Chou-Fasman Method Research Articles

Multi-Output Interval Type-2 Fuzzy Logic System for Protein Secondary Structure Prediction

A new multi-output interval type-2 fuzzy logic system (MOIT2FLS) is introduced for protein secondary structure prediction in this paper. Three outputs of the MOIT2FLS correspond to three structure classes including helix, strand (sheet) and coil. Quantitative properties of amino acids are employed to characterize twenty amino acids rather than the widely used computationally expensive binary encoding scheme. Three clustering tasks are performed using the adaptive vector quantization method to construct an equal number of initial rules for each type of secondary structure. Genetic algorithm is applied to optimally adjust parameters of the MOIT2FLS. The genetic fitness function is designed based on the Q3 measure. Experimental results demonstrate the dominance of the proposed approach against the traditional methods that are Chou-Fasman method, Garnier-Osguthorpe-Robson method, and artificial neural network models.

Analysis of the secondary structure of a protein's N-terminal

The major protein component from aleurone cells of barley (Hordeum vulgare L.), PACB, is related to 7S globulins present in other cereals and to the vicilin-type 7S globulins of legumes and cotton seed. It contains 4 subunits of about 20, 25, 40 and 50 kDa molecular weights. The N-terminal sequence of 16 amino acids (over 260 atoms) in the protein was previously determined, and our aim is the prediction of its secondary structure. The empirical Chou-Fasman method was applied in an improved version as well as the empirical DSC method (discrimination of protein secondary structure class) with quite similar results. A molecular dynamics simulation was also performed, using the FF99SB forcefield within AMBER version 9.0. Solvation effects were incorporated using the Born model. The results are compared and a 3D model is proposed.

Alpha-helix structure of parathyroid hormone fragment (1-34) predicted by Monte Carlo simulated annealing.

Tertiary structure of parathyroid hormone fragment (1-34) is predicted by the Monte Carlo simulated annealing method. Among the 20 structures obtained after completely unbiased calculations, the lowest-energy conformation exhibits two alpha-helices around residues 2-10 and 18-22. This structure agrees with the models, especially with the location of helices, deduced from experiments. In addition, the simulation supports empirical implications in the following two points. (1) The helix near the N-terminus is more stable than the C-terminal one. (2) The rest of the peptide segments are flexible and do not tend to have any definite structure. Our calculation correctly predicts only an alpha-helix, whereas previous analyses by the Chou-Fasman method leave an ambiguity between an alpha-helix and a beta-strand.

Improved Chou-Fasman method for protein secondary structure prediction

BackgroundProtein secondary structure prediction is a fundamental and important component in the analytical study of protein structure and functions. The prediction technique has been developed for several decades. The Chou-Fasman algorithm, one of the earliest methods, has been successfully applied to the prediction. However, this method has its limitations due to low accuracy, unreliable parameters, and over prediction. Thanks to the recent development in protein folding type-specific structure propensities and wavelet transformation, the shortcomings in Chou-Fasman method are able to be overcome.ResultsWe improved Chou-Fasman method in three aspects. (a) Replace the nucleation regions with extreme values of coefficients calculated by the continuous wavelet transform. (b) Substitute the original secondary structure conformational parameters with folding type-specific secondary structure propensities. (c) Modify Chou-Fasman rules. The CB396 data set was tested by using improved Chou-Fasman method and three indices: Q3, Qpre, SOV were used to measure this method. We compared the indices with those obtained from the original Chou-Fasman method and other four popular methods. The results showed that our improved Chou-Fasman method performs better than the original one in all indices, about 10–18% improvement. It is also comparable to other currently popular methods considering all the indices.ConclusionOur method has greatly improved Chou-Fasman method. It is able to predict protein secondary structure as good as current popular methods. By locating nucleation regions with refined wavelet transform technology and by calculating propensity factors with larger size data set, it is likely to get a better result.

