Karle
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GIy - L - Pro- L-Ser-n- A la- L - Pro
Conformation of the Cyclic Pentapeptide Gly-L-Pro-L-Ser-D-Ala-L-Pro in the Crystalline State and an Example of Rotational “Isomerism” between Analogues Isabella L. Karle Contribution f r o m the Laboratory f o r the Structure of Matter, Naval Research Laboratory. Washington, D.C. 20375. Receiced May 15, I978
Gly1-~-Pro2-L-Ser3-~-Ala4-~-Pro5 (ClgH27N506) contains all trans peptide units with significant deviations from planarity in three of them where 0 3 = - 165’, w4 = 160’. and 0 5 = 169’. I f the side groups are disregarded, the conforpreviously remation of the cyclic backbone is almost identical with that found in cyclic Gly1-L-Pro2-Gly3-D-Ala4-L-Pro’. ported, with the exception that the backbones in the two molecules are related by a mirror. I f the peptide backbones of both molecules are held in the same orientation, the side groups of the Ser-containing molecule have progressed by one peptide unit along the backbone as compared to the Gly3 molecule. One transannular 4-1 hydrogen bond (type 11’) is formed encompassing Gly’-L-Pro* with = 58’, $I = - 1 28’, $2 = -75’, and $2 = 20’. This is a first observation, at least in crlstals of relatively small pe tides, for the second corner of a @ turn to contain a Pro group. The space group is P21 with a = 12.392 (7) A, b = 9.149 (8) c = 10.428 (4) A, @ = 97.3’, and Z = 2. The peptide molecules are stacked in the crystal with NH-O=C and OH-.O=C hydrogen bonds between molecules in a stack. The stacks of peptide molecules are separated by layers of solvent molecules, CHlC12.
Abstract: Cyclic
1,
the isotropic and anisotropic refinements, and the relatively large value Parallel studies on the solution and crystalline conformafor the final R factor, must be due in large part to the CH*Clz moletions of cyclic Gly’-L-Pro2-L-Ser3-D-Ala4-t -Pro5 have been cule that cocrystallizes with the peptide molecule. The thermal pacarried out by N M R and X-ray diffraction analysis, respecrameters for the CI atoms are very large and anisotropic. In fact, in tively. The results of the conformational analysis of this cyclic the E map the weights of the CI atoms are no larger than the weights pentapeptide in solution are reported in an accompanying of the C and 0 atoms. Moreover, atoms in the side groups of the paper.’ This paper concerns the conformation and structure peptide, particularly C57 and CqP, also have very large thermal pain the crystalline state. There are both similarities and signiframeters, indicating a considerable degree of disorder. and contribicant differences in conformation and intramolecular hydrogen uting to a large R factor. bonding between the present cyclic pentapeptide and its anaThe labeling of the atoms is shown in Figure I , the coordinates for l o g ~ e , cyclic ~ , ~ Glyl-~-Pro~-Gly~-~-Ala~-~-Pro,~ where the the atoms, other than hydrogen. are listed in Table I. the bond lengths and bond angles are shown in Table I I , while the conformational anonly chemical difference is the substitution of ~ - S e for r~ gles are shown in Table 1 1 1 . Gly3.
