Environments and conformations of tryptophan side chains of gramicidin A in phospholipid bilayers studied by Raman spectroscopy

Takeuchi, Hideo; Nemoto, Yasuhisa; Harada, Issei

doi:10.1021/bi00458a031

Cited by 58 publications

(57 citation statements)

References 54 publications

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“…Indole orientations determined for the Trp side chains are consistent with Raman scattering (18) which requires 2 to be approximately Ϯ90°. Furthermore, it has been shown that the extent of lipid ; however, all four Trp residues interact with the hydrophobic acyl chains of the lipid (19). The DSDH dimer conformation is fully consistent with these observations having Trp 15 exposed to water near the top and bottom of the dimer and Trp 9 exposed only to lipid.…”

Section: The Dsdh Conformation In Lipid Membranessupporting

confidence: 74%

The conducting form of gramicidin A is a right-handed double-stranded double helix

Burkhart

Langs

et al. 1998

Proc. Natl. Acad. Sci. U.S.A.

123

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The linear pentadecapeptide antibiotic, gramicidin D, is a naturally occurring product of Bacillus brevis known to form ion channels in synthetic and natural membranes. The x-ray crystal structures of the right-handed double-stranded double-helical dimers (DSDH ) reported here agree with 15 N-NMR and CD data on the functional gramicidin D channel in lipid bilayers. These structures demonstrate single-file ion transfer through the channels. The results also indicate that previous crystal structure reports of a left-handed double-stranded double-helical dimer in complex with Cs ؉ and K ؉ salts may be in error and that our evidence points to the DSDH as the major conformer responsible for ion transport in membranes.

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Section: The Dsdh Conformation In Lipid Membranessupporting

confidence: 74%

The conducting form of gramicidin A is a right-handed double-stranded double helix

Burkhart

Langs

et al. 1998

Proc. Natl. Acad. Sci. U.S.A.

123

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“…As indicated by the significant contribution from the electrostatic interaction, the tryptophan side chains are capable of forming hydrogen bonds with the ester carbonyl groups ofthe lipids and the water, whereas the leucine side chains are not. The existence of these hydrogen bonds for the tryptophans are consistent with 2H exchange and IR studies (27,28). For both leucine and tryptophan side chains, the alkane chains are energetically the strongest interacting component.…”

supporting

confidence: 80%

Molecular dynamics simulation of the gramicidin channel in a phospholipid bilayer.

Woolf

Roux

1994

Proc. Natl. Acad. Sci. U.S.A.

283

231

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A molecular dynamics simulation of the gramicidin A channel In an explicit dimyrsoyl posphatidylcholine bilayer was generated to study the details of lipidprotein interactions at the microscopic level. Solid-state NMR properties of the channel averaged over the 500 psec trajectory are in excellent agreement with available experimental data. In contrast with the aption of macroscopic models, the membrane/solution interface region is found to be at leat 12 A thick. The tryptophan side chains, located within the interface, are found to form hydrogen bonds with the ester carbonyl groups of the lipids and with water, suggeng thelr important contribution to the stability of membrane proteins. Individual lipid-protein interactions are seen to vary from near 0 to -50 kcal/mol. The most strongly interacting formations are short-lived and have a nearly equal contribution from both van der Waals and electrostatic energ. This approach for per. forming molecular dynamics simulations of membrane proteis in explicit phosphollpid bilayers should help In studying the structure, dynamics, and energetics of lipid-protein interactions.The scarcity of information about the structure of membrane proteins, along with the complexity of the bilayer environment, makes an understanding of lipid-protein microscopic interactions difficult. Structure prediction algorithms of membrane proteins often represent the membrane/solution interface as a sharp demarcation between a hydrophobic and a hydrophilic environment (1, 2). Such a simplified view may not be sufficient. For example, although the amino acids of membrane proteins are generally distributed according to their hydrophobicity (2), the reasons why tryptophan and other aromatic residues are often found at the membrane/solution interface are not well understood (3). Despite numerous experimental studies, little or no detailed information is available about the microscopic nature ofthe lipid bilayer/protein bulk solution interface and its implications for lipid-protein interactions. In principle, the powerful molecular dynamics approach for studying biological macromolecules (4) can be used to gain insight into the structure and dynamics of membraneprotein complexes. In practice, extension of current computational methods to simulate a protein in an explicit phospholipid bilayer represents a major challenge. The dynamical stability and the computed properties of the system will depend on two important factors: (i) the choice of a carefully constructed starting configuration (5) and (ii) the ability of the empirical potential function to represent accurately the balance between hydrophobic and hydrophilic forces. The selection of a model system is important in that a large body ofexperimental data should be available for assessing the simulation's validity. This paper describes a systematic approach for constructing the starting configuration for molecular dynamics simulations of intrinsic membrane proteins and reports on the results of a 500-psec trajectory for an 8:1 dimyristoyl ...

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“…In the case of the Trp-Trp dipeptide the negative ellipticity in the near-UV region was attributed to a restriction of the side-chain torsional angles xi and X2 although one might expect their actual values and not just their variability to be important. Raman spectroscopy has indicated a narrow range of Trp X2 angles in the channel form of gramicidin [12]. This corroborates energy calculations which have indicated large barriers for side chain rotation [13].…”

Section: Peptide and Prolein Conformationsupporting

confidence: 83%

Circular Dichroism Studies of Tryptophan Residues in Gramicidin

Woolley¹,

Wallace²

1992

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Environments and conformations of tryptophan side chains of gramicidin A in phospholipid bilayers studied by Raman spectroscopy

Cited by 58 publications

References 54 publications

The conducting form of gramicidin A is a right-handed double-stranded double helix

The conducting form of gramicidin A is a right-handed double-stranded double helix

Molecular dynamics simulation of the gramicidin channel in a phospholipid bilayer.

Circular Dichroism Studies of Tryptophan Residues in Gramicidin

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