Conformation and ion-binding properties of cyclic and bicyclic peptides

Abstract

The structure-function relationship of biomolecules is one of the important problems in modern biology and can be understood to a large extent by investigating the conformational aspects of biomolecules with biological relevance. One such class of biomolecules of interest is cyclic peptides. Cyclic peptides are a special class of peptides well known for their biological functions such as hormones, antibiotics, toxins, and regulators of ion transport. Many naturally occurring cyclic peptides serve important functions in inducing transport of ions across membranes. Their biological activity originates from their 3D structure and ionbinding properties. Some of these peptides are specific towards particular metal ions. The conformational study of synthetic cyclic peptides with varying ring size, amino acid composition, and cations is important to understand their structural variability and ion specificity. A study of synthetic cyclic and bicyclic peptides, their 3D structures, and ionbinding properties using NMR, CD, and Xray crystallography is reported in this thesis. This thesis consists of six chapters and an appendix.

Chapter I Chapter I describes the general features of cyclic peptides, their specificity toward metal ions, and criteria for designing peptides to serve as ion transporters. Lehn’s idea of threedimensional cavity molecules and their translation to bicyclic peptides is discussed. Methods used for the study-NMR, CD, and Xray crystallography-are briefly surveyed. Special 2D NMR techniques such as NOESY and ROESY are described. This chapter also includes details of the materials used.

Chapter II Chapter II describes conformational studies on the symmetric cyclic octapeptide cyclo(AlaLeuProGly). CD studies on this peptide and its ionbinding properties are presented. Detailed conformational studies of this peptide in its free and calciumcomplexed forms using NMR are discussed. This peptide binds both monovalent and divalent cations, with greater specificity toward divalent ions. In the free state, the peptide is stabilized by and turns. In the calcium complex, the turn is weakened or broken, whereas the turn persists. Four carbonyl groups point outward to bind the Ca² ion. The peptide forms both 1:1 and 2:1 complexes, with the 2:1 complex being predominant in solution.

Chapter III Chapter III describes crystallographic studies on the cyclo(AlaLeuProGly)-calcium complex. Two types of crystal structures-orthorhombic and monoclinic-were observed. Their structures, coordination with Ca², and comparison with solution conformations are presented. The peptide adopts a bowlshaped conformation in which the Ca² ion sits inside the cavity. One side of the molecule is hydrophobic (Leu and Pro side chains), and the other forms a hydrophilic cavity suitable for cation binding. The overall conformation is similar in both crystal forms and in solution, indicating a rigid structure unaffected by packing forces or solvents. The free peptide and its calcium complex also do not differ significantly.

Chapter IV Chapter IV presents the conformation and ionbinding properties of two cyclic octapeptides cyclo(DPheProXGly), where X = Ala or Sar. For X = Ala, the CDCl conformation exhibits C symmetry on the NMR timescale and contains two 51 intramolecular hydrogen bonds:

NH of DPhe(1) C=O of DPhe(2) NH of DPhe(2) C=O of DPhe(1)

The PhePro bond adopts a trans conformation, producing two helical turns joined at the DPhe residue. CD spectra show changes only upon binding to divalent cations. When alanine is replaced by sarcosine, two conformers are obtained:

Conformer A (predominant at low concentration): stabilized by two turns. Conformer B (predominant at high concentration): contains no intramolecular hydrogen bonds and possibly forms a dimer.

Chapter V Chapter V describes the conformation of a cyclic tetrapeptide cyclo(DPheProSarGly). NMR studies revealed two conformers:

cis-trans-cis-trans trans-cis-trans-cis

Xray crystallography showed only one type (the major NMR conformer). The dependence of conformation on chirality, sequence, and symmetry-predicted theoretically for tetrapeptides-is discussed. CD studies with monovalent cations indicated that only one conformer binds to the cation.

Chapter VI Chapter VI discusses spherical recognition in bicyclic peptides. The bicyclic peptide studied has the sequence: cyclo(Lys¹Pro²Gly³ProGluProGlyLeu)-cyclo(Leu-Phe-Ala) where Lys and Glu side chains are crosslinked via Phe and Ala. This peptide shows high specificity for Ca², forming a 1:1 complex. The monocyclic analogue cyclo((Ac)LysLeuProGly(tBu)GluLeuProGly) binds Ca², Mg², and Ba², with slight preference for Ca². The summary and conclusions emphasize that cation specificity increases markedly when moving from a monocyclic peptide to a bicyclic peptide containing a welldefined 3D cavity.

Appendix A brief account is given of studies on the solution conformation of a linear tetradecapeptide from wasp venom-Polistes mastoparan: ValAspTrpLysLysIleGlyGlnHisIleLeuSerValLeuNH.