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Abstract
An analysis of protein structures indicates the existence of a novel, fused five-membered rings motif, comprising of two residues (i and i + 1), stabilized by interresidue Ni+1–H∙∙∙Ni and intraresidue Ni+1–H∙∙∙O=Ci+1 hydrogen bonds. Fused-rings geometry is the common thread running through many commonly occurring motifs, such as β-turn, β-bulge, Asx-turn, Ser/Thr-turn, Schellman motif, and points to its structural robustness. A location close to the beginning of a β-strand is rather common for the motif. Devoid of side chain, Gly seems to be a key player in this motif, occurring at i, for which the backbone torsion angles cluster at ~(−90°, −10°) and (70°, 20°). The fused-rings structures, distant from each other in sequence, can hydrogen bond with each other, and the two segments aligned to each other in a parallel fashion, give rise to a novel secondary structure, topi, which is quite common in proteins, distinct from two major secondary structures, α-helix and β-sheet. Majority of the peptide segments making topi are identified as aggregation-prone and the residues tend to be conserved among homologous proteins.
Highlights
An analysis of protein structures indicates the existence of a novel, fused five-membered rings motif, comprising of two residues (i and i + 1), stabilized by interresidue Ni+1–H∙∙∙Ni and intraresidue Ni+1– H∙∙∙O=Ci+1 hydrogen bonds
The N–H∙∙∙O angle in the motif deviates considerably from linearity the evidence for the occurrence of the intra-residue hydrogen bond has come from FT-IR and NMR experimental data acquired on a number of peptides containing non-proteinogenic, Cα,α-disubsituted Gly residues, and from the fact that in many of the crystal structures the internal N–H donors and C=O acceptors do not participate in any competing intermolecular hydrogen bonds[15]
As the hydrogen bond involves the pz orbital of the acceptor it is designated as N–H∙∙∙N(pz) interactions and appears to be very common in protein structures (Table 1)
Summary
An analysis of protein structures indicates the existence of a novel, fused five-membered rings motif, comprising of two residues (i and i + 1), stabilized by interresidue Ni+1–H∙∙∙Ni and intraresidue Ni+1– H∙∙∙O=Ci+1 hydrogen bonds. C–H∙∙∙O interaction seen in peptide structures[6] has been found to be of common occurrence in proteins leading to the identification of ω-turn, a new type of β-turn mimic[7] Both conventional and non-conventional hydrogen bonds, such as C–H∙∙∙πinteractions, seen in small molecule crystals are important for the structure and function of protein molecules[8,9]. The N–H group is associated with another conventional hydrogen bond (Fig. 1a) Another two-residue motif is the basic unit of 2.05-helix[11], which has the backbone in the fully-extended conformation (φ, ψboth ≈ 180°). The results have implications for protein folding problem as it is seen that the two fused-rings motifs, distant in sequence along the protein, can recognize and interact with each other giving rise to structure with distinct topology
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