Peptide nanotubes with filled and empty pores and close-packed structures are formed in closely related pentapeptides. Enantiomorphic sequences, Boc-(D)Pro-Aib-Xxx-Aib-Val-OMe (Xxx = Leu, 1; Val, 2; Ala, 3; Phe, 4) and Boc-Pro-Aib-(D)Xxx-Aib-(D)Val-OMe ((D)Xxx = (D)Leu, 5; (D)Val, 6; (D)Ala, 7; (D)Phe, 8), yield molecular structures with a very similar backbone conformation but varied packing patterns in crystals. Peptides 1, 2, 5, and 6 show tubular structures with the molecules self-assembling along the crystallographic six-fold axis (c-axis) and revealing a honeycomb arrangement laterally (ab plane). Two forms of entrapped water wires have been characterized in 2: 2a with d(O...O) = 2.6 A and 2b with d(O...O) = 3.5 A. The latter is observed in 6 (6a) also. A polymorphic form of 6 (6b), grown from a solution of methanol-water, was observed to crystallize in a monoclinic system as a close-packed structure. Single-file water wire arrangements encapsulated inside hydrophobic channels formed by peptide nanotubes could be established by modeling the published structures in the cases of a cyclic peptide and a dipeptide. In all the entrapped water wires, each water molecule is involved in a hydrogen bond with a previous and succeeding water molecule. The O-H group of the water not involved in any hydrogen bond does not seem to be involved in an energetically significant interaction with the nanotube interior, a general feature of the one-dimensional water wires encapsulated in hydrophobic environments. Water wires in hydrophobic channels are contrasted with the single-file arrangements in amphipathic channels formed by aquaporins.
BackgroundKrishna Tulsi, a member of Lamiaceae family, is a herb well known for its spiritual, religious and medicinal importance in India. The common name of this plant is ‘Tulsi’ (or ‘Tulasi’ or ‘Thulasi’) and is considered sacred by Hindus. We present the draft genome of Ocimum tenuiflurum L (subtype Krishna Tulsi) in this report. The paired-end and mate-pair sequence libraries were generated for the whole genome sequenced with the Illumina Hiseq 1000, resulting in an assembled genome of 374 Mb, with a genome coverage of 61 % (612 Mb estimated genome size). We have also studied transcriptomes (RNA-Seq) of two subtypes of O. tenuiflorum, Krishna and Rama Tulsi and report the relative expression of genes in both the varieties.ResultsThe pathways leading to the production of medicinally-important specialized metabolites have been studied in detail, in relation to similar pathways in Arabidopsis thaliana and other plants. Expression levels of anthocyanin biosynthesis-related genes in leaf samples of Krishna Tulsi were observed to be relatively high, explaining the purple colouration of Krishna Tulsi leaves. The expression of six important genes identified from genome data were validated by performing q-RT-PCR in different tissues of five different species, which shows the high extent of urosolic acid-producing genes in young leaves of the Rama subtype. In addition, the presence of eugenol and ursolic acid, implied as potential drugs in the cure of many diseases including cancer was confirmed using mass spectrometry.ConclusionsThe availability of the whole genome of O.tenuiflorum and our sequence analysis suggests that small amino acid changes at the functional sites of genes involved in metabolite synthesis pathways confer special medicinal properties to this herb.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-015-0562-x) contains supplementary material, which is available to authorized users.
The crystallographic observation of a hydrophobic, empty channel (diameter approximately 5.2 A) in the peptide Boc-(D)Pro-Aib-Leu-Aib-Val-OMe, prompted the investigation of the analog Boc-(D)Pro-Aib-Val-Aib-Val-OMe in which the side chain at position 3 was shortened, resulting in the structure of a channel (diameter approximately 7.5 A) containing a one-dimensional wire of water molecules. Crystallization in the space group P6(5) facilitates formation of a pore lined entirely by hydrocarbon side chains. Two forms of the entrapped water wires, with O...O separations of 3.5 and 2.6 A, are discussed. A lone hydrogen bond between the adjacent pairs of water molecules in the wire, with no strong interactions between the second water hydrogen and the hydrophobic walls of the channel, is a feature of the one-dimensional array. The structure provides the first crystallographic characterization of a water wire in a hydrophobic channel with implications in water and proton transport in membranes and carbon nanotubes.
A one-dimensional water wire has been characterized by X-ray diffraction in single crystals of the tripeptide Ac-Phe-Pro-Trp-OMe. Crystals in the hexagonal space group P6(5) reveal a central hydrophobic channel lined by aromatic residues which entraps an approximately linear array of hydrogen bonded water molecules. The absence of any significant van der Waals contact with the channel walls suggests that the dominant interaction between the "water wire" and "peptide nanotube" is electrostatic in origin. An energy difference of 16 kJ mol(-1) is estimated for the distinct orientations of the water wire dipole with respect to the macrodipole of the peptide nanotube. The structural model suggests that Grotthuss type proton conduction may, through constricted hydrophobic channels, be facilitated by concerted, rotational reorientation of water molecules.
The alpha-aminoisobutyric acid-D-proline (Aib-(D)Pro) dipeptide is an obligatory Type I' beta-turn forming segment that nucleates hairpin formation.
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