Vibrational spectroscopic studies of L,D‐alternating phenylalanine peptides

Naik, V. M.

doi:10.1111/j.1399-3011.1993.tb00488.x

Cited by 10 publications

(3 citation statements)

References 30 publications

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“…However, when they studied the normal modes of gramicidin A, the 3D structure had not been determined yet and they assumed it to be a left-handed b-helix conformation instead of the correct right-handed b-helix. Naik and Krimm [27][28][29] have also reported on vibrational analyses of gramicidin A and other D,Lalternating polypeptides. However, their studies mainly focused on amide vibration at high frequencies (600 -1700 cm 21 ) that may not be directly relevant to channel functions.…”

Section: Introductionmentioning

confidence: 93%

Dynamic structure of the polytheonamide B channel studied by normal mode analysis

Mori

Kokubo

Oiki

et al. 2011

Molecular Simulation

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Polytheonamide B is a linear 48-residue peptide with alternating D-and L-amino acids. It forms a single b 6.3 -helix structure and acts as a cation-selective ion channel. We performed normal mode analysis to investigate the dynamical properties of the polytheonamide B channel. We calculated root-mean-square (RMS) displacements of all backbone atoms, RMS fluctuations of the backbone dihedral angles f and c, and correlation factors for the C a atom and for dihedral angle fluctuations. The analysis revealed that polytheonamide B has elastic rod properties in very low-frequency modes and that the librational motions of backbone amide planes have the modes with relatively low frequencies, which is relevant to the function of polytheonamide B. The librational motions occur almost independently and are weakly anti-correlated with those of the neighbouring hydrogen-bonded amide planes. Backbone fluctuations show that polytheonamide B is roughly uniformly flexible over the entire helix. We also compared our results with those of gramicidin A, an analogue of polytheonamide B and found some common features in the dynamics of the 'channel wall'. It was suggested that polytheonamide B utilises similar mechanisms to gramicidin A for conducting cations across the membrane.

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Section: Introductionmentioning

confidence: 93%

Dynamic structure of the polytheonamide B channel studied by normal mode analysis

Mori

Kokubo

Oiki

et al. 2011

Molecular Simulation

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“…Pongamia crude oils have many properties for different applications. For example, the properties of raw pongamia oil have been used in agriculture, especially for bioinsecticides, pharmaceutical products, and raw materials for the synthesis of fatty acid methyl esters [8,[15][16][17].…”

Section: Methyl Of Palmitoleate and Lenoleate Compoundmentioning

confidence: 99%

“…Analysis of methyl compounds in crude P. pinnata oil, referred to as Pongamia oil, is therefore important to support its use as biodiesel. Several studies analyzing constituents of Pongamia crude oil have been reported [10,[16][17]. To complete the baseline information of P. pinnata as biodiesel, this study was conducted.…”

Section: Introductionmentioning

confidence: 99%

Analysis of methyl compounds variation in the crude Pongamia pinnata oil from Banten, West Java and North Java populations

Jayusman

Hakim

Dalimunthe

et al. 2022

IOP Conf. Ser.: Earth Environ. Sci.

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Identification of methyl compounds from crude oil is an important baseline provenance to support the development of renewable bioenergy resources in Indonesia. Pongamia pinnata, known as Malapari, has great potential to be an alternative to renewable bioenergy resources and an environmentally friendly substitute for fossil fuels. Our analysis of four provenances of crude Pongamia oil has identified eight (8) methyl compounds with a relative value of >1%, i.e. palmitoleate, lenoleate, eicostrienoic, erucate, docosadienoic, nervonate, eicosapentaenoate and arachidate. The value of the individual methyl compounds varied in each provenance. The unsaturated fatty acid content of Pongamia crude was higher and needs to be balanced to maintain the physical properties of Pongamia biodiesel. In addition, the quality of the tested Pongamia crude oil from all provenances that show high acidity and water content in the crude oil but exceed the standard for biodiesel (SNI 04-7182-2006) shows a need for improvement advanced process. The variations of the methyl compounds found in each provenance can be used as a selection basis for the development of products in the pharmaceutical and agricultural sectors.

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Engineering a β‐Helical d,l‐Peptide for Folding in Polar Media

Kulp

Clark

2009

Chemistry A European J

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Beta helices--helices formed by alternating D,L-peptides and stabilized by beta-sheet hydrogen bonding--are found naturally in only a handful of highly hydrophobic peptides. This paper explores the scope of beta-helical structure by presenting the first design and biophysical characterization of a hydrophilic D,L-peptide, 1, that forms a beta helix in methanol. The design of 1 is based on the beta-hairpin/beta helix--a new supersecondary that had been characterized previously only for hydrophobic peptides in nonpolar solvents. Incorporating polar residues in 1 provided solubility in methanol, in which the peptide adopts the expected beta-hairpin/beta-helical structure, as evidenced by CD, analytical ultracentrifugation (AUC), NMR spectroscopy, and NMR-based structure calculations. Upon titration with water (at constant peptide concentration), the structure in methanol (1 m) transitions cooperatively to an extended conformation (1 w) resembling a cyclic beta-hairpin; observation of an isodichroic point in the solvent-dependent CD spectra indicates that this transition is a two-state process. In contrast, neither 1 m nor 1 w show cooperative thermal melting; instead, their structures appear intact at temperatures as high as 65 degrees C; this observation suggests that steric constraint is dominant in stabilizing these structures. Finally, the (1)H NMR C alphaH spectroscopic resonances of 1 m are downfield-shifted with respect to random-coil values, a hitherto unreported property for beta helices that appears to be a general feature of these structures. These results show for the first time that an appropriately designed beta-helical peptide can fold stably in a polar solvent; furthermore, the structural and spectroscopic data reported should prove useful in the future design and characterization of water-soluble beta helices.

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Vibrational spectroscopic studies of L,D‐alternating phenylalanine peptides

Cited by 10 publications

References 30 publications

Dynamic structure of the polytheonamide B channel studied by normal mode analysis

Dynamic structure of the polytheonamide B channel studied by normal mode analysis

Analysis of methyl compounds variation in the crude Pongamia pinnata oil from Banten, West Java and North Java populations

Engineering a β‐Helical d,l‐Peptide for Folding in Polar Media

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