Synthesis and properties of chiral peptide nucleic acids with a N-aminoethyl-D-proline backbone.

A synthon of D-proline substituted at the 4-position by thymine and at N by a flexible aminoethyl linker, has been used to prepare a novel chiral peptide nucleic acid (cPNA) with (2R,4R) stereochemistry using solid phase methodology. The homothymine decamer cPNA binds to complementary polyadenylic acid to form a 2:1 hybrid with high affinity and specificity according to UV and CD studies, whereas no binding to the corresponding polydeoxyadenylic acid was observed.

An analysis of the origins of a cooperative binding energy of dimerization.

The cooperativity between binding of cell wall precursor analogs (ligands) to and antibiotic dimerization of the clinically important vancomycin group antibiotics was investigated by nuclear magnetic resonance. When dimerization was weak in the absence of a ligand, the increase in the dimerization constant in the presence of a ligand derived largely from changes associated with tightening of the dimer interface. When dimerization was strong in the absence of a ligand, the increase in the dimerization constant in the presence of a ligand derived largely from changes associated with tightening of the ligand-antibiotic interface. These results illustrate how, when a protein has a loose structure, the binding energy of another molecule to the protein can derive in part from changes occurring within the protein.

Induction of asymmetry into homodimers.

The self-regulation of biological signalling receptors via homodimerization is discussed in relation to the symmetry changes occurring when these receptors bind their target ligand. The idea of positive and negative cooperativity between dimerization and ligand binding, mediated by changes in the symmetry of the system as a source of signalling control is considered; an analogy made with the homodimerization of a glycopeptide antibiotic, ristocetin A, which displays negative cooperativity. Finally, the regulation of the bacterial aspartate receptor and the human growth hormone receptor is discussed as a function of ligand-induced asymmetry.

Weak interactions and lessons from crystallization.

Ideas derived from the study of the process of crystallization may provide insights into molecular recognition in biological systems. Both processes exploit the cooperativity which arises from the formation of a large array of weak interactions.

Cooperativity and anti-cooperativity between ligand binding and the dimerization of ristocetin A: asymmetry of a homodimer complex and implications for signal transduction.

BACKGROUND: Recent work has indicated that dimerization is important in the mode of action of the vancomycin group of glycopeptide antibiotics. NMR studies have shown that one member of this group, ristocetin A, forms an asymmetric dimer with two physically different binding sites for cell wall peptides. Ligand binding by ristocetin A and dimerization are slightly anti-cooperative. In contrast, for the other glycopeptide antibiotics of the vancomycin group that have been examined so far, binding of cell wall peptides and dimerization are cooperative. RESULTS: Here we show that the two halves of the asymmetric homodimer formed by ristocetin A have different affinities for ligand binding. One of these sites is preferentially filled before the other, and binding to this site is cooperative with dimerization. Ligand binding to the other, less favored half of the dimer, is anti-cooperative with dimerization. CONCLUSIONS: In dimer complexes, anti-cooperativity of dimerization upon ligand binding can be a result of asymmetry, in which two binding sites have different affinities for ligands. Such a system, in which one binding site is filled preferentially, may be a mechanism by which the cooperativity between ligand binding and dimerization is fine tuned and may thus have relevance to the control of signal transduction in biological systems.

The "n' effect in molecular recognition.

The cooperativity which exists in crystal melting and many biological molecular recognition phenomena arises from extended arrays of weak interactions. We present a correlation between the melting temperature of a crystal and the intermolecular energy (which is evident only when compounds possessing several or many internal rotors are excluded). The correlation is used as the basis for a model of crystal melting which is capable of estimating the melting temperature of crystals. This model provides the basis for an understanding of the sharpness of the crystal melting transition for organic and inorganic substances. The cooperativity illustrated by the extended arrays of weak interactions, or the "n' effect, is extended to analogous order/disorder transitions in biological systems, such as the "melting' of DNA and RNA duplexes, providing insights into the physical properties of these structures.

Two conformers of the glycopeptide antibiotic teicoplanin with distinct ligand binding sites.

The clinically important vancomycin group glycopeptide antibiotics, which act by blocking cell wall synthesis, are crucial in the treatment of methicillin resistant Staphylococcus aureus. All of the group members studied so far, with the apparent exception of teicoplanin, enhance their antibiotic action by the formation of an asymmetric homodimer. Teicoplanin exists in two main conformers which differ by a rotation of approximately 180 degrees of a sugar residue. From NMR studies and molecular modelling, we present structures for the two conformers and conclude that they have different binding affinities for cell wall analogues. The two conformers of teicoplanin are closely analogous to those adopted by each half of the asymmetric dimers of the other vancomycin group antibiotics.