Theonellapeptolide-Id Date: Dec.1999 Mtx-Val-D-mLeu-(-Thr-bAla-D-Leu-mIle-bAla-D- alloIle-mVal-mAla-bAla-D-Leu-malloIle-), 13-water hydrates Mtx=methoxyacetate, m=N-methyl, bAla=beta-alanine

Chemical scheme is here. Left: Amphiphatic layer structure in the crystal. Colored balls represent the solvated water molecules and the arrows show the water-layers. Drawn radius is 35 A.

Abstract: Theonellapeptolide-Id (TNLP), a cyclic tridecapeptide lactone, was crystallized from dimethylformamide-water solution. In the asymmetric unit, two peptide molecules were existed with solvent molecules, and total molecular weight were over 3000 Dalton. The crystal structure including solvent molecules was finally determined at 0.80 A resolution by using synchrotron radiation. The conformations of two independent molecules were similar to each other and were also similar to the previously reported structure (Doi, Ishida, Kobayashi, Deschamps & Flippen-Anderson (1999) Acta Crystallogr., Sect. C, 55, 796-798). About thirteen hydrated waters were found at disordered nineteen sites, and they were located on a certain region to avoid the contacts with aliphatic side chains of peptolide in the crystal. The spatial dispositions of solvent molecules and peptides subsequently created the amphipathic layer structure. This unique behavior was elucidated by X-ray analysis as a noteworthy characteristic of TNLP-Id.

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Paper:

Tile: Amphipathic Structure of Hydrated Theonellapeptolide-Id, a Hydrophobic Tridecapeptide Lactone from the Okinawa Marine Sponge Theonella swinhoei
Authors: Mitsunobu Doi, Toshimasa Ishida, Motomasa Kobayashi, Yoshio Katsuya, Yushihiro Mezaki, Masahiro Sasaki, Akira Terashima, Taizo Taniguchi and Chikako Tanaka
Journal: Biopolymers 54, 27-34 (2000)

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References of theonellapeptolide:

1. Kobayashi, M., Lee, N. K., Shibuya, H., Momose, T. & Kitagawa, I. (1991) Chem. Pharm. Bull. 39, 1177-1184.
2. Kobayashi, M., Kanzaki, K., Katayama, S., Ohashi, K., Okada, H., Ikegami, S. & Kitagawa, I. (1994) Chem. Pharm. Bull. 42, 1410-1415.
3. Kobayashi, M., Kawazoe, K., Okamoto, T., Sasaki, T. & Kitagawa, I. (1994) Chem. Pharm. Bull. 42, 19-26.
4. Kobayashi, J., Itagaki, F., Shigemori, H., Ishibashi, M., Takahashi, K., Ogura, M., Nagasawa, S., Nakamura, T., Hirota, H., Ohta, T. & Nozoe, S. (1991) J. Am. Chem. Soc. 113, 7812-7813.
5. Kobayashi, M., Kawazoe, K., Katori, T. & Kitagawa, I. (1992) Chem. Pharm. Bull. 40, 1773-1778.
6. Kitagawa, I., Lee, N.K., Kobayashi, M. & Shibuya, H. (1987) Chem. Pharm. Bull. 35, 2129-2132.
7. Kitagawa, I., Lee, N.K., Kobayashi, M. & Shibuya, H. (1987) Tetrahedron, 47, 2169-2171.
   Structure...
8. Doi, M., Ishida, T., Kobayashi, M., Deschamps, J. R. & Flippen-Anderson, J. L. (1999) Acta Crystallogr., Sect. C, 55, 796-798. (see orthorhombic [monomeric] structure)
9. Bernardinelli, G., Jefford, C.W., Sakai, R. & Higa, T. (1992) Abstracts of Papers, 7th International Symposium on Marine Natural Products, p29-30, Capri, Italy.

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ORTEP-III (Burnett, 1996) drawing of Molecule 1.

ORTEP-III (Burnett, 1996) drawing of Molecule 2.

The conformation of Molecules 1 & 2 are similar to each other except for N-terminus and some loop. The other feature is cis amide bond between Val and Ala (lower coner in the figure).

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Side view of Molecule 1. Main chain is thick line and fairely winded.

Side view of Molecule 2. Shape is like as a "bottom of ship".

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X-Ray Data Summary

formula	2(C70H125N13O16), 12.9H2O
weight	3043.4
symmetry	monoclinic
space group	P21
Cell		Crystal
a	11.9955(3) Ang.	description	block
b	36.9917(10) Ang.	colour	Colorless
c	19.7887(3) Ang.	size (mm)	0.3x0.2x0.2
alpha	90.0 deg.	Dx (g/ml)	1.069
beta	96.1623(15) deg.	F(000)	3056
gamma	90.0 deg.	mu(CuKa)	0.076
volume	8730.2(3) Ang^3	wave length	0.834 A
Z	4	temperature	100(2)
Diffrn measurement		Refinementspace
device type	Rigaku RAXIS-4	Flack	0.5(11)
radiation source	SPring-8/BL24XU-A*	parameters	2002
index limit	0~h~15, 0~k~46, -24~L~24	restraints	396
theta (deg.)	2.3-31.5	R_factor_gt	0.0865
total reflections	16300	wR_factor_gt	0.2492
reflections(obs)	14826 .gt. 2sigma(I)	dela rho_max	0.802 e A^3
Structure		delta rho_min	-0.428 e A^3
solution	SnB	shift/su_max	7.069
refinement	SHELXL-97	Goodness of fit	1.111

^*The machine time of the synchrotron was given from Hyogo prefecture and Japan Synchrotron Radiation Research Institute with the proposal No. C99A24XU-005N.

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