Amino Acid Residues Gln4020 and Lys4021 of the Ryanodine Receptor Type 1 Are Required for Activation by 4-Chloro-m-cresol

The ryanodine receptor type 1 (RyR1) and type 2 (RyR2), but not type 3 (RyR3), are efficiently activated by 4-chloro-m-cresol (4-CmC). We previously showed that a 173-amino acid segment of RyR1 (residues 4007-4180) is required for channel activation by 4-CmC (Fessenden, J. D., Perez, C. F., Goth, S., Pessah, I. N., and Allen, P. D. (2003) J. Biol. Chem. 278, 28727-28735). In the present study, we used site-directed mutagenesis to identify individual amino acid(s) within this region that mediate 4-CmC activation. In RyR1, substitution of 11 amino acids conserved between RyR1 and RyR2, but divergent in RyR3, with their RyR3 counterparts reduced 4-CmC sensitivity to the same degree as substitution of the entire 173-amino acid segment. Further analysis of various RyR1 mutants containing successively smaller numbers of these mutations identified 2 amino acid residues (Gln(4020) and Lys(4021)) that, when mutated to their RyR3 counterparts (Leu(3873) and Gln(3874)), abolished 4-CmC activation of RyR1. Mutation of either of these residues alone did not abolish 4-CmC sensitivity, although Q4020L partially reduced 4-CmC-induced Ca(2+) transients. In addition, mutation of the corresponding residues in RyR3 to their RyR1 counterparts (L3873Q/Q3874K) imparted 4-CmC sensitivity to RyR3. Recordings of single RyR1 channels indicated that 4-CmC applied to either the luminal or cytoplasmic side activated the channel with equal potency. Secondary structure modeling in the vicinity of the Gln(4020)-Lys(4021) dipeptide suggests that the region contains a surface-exposed region adjacent to a hydrophobic segment, indicating that both hydrophilic and hydrophobic regions of RyR1 are necessary for 4-CmC binding to the channel and/or to translate allosteric 4-CmC binding into channel activation.

Unreliability of the Chou-Fasman parameters in predicting protein secondary structure.

The Chou-Fasman method has been widely used for predicting protein secondary structure. It is based on knowledge of the potential of amino acid residues to form alpha-helical or beta-sheet regions in proteins. Our main interest in this study was to examine the reliability of these Chou-Fasman parameters. We calculated the Chou-Fasman parameters, with 95% confidence limits, of 144 non-homologous proteins consisting of 155 chains, and a total of 33 118 amino acid residues. All of the protein chains used were X-ray structures known at a resolution of at least 2.5 A. We compared the results of our calculations with those previously done by Chou and Fasman. Our results show that Chou and Fasman classified four amino acid residues wrongly in alpha-helical regions and one in a beta-sheet region. This is so, because the confidence limits we calculated did not include the values determined by Chou and Fasman. Moreover, the confidence limit calculations contradict most of the Chou-Fasman classification of amino acid residues.

Capillary zone electrophoresis studies of motilin peptides: Effects of charge, hydrophobicity, secondary structure and length

Motilin is a gut hormone, which is involved in gastrointestinal motility. Capillary electrophoresis studies were made on 24 peptides that are N-terminal, C-terminal or internal fragments of motilin. The isoelectric point, total charge and hydrophobicity were calculated for all of the peptides. The effects of buffers and pH on migration time and resolution were studied. These included citrate buffer, pH 2.5; phosphate buffer, pH 7.0 and borate buffer, pH 10.0. A capillary zone electrophoresis method was developed to resolve 14 of the motilin peptides. Secondary structure predictions were made using the Chou-Fasman method. Circular dichroism spectra were collected to confirm presence of α-helix in several fragments. Effects of charge, hydrophobicity, secondary structure and length of the motilin fragments on migration time were studied.

Synthetic, immunological and structural studies on repeat unit peptides of Plasmodium falciparum antigens

Using solid phase methodology, we have synthesized five peptides (16-18 residues long) corresponding to repeat sequences of four antigens of a human malarial parasite, Plasmodium falciparum. Three of these antigens (RESA, FIRA, and ABRA) are found in the asexual blood-stages of the parasite, while the remaining one (CSP) is found in the sporozoites. The synthetic peptides, conjugated to bovine serum albumin, elicited high levels of antibodies in rabbits, and these antibodies were found to cross-react with the heterologous peptides. The degree of cross-reactivity, as estimated in an ELISA, was quite remarkable among all the peptides. The peptide corresponding to the RESA tetrapeptide repeat was found to be the most immunogenic and highly cross-reactive. For this reason this tetrapeptide repeat unit, peptide 1, may be a suitable candidate for inclusion in a multiple epitope polypeptide vaccine design. Conformational studies using circular dichroism spectroscopy show that these peptides have similar conformational characteristics with a common feature of approximately 30% and approximately 50% helical content water and TFE respectively. Theoretical predictions regarding conformation using the Chou-Fasman method have also been presented.

