Involvement of side functions in peptide structures: the Asx turn. Occurrence and conformational aspects

Abbadi, A.; Mcharfi, Mohammed; Aubry, A.; Premilat, S.; Boussard, Guy; Marraud, Michel

doi:10.1021/ja00007a056

Cited by 84 publications

(76 citation statements)

References 7 publications

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“…The peptide backbone was shown to adopt a special Asx-turn conformation (Abbadi et al, 1991;Imperiali et al, 1992). Some of these conformations fall in the speci®ed clustering region.…”

Section: Resultsmentioning

confidence: 99%

A database analysis of potential glycosylating Asn-X-Ser/Thr consensus sequences

Christlet

Biswas

Veluraja

1999

Acta Crystallogr D Biol Cryst

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An analysis of the frequency of occurrence of various residues at position X was carried out on the consensus glycosylating sequence Asn-X-Ser/Thr using the PDB three-dimensional database. 488 non-homologous proteins bearing 696 Asn-X-Ser/Thr (X T Pro) sequences were analysed. More than 65% of Asn residues, when they occur as part of the consensus sequence, lie on the surface of the protein, implying a potentiality for glycosylation. A deviation parameter (DP) was calculated as a measure of preferential (positive) or nonpreferential (negative) selection. At the X position in the consensus-sequence segment, the amino acids Gly, Asn and Phe have statistically signi®cant positive DP values. The high value of DP for Asn is a consequence of the preferential occurrence of homodoublets, while for Phe it may be a consequence of the stacking interaction of the aromatic ring with the glycan. Gly at the X position in the consensus glycosylating sequence may be functionally signi®cant owing to its preference and its high percentage of occurrence in proteins. The Ramachandran (È,É) angles around Gly in the consensus sequence show clustering in the region which is disallowed for non-glycyl residues. In this region, a hydrogen bond between the side chain of Asn and the peptide backbone/side chain of Ser/Thr is possible, re¯ecting a positional as well as a conformational role in the consensus glycosylating sequence. For the 44 con®rmed N-glycosylating sequences, an in-depth analysis of the (É N , È X , É X , È S/T ) dihedral angles, which position the side chains of Asn and Ser/Thr, shows that these can be grouped into nine conformational states. In most cases, a direct or watermediated hydrogen bond between OD1 of Asn and OG of Ser/Thr is possible, re¯ecting the possible importance of this hydrogen bonding in the glycosylation process.

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“…The peptide backbone was shown to adopt a special Asx-turn conformation (Abbadi et al, 1991;Imperiali et al, 1992). Some of these conformations fall in the speci®ed clustering region.…”

Section: Resultsmentioning

confidence: 99%

A database analysis of potential glycosylating Asn-X-Ser/Thr consensus sequences

Christlet

Biswas

Veluraja

1999

Acta Crystallogr D Biol Cryst

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“…Residues C5-Y10 and C38-A43 form a series of Types-I, -11, and -111 NH-S tight turns, and residues D13-G17, D18-G22, K28-L32, and P44-F48 are folded to form four 310-helical corners. In addition, the side chain of Dl3 appears to be hydrogen bonded to the amide of D15, forming an Asx turn (Richardson, 1981;Rees et al, 1983;Abbadi et al, 1991), and residues P25"27 and P33-W36 form Types-I and -11 @-turns, respectively. The hydrophobic side chains of residues W3, Y10, Y 12,123, F29, L32, W36, and F48 contribute to the hydrophobic core of the protein, with apparent stacking of the six-membered aromatic rings of Trp 3 and Phe 29 ( Fig.…”

Section: Description Of the Folding And Comparison With C Pasteurianmentioning

confidence: 99%

Solution‐state structure by NMR of zinc‐substituted rubredoxin from the marine hyperthermophilic archaebacterium pyrococcus furiosus

