WATER-BRIDGED HELICAL PEPTIDE MOLECULES IN THE STRUCTURE OF THE OCTAPEPTIDE PARABROMOBENZOYL-(D-IVA)8-OTBU
M. Crisma1, F. Formaggio1, A. Moretto1, C. Toniolo1, and Q.B. Broxterman2
1Biopolymer Research Centre,
CNR, Department of Organic Chemistry, University of Padova,
I-35131 Padova, Italy
2DSM Research, Organic Chemistry and
Biotechnology Section, 6160 MD Geleen, The Netherlands
Keywords: 310-helix, isovaline, peptides,
peptide hydration
Isovaline (Iva; Ca-ethyl,Ca-methyl-glycine) is the simplest chiral Ca-tetrasubstituted a-amino acid. As part of our ongoing effort towards the understanding of the conformational preferences of peptides containing Ca-tetrasubstituted a-amino acids [1], herewith we report on the crystal structure of pBrBz-(D-Iva)8-OtBu dihydrate (pBrBz, parabromobenzoyl; OtBu, tertbutyl ester). This structure represents the longest Iva homopeptide so far characterized at atomic resolution [2,3].
Single crystals of pBrBz-(D-Iva)8-OtBu dihydrate (C51H85BrN8O10 2 H2O) were grown by slow evaporation from ethyl acetate. Crystals are monoclinic, space group P21, with a = 14.740(2), b = 13.447(2), c = 15.559(2) Å, b = 102.66(5)°, Z = 2, V = 3009.0(7) Å3, Dcalc = 1.199 Mg m-3.
4696 independent reflections were collected on a Philips PW110 diffractometer, using graphite monochromated CuKa radiation (l = 1.54178 Å), q-2q scan mode up to qmax = 60°. The structure was solved by direct methods of SHELXS 86 program [4] and refined on F2, using all data, with SHELXL 93 program [5]. The refinement converged to R1 = 0.044 [on F 4s(F)] and wR2 = 0.122 (on F2, all data).
The peptide molecule is folded into a left-handed 310-helix [6], stabilized by six consecutive intramolecular NH ... O=C H-bonds of the i+3 i type (b-bends or C10 structures). The first five b-bends, starting from the N-terminus, are of the type III' (average f,y = +53.0, +30.2° for residues 1-6), while the sixth b-bend, with f,y = +78.8, -4.3° for Iva(7) at the i + 2 position, is of type I' [7]. The C-terminal Iva(8) residue is semi-extended, with f,y = +50.6(7), -135.8(5)°. The adoption of a semi-extended conformation by a C-terminal chiral Ca-tetrasubstituted a-amino acid in a 310-helical peptide ester is a unusual finding, the most common conformation being helical with either the same or the opposite screw-sense with respect to the preceding residues.
In the present case the uncommon conformation of the C-terminal residue may be related to the presence of two co-crystallized water molecules (W1 and W2) and their influence on the packing mode. Each water molecule acts as a bridge connecting two helical peptide molecules. More specifically, the W1 water molecule is H-bonded, as the acceptor, to the N1-H group (within the same asymmetric unit) and as the H-bond donor to the (peptide) O6 and (ester) O8 carbonyl oxygens of a (1+x, y, 1+z) symmetry related peptide molecule. It has to be noted that, in order for the O1W ... O8 H-bond to occur concomitantly to the O1W ... O6 H-bond, the C-terminal residue is forced to adopt the semi-extended conformation. Were it helical, the ester carbonyl O8 atom would be replaced by the methoxy oxygen atom of the ester group. Conversely, the W2 water molecule accepts a H-bond from the N2-H group (x, y, z), and donates one H-bond to the O7 carbonyl oxygen of a (-x, -1/2+y, -z) symmetry related peptide molecule, and the other H-bond to O1W within the same asymmetric unit. Therefore, infinite head-to-tail peptide helical rows, interleaved by W1 water molecules, are formed along the 101 direction, while W2 bridges peptide molecules related by the twofold screw axis in a zig-zag motif along the y direction.
To the best of our knowledge, this structure represents the
first example of a 310-helical peptide where all
NH and C=O potential H-bonds donors and acceptors not satisfied
by the intramolecular H-bonding scheme participate in H-bonds
with co-crystallized water molecules.