Protein secondary structure and homology by neural networks The α-helices in rhodopsin

Neural networks provide a basis for semiempirical studies of pattern matching between the primary and secondary structures of proteins. Networks of the perceptron class have been trained to classify the amino-acid residues into two categories for each of three types of secondary feature: α-helix or not, β-sheet or not, and random coil or not. The explicit prediction for the helices in rhodopsin is compared with both electron microscopy results and those of the Chou-Fasman method. A new measure of homology between proteins is provided by the network approach, which thereby leads to quantification of the differences between the primary structures of proteins.

Examination of the secondary structure of the kringle 4 domain of human plasminogen

The structure of a small region of human plasminogen (F4), consisting of amino acid residues Val 354Ala 439 and containing its kringle 4 (K4) domain (residues Cys 357Cys 434), has been predicted from Chou-Fasman calculations and hydropathy profiles, and compared to circular dichroism (CD) measurements on the isolated fragment. Calculations, by the Chou-Fasman method, of the probabilities of various types of secondary structures that exist in this region reveal that no helical structures are present. Of the total of 86 amino acid residues present in this K4-containing peptide region, 37% can adopt conformations of β-pleated sheets, 48% of the amino acids can exist in β-turns, and 15% of the residues can be present as coils. The structure of F4 in dilute aqueous solution has been experimentally evaluated by CD measurements. At pH = 7.4, in dilute salt solutions, a total of 64% β-structures, 30% β-turns, and 6% coiled structures is estimated to be present in this peptide region. Consideration of the marginal stability of many of the conformational regions of F4, as predicted by Chou-Fasman calculations, suggests that secondary structural flexibility is present in this fragment, which could result in ready adoption of new conformations. The hydropathy profile of F4 has been determined and suggests that this polypeptide is highly hydrophilic, especially in the regions of residues His 387Tyr 396 and Cys 406Lys 413. Thus, it appears as though a large portion of the surface of F4 can be exposed to solvent in its native conformation.

Structural homology of corticotropin-releasing factor, sauvagine, and urotensin I: circular dichroism and prediction studies.

Three recently isolated peptides, whose sequences have been determined--the corticotropin (adrenocorticotropic hormone)-releasing factor of ovine origin, sauvagine, from the skin of the frog Phyllomedusa sauvagei, and urotensin I from the teleost fish, Catostomus commersoni--show high (greater than 50%) sequence homology. CD spectra of the three peptides in trifluoroethanol indicate predominantly helical character for these peptides. Analysis of the secondary structures by the Chou-Fasman method predicts that the overall structural organization of the peptides is the same. All three possess a long internal helix, spanning about 25 residues, connected by a turn region to a COOH-terminal structural element that is an alpha-helix in corticotropin-releasing factor and urotensin I and a beta-sheet in sauvagine. The values for helical content estimated from the prediction method agree reasonably well with those computed from the CD spectra. This agreement as well as the CD spectra of corticotropin-releasing factor fragment 5-33 support the specific assignments of helical regions derived from the Chou-Fasman analysis. The three peptides exhibit significantly less helical structure in water than in trifluoroethanol as indicated by CD spectra. Hydrophilicity profiles provided comparison of the three peptides in terms of their overall hydrophilicity and the location of the regions of maximal hydrophilicity. A unique distribution of hydrophilic and hydrophobic residues within the internal helices is revealed by helical wheel analysis. Patches of both types of residues are formed following a heptad (four/three) rule. Since the two patches are shifted by one residue relative to one another, together they occupy only one face of the helical surface, a feature distinct from other amphiphilic structures.

