Hydrophobic sequences

Singer, S. J., and Yaffe, M. R, 1990. Embedded or not Hydrophobic sequences and membranes. Trends in Biochemical Sciences 15 369-373. 

Rieske proteins are constituents of the be complexes that are hydro-quinone-oxidizing multisubunit membrane proteins. All be complexes, that is, bci complexes in mitochondria and bacteria, b f complexes in chloroplasts, and corresponding complexes in menaquinone-oxidizing bacteria, contain three subunits cytochrome b (cytochrome 6e in b f complexes), cytochrome Ci (cytochrome f in b(,f complexes), and the Rieske iron sulfur protein. Cytochrome 6 is a membrane protein, whereas the Rieske protein, cytochrome Ci, and cytochrome f consist of water-soluble catalytic domains that are bound to cytochrome b through a membrane anchor. In Rieske proteins, the membrane anchor can be identified as an N-terminal hydrophobic sequence (13). 

PelZ is a hydrophilic protein of 420 amino acids with a short hydrophobic sequence at its N-terminal end which has Ae characteristics of the signal sequences of exported proteins. The signal peptide may be 24 amino acids long, which would corroborate wiA the usual length encountered in prokaryotes. The molecular cloning of the pelZ gene in an expression vector pT7-6 allowed for the specific 35S-cysteine-methionine raAo-labelling of PelZ in E. coli K38. We could detect, in crude extracts, the presence of a precursor and a mature form of PelZ. After cell fractionation, Ae mature form of PelZ could be localized in Ae periplasm of E. coli. So PelZ appears to be a protein exported by Ae Sec-dependent system of translocation. 

The association of PDE isozymes with the cell membrane is mediated by a conserved, hydrophobic sequence in the amino terminus of the proteins. This has been most convincingly demonstrated for PDE4A when the amino terminus is removed PDE4A is no longer localized to the membrane fraction. A similar amino terminus sequence is found in the membrane-bound forms of PDE2, and may also mediate the membrane-association of certain PDE3 isozymes. 

Proteins that are destined to be secreted or to end up as transmembrane proteins are synthesized with an N-terminal signal peptide. Signal peptides are highly hydrophobic sequences of variable length. Proteins synthesized with signal peptides are termed preproteins. For example, insulin is a secreted protein. It is therefore synthesized as a preprotein. It is also synthesized in inactive form a proprotein. Insulin as initially synthesized is, in consequence, a preproprotein. 

Histone methylation was first reported in 1964 [118], Core histones H2B, H3, and H4 are modified by methylation (Fig. 1). H3 and H4 are modified at lysines and arginines located primarily in the N-terminal tail. Histone methylation does change the charge of the protein at physiological pH. However, methylation does increase the hydrophobicity of the lysine residue and reduces its ability to form hydrogen bonds [119]. The sites of methylation (Lys-20 in H4 and Lys-27 in H3) are positioned at the boundary between the very basic N-terminal tail domain and the more hydrophobic sequence of the remainder of the molecule. Lys-20 of histone H4 is also in the basic region that binds to nucleosomal DNA [120]. Methylation at these sites may alter nucleosome structure [121,122]. 

Membrane translocation domains have been identified in toxins and viruses and derived from signal sequences of secreted proteins. When derived from a signal seqnence the translocation domain contains hydrophobic sequences [146-148] while the toxin and viral translocation domains contain mostly basic residues [149,150]. 

Phosphohpase Cy and protein tyrosine phosphatase Syp possess an SH2 domain of class 3. Their substrate binding site has mostly hydrophobic character. The substrate is boimd in a stretched form in a flat pit where contacts are formed to a hydrophobic sequence section of the substrate, including 5—6 amino acids on the C-terminal side of the phosphotyrosine residue. 

