Directing macromolecular conformation through halogen bonds

Abstract

The halogen bond, a noncovalent interaction involving polarizable chlorine, bromine, or iodine molecular substituents, is now being exploited to control the assembly of small molecules in the design of supramolecular complexes and new materials. We demonstrate that a halogen bond formed between a brominated uracil and phosphate oxygen can be engineered to direct the conformation of a biological molecule, in this case to define the conformational isomer of a four-stranded DNA junction when placed in direct competition against a classic hydrogen bond. As a result, this bromine interaction is estimated to be Ϸ2-5 kcal/mol stronger than the analogous hydrogen bond in this environment, depending on the geometry of the halogen bond. This study helps to establish halogen bonding as a potential tool for the rational design and construction of molecular materials with DNA and other biological macromolecules.biomolecular engineering ͉ DNA structure ͉ molecular interactions H alogen bonds have recently seen a resurgence of interest as a tool for ''bottom-up'' molecular design. Chlorines, bromines, and iodines in organic and inorganic compounds are known to polarize along their covalent bonds to generate an electropositive crown; the halogen thus acts as a Lewis acid to pair with Lewis bases, including oxygens and nitrogens. These electrostatic pairs, originally called charge-transfer bonds (1), are now known as halogen bonds (X-bonds), recognizing their similarities to hydrogen bonds (H-bonds) in their strength and directionality (2). In chemistry, X-bonds are being exploited in the design and engineering of supramolecular assemblies (3) and molecular crystals (for review, see ref. 4), with an iodine X-bond estimated to be Ϸ3.5 kcal/mol more stable than an O-H⅐⅐⅐O H-bond in organic crystals (5).The X-bond, however, has not generally been a part of the biologist's lexicon. Although halogens are widely used in drug design and to probe molecular interactions, X-bonds have only recently been recognized as a distinct interaction in ligand recognition and molecular folding and in the assembly of proteins and nucleic acids (6, 7). With the growing application of biological molecules (biomolecule), particularly nucleic acids (for review, see ref. 8), in the design of nanomechanical devices, we ask here whether specific X-bonds can be engineered to direct conformational switching in a biomolecule.To compare X-and H-bonds in the complex environment of a biomolecule, we have designed a crystallographic assay to determine whether an intramolecular X-bond could be engineered to direct the conformational isomerization of a DNA Holliday junction by competing an X-bond against a classic H-bond and, consequently, we are able to compare the stabilization energies afforded by these two types of interactions. The stacked-X form of the DNA Holliday junction (Fig. 1), seen in high-salt solutions (9) and in crystal structures (10 -12), is a simple and well controlled biomolecular assay system that can isomerize between two nearly isoenergetic an...

The shape of the halogen atom—anisotropy of electron distribution and its dependence on basis set and method used

“…Among different noncovalent interactions, the halogen bond (X-bond) attracts particular attention of researchers because, similarly as the hydrogen bond (H-bond), it is responsible for physical, chemical, and biologic properties of a large group of chemical species [1][2][3][4][5][6][7][8][9][10][11][12][13][14][15][16]. The X-bond is of the strength close to that of H-bond [1] and is strongly directional [17].…”

Halogen and Hydrogen Bonding in Multicomponent Crystals of Tetrabromo-1H-Benzotriazole

“…The specific role of halogen atoms in pinning a drug at the active site of the target enzyme via XB has been proven. In general, the role of XB in affecting binding and recognition phenomena between halogenated residues and biomacromolecules is attracting growing interest [26][27][28]. In this context, we have recently shown that the formation of halogen-bonded API-CCF cocrystals is a further opportunity offered by this interaction in biopharmacology [29,30].…”

Halogen bonding at the ATP binding site of protein kinases: Preferred geometry and topology of ligand binding

“…Specific interactions between the halogen atoms (Cl, Br, I) of halogenated ligands and the electron pairs of oxygen/nitrogen/sulfur have been identified in many crystal structures of supramolecular ensembles [1][2][3] as well as in complexes between biomolecules and halogenated ligands [4][5][6][7][8]. In both cases this is based in part on the observation that the distance between a halogen atom and its electron-donating partner is significantly lower than the sum of their vdW radii ( Figure 1).…”

“…Statistical analysis showed that such halogen bonds exhibit a geometry similar to that of hydrogen bonds [4], including a directional preference. However, despite the clear evidence of short halogen-bonding contacts in many protein-ligand structures, their energetic contribution is still under active debate [2,6,[11][12][13][14][15][16][17][18][19].…”