Hydrophobicity plots

Hydrophobicity plots of AQPs indicated that these proteins consist of six transmembrane a-helices (Hl-H6 in Fig. la) connected by five connecting loops (A-E), and flanked by cytosolic N- and C-termini. The second half of the molecule is an evolutionary duplicate and inverse orientation of the first half of the molecule. Loops B and E of the channel bend into the membrane with an a-helical conformation (HB, HE in Fig. lb) and meet and each other at their so-called Asn-Pro-Ala (NPA) boxes. These NPA motifs are the hallmark of AQPs and form the actual selective pore of the channel, as at this location, the diameter is of that of a water molecule (3 A Fig. la and b). Based on the narrowing of the channel from both membrane sides to this small... 

Several methods exist for predicting the secondary stmcture of proteins. These methods are often applied in nnison with hydrophobicity plots with the purpose of identifying stractural features of importance for the interpretation and srrbsequent modification of the protein stmcture. Urrfortrrrrately, none of them are very accrrrate, but certain important features can often be deducted from such predictiorrs. In... 

Hydrophobicity plot for the transmembrane protein opsin. Note the peaks in hydrophobicity which roughly denote the putative membrane spanning regions. 

Figure 10.16 Hydrophobicity plot for the bacteriorhodopsin molecule depicted in Figure 10.15. 

Figure 3.11. Top. Single-residue hydrophobicity average) for proinsulin. The T,-based hydrophobicity plot of porcine proinsulin. At each residue position scale is derived in Chapter 5 and utilized in Chapters the hydrophobicity of the residue is given as derived 7 and 8 to understand the hydrophobic associations from the T,-based hydrophobicity scale. Bottom, attending function for selected protein systems. Mean residue hydrophobicity plot (11-residue...

Insights into Association of Chains from the Single Residue T,-based Hydrophobicity Plots... 

Figure 7.2. Single residue hydrophobicity plots for the a- and P-chains of hemoglobin and for myoglobin. Note the marked decrease in polar residues (the negative deflections) in the plots for the a- and p-...

Hydrophobic Interfaces Between Subunits Identified by Mean Residue Hydrophobicity Plots... 

Mean Residue Hydrophobicity Plots for the Hemoglobin a- And P-Chains and for Myoglobin... 

Figure 7.9 provides a comparison of the T,-based mean residue hydrophobicity plots of the a- and P-chains and myoglobin as a function of... 

Formation of a blood clot involves a complex cascade of enzymatically controlled reactions the penultimate step of which is the formation of thrombin. Thrombin then cleaves peptides from fibrinogen to form fibrin monomers that associate to form the fibrin clot. Fibrin clot formation is a carefully poised process whereby a relatively minor injury will not allow excessive bleeding and result in death and whereby excessive clot formation will not block blood flow and result in death. As will be seen by examination of the relevant molecular structures, regardless of the balance struck, the key process of clot formation is the hydrophobic association of fibrin monomers. In demonstrating this perspective, the same T,-based mean residue hydrophobicity plot will be used as was used above in Figure 7.9 for understanding the hydrophobic association of hemoglobin subunits. 

Trbased Hydrophobicity Plots of Human Fibrinogen Chains... 

Figure 7.29. Single residue (A) and mean residue (B) hydrophobicity plots of human y-fibrinogen. The most striking feature of the mean residue plot is the hydrophobic sequence, residues 337 to 379, experimentally shown to provide the Ea site for interaction with the a-chain amino-terminus on removal of the A peptide and exposure of GPRP and its surrounding hydrophobic residues for association with the hydrophobic domain of the Ea site shown in Figure...

The mean residue hydrophobicity plot of BP-fibrinogen in Figure 7.30B exhibits two minor hydrophobic sequences near residues 115 and 375 that could serve hydrophobic folding and assembly within the fibrinogen molecule, but would be less likely to participate in the hydrophobic association between molecules. 

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