Kyte-Doolittle hydropathy scale

Uversky and co-workers recently used a pair of sequence attributes, specifically the Kyte-Doolittle hydropathy scale and net charge, to... 

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]. 

The SPLIT algorithm was optimized for predicting transmembrane a-helices by using the Kyte-Doolittle hydropathy scale to create profile of a-helix preferences. The digital version of prediction for transmembrane a-helices is designated as the TMH predictor. Predicted profile of P-strand preferences can be used to find sequence location of potential membrane-embedded or surface-attached P-strands. The score for potential membrane-attached P-strand... 

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.

Two data bases of soluble proteins of known structure used to find false positive prediction results (Table I and Table II). Gaussian parameters needed for evaluation of preference functions based on the Kyte-Doolittle hydropathy scale [17] (Table III). Table with detailed prediction results for transmembrane helices in 168 integral membrane proteins (Table IV). Table with a detailed comparison of prediction results for 10 best known membrane proteins for our and three other algorithms (Table V). All these tables together with the FORTRAN 77 source code are available from the anonymous ftp server mia.os.camet.hr in the /pub/pssp directory. The anonymous login is ftp and the e-mail address is accepted as password. The list of files with short descriptions is contained in the 00index.txt file. 

MODKD Modified Kyte- This work (Table 4) Doolittle hydropathy scale 0 711 95.7 76.8... 

Our algorithm can give partial answer to the question what attributes are optimal predictors for specific folding motifs. Kyte-Doolittle type hydropathy values and Chou-Fasman type conformational preferences are two obvious answers to the question what amino acid attributes are good predictors for majority of transmembrane helices. Indeed, three such scales MODKD, KYTDO and CPREF (Table 4), are on the very top of the list of the best amino acid scales (Table 5). Performance parameters that punish overprediction (A-j y and Qp) give advantage to hydropathy values. Modifications to the Kyte-Doolittle values in the MODKD... 

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.

Hydrophilic and hydrophobic are terms used to denote the relative water-attracting and water-repelling property, respectively, of the side-chain when the amino add is condensed into a polypeptide (see Chapter 5). The term hydropathy index may be used to place the amino acids in order of their hydrophilicity (Kyte and Doolittle, 1985), and their relative positions are shown here on an arbitrary scale. 

---