Acetylated Gramicidin S

BrGS: cyclo(-Val-Orn(BrBz)-Leu-D-Phe-Pro-)2
TcGS: cyclo(-Val-Orn(Tc)-Leu-D-Phe-Pro-)2
[BrBz=m-bromobenzoicyl, Tc=trichloroacetyl]

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Backbone: show beta-sheet
Amphipathic
Spacefilling

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X-Ray diffraction data were measured on SPring-8/BL24XU-A with the approval from Hyogo Prefecture and Japan Synchrotron Radiation Research Institute (C00A24XU-5003N).
Reference: Doi, M., Fujita, S., Katsuya, Y., Sasaki, M., Taniguchi, T. and Hasegawa, H.
Antiparallel Pleated beta-Sheets Observed in Crystal Structures of N,N-Bis(trichloroacetyl) and N,N-Bis(m-bromobenzoyl) Gramicidin S.
Arch. Biochem. Biophys. (2001). 395, 85-93.
Gramicidin S (GS), cyclo(-Val-Orn-Leu-D-Phe-Pro-)2, is an amphiphilic cyclosymmetric decapeptide isolated from garden soil of the former Soviet Union in 1944, having antibacterial activities against Gram-positive bacteria. Since gramicidin, a linear peptide antibiotic, was found prior to GS in 1941, the letter 'S' was taken from the name "Soviet" and attached to the name of this cyclic peptide.

The conformational properties of GS and its analogues have also been studied since mid-1950s by spectroscopic methods. In early studies, alpha-helical characteristics were speculated from ORD and CD spectra. However, NMR studies showed agreements with the beta-sheet model presented by Hodgkin and Oughton, and Schwyzer and Ludescher. Other spectroscopic and X-ray diffraction studies also support this model, and the Hodgkin and Oughton's model has been widely adopted thus. Oughton and his group also attempted X-ray structural analyses of GS salts, and of its analogues, N-acetyl, N-chloroacetyl, N-iodoacetyl, chloroaurate and N-(2,4-dinitrophenyl) GS. Furthermore, Hong et al. independently studied the crystals of GS hydrochloride. However, the crystal structure of GS or its analogues is not known, except for the GS-urea complex.

Therefore, we have attempted the X-ray structure analyses of GS and acetyl GS (AcGS), but the structure was not clarified in spite of exhaustive trials using advanced methods such as SnB and LODEM. Therefore, we focused on the N-acetyl groups of GS analogues to obtain crystals suitable for the X-ray diffraction method. The amino groups of Orn residues were capped using trichloroacetic acid (TCA) and m-bromobenzoyl acid (BrBz). Crystals of N,N-bis(trichloroacetyl) gramicidin S (TcGS) and N,N-bis (m-bromobenzoyl) gramicidin S (BzGS) were grown in aqueous dimethylformamide (DMF) solution. Although it is well know that AcGS yields hexagonal crystals in aqueous alcohol solutions, the crystals of TcGS and BzGS belong to the monoclinic and orthorhombic system, respectively. The structures of TcGS and BzGS were determined without exhaustive trials as in the case of AcGS. These structures are the first structural examples of acetylated GS and reflect the amphiphilic properties revealed by spectroscopic studies.
Needle crystals (hexagonal) of TcGS grown from aqueous iso-propanol,
and diffraction image. (structure not determined)
Plate crystals (monoclinic) of TcGS grown from aqueous DMF,
and diffraction image. (structure solved)
Weak satelite spots are recorded at low resolution.
It is postulated that these cell are close to hexagonal cell.
Left: Diffraction image of AcGS, which is similar to that of needle crystalss of TcGS.

This is a typical one for hexagonal crystals of AcGS. (structure not determined)

P6122 or P6522
a=b=28.3 A
c=54.9 A
alpha=beta=90 deg.
gamma=120 deg.
V=36,000 A3

Schmidt, G. M. J., Hodgkin, D. C., and Oughton, B. M. (1957). Biochem. J. 65, 744-751.    Oh! My birth year!

Structure and beta-sheet of TcGS.

Structure and beta-sheet of BrGS.
Structers are drawon by ORTEP-III, and sheets were drawn by Raster3D and POV layer.
Get PDB coordinates: TcGS BrGS
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Date: Nov. 2001