Chain reversals in proteins

Lewis, Peter N.; Momany, Frank A.; Scheraga, Harold A.

doi:10.1016/0005-2795(73)90350-4

Cited by 679 publications

(470 citation statements)

References 14 publications

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“…The large 3 J~~u coupling constant for T11 (8.7 Hz) and the strong NOE between amide protons of T11 and S12 indicate that residues S9-Sl2 form a type I @-turn. The y-hydroxyproline at position 2 of the turn can be accommodated in a type I turn (Lewis et al, 1973). In addition, the [(&, &), (43, q3)l torsion angles for residues P10 and T11 in the average structure are [(-61", -13"), (-90", -47")], respectively, which is consistent with a type I 0-turn.…”

Section: Three-dimensional Structure Calculationsmentioning

confidence: 54%

“…The conformation of the loop and turn regions of the peptides were identified by the NOE patterns, the J values, and the [(&, &), (43, $3)] torsion angles (Wiithrich, 1986;Lewis et al, 1973) in the 20 final refined structures and the refined average GVIA structure. The large 3 J~~u coupling constant for T11 (8.7 Hz) and the strong NOE between amide protons of T11 and S12 indicate that residues S9-Sl2 form a type I @-turn.…”

Section: Three-dimensional Structure Calculationsmentioning

confidence: 99%

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Solution structure of the calcium channel antagonist ω‐conotoxin GVIA

et al. 1993

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The three-dimensional solution structure is reported for w-conotoxin GVIA, which is a potent inhibitor of presynaptic calcium channels in vertebrate neuromuscular junctions. Structures were generated by a hybrid distance geometry and restrained molecular dynamics approach using interproton distance, torsion angle, and hydrogenbonding constraints derived from 'H NMR data. Conformations of GVIA with low constraint violations converged to a common peptide fold. The secondary structure in the peptide is an antiparallel triple-stranded &sheet containing a &hairpin and three tight turns. The NMR data are consistent with the region of the peptide from residues S9 to C16 being more dynamic than the rest of the peptide. The peptide has an amphiphilic structure with a positively charged hydrophilic side and an opposite side that contains a small hydrophobic region. Residues that are thought to be important in binding and function are located on the hydrophilic face of the peptide.

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Section: Three-dimensional Structure Calculationsmentioning

confidence: 54%

Section: Three-dimensional Structure Calculationsmentioning

confidence: 99%

Solution structure of the calcium channel antagonist ω‐conotoxin GVIA

et al. 1993

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“…The remaining turns were grouped into 7 classes using the @ and $ angles of residues i + 1 and i + 2. These angles were allowed to vary by k30" from the ideal values for each class, with one angle being allowed to deviate by as much as 45" (Lewis et al, 1973). The definitions used for the 4, $ angles of the type VI turns were taken from Richardson et al (1981).…”

Section: Methodsmentioning

confidence: 99%

A revised set of potentials for β‐turn formation in proteins

1994

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Three thousand eight hundred ninety-nine P-turns have been identified and classified using a nonhomologous data set of 205 protein chains. These were used to derive &turn positional potentials for turn types I' and 11' for the first time and to provide updated potentials for formation of the more common types I, 11, and VIII. Many of the sequence preferences for each of the 4 positions in turns can be rationalized in terms of the formation of stabilizing hydrogen bonds, preferences for amino acids to adopt a particular conformation in 4, rC. space, and the involvement of turn types I' and 11' in &hairpins. Only 1,632 (42%) of the turns occur in isolation; the remainder have at least 1 residue in common with another turn and have hence been classified as multiple turns. Several types of multiple turn have been identified and analyzed.

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“…Although they are considered a-helical by DSSP, residues 352-357 are not included in helix TH9 because residues 352-354 are poorly ordered and residues 355-357 d o not form hydrogen bonds with the corresponding i + 4 residues in TH9. Hydrogen bonded turns were classified into standard types (Richardson, 1981;Wilmot & Thornton, 1990) on the basis of their main-chain torsion angles at the i + 1 and i + 2 residues according to the criteria of Lewis et al (1973). In all turns, the hydrogen bond donor and acceptor atoms of the i and i + 3 residues are less than …”

Section: J Bennett Et Almentioning

confidence: 99%

Refined structure of dimeric diphtheria toxin at 2.0 Å resolution

1994

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The refined structure of dimeric diphtheria toxin (DT) at 2.0 A resolution, based on 37,727 unique reflections ( F > l o ( F ) ) , yields a final R factor of 19.5% with a model obeying standard geometry. The refined model consists of 523 amino acid residues, 1 molecule of the bound dinucleotide inhibitor adenylyl 3'-5' uridine 3' monophosphate (ApUp), and 405 well-ordered water molecules. The 2.0-A refined model reveals that the binding motif for ApUp includes residues in the catalytic and receptor-binding domains and is different from the Rossmann dinucleotide-binding fold. ApUp is bound in part by a long loop (residues 34-52) that crosses the active site. Several residues in the active site were previously identified as NAD-binding residues. Glu 148, previously identified as playing a catalytic role in ADP-ribosylation of elongation factor 2 by DT, is about 5 A from uracil in ApUp.The trigger for insertion of the transmembrane domain of DT into the endosomal membrane at low pH may involve 3 intradomain and 4 interdomain salt bridges that will be weakened at low pH by protonation of their acidic residues. The refined model also reveals that each molecule in dimeric DT has an "open" structure unlike most globular proteins, which we call an open monomer. Two open monomers interact by "domain swapping" to form a compact, globular dimeric DT structure. The possibility that the open monomer resembles a membrane insertion intermediate is discussed.Keywords: ADP-ribosyltransferase; diphtheria; membrane insertion Diphtheria toxin (DT) is secreted from toxic strains of the bacterium Corynebacterium diphtheriae. Toxigenic conversion of C. diphtheriae occurs by lysogenization with corynephage 0 (Freeman, 1951), which carries the DT gene encoding a 535-residue protein (M, 58,342) (Uchida et al., 1971; Greenfield et al., 1983). DT kills eukaryotic cells by inactivating an essential component of the protein translation machinery, elongation factor 2 (EF-2) (Collier, 1975).DT is produced as a protomer of 2 fragments connected by a loop containing a proteolysis site and a disulfide bond. Limited proteolysis with trypsin and reduction of the disulfide separates the 2 fragments, which are denoted fragment A and fragment B (Drazin et al., 1971). Fragment A consists of an independent folding domain, the catalytic (C) domain (residues 1-190) (Choe et al., 1992). Fragment B consists of 2 folding domains, the transmembrane (T) domain (residues 191-378) and receptor-binding (R) domain (residues 379-535) (Choe et al., 1992).

show abstract

Chain reversals in proteins

Cited by 679 publications

References 14 publications

Solution structure of the calcium channel antagonist ω‐conotoxin GVIA

Solution structure of the calcium channel antagonist ω‐conotoxin GVIA

A revised set of potentials for β‐turn formation in proteins

Refined structure of dimeric diphtheria toxin at 2.0 Å resolution

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