Chou-Fasman method

The most widely used prediction scheme for protein secondary stracture has been, beyond doubt, the Chou-Fasman method (Prevelige and Fasman, 1989 Fasman, 1989 1985 Chou and Fasman, 1974a 1974b 1977 1978 1979). The Chou-Fasman method relies on the calculation of coirformational parameters Pa, PlS and P , which are the ratios... 

Whereas the output space in the Chou-Fasman method is limited to 3 states df, and coil the GOR method utilizes up to 81 states (Gamier, Osguthorpe and Robson, 1978 Gamier and Robson, 1989 Gibrat, Gamier and Robson, 1987). The approaeh uses information theory as its basis and represents protein straetures by residue torsion angels... 

It is difficult to compare quantitatively the GOR method with the Chou-Fasman method since it is implicit that a method operating with a much larger number of output categories will exhibit a lower success rate. The authors of the present paper rather recommend use of more than one scheme for predicting protein secondary stracture. 

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-... 

The most frequently used predictive method for secondary structures was developed by Chou and Fasman. They proposed that an a helix is present where four of six adjacent amino acids are a helix formers and if their average Pa > 1.0 and their P < 1. The a helix continues until a Pro residue is reached or the average P of four consecutive residues is less than 1. A pleated sheet is preferred when three of five consecutive residues are pleated sheet formers, where their average Pp> 1.04 and their Pa < 1. Again, this conformation is continued until the average P of four adjacent residues is less than one. A turn is encountered where four adjacent amino adds are turn formers. The Chou-Fasman method, as well as others, are not perfect, but they do provide a starting point from which... 

For comparison, Huang and co-workers also investigated three other prediction methods (Chou and Fasman, 1978 Gamier et al, 1978 and the PHD method by Rost and Sander, 1994), where the protein was not designated to be fully a helical. In those cases, the secondary structure predictions for H1-H3 were ambiguous. The Chou-Fasman method predicted HI, H2, and H4 to be helical and H3 to adopt (3 structure. The Garnier-Robson method was the same except that H2 was also predicted to be a P strand. Finally, PHD predicted that H3 and H4 were helical and HI and H2 were unknown. Given that H3 and H4 are... 

Discrepancies between retention properties and either summated hydrophobicity or linear hydropathy parameters are expected to become more significant as the molecular size of the solute increases. A number of algorithms are available to predict the secondary structure of peptides and proteins such as the Chou-Fasman [51] method for predicting a-heUx and j8-sheet formation and other procedures [52,53] which determine the probability of heUx formation in a particular solvent environment. These approaches assist in the location of potential hydrophobic areas on the surface of a molecule via characterisation of amphipathic regions. For example, the probability profile shown in Fig. 11 indicates that an amphipathic a-helix can form in the C-terminal region of human )8-endorphin, a peptide which... 

By model building it was found that only a-helix could be constructed, due to steric hindrances introduced by 1-11 and 3-15 disulphide links. The presence of a-helical region in apamin is in accord with CD(IO) and laser Raman spectra(ll), and also with the secondary structure prediction(12) based on the Chou and Fasman method. 

Over 20 different methods have been proposed for predictions of secondary stmcture they can be categorized in two broad classes. The empirical statistical methods use parameters obtained from analyses of known sequences and tertiary stmctures. All such methods are based on the assumption that the local sequence in a short region of the polypeptide chain determines local stmcture as we have seen, this is not a universally valid assumption. The second group of methods is based on stereochemical criteria, such as compactness of form with a tightly packed hydrophobic core and a polar surface. Three frequently used methods are the empirical approaches of P.Y. Chou and G.D. Fasman and of J. Gamier, D.J. Osguthorpe and B. Robson (the GOR method), and third, the stereochemical method of V.l. him. 

Empirical statistical methods that use parameters derived from known 3D structures (Chou and Fasman, 1974). 

Analysis of the CD spectrum has yielded values of 14% a helix and 31 % p strand, with a possible increase in helix content observed with increase of temperature (Loucheaux-Lefebvre et al., 1978). In a more recent study (Ono et al., 1987), a lower fraction of a helix was calculated, but the results vary with the method of calculation. Structure prediction methods have also been applied to this protein and have given results that encourage the view that K-casein has a number of stable conformational features. Loucheaux-Lefebvre et al. (1978) applied the Chou and Fasman (1974) method and predicted an a-helical content of 23%, with 31% P strand and 10% p turns. Raap et al. (1983) preferred the method of Lim (1974) to predict a-helix and P-strand content, because the method of Chou and Fasman, as published in 1974, was considered to overpredict these elements (Lenstra, 1977). They also tested their predictions for the structure about the chymosin-sensitive bond using the later boundary analysis method... 

A software package called MultPred (Multiple Predictions) was developed in C++ language and implements all but C F (Chou and Fasman, 1974) and GGR (Gibrat et al., 1987) methods which were taken from the program ANTHEPROT (Deleage and Roux. 1989). 

Wootton 43a) has used the method of Chou and Fasman 43h) to predict secondary structural elements of Neurospora and beef GluDH. By combining the anticipated sequence of sheets and helices in a dinucleotide binding domain with the requirement for such functional residues as are shown in Table IV, he was able to predict the position of two such domains within the polypeptide chain. One of these corresponds to the prediction of Rossmann et al. 28). 

The first step in this procedure requires the secondary structural elements to be predicted. In other words, each amino acid must be assigned to one of three classes a-helix, / -strand or coil (i.e. neither helix nor strand) Some approaches also predict whether an amino acid is present in a turn structure. One of the first methods for secondary structure prediction was devised by Chou and Fasman [Chou and Fasman 1978]. Theirs is a statistical method, based upon the observed propensity of each of the 20 amino acids to exist as a-helix, / -strand and coil. These propensities were originaUy determined by analysing 15 protein X-ray structures. The fractional occurrence of each amino acid in each of these three states was calculated, as was the fractional occurrence of the amino acid over all 15 structures. The propensity of that residue for a given t3rpe of secondary structure then equals the ratio of these two values. Each residue was also classified according to its propensity to act as an initiator or as a breaker of a-helices and /3-strands. To predict the secondary structure, the amino acid sequence is searched for potential a-helix or /3-strand initiating... 

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