Kyte-Doolittle method

Figure 14. Hydrophobicity analysis of five P-type ATPases according to the Kyte-Doolittle method. A hydrophobicity value between -4.5 and +4.5 is assigned to each type of amino acid residue and mean values are successively calculated along the peptide sequence using a window of 18 residues. Segments corresponding to the transmembrane helices M1-M10 in the structural model in Figure 15 are shaded. Modified from Verma et al., 1988.

The best known and most used procedure is the Kyte-Doolittle method which computes within the sliding window of specific width the hydrophobicity/am-phiphilicity of the segment. This represents a certain probability that the specific segment will or will not be present in the membrane. 

It can be seen from the AflX) profiles shown for several proteins in this report that the profiles in the present version of the PREF method are much clearer than in the earlier version. These profiles are far clearer than those obtained by the Kyte-Doolittle method on the example of cyoe ecoli. ... 

Membrane-bound proteins extend from the cytoplasmic membrane. Analysis by the method of Kyte and Doolittle 186> is quite useful for predicting the protein segments extending into the cytoplasmic membrane. The Kyte and Doolittle method, the so-called hydropathic index method, if it is coupled with the Chou-Fasman method, safely differentiates the protein segment which is located outside the membrane, from the helices within the membrane. The best examples are cytochrome P-450 187), cytochrome b5188), reaction centers 189,190) and light-harvesting protein comple-... 

By using the cross-validation statistical procedure and Kyte-Doolittle hydropathy scale, the prediction results for TMH in the training data base of 63 membrane proteins common to us and to Rost et al. [9] and also to Jones et al. [33] were similar in accuracy by all three methods. When training data base is enlarged to 168 proteins, we maintain the 95% accuracy for predicted transmembrane helices and almost 80% (78.6%) of proteins are predicted with 100% correct transmembrane topology. When 168 proteins are divided in the above mentioned training set of 63 proteins and an independent test set of 105 proteins, all performance parameters for TMH prediction associated with a set of 105 proteins exhibited a decrease which was smaller in our case than for Rost et al. [9]. 

Ten integral membrane proteins of well known structure (BESTP, Methods) have been tested first. Only the Kyte-Doolittle and our modification of the Kyte-Doolittle scale (MODKD, 83) were able to predict all od these ten membrane proteins with 100% correct transmembrane topology, i.e. all transmembrane helices were correctly predicted at their observed sequence locations and there were no overpredicted TMH (Table 7). Only the Chothia buried surface scale (CHOTH, 29) did not recognize one of ten membrane proteins as the membrane protein (the subunit H fi-om the photosynthetic reaction center from R. viridis). Nine long extramembrane helices in these 10 proteins were not predicted as TMH by any of 12 tested amino acid scales. That these sensitive tests of our predictor do not depend on the chosen training procedure was checked by using different training procedures. After... 

Figure 3 Score profiles for cxlbjarde (Figure 3A) and for cox3 parde (Figure 3B) of cytochrome oxidase from Paracoccus denitrificans [14] are obtained by substraction of turn preferences from a-helix preferences (full line). Digital predictions, as outcome of the best training procedure for the SPLIT algorithm with Kyte-Doolittle hydropathy scale (Methods), are shown as bold horizontal bars at the score level 0.5. Observed location of TMH segments are shown as bold horizontal bars at the score level 0.2.

The Kyte-Doolittle scale is used in each case See Methods for performance parameters. 

Kyte, J., Doolittle, R.F. A simple method for displaying the hydropathic character of a protein. /. Mol. Biol. 

The parsing of the transporter sequences into the TM domains shown in Fig. 1A represents the consensus result of three different methods. Average hydrophobicity was calculated with ProperTM using different window sizes and the Kyte and Doolittle scale (7). TMHMM, a hidden Markov model-based approach (8), and PHDHTM, a profile-based neural network method (9), were then utilized to refine the predictions. 

In the method by Schirmer and Cowan (1993), a kind of hydropho-bicity plot like the hydropathy plot of Kyte and Doolittle (1982) is used. The amino acid index representing hydrophobicity is modified to emphasize the effect of aromatic residues. Considering the structural feature of /3 strands, the averaged value of 4 positions (i — 2, i, i + 2, and i + 4 for position i) is taken, and the plot is drawn for both even- and odd-numbered positions. The peaks correspond well to the observed positions of the /3 strands. 

A scale combining hydrophobicity and hydrophilicity of R groups it can be used to measure the tendency of an amino acid to seek an aqueous environment (- values) or a hydrophobic environment (+ values). See Chapter 11. From Kyte, J. Doolittle, R.F (1982) A simple method for displaying the hydropathic character of a protein. J. Mot. Biol. 157, 105-132. 

J Kyte and RF Doolittle (1982) A simpie method for displaying the hydropathic characterof a protein. J Mol Biol 157 105-132... 

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