Lysine relative hydrophobicity

For assembly of novel three-dimensional (3D) structures, block copolypeptides are required that have structural domains (i.e., amino acid sequences) whose size and composition can be precisely adjusted. Such materials have proven elusive using conventional techniques. Strong base-initiated NCA polymerizations are very fast. These polymerizations are poorly understood and well-defined block copolymers cannot be prepared. Primary amine-initiated NCA polymerizations are also not free of side reactions. Even after fractionation of the crude preparations, the resulting polypeptides are relatively ill-defined, which may complicate unequivocal evaluation of their properties and potential applications. Nevertheless, there are many reports on the preparation of block copolypeptides using conventional primary amine initiators. Examples include many hydrophilic-hydrophobic and hydrophilic-hydrophobic-hydrophilic di- and triblock copolypeptides (where hydrophilic residues were glutamate and lysine, and hydrophobic residues were leucine, valine, isoleucine, phenylalanine, and alanine" ) prepared to study... 

Positive ROA bands in the range 1297-1312 cm-1 are also characteristic of a-helix. These are observed at 1300 cm-1 in human serum albumin (Fig. 4) and at 1297 cm-1 in a-helical poly-L-lysine (Fig. 3). These additional bands appear to be associated with a-helix in a more hydrophobic environment (Barron etal., 2000). The striking absence of a positive ROA band in the range 1297-1312 cm-1 in a-helical poly-L-glutamic acid would then suggest that only the hydrated form of a-helix is present, possibly due to the shorter side chains relative to poly-L-lysine,... 

Further investigations with bimanyl-labeled K-Ras4B peptides demonstrated that relatively small differences in membrane charging (approximately 10 mol %) are sufficient for an electrostatic enrichment in the more negative environment [230]. With the farnesyl group as a hydrophobic anchor, the peptide is still mobile and can swap between vesicles but may find its target membrane with the sensitive surface potential-sensing function of its lysine residues. 

Histone methylation participates in the regulation of gene expression patterns. Unlike histone acetylation, histone methylation does not alter the charge of the amino acid and hence the histone tail. There are changes in the basicity and the hydrophobicity which are relatively small when viewed at the scale of the histone but still influence the affinity of the histone tails to certain proteins, for example transcription factors, which in turn result in certain signaling events. The histone methyltransferases are usually subdivided into three classes SET domain lysine methyltransfeases, nonSET domain lysine methyltransferases and arginine methyltransferases (PRMTs). All of them utilize S-adenosylmethionine (SAM) as cosubstrate for the methylation reaction... 

A more extensive study of mobilities of 3H- and 14C-labeled amino acids again found that amino acids labeled with 14C at Cl or C2 are retained on the column, relative to the unlabeled forms.135 Lysine is an exception. Tritiation at C3 also increases the retention time, but tritiation at C2 of glycine or at C4, C5, or C6 of lysine decreases it, and large decreases are seen with methionine tritium-labeled in the methyl and with tyrosine tritium-labeled at C3, 5. The 14C IEs can be attributed to a decrease of acidity, but the IEs of distant 3H may be due to hydrophobic interactions with the resin. A remarkable result is that intramolecular isotopic isomers (isotopomers) can be distinguished on the basis of their chromatographic mobilities. 

Database searches aimed at identifying related proteins found that the closest structural relative to bacteriocin AS-48 is the effector polypeptide from porcine lymphocytes, NK-lysin.63 Similar to AS-48, this 76-residue protein adopts a globular fold with five helices surrounding a hydrophobic core but lacks a circular backbone.64 Instead, NK-lysin comprises three cross-bracing disulphide bonds that stabilise the structure. Despite the linear backbone of NK-lysin creating differences in the orientation of helix 5 in relation to the one in AS-48, and despite no significant sequence homology between them, the backbone... 

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