Transmembrane INDEX

Figure 12.23 Hydropathy plots for the polypeptide chains L and M of the reaction center of Rhodobacter sphaeroides. A window of 19 amino acids was used with the hydrophohicity scales of Kyte and Doolittle. The hydropathy index is plotted against the tenth amino acid of the window. The positions of the transmembrane helices as found by subsequent x-ray analysis by the group of G. Feher, La Jolla, California, ate indicated by the green regions.

We have developed a common residue numbering scheme that facilitates comparison of the sequences of different NTs. The numbering scheme is informative of the relative position of each amino acid, the amino acid present at that position, and the actual amino acid number in a particular transporter. Each index number starts with the number of the transmembrane segment (TM), e.g., 1 for TM1, and is followed by a number indicating the position relative to a reference residue that is the most conserved position in that TM. That reference residue is arbitrarily assigned the number 50. For exam-... 

The transmembrane arrangement of these subunits of the Cyt b f complex is also evident in the hydropathy index plots determined from the deduced amino acid sequences obtained from the sequencing of the chloroplast-encoded genes of Cyt /, Cyt 6-563, and the 17 kDa protein (cf. Refs. 4 and 16). Cyt/is anchored in the membrane by a single a-helix located close to the C-terminal end (= 20 amino acid residues). Most of the mainly hydrophilic polypeptide chain ( 250 amino acid... 

Fig. 3. A putative transmembrane arrangement of the subunits of the Cyt bif complex using (a) data derived from proteases and antibody labelling [24], and (b) from gene sequences and hydropathy index plots [16],...

Figure 10. Dielectric model of the protein. Within this model, the protein medium (i.e., the medium with the refractive index of n = 1.2) is represented with a set of cylinders. The cross section of these cylinders is shown with white circles. The real location of the transmembrane part of a-helices in PSI are indicated by coiled structures. Chlorophylls are presented as Mg-chlorin rings, lacking the phytyl tail. Chlorophyll Mg atoms are shown in van der Waals representation. See color insert.

Hydropathy plot. The hydropathic index is plotted on they axis, with hydrophobic domains at the top and hydrophilic domains at the bottom. The x axis shows the amino-acid residue number from the amino to the carboxy terminus. The protein shown is a 7-transmembrane receptor (the serotonin receptor), analogous to the epinephrine (adrenalin) receptor. The approximate positions of the seven transmembrane segments are indicated by the purple bars. (Original plot graciously provided by... 

Figure 11.5. Partial output from a PHDtopology prediction. The input sequence is pendrin, which is responsible for Pendred syndrome (Everett et al., 1998). The row labeled aa shows a portion of the input sequence, and the row labeled Rel htm gives the reliability index of prediction at each position of the protein values range from 0 to 9, with 9 representing the maximum possible confidence for the assignment at that position. The last line, labeled PHDThm, contains one of three letters a T represents a transmembrane region, whereas an i or o represents the orientation of the loop with respect to the membrane (inside or outside).

Figure 1.3. Diagrammatic scheme showing the possible folding of the Dj polypeptide through a thylakoid membrane in five transmembrane segments. Numbers refer to the amino acid residues. Based on predictions from hydropathy index plots by Trebst. See also Marder and Barber. ...

For constant flux feed, the fouling index I can be determined from the slope of the linear region in a plot of transmembrane pressure (AF) versus time using Eq. (6.7). The MFI can then be calculated from Eq. (6.8) ... 

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