At all temperatures, asl-CN B and C are insoluble in calcium-containing solutions and form a coarse precipitate at Ca2+ concentrations greater than about 4 mM. asl-CN A, from which the very hydrophobic sequence, residues 13-26, is deleted, is soluble at [Ca2+] up to 0.4 M in the temperature range 1-33°C. Above 33°C, it precipitates but redissolves on cooling to 28°C. The presence of asl-CN A modifies the behaviour of asl-CN B so that an equimolar mixture of the two is soluble in 0.4 M Ca2+ at 1°C asl-CN B precipitates from the mixture at 18°C and both asl-CN A and B precipitate at 33°C. aBl-CN A does not form normal micelles with K-casein. Since asl-CN A occurs at very low frequency, these abnormalities are of little consequence in dairy processing but may become important if the frequency of asl-CN A increases as a result of breeding practices. 

Some membrane proteins span the lipid bilayer several times, with hydrophobic sequences of about 20 amino acid residues forming transmembrane a helices. Detection of such hydrophobic sequences in proteins can be used to predict their secondary structure and transmembrane disposition. Multistranded... 

Another recent trend is to show the importance of hydrophobic profiles rather than molecular hydrophobicity. Giuliani et al. (2002) suggested nonlinear signal analysis methods in the elucidation of protein sequence-structure relationships. The major algorithm used for analyzing hydrophobicity sequences or profiles was recurrence quantification analysis (RQA), in which a recurrence plot depicted a single trajectory as a two-dimensional representation of experimental time-series data. Examples of the global properties used in this... 

The incorporation yields of the stabilizers are always very limited, but the highest value is obtained for the PEO-MA macromonomer, and the lowest for the amphiphilic compound (surfmer) with the longest hydrophobic sequence ca. 0.5% ... 

With the exception of the plantacyanins, phytocyanins are chimeric proteins in their mature forms. They are composed of two structurally distinct sequence motifs, a 100-109-amino acid blue copper domain followed by a domain that varies in length between 30-220 amino acids, lacks any obvious consensus sequence, but resembles heavily glycosylated arabinogalactan proteins (AGP). Where such AGP domains are present, they are followed by a hydrophobic sequence predicted to provide a signal for the attachment of a GPI moiety, which anchors the protein to the cell surface (Figure 2). This cell-surface attachment of phytocyanins... 

Hydrophobic sequences. Including membrane translocating sequences (MTS) (16-18). 

N-terminus of the mature polypeptide and a single hydrophobic sequence, which may be involved in anchoring Cyt/in the thylakoid membrane, is located near the C-terminus. A model of Cyt / with a single membrane-spanning a-helix and the bulk of the polypeptide in the intrathylakoid space has been proposed and tested by partial proteolytic cleavage [105],... 

There is a close homology in the P subunits of EF, CFj (66% of EF, in maize, 67% in spinach) and MFj (72% of EF, in beef heart, 70% in S. cerevisiae). Chloroplast cDNA shows some homology with the gene for e subunit of EFj (23% for maize [36] and 26% in spinach [35]). EFq shows some homology with MFq of S. cerevisiae in both the a and c subunit [66]. All the c subunits of nine species examined (animal, plants, and mesophilic and thermophiUc prokaryotes) have two hydrophobic sequences connected by a central polar sequence [67]. DCCD binds to a Glu (or Asp) residue in the center of the second hydrophobic sequence from the amino terminus [67]. ATPase inhibitory peptides of beef heart [33] and yeast [34] also show some homology. 

D) contain a hydrophobic sequence at the C-terminal end that is embedded in the membrane of secretory vesicles... 

Secretory vesicles bud from the Golgi, and the proteins are secreted from the cell by the process of exocytosis. If the proteins have a hydrophobic sequence that embeds in the membrane, they remain attached and are not secreted. 

Glycoproteins play major roles in antigen-antibody reactions, hormone function, enzyme catalysis, and cell-cell interactions. Membrane glycoproteins have domains of hydrophilic and hydrophobic sequences and are amphi-pathic molecules. The carbohydrate moieties of glycoproteins are distributed asymmetrically in cell membranes, cluster near one end of the protein molecule (Figure 10-7), and constitute a hydrophilic domain of amino acid residues (Chapter 21) as well as carbohydrates. The hydrophobic domain of the molecule interacts with the lipid bilayer. 

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