, L., Pattabhi, V., and Durani, S. (2001) Conformational preferences of heterochiral peptides. Crystal structures of heterochiral peptides Boc-(d) Val-(D) Ala-Leu-Ala-OMe and Boc-Val-Ala-Leu(D) Ala-OMe-enhanced stability of p-sheet through CH- -O hydrogen bonds, J. Biomol. Struct. Dyn. 18, 579-594. 

More than 100 members of the AS family of enzymes have been reported in the literature, but only for malonamidase (MAE2) (Shin et al., 2002) and C-terminal peptide amidase (PAM) (Labahn et al., 2002), two soluble bacterial enzymes, structural data are available. All three resolved structures of AS enzymes (FAAH, MAE2, and PAM) revealed a common core, consisting of a twisted p-sheet of 11 mixed strands, surrounded by a large number of a-helices (those of FAAH are shown in Fig. 4.3). Compared to other AS enzymes, which are mostly soluble proteins, FAAH displays two distinguished features i) integration into membranes, and ii) strong preference for hydrophobic substrates. 

When a third strand is added, the relative frequencies of occurrence of the possible motifs reflect the same preferences for antiparallel compared with parallel, and for sequential strands to be adjacent in the structure. Tkble 15.3 shows the possible topologies for three consecutive strands that are adjacent in the same P sheet and their frequency of occurrence in our data set. The most commonly occurring pattern is the P meander (Figure 15.15), which consists of two consecutive P hairpin ( 4-1 ) connections. Many of these meanders exist as isolated units, i.e. no other strands are... 

In effect, our method predicts 6 different secondary structure conformations a-helical, p-sheet, turn, undefined, TMH and TMBS. Only primary structure segments with predicted long uninterrupted stretches of a-helical residues with high maximum preference for helical configuration are considered as candidates for the TMH. Longer P-strands are also predicted and, at least in porins, are never confused with TMH. We have no false positive predictions of TMH in porins, but we do have false positive predictions of TMH in some soluble proteins. 

One letter amino acid codes are used in the second column (AA). Predicted structure (PS) in the third column can be a-helix (H), P-sheet (B) or coil (C) structure that includes turn and undefined structure. Residues predicted in the transmembrane helix configuration (PTM) in the fourth column are labeled with letter NT except for highly probable TMH conformation when letter O is used. Residues with a potential to form transmembrane P-strands are labeled with letter E in the fourth column. The coil (C) conformation from third column is specified as undefined (U) or turn (T) conformation in the fourth column. Fifth to eighth column contain smoothed preferences for a-helix (PH), P-sheet (PB), turn (PT) and undefined (PU) conformation. The columns 9 and 10 contain numerical values for hydrophobic moments calculated in the case of assumed a-helix configuration (MA) and for moments calculated for assumed P-sheet configuration (MB). Last two columns contain PH-PT difference of preferences (H-T) that helps in visual identification of predicted transmembrane helices and PB+MB-2.0 scores that help in prediction of potential membrane-embedded P-strands. 

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