Recognition of α-helical segments in proteins of known primary structure

Periti, P; Quagliarotti, Giancarlo; Liquori, A. M.

doi:10.1016/0022-2836(67)90336-1

Cited by 43 publications

(10 citation statements)

References 5 publications

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“…The predictive method was also extensively applied to indicate a predominant a-and 0-regions in many of the ribosomal proteins sequenced in Wittmann's laboratory (112)(113)(114)(115)(116)(117)(118)(119)(120)(121)(122)(123)(124)(125). Experimental studies showed a correlation of the helix-forming potential of synthetic ribonuclease S- (1)(2)(3)(4)(5)(6)(7)(8)(9)(10)(11)(12)(13)(14)(15)(16)(17)(18)(19)(20) peptides with binding to the S-protein (126). The helical residue Glu 9 of ribonuclease S-peptide was replaced by Leu and Giy.…”

Section: Prediction Of Other Proteins By T H E Chou-fasman Methodsmentioning

confidence: 99%

“…Prothero (16) classified Ala, Val, Leu, Glu as helix formers and was able to predict five of the six helices in lysozyme correctly. Periti et al (17) utilized helical and antihelical pairs obtained from statistical analysis of myoglobin and hemoglobin in predicting the helices of lysozyme. Low et al (18) followed a conservative approach and used matching helical fragments of known structure to avoid overprediction of helices in proteins.…”

Section: Historical Introductionmentioning

confidence: 99%

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Prediction of the Secondary Structure of Proteins from their Amino Acid Sequence

Chou

Fasman

1979

Advances in Enzymology - And Related Areas of Molecular Biology

1,538

545

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Section: Prediction Of Other Proteins By T H E Chou-fasman Methodsmentioning

confidence: 99%

Section: Historical Introductionmentioning

confidence: 99%

Prediction of the Secondary Structure of Proteins from their Amino Acid Sequence

Chou

Fasman

1979

Advances in Enzymology - And Related Areas of Molecular Biology

1,538

545

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“…When the method was applied to the variable-region subclasses of light, and heavy chains of immunoglobulins, upper limits of about 12 and 17% for the helix contents respectively, were found. This is in general agreement with the results of optical rotatory dispersion and circular dichroism studies, which also indicate little or no a-helix (28).…”

Section: Discussionmentioning

confidence: 99%

“…However, several empirical procedures (7)(8)(9)(10)(11)(12) have been developed to compare amino-acid sequences with identical or similar sequences in proteins of known three-dimensional structure. In a recent paper on the structure of cytochrome c, Dickerson et al (13) remark on the value of such methods and compare the predictions with the structure.…”

mentioning

confidence: 99%

An Attempt to Locate the Non-helical and Permissively Helical Sequences of Proteins: Application to the Variable Regions of Immunoglobulin Light and Heavy Chains

Kabat²

1971

Proc. Natl. Acad. Sci. U.S.A.

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From a consideration of (qO, k6) values of the amino acids of myoglobin, lysozyme, the a and ft chains of horse oxyhemoglobin, tosyl-a-chymotrypsin, and carboxypeptidase A, an empirical procedure of predicting whether amino-acid residues in proteins are in a non-helical or may be in a helical conformation has been developed. The conformation of an amino acid at any position n is considered to be influenced by its nearest neighbors (the amino acids at positions n + 1 and n -1), and the (v,, (n -I)-(n)-(n + 1) taken sequentially for the entire chain was constructed; it lists the number of instances in which helical and non-helical conformations for the amino acids at position n were found. Certain sequences are found to be associated exclusively with non-helical and others exclusively with helical conformations, whereas many sequences may be either helical or non-helical. The distribution of non-helical residues serves to limit stretches of permissively helical regions; these are then further examined by the helical wheel method. As applied to cytochrome c from 18 species, the only permissively helical segment found was the stretch 91-101 near the Cterminus. For the variable regions of three light and three heavy chains of immunoglobulins, upper limits of 12 and 17% a-helix, respectively, were obtained.The prediction of secondary and tertiary structures of protein molecules from their primary sequence has been explored by Scheraga (1) and by Levinthal (2) for ribonuclease and cytochrome c respectively, following the suggestion by Anfinsen and Redfield (3) that the minimum energy state of a peptide chain should determine its folding pattern. Unfortunately, nonbonding interactions between atoms have not been determined with sufficient precision (4), and experimental findings on the structures of ribonuclease (5) and cytochrome c (6) have not substantiated the earlier theoretical predictions.However, several empirical procedures (7-12) have been developed to compare amino-acid sequences with identical or similar sequences in proteins of known three-dimensional structure. In a recent paper on the structure of cytochrome c, Dickerson et al. (13) remark on the value of such methods and compare the predictions with the structure.In this communication we are using the c and ,6 angles (14) of sequences in five known proteins to estimate the probability of any given residue being in a non-helical conformation or of permitting it to be in a helical conformation. 1501The method involves estimating the influence of the nearestneighbor amino acid on the conformation of each residue, location of helix-breaking sequences from a frequency table of helical and non-helical occurrences, and then examining the permissively helical sequences by the helical wheel analysis (10). The procedure, as applied to cytochrome c sequences from 18 species, identified the sole helical segment as 91-101, near the C-terminus. Numerous helix-breaking residues could be seen in ribonuclease, and several helices predicted by others could be e...

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“…Secondary structure predictions have been performed by various methods (Szent-Györgyi & Cohen, 1957;Periti et al, 1967;Ptitsyn, 1969;Pain & Robson, 1970;Robson & Pain, 1971), ever since Pauling suggested that proteins form certain local conformational patterns like helices and strands .…”

Section: Figure 1 Number Of Proteins Whose Structures Are Knownmentioning

confidence: 99%

Regression Analysis to Predict the Secondary Structure of Proteins

Akcesme

2014

scjournal

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A method is presented for protein secondary structure prediction based on the use of multidimensional regression. 200 proteins are chosen from RCSB Protein Database. Their secondary structures obtained through xray crystallography analyses are downloaded from the same source. Primary and secondary structure of proteins are concatenated separately to create a sequence of 169 026 residues. First 150 000 of the amino acid residues and corresponding secondary structures are chosen to create a regression model. The remaining 19 026 residues are used for testing. Since we expect three outputs α-helices "S", β-sheets "H", and coiled coils "C", our regression modes consists of 3 × 20 × 23 parameters. These parameters are tuned and a correct classification rate of 62.50% is achieved on the test data. Furthermore, the performance of the regression model compared with online secondary structure estimation algorithms on 14 unused proteins, and the performance of the regression model is found comparable with the online estimation tools.

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Recognition of α-helical segments in proteins of known primary structure

Cited by 43 publications

References 5 publications

Prediction of the Secondary Structure of Proteins from their Amino Acid Sequence

Prediction of the Secondary Structure of Proteins from their Amino Acid Sequence

An Attempt to Locate the Non-helical and Permissively Helical Sequences of Proteins: Application to the Variable Regions of Immunoglobulin Light and Heavy Chains

Regression Analysis to Predict the Secondary Structure of Proteins

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