Prediction of β‐sheets in immunoglobulin chains. Comparison of various methods and an expanded 20 × 20 table for evaluation of the effects of nearest‐neighbors on conformations of middle amino acids in proteins

Wu, Tai Te; Szu, Shousun C.; Jernigan, Robert L.; Bilofsky, Howard S.; Kabat, Elvin A.

doi:10.1002/bip.1978.360170303

Cited by 10 publications

(5 citation statements)

References 59 publications

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“…Only the Chou-Fasman procedure predicts a-helix in both loops. Thus the Robson and Chou-Fasman algorithms agree on the presence of two or four turns of a-helix in the region of Tyr-135 in loop 3-4, and the procedure of Wu et al (1978) finds this region from residues 135-142 to be permissively helical. The length of the a-helix predicted in loop 1-2 of the human MBP by the Chou-Fasman algorithm is restricted by the presence of Pro residues at positions 63 and 73.…”

Section: Organization Of the Loop Regions Of Mbpmentioning

confidence: 88%

“…To locate permissively helical regions, helix-breaking residues were identified on the basis of nearest-neighbor effects on residue conformation (Wu et al, 1978). The unified numbering system for MBP amino acid sequences from various species is from Martenson (1981).…”

Section: Secondary Structure Predictionmentioning

confidence: 99%

“…The Lim procedure does not predict any a-helix in the molecule (Martenson, 1981). The procedure of Wu et al (1978), which locates permissively helical regions, identifies two helix-breaking residues in each proposed a-helix (residues Ala-67 and Leu-72 in the first and Asp-134 and Lys-143 in the second). The Robson procedure predicts a-helix in loop 3-4, but not in loop 1-2 in either the human or bovine sequences if DC, = DC, = 0.…”

Section: Organization Of the Loop Regions Of Mbpmentioning

confidence: 99%

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Predicted Folding of β‐Structure in Myelin Basic Protein

Stoner

1984

Journal of Neurochemistry

111

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Predictions of myelin basic protein secondary structure have not previously considered a major role for beta-structure in the organization of the native molecule because optical rotatory dispersion and circular dichroism studies have provided little, if any, evidence for beta-structure, and because a polycationic protein is generally considered to resist folding into a compact structure. However, the Chou-Fasman, Lim, and Robson algorithms identify a total of five beta-strands in the amino acid sequence. Four of these hydrophobic amino acid sequences (37-45, 87-95, 110-118, and 150-158) could form a hairpin intermediate that initiates folding of a Greek-key-type beta-structure. A second fold on the more hydrophobic side, with the addition of a strand from the N-terminus (residues 13-21), would complete the five-stranded antiparallel beta-sheet. A unique strand alignment can be predicted by phasing the hydrophobic residues. The unusual triproline sequence of myelin basic protein (100-102) is enclosed in the 14-residue hairpin loop. If these prolines are in the trans conformation, models show that a reverse turn could occur at residues 102-105 (Pro-Ser-Gln-Gly). Algorithms do not agree on the prediction of alpha-helices, but each of the two large loops could accommodate an alpha-helix. Myelin basic protein is known to be phosphorylated in vivo on as many as five Ser/Thr residues. Phosphorylation might alter the dynamics of folding if the nascent polypeptide were phosphorylated in the cytoplasm. In particular, phosphorylation of Thr-99 could neutralize cationic residues Lys-106 and Arg-108 within the hairpin loop. In addition, the methylation of Arg-108 might stabilize the hairpin loop structure through hydrophobic interaction with the side chain of Pro-97. The cationic side chains of arginine and lysine residues located on the faces of the beta-sheet (Arg-43, Arg-114, Lys-13, Lys-92, Lys-153, and Lys-156) could provide sites for interaction with phospholipids and other anionic structures on the surface of the myelin lipid bilayer.

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Section: Organization Of the Loop Regions Of Mbpmentioning

confidence: 88%

Section: Secondary Structure Predictionmentioning

confidence: 99%

Section: Organization Of the Loop Regions Of Mbpmentioning

confidence: 99%

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Predicted Folding of β‐Structure in Myelin Basic Protein

Stoner

1984

Journal of Neurochemistry

111

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“…These values were computed according to Wu and Kabat31 using the most recent 20 X 20 table based on 19 proteins. 23 Breaking tripeptides are not taken to be contradictory to predictions if, for helix, they occur in the three terminal residues at either end, or if for 0-strand, they appear at either terminal residue.…”

Section: Methodsmentioning

confidence: 97%

Composite predictions of secondary structures of lac repressor

et al. 1979

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SynopsisThe secondary structure of the lac repressor protein proposed by Chou et al. has been modified to include the recent revisions in sequence. In addition to the Chou and Fasman method, five other methods were used; they include those of (1) Lim, (2) Ptitsyn and Finkelstein, (3) Burgess et al., (4) Bunting et al., and (5) Wu and Kabat. Any two individual methods gave results differing sharply from one another. Three or more methods were in agreement for 91,39, and 126 residues in helix, in 0, and in combined coil plus turn conformations, respectively; there were such agreements for a total of 256 of the 360 residues. Agreements in the amino-terminal third of the molecule were found for 68% of the residues, whereas in the remainder of the molecule only 53% of the residues showed such agreements. Only two helix-breaking and two P-breaking tripeptides were inconsistent with the composite predictions by three or more methods. The large number of disagreements among the results for different methods indicates that only very limited information is provided by each method and that the basis on which they operate is not clear. There is no a priori reason for a composite prediction to be more reliable than any individual prediction, and such a procedure does not permit the determination of an unambiguous secondary structure. Since these methods were applied to lac repressor before any three-dimensional crystallographic structure was known, the methods may ultimately be evaluated should such a structure become available.

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“…The VH region sequence is longer by two amino acids than other PC-binding myeloma proteins. X-ray crystallographic 3D structure (35) and sequence-conformation analyses of M603 (36) and T15 have revealed correlations between the light chain sequence and combining site conformations. The M603 combining site for PC has ample room for a polysaccharide backbone, such as C-ps, to approach the combining region; this phenomenon may be extrapolated to the HYPC1613.…”

mentioning

confidence: 99%

Protection against pneumococcal infection in mice conferred by phosphocholine-binding antibodies: specificity of the phosphocholine binding and relation to several types

Szu¹,

Clarke²,

Robbins³

1983

Infect Immun

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Some anti-phosphocholine antibodies protect mice against challenge with certain, but not all, pneumococcal types. We found that both their isotype and reactivity with the cell wall C-polysaccharide of encapsulated pneumococci, as measured by immunodiffusion, were important in predicting the protective activity of anti-phosphocholine antibodies. We propose that the specificity of the protective antibodies includes the backbone of the phosphocholine-containing structure.

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Prediction of β‐sheets in immunoglobulin chains. Comparison of various methods and an expanded 20 × 20 table for evaluation of the effects of nearest‐neighbors on conformations of middle amino acids in proteins

Cited by 10 publications

References 59 publications

Predicted Folding of β‐Structure in Myelin Basic Protein

Predicted Folding of β‐Structure in Myelin Basic Protein

Composite predictions of secondary structures of lac repressor

Protection against pneumococcal infection in mice conferred by phosphocholine-binding antibodies: specificity of the phosphocholine binding and relation to several types

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