Role of N‐t‐Boc group in helix initiation in a novel tetrapeptide

Ganesh, S.; Jayakumar, R.

doi:10.1034/j.1399-3011.2002.02989.x

Cited by 18 publications

(25 citation statements)

References 52 publications

(52 reference statements)

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“…More recently, an a-helical turn conformation has been proposed for the sequence Boc-Ala-Ile-Ile-Gly-OMe, on the basis of a characteristic CD signature in trifluoroethanol-containing methanol solution. [27] The CD spectrum of the oxopeptide Boc-Ala-Gly-Ala-Aib-OMe in acetonitrile, on the other hand, shows only a weak negative signal at 230 nm, with a negative minimum near 198 nm. As the temperature is lowered, the 198 nm minimum becomes more pronounced, while a small positive signal near 215 nm partially fills the 240 nm dip observed at room temperature (data not shown).…”

Section: Full Papermentioning

confidence: 98%

Coexistence of Hydrogen‐Bonded Loop and Extended Tetrapeptide Conformations

Cervetto

Pfister

Kolano

et al. 2007

Chemistry A European J

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The conformations of a protected tetrathiopeptide have been analysed by isotope labelling and two-dimensional infrared spectroscopy (2D-IR). It has been found that Boc-Ala-Gly(=S)-Ala-Aib-OMe in acetonitrile, as well as its oxopeptide analogue, can adopt a hydrogen-bonded loop conformation in coexistence with less restricted structures. The two types of conformations interconvert too quickly to be resolved on the nuclear magnetic resonance (NMR) timescale, but give rise to different cross peaks in two-dimensional infrared spectra. The hydrogen bond between the Boc terminal group and the amide proton of Aib can be broken by photoisomerisation of the thioamide bond.

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Section: Full Papermentioning

confidence: 98%

Coexistence of Hydrogen‐Bonded Loop and Extended Tetrapeptide Conformations

Cervetto

Pfister

Kolano

et al. 2007

Chemistry A European J

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“…Protecting groups, which alter the polarity of the N-or C-terminus, may influence the conformational preference of small peptides [37], and such changes are detected by using MD/cluster analysis for MIFAGIK ϩ ions. It is unclear whether these differences arise as a result of different structures or differences in the spatial projections of the Fmoc group, but more detailed studies on similar effects are currently underway.…”

Section: N-and C-terminal Derivatives Of Mifagikmentioning

confidence: 99%

The contributions of molecular framework to IMS collision cross-sections of gas-phase peptide ions

Tao

Dahl

Pérez

et al. 2009

J. Am. Soc. Mass Spectrom.

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Molecular dynamics (MD) is an essential tool for correlating collision cross-section data determined by ion mobility spectrometry (IMS) with candidate (calculated) structures. Conventional methods used for ion structure determination rely on comparing the measured cross-sections with the calculated collision cross-section for the lowest energy structure(s) taken from a large pool of candidate structures generated through multiple tiers of simulated annealing. We are developing methods to evaluate candidate structures from an ensemble of many conformations rather than the lowest energy structure. Here, we describe computational simulations and clustering methods to assign backbone conformations for singly-protonated ions of the model peptide (NH 2 -Met-Ile-Phe-Ala-Gly-Ile-Lys-COOH) formed by both MALDI and ESI, and compare the structures of MIFAGIK derivatives to test the 'sensitivity' of the cluster analysis method. Cluster analysis suggests that [MIFAGIK ϩ H] ϩ ions formed by MALDI have a predominantly turn structure even though the low-energy ions prefer partial helical conformers. T he emphasis of mass spectrometry based biological chemistry is shifting from compound identification to structural studies of large biomolecules and biomolecule complexes [1][2][3][4][5][6][7], including membrane proteins [8]. The next phase of 'omics' related research must be aimed at obtaining and predicting additional dimensions of information, such as secondary, tertiary, and quaternary structures and linkage-specific information for glycans. Although sophisticated structural characterization tools, such as NMR and XRD, provide the most information, high throughput analysis of complex biological mixtures obtained by using these techniques is an underdeveloped technology. On the other hand, IMS is much more than a separation device, the structural information derived from 2D conformation space afforded by IM-MS is potentially well-suited to both high throughput applications and complex biological samples.A number of laboratories have focused their research on developing IM-MS for biophysical studies of peptides and proteins [9 -14]. In previous work, we showed that a large proportion of singly charged peptide ions (formed by MALDI) appear on a single trendline in 2D mobility-m/z plots, i.e., plots of arrival-time distribution (ATD) or ion-neutral collision cross-section (⍀) versus m/z [15]; however, a few ion signals deviate (Ͼ3% to ϳ20%) from the expected trendline and nonpeptidic ion signals appear on separate, compound class specific trendlines [14,15]. Ruotolo et al. showed that gas-phase [M ϩ H] ϩ ions of LLGNVLVVVLAR (derived from bovine hemoglobin) prefer extended (helical) structure(s) resulting in a larger collision cross-section than random coil structures having the same or similar m/z values [12,13], while some post-translationally modified (PTM) peptide ions (phosphopeptides) tend to pack more tightly than the unmodified protonated peptide ions owing to intra-molecular charge-solvation and/or formation of salt-...

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“…Synthesis and characterization of peptide A has been described in our earlier report [10]. Details of spectroscopic and MALDI characterization of peptide B is given in this investigation.…”

Section: Methodsmentioning

confidence: 99%

“…3, curve a) shows stronger amide II band at 1538 cm À1 than the amide I band at 1649 cm À1 indicating that the helix axes of peptide A are oriented in the direction parallel to solid surface in the compressed form. We have shown earlier that the involvement of intramolecular hydrogen boding between urethane carbonyl and NH of Gly in the helical turn formation of peptide A [10]. It should be noted that three amide protons and carbonyl group of peptide A (from Ala, Ile, Ile) in the middle of the helical turn are not involved in the hydrogen bonding and would be hydrated when it is spread at the air/water interface.…”

Section: Determination Of Secondary Structure In the Air/ Solid Intermentioning

confidence: 95%

“…In the Chemical Physics Letters 380 (2003) 681-688 www.elsevier.com/locate/cplett present work, the conformational analysis of two protected tetrapeptides A and B (Scheme 1) are investigated at the air/water, air/solid interfaces and micellar medium. Recently, we have shown that peptide A takes helical turn conformation in alcoholic solvents [10]. We felt it is worthwhile to investigate the self-assembly studies of peptide A and B at the air/water and air/solid interfaces because these peptide sequences are present in the hydrophobic nucleating regions of beta amyloid peptide (bAP) and Islet amyloid peptide (IAP), respectively [11,12].…”

Section: Introductionmentioning

confidence: 99%

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