“Cross-β” conformation in proteins

Geddes, A. J.; Parker, Kate; Atkins, E. D. T.; Beighton, E.

doi:10.1016/0022-2836(68)90014-4

Cited by 405 publications

(298 citation statements)

References 9 publications

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“…The patterns all indicate a short-range repetitive spacing along the fibre axis of 4.51 -4.75 Å, consistent with the expected distance between hydrogenbonded ß-strands. 38,39 Similar values have been found elsewhere for Fmoc-dipeptides, and have been ascribed to either distances between ß-sheets or distances between the Fmoc groups. 32,[40][41][42] The interstrand separation in Å, indicated by the strongest meridional signals, are generally grouped by the identity of the naphthalene group since HNap-AA and H-Nap-AV show a meridional repeat of 4.68 -4.70 Å whilst the peptides containing Br or CN have shorter repeats closer to 4.55 Å (Table S3).…”

Section: Molecular Packing Is Governed By the Naphthalene Moietysupporting

confidence: 78%

Structural determinants in a library of low molecular weight gelators

et al. 2015

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ARTICLELow molecular weight hydrogels are formed by molecules that form a matrix that immobilises water to form a self-supporting gel. Such gels have uses as biomaterials such as molecular scaffolds and structures for tissue engineering. One class of low molecular weight gelators (LMWG), naphthalene-conjugated dipeptides, has been shown to form hydrogels via selfassembly following a controlled drop in pH. A library of naphthalene-dipeptides has been generated previously although the relationship between the precursor sequence and the resulting self-assembled structures remained unclear. Here, we have investigated the structural details of a set of dipeptide sequences containing alanine (A) and valine (V) conjugated to naphthalene groups substituted with a Br, CN or H at the 6-position. Electron microscopy, circular dichroism and X-ray fibre diffraction shows that these LMWG may be structurally classified by their composition: the molecular packing is determined by the class of conjugate, whilst the chirality of the self-assemblies can be attributed to the dipeptide sequence. This provides insights into the relationship between the precursor sequence and the macromolecular and molecular structures of the fibres that make up the resulting hydrogels. IntroductionThe formation of hydrogels from low molecular weight gelators (LMWG) is a useful route to the production of materials for a wide range of applications. 1, 2 A recent expansion in the number of LMWG systems reported has led to a rapid growth in reports of characterisation and applications of a particular class of this type of molecule, namely aromatic conjugated dipeptide LMWG. 3-8 These systems typically consist of a hydrophobic, often aromatic, dipeptide sequences conjugated to Fmoc (9-fluorenylmethoxycarbonyl) 9, 10 or naphthalene 3, 4 ; further conjugations have also been reported. 11,12 Through the use of an environmental cue, 13 such as an enzymatic trigger, 14 temperature, 15,16 or light 12 some of these conjugates selfassemble into anisotropic fibrils that can eventually cause hydrogelation through the immobilisation of water by the fibrillar network. There are now a large number of systems reported in the literature. 17 It is apparent from previous work that two LMWG molecules that differ only by a single amino acid can give rise to hydrogels with dramatically different rheological and phase properties. 3,4,10,18 However, the structural basis for these differences in material properties is not understood.The short-range molecular architecture of some LMWG systems has been studied. For example, the chirality of assembled naphthalene conjugated dipeptides has been reported to correlate to the D-or L-enantiomer of the incorporated amino acids with left-and right-handed assemblies being formed respectively. 3 Other reports have indicated that proteinaceous additives induce changes to the chiral organisation of the self-assembled hydrogelating molecules. 19 In addition to the plethora of molecular hydrogels with varying material properties available, the...