Blue copper sites and analogous sites in copper-containing oxidases: a structural description

The secondary structure of the C-terminal region of all blue copper proteins can be assigned to two beta strands and a connecting segment that contains a potential histidine ligand. A similar assignment is made for the second probable blue (Type 1 ) site that is located in the middle fragment of ceruloplasmin also. The secondary structure regions for stellacyanin and subunit II of cytochrome oxidase predicted by the Chou-Fasman method are compared to those found in the crystal structures of plastocyanin and azurin.

Assessment of secondary-structure prediction of proteins comparison of computerized chou-fasman method with others

A method predicting protein secondary structure from sequence information could be assessed for its real efficiency by applying it to a number of proteins which lie completely outside a given data set. This type of test is performed for the three methods of Chou and Fasman (Adv. Enzymol. 47 (1978) 45–148), Robson and co-workers (J. Mol. Biol. 120 (1978) 97–120) and Lim (J. Mol. Biol. 88 (1974) 873–894) by using data of 19 proteins for the former two methods and 11 proteins for the method of Lim. The prediction abilities of these methods turn out to be of almost the same level, but unexpectedly low: their average scores are commonly less than 55% measured by the three-state assessment (α, β and coil) or less than 45% measured by the four-state assessment (α, β, turn and coil). This level of accuracy is more than 20% lower than that of current expectations as summarized by Schulz and Schirmer (Principles of Protein Structure (1979) Ch. 6, Springer, New York). A joint prediction attempted with the simultaneous usage of the three prediction methods did not improve the results. Causes and implications of the unsatisfactory results are discussed. In this study, computer programs were prepared for the methods of Chou and Fasman and of Robson and co-workers. While difficulties arose in the course of the computerization of the Chou-Fasman method, the prediction algorithm was arranged in a fully automatic form with optimization of the original rules as well as introduction of a modified treatment for solving the overlap among initially predicted regions of the secondary structures. Large discrepancies observed between the original results and those obtained by the computerized method are examined.

Model for mammalian metallothionein structure.

The results of physicochemical studies of mammalian metallothioneins are summarized and used to propose a model of the protein. The primary structures of all mammalian metallothioneins are very homologous; there are 38 invariant residues and 20 of them are cysteines. The results of UV and CD optical studies indicated that all 20 cysteines are involved in the ligation of 7 mol of metal per mol of metallothionein and that the protein does not contain any alpha-helix structure. A theoretical analysis by the Chou-Fasman method has predicted 11 beta-bends, each one involving at least one cysteine residue. The most significant structural data, provided by 113Cd NMR, demonstrated that the 7 mol of bound Cd2+ are arranged in two separate metal clusters, one containing four metal ions and the other containing three, with all Cd2+ tetrahedrally coordinated to cysteine thiolate ligands. The 11 cysteine residues of the carboxyl-terminal portion of the metallothionein chain (residues 30-61) are ligated to the 4-metal cluster as shown by 113Cd NMR of this enzymatically cleaved fragment. The remaining cysteine residues from the amino-terminal polypeptide portion (residues 1-29) form the 3-metal cluster. Such a division of the chain is consistent with the presence of an intron in the mouse metallothionein-1 gene corresponding to residue 32 in the polypeptide chain. A two-domain molecular model has been constructed based on an analysis of all the available data and is described in detail. The accuracy of this model was tested by 1H NMR at 500 MHz and the data are in agreement with our proposed structure.

A STRUCTURAL APPROACH TO THE COPPER SITES OF THE BLUE ELECTRON TRANSFER PROTEINS

Abstract The copper-binding regions of plastocyanins and azurins are examined by the Chou-Fasman method. Similar structural features are found in the proposed copper-binding site for stellacyanin. These structural features are related to the copper-ligand bond lengths and to the reduction potentials of the blue copper proteins. The range of reduction potentials observed in these proteins is considered to be a function of the chelating peptide loop sizes and of the nature of the amino acid side chains in the loop region. A copper core of two histidines, a cysteine and a methionine is proposed for rusticyanin with a tighter chelate loop structure in the C-terminal region than is found in plastocyanin and azurin.

Phosphoproteins in the parotid saliva from the subhuman primate Macaca fascicularis. Isolation and characterization of a proline-rich phosphoglycoprotein and the complete covalent structure of a proline-rich phosphopeptide.