Experimental Section Clear, lath-shaped crystals of c-Gly-Pro-Ser-D-Ala-Pro grown from CH*Clz/hexane solution were obtained from Pease and Niu.’ X-ray intensity data were collected on a four-circle automatic diffractometer ) with the 0-20 scan mode using a scan of 2.0’ t 2 0 ( 0 ? ) - 2 1 9 ( ( ~ 1and a scan speed of 2’/niin. Data were collected with Cu K O radiation to a scattering angle of 20 = 120’ for a total of I864 reflections. Lorentz and polarization corrections were applied and normalized structure factors were derived with the aid of a K curve. The space group is P21 with cell parameters a = 12.392 (7) A, b = 9.149 (8) A, c = 10.428 (4) A, p = 97.31 (3)O, z = 2, c = 1 172.7 A3, and a calculated density of 1.400 g/cm3 for two peptide molecules plus two CHzClz molecules per unit cell. The structure of the crystal was solved with some difficulty by the direct method4 of phase determination using symbolic addition. The fragment of the molecule obtained from the determined phases was misplaced with respect to the twofold screw axis. The procedure for reducing the symmetry of the cell to space group PI,and consequently doubling the number of atoms to be placed in the cell, yielded the s t r ~ c t u r eSubsequently, .~ the structure was solved more directly by a new automated procedure.h Full-matrix least-squares refinement’ on the 32 nonhydrogen atoms, with weighting based on counting statistics,8 led to an R factor of 17% for isotropic thermal parameters and 10.4% for anisotropic thermal parameters. Scattering factors used were those listed in Vol. I l l of the “International Tables for Crystallography” and the function minimized was Z w ( IFo\ - JF,Jj2. Most of the hydrogen atoms were located i n a difference map and coordinates for the remaining hydrogen atoms were calculated for idealized positions. In the final cycles of refinement the coordinates of the hydrogen atoms were not varied, except for the H on N3.The R factor, where R = ZllFol - I F , ~ ~ / Z ~ F , , for all the observed data was 8.5%, and 8.2% for the I8 16 reflections greater than 6.The large decrease in the value of the R factor between T h i s article not subject to US. Copyright.
Results The Molecule. The most striking feature of this molecule is the similarity of the conformation of the backbone with that in the Gly3 analogue,2 which can be seen by comparing Figures 1 and 2. The backbones in the two molecules are related by a mirror. The side groups, however, have been moved by one peptide unit along the backbone (Figure 3). A possible explanation for the rotation of the side groups may be that the conformation for the ring is quite stable for the chiral sequence D L D D L (or the mirror image L D L L D ) . From the values of the torsional angles 6 and plotted on the graph in Figure 4, it is seen that the Gly residues in the Gly3 pentapeptide behave as if they had the D hand. A replacement of such a Gly residue with L-Ser results i n the chiral sequence D L L D L . I f the side groups are shifted around the ring to the next Cck,then the chiral sequence becomes LDLLD, the mirror image of the first pentapeptide. Perhaps, if D-Ser rather than L-Ser were substituted for Gly3, the two pentapeptide analogues would remain isostructural, rather than exhibit rotational “isomerism”, i.e., the same backbone shape but a shifting of the side groups to the next Ccratom. A comparison of the 4 and values for the two analogues (Figure 4) shows that the difference in the values are very small around the two Ccratoms which form the corners of the 4- I transannular hydrogen bonds and the differences become larger, 30’ and up to 50°,for the remaining three Cll atoms. These differences in 4 and J. are accounted for by the occurrence of a 3+ 1 transannular hydrogen bond encompassing Pro5 in the Gly3 analogue and the impossibility for such hydrogen bonding in the Ser3 analogue since a Pro residue has
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+
Published 1979 by the American Chcniical Socicty
I82
Journal o f t h e American Chemical Society
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101.1
/ January 3, 1979
n
5.
PRO
R .4
.1
&-ALA '5
Figure 1. Conformation of cyclic (Gly-Pro-Ser-o-Ala-Pro) in the crystalline state. The thermal ellipsoids for the C. N,and 0 atoms are drawn at the 50% probability level. Hydrogen atoms are indicated by small spheres and the hydrogen bond (4+1, type 11') is indicated by the thin line.
, I
-,23,
.
c ( s i y - ~ r ~ . s ~: -yF ,-O~J ~ 4
I
atly
3r3
Ser-D A a
>rot
t r p i ~ o imm3get
Figure 4. The conformational angles 4 and $ rcprescnting the torsions about the N,-C,c' bonds and the C,'"-C,' bonds. respectively. The signs for all the valbes for thc Ser3analogue have been changed (the cquivnlcnt analogue. of a mirror image) in order to compare directl! H i t h the
L- P R O Table 1. Fractional Coordinates
atom
NI C" 1 C' I
0,
N? Ccv2 C'? 0 2
C'j?
c-12
Ch? 3 3
Ctl, C'3 0 3
Figure 2. Conformation of cyclic (Gly-Pro-GIy-D-Ala-Pro)in the crystalline state,? ah analogue and rotational "isomer" of molecule i n Figure I.
C"1 013
NJ C