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Section: Molecular Packing Is Governed By the Naphthalene Moietysupporting

confidence: 78%

Structural determinants in a library of low molecular weight gelators

et al. 2015

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“…All of the diffraction patterns show the main features of a "cross-␤" diffraction pattern (44). This type of diffraction pattern, along with evidence from electron microscopy and Congo Red staining, has become one of the main indicators of amyloidtype structures (45).…”

Section: Secondary Structure Of the Peptides In Their Fibrillar Statementioning

confidence: 91%

Amyloid Fibril Formation from Sequences of a Natural β-Structured Fibrous Protein, the Adenovirus Fiber

Papanikolopoulou

Schoehn

Forge

et al. 2005

Journal of Biological Chemistry

112

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Amyloid fibrils are fibrous ␤-structures that derive from abnormal folding and assembly of peptides and proteins. Despite a wealth of structural studies on amyloids, the nature of the amyloid structure remains elusive; possible connections to natural, ␤-structured fibrous motifs have been suggested. In this work we focus on understanding amyloid structure and formation from sequences of a natural, ␤-structured fibrous protein. We show that short peptides (25 to 6 amino acids) corresponding to repetitive sequences from the adenovirus fiber shaft have an intrinsic capacity to form amyloid fibrils as judged by electron microscopy, Congo Red binding, infrared spectroscopy, and x-ray fiber diffraction. In the presence of the globular C-terminal domain of the protein that acts as a trimerization motif, the shaft sequences adopt a triple-stranded, ␤-fibrous motif. We discuss the possible structure and arrangement of these sequences within the amyloid fibril, as compared with the one adopted within the native structure. A 6-amino acid peptide, corresponding to the last ␤-strand of the shaft, was found to be sufficient to form amyloid fibrils. Structural analysis of these amyloid fibrils suggests that perpendicular stacking of ␤-strand repeat units is an underlying common feature of amyloid formation.

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“…The conformation defined by Venkatachalam as type 1, with dihedral angles ~2, ~'2, ~03, and ///3 equal approximately to -60 °, -30 °, -90 °, and 0 ° respectively, is clearly the one adopted by these three peptides. This type of conformation has been referred to as a fl-twist (Urry & Ohnishi, 1970) a fl-fold (Geddes, Parker, Atkins & Beighton, 1968), a 3~0-bend (Dickerson et al, 1971), or a U-fold (Ueki et al, 1971). It has been found in cyclohexaglycyl (Karle & Karle, 1963), lysozyme (Blake, Johnson, Mair, North, Phillips & Sarma, 1967), and other peptides and proteins.…”

Section: Discussionmentioning

confidence: 99%

The crystal structure of S-benzyl-L-cysteinyl-L-prolyl-L-leucylglycinamide and its selenium analog

Rudko¹,

Low²

1975

Acta Crystallogr Sect B

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The crystal structure of the protected C-terminal tetrapeptide fragment of oxytocin, S-benzyl-L-cysteinyl-L-prolyl-L-leucylglycinamide, has been determined, as well as that of the analogous peptide in which sulfur is replaced by selenium. The crystals of both compounds are monoclinic, space group P21. Lattice constants are a= 13.65, b=8.97, c=20.27 A,, fl=93.33 ° for the sulfur peptide and a= 13.71, b = 9.07, c= 20.31A., fl= 94-00 ° for the nearly isomorphous selenium peptide. The selenium analog structure was solved by the heavy-atom method. The atomic parameters so derived were used as a starting point for the refinement of both structures. The least-squares refinement was not straightforward; the selenium peptide would refine to an R value of only 0.21, while the sulfur peptide was finally refined to an R value of 0.085. There are two molecules in the asymmetric unit with very similar conformations and orientations, related by a translation of approximately ¼b+½c. The peptides are in a compact '3L0 bend' conformation with an intramolecular hydrogen bond between the carbonyl oxygen of the cysteinyl residue and the amide nitrogen of the leucyl residue. In one of the molecules in the asymmetric unit there is a second hydrogen bond between the carbonyl oxygen of the prolyl residue and the C-terminal amide nitrogen.

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“Cross-β” conformation in proteins

Cited by 405 publications

References 9 publications

Structural determinants in a library of low molecular weight gelators

Structural determinants in a library of low molecular weight gelators

Amyloid Fibril Formation from Sequences of a Natural β-Structured Fibrous Protein, the Adenovirus Fiber

The crystal structure of S-benzyl-L-cysteinyl-L-prolyl-L-leucylglycinamide and its selenium analog

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