Parotid saliva from the cynomolgus monkey (Macaca fascicularis) and from pooled human collections displayed the same groups of proteins when fractionated by anion exchange and gel filtration chromatography. We have isolated and characterized a proline-rich phosphoglycoprotein (MPRP) and a proline-rich phosphopeptide (M-statherin) from macaque parotid saliva. MPRP has an apparent molecular weight of 16,900 and displays an unusual chemical composition. It is enriched in proline, glycine, and acidic amino acids, but lacks cysteine, methionine, and tyrosine. MPRP contains 25% (w/w) carbohydrate with 7.0 mol of neutral hexoses, 5.3 mol of galactosamine, 5.9 mol of sialic acid, and 3 mol of phosphorus/mol of protein. M-statherin is a 42-residue phosphopeptide with a high proline, glutamic acid, and tyrosine content, but which lacks threonine, valine, cysteine, methionine, isoleucine, and histidine. The complete covalent structure of M-statherin (Mr = 5,368) is: NH2-Asp-Pse-Pse-Glu-Glu-Lys-Phe-Leu-Arg-Arg-Leu-Arg-Arg-Phe-Asp-Glu-Gly-Arg-Tyr- -Gly-Pro-Tyr-Gln-Pro-Phe-Ala-Pro-Gln-Pro-Leu-Tyr-Pro-Gln-Pro-Tyr-Gln-Pro-Tyr-Gln-Pro-Gln-Tyr-COOH This is the first complete amino acid sequence of a component in the salivary secretion of a subhuman primate. Phosphoserine occurs at residues 2 and 3. All 13 acidic and basic amino acids are located in the NH2-terminal half of the molecule. The carboxyl-terminal half of the molecule is hydrophobic where the tripeptide Tyr-Gln-Pro is repeated three times, the dipeptide Gln-Pro occurs twice, and the tripeptides Tyr-Gly-Pro, Phe-Ala-Pro, and Leu-Tyr-Pro occur once. Evaluation of secondary structure by the Chou-Fasman method predicts an alpha helix in the NH2-terminal half (residue 4-16) and a beta pleated sheet in the carboxyl-terminal half (residues 22-26; 38-42) of the molecule. Both MPRP and M-statherin inhibit spontaneous and seeded precipitation from solutions supersaturated with respect to calcium phosphate salts. This suggests that these macaque compounds may function by maintaining saliva supersaturated with respect to calcium phosphate salts, a necessary requirement for stabilization of hydroxyapatite in the surface layers of teeth.U

Chou-Fasman analysis of the secondary structure of F and Le interferons

The Chou-Fasman method for calculating the secondary structure of F and Le interferons from their amino acid sequences predicts several regions of homologous structure in the two interferons. Those areas tend to be located in the middle and C- terminal ends of the molecules. Total predicted content of α helix is 55% for Le interferon and 36% for F interferon. Predicted β-pleated sheet residues total 33% for F and 16% for Le .

Conformational studies of peptide heart stimulant anthopleurin A. Laser Raman, circular dichroism, fluorescence spectral studies, and Chou-Fasman calculations.

Sea anemone contain a number of closely related peptide heart stimulants. In the present investigation, the conformation of anthropleurin A from Anthopleura xanthogrammica was investigated by laser Raman, circular dichroism, and fluorescence spectral methods and by the Chou-Fasman method using sequence data. The recent 13C NMR data of the peptide (Norton, R.S., and Norton, T.R. (1979) J. Biol. Chem., in press) provided useful information for the interpretation of the above-mentioned spectral data. The results from these spectral methods suggested that anthropleurin A and the related sea anemone peptides are roughly spherical in shape due to the presence of some beta-bends, possibly due to a beta-pleated sheet region and due to the 3 cystine residues in the peptide which exist in the gauche-gauche-gauche configuration. The sole tyrosine residue is exposed to the solvent, a finding which has now been confirmed by 13C NMR. The laser Raman and fluorescence spectral procedures showed that one or more of the tryptophan residues are buried. Interestingly, the reduction of the native protein with dithioerythritol did not change the spherical shape even in the presence of 5 M guanidine HCl and the carboxymethylcysteine derivative of the peptide was folded even in the presence of the denaturing agent, guanidine HCl.