Protein residue sheets

Preparation of Protein Residue Sheets. Individual abdomen stratum corneum sheets were placed in 20 ml 1 2 0.8 chloroform methan-ol water and agitated lightly continually for 24 hours. The solution was then removed and replaced daily with methanol. Stratum corneum sheets were extracted for a total of two, four, seven or thirteen days. The extracted protein residue sheets were placed on Teflon sheets and dried in a vacuum oven (10- Torr, 25°C) for eight hours and then stored under vacuum. 

Calorimetric results for the hairless mouse stratum corneum and isolated components confirmed thermal transitions associated with increased mobility occurred in the temperature region where large increases in permeability of lipophilic components also occurred. Thermal transitions for the extracted lipids were in the 27 to 67°C range, while the protein residue sheets (primarily... 

Ethanol and methanol have been used to swell other types of keratinized protein without loss of the a-helieal structure in the presence or after removal of the alcohols (46). Polar lipids such as the ceramides or sphingolipids are soluble in methanol (47). Therefore, extensive extraction periods in methanol could have provided sufficient time to swell the keratinized protein and allow the highly polar lipids entrapped within the protein fibrils to diffuse from the stratum corneum sheet. The resultant protein residue sheets retained the a-keratin conformation throughout the extensive extraction process. 

Differential scanning calorimetric and infrared spectroscopic investigations of intact stratum corneum, extracted lipids and keratinized protein residue sheets suggested the thermal transitions occurring within the 30 to 70°C region were associated with increased molecular mobility of the lipids. The permeability coefficients of lipophilic molecules through hairless mouse skin increased by several orders of magnitude over the same temperature... 

HELIX, SHEET, TURN, CISPEP, and SITE lines, listing the elements of secondary structure in the protein, residues involved in cis-peptide bonds (almost always involving proline as the second residue), and residues in the active site of the protein. 

The p Sheet Another type of secondary structure, the p sheet, consists of laterally packed p strands. Each p strand is a short (5- to 8-residue), nearly fully extended polypeptide segment. Hydrogen bonding between backbone atoms in adjacent p strands, within either the same polypeptide chain or between different polypeptide chains, forms a p sheet (Figure 3-4a). The planarity of the peptide bond forces a p sheet to be pleated hence this structure is also called a 3 pleated sheet, or simply a pleated sheet. Like a helices, p strands have a directionality defined by the orientation of the peptide bond. Therefore, in a pleated sheet, adjacent p strands can be oriented in the same (parallel) or opposite (antiparallel) directions with respect to each other. In both arrangements, the side chains project from both faces of the sheet (Figure 3-4b). In some proteins, p sheets form the floor of a binding pocket the hydrophobic core of other proteins contains multiple P sheets. 

Fig. C5.9 One of the two most common secondary structures of protein /3-sheet. It is stabilized by hydrogen bonds between atoms of the main polypeptide chain, not involving the aminoacid residues side groups, which extend above and below the sheet. As in case of a-helix, only the least bulky amino acid residues, glycine and alanine, are used for this...

Fig. 2. Protein secondary stmcture (a) the right-handed a-helix, stabilized by intrasegmental hydrogen-bonding between the backbone CO of residue i and the NH of residue t + 4 along the polypeptide chain. Each turn of the helix requires 3.6 residues. Translation along the hehcal axis is 0.15 nm per residue, or 0.54 nm per turn and (b) the -pleated sheet where the polypeptide is in an extended conformation and backbone hydrogen-bonding occurs between residues on adjacent strands. Here, the backbone CO and NH atoms are in the plane of the page and the amino acid side chains extend from C ...

Fig. 1. The two principal elements of secondary stmcture in proteins, (a) The a-helix stabilized by hydrogen bonds between the backbone of residue i and i + 4. There are 3.6 residues per turn of helix and an axial translation of 150 pm per residue. represents the carbon connected to the amino acid side chain, R. (b) The P sheet showing the hydrogen bonding pattern between neighboring extended -strands. Successive residues along the chain point...

Attempts have also been made at predicting the secondary stmcture of proteins from the propensities for residues to occur in the a-helix or the P-sheet (23). However, the assignment of secondary stmcture for a residue only has an average accuracy of about 60%. A better success rate (70%) is achieved when multiple-aligned sequences having high sequence similarity are available. 

An off-lattice minimalist model that has been extensively studied is the 46-mer (3-barrel model, which has a native state characterized by a four-stranded (3-barrel. The first to introduce this model were Honeycutt and Thirumalai [38], who used a three-letter code to describe the residues. In this model monomers are labeled hydrophobic (H), hydrophilic (P), or neutral (N) and the sequence that was studied is (H)9(N)3(PH)4(N)3(H)9(N)3(PH)5P. That is, two strands are hydrophobic (residues 1-9 and 24-32) and the other two strands contain alternating H and P beads (residues 12-20 and 36-46). The four strands are connected by neutral three-residue bends. Figure 3 depicts the global minimum confonnation of the 46-mer (3-barrel model. This (3-barrel model was studied by several researchers [38-41], and additional off-lattice minimalist models of a-helical [42] and (3-sheet proteins [43] were also investigated. 

The basic structural unit of these two-sheet p helix structures contains 18 amino acids, three in each p strand and six in each loop. A specific amino acid sequence pattern identifies this unit namely a double repeat of a nine-residue consensus sequence Gly-Gly-X-Gly-X-Asp-X-U-X where X is any amino acid and U is large, hydrophobic and frequently leucine. The first six residues form the loop and the last three form a p strand with the side chain of U involved in the hydrophobic packing of the two p sheets. The loops are stabilized by calcium ions which bind to the Asp residue (Figure S.28). This sequence pattern can be used to search for possible two-sheet p structures in databases of amino acid sequences of proteins of unknown structure. 

A more complex p helix is present in pectate lyase and the bacteriophage P22 tailspike protein. In these p helices each turn of the helix contains three short p strands, each with three to five residues, connected by loop regions. The p helix therefore comprises three parallel p sheets roughly arranged as the three sides of a prism. However, the cross-section of the p helix is not quite triangular because of the arrangement of the p sheets. Two of the sheets are... 

The thioredoxin domain (see Figure 2.7) has a central (3 sheet surrounded by a helices. The active part of the molecule is a Pa(3 unit comprising p strands 2 and 3 joined by a helix 2. The redox-active disulfide bridge is at the amino end of this a helix and is formed by a Cys-X-X-Cys motif where X is any residue in DsbA, in thioredoxin, and in other members of this family of redox-active proteins. The a-helical domain of DsbA is positioned so that this disulfide bridge is at the center of a relatively extensive hydrophobic protein surface. Since disulfide bonds in proteins are usually buried in a hydrophobic environment, this hydrophobic surface in DsbA could provide an interaction area for exposed hydrophobic patches on partially folded protein substrates. 

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