et al. 1992

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The three-dimensional solution-state structure is reported for the zinc-substituted form of rubredoxin (Rd) from the marine hyperthermophilic archaebacterium Pyrococcus furiosus, an organism that grows optimally at 100 " c . Structures were generated with DSPACEB by a hybrid distance geometry (DG)-based simulated annealing (SA) approach that employed 403 nuclear Overhauser effect (N0E)-derived interproton distance restraints, including 67 interresidue, 124 sequential ( i -j = I), 75 medium-range ( i -j = 2-5), and 137 long-range ( i -j > 5) restraints.All lower interproton distance bounds were set at the sum of the van Der Waals radii (1.8 A), and upper bounds of 2.7 A, 3.3 A, and 5.0 A were employed to represent qualitatively observed strong, medium, and weak NOE cross peak intensities, respectively. Twenty-three backbone-backbone, six backbone-sulfur (Cys), two backboneside chain, and two side chain-side chain hydrogen bond restraints were include for structure refinement, yielding a total of 436 nonbonded restraints, which averages to >16 restraints per residue. A total of 10 structures generated from random atom positions and 30 structures generated by molecular replacement using the backbone coordinates of Clostridiumpusteuriunum Rd converged to a common conformation, with the average penalty (= sum of the square of the distance bounds violations; +standard deviation) of 0.024 f 0.003 A 2 and a maximum total penalty of 0.035 A*. Superposition of the backbone atoms (C, Ca, N) of residues A1-L51 for all 40 structures afforded an average pairwise root mean square (rms) deviation value (fSD) of 0.42 f 0.07 A. Superposition of all heavy atoms for residues AI-L51, including those of structurally undefined external side chains, afforded an average pairwise rms deviation of 0.72 k 0.08 A . Qualitative comparison of back-calculated and experimental two-dimensional NOESY spectra indicate that the DG/SA structures are consistent with the experimental spectra. The global folding of P. furiosus Zn(Rd) is remarkably similar to the folding observed by X-ray crystallography for native Rd from the mesophilic organism C. pusteuriunum, with the average rms deviation value for backbone atoms of residues Al-LSI of P. furiosus Zn(Rd) superposed with respect to residues K2-V52 of C. pusteuriunum Rd of 0.77 +_ 0.06 A. The conformations of aromatic residues that compose the hydrophobic cores of the two proteins are also similar. However, P. furiosus Rd contains several unique structural elements, including at least four additional hydrogen bonds and three potential electrostatic interactions. Four of these interactions involve the nonconservatively substituted Glu 14, Ala 1, and Trp 3 residues. The combined findings are consistent with the proposal that stabilization of the N-terminal residues inhibits the &sheet from "unzipping" at elevated temperatures (Blake, P.R., Park, J.-B., Bryant, EO., et al., 1991, Biochemistry30, 10885-10895). In view of the high structural similarities between this hyperthermophilic protein and C...

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“…The capital conformational perturbation induced by the AzAsx/Asx substitution results in the absence of any type of Asx-turn in the two azadipeptides I and II, contrary to the cognate dipeptides [7], Where an intramolecular hydrogen bond between the side chain acceptor CvO v (j) and the backbone donor NH(j+2) stabilizes the Asxturn disposition. Furthermore, the presence of the AzAsx residue in position i+l does not prevent [3-turn formation, even in the rather unfavorable case where proline occupies the i+2 position.…”

Section: Discussionmentioning

confidence: 98%

Synthesis and conformational analysis of AzAsx-containing oligopeptides

et al. 1995

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For the sake of improving synthetic methods and evaluating the conformational perturbation induced by the substitution of AzAsx for the Asx residue in the cognate dipeptide R-CO-Asx-Pro-NHR', we prepared the AzAsxdipeptide sequence by making use of the crystalline triphosgene. This reagent allows, in situ and under very mild experimental conditions, both the carbonylation and the activation of the properly substituted and N-protected hydrazine before coupling with the proline partner. With regard to conformational behaviour, the azadipeptide sequence displays a 13-fold, unlike the cognate dipeptide which adopts an Asx-turn.

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Involvement of side functions in peptide structures: the Asx turn. Occurrence and conformational aspects

Cited by 84 publications

References 7 publications

A database analysis of potential glycosylating Asn-X-Ser/Thr consensus sequences

A database analysis of potential glycosylating Asn-X-Ser/Thr consensus sequences

Solution‐state structure by NMR of zinc‐substituted rubredoxin from the marine hyperthermophilic archaebacterium pyrococcus furiosus

Synthesis and conformational analysis of AzAsx-containing oligopeptides

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