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Unformatted text preview: Halogen bonds in biological molecules Pascal Auffinger †‡ , Franklin A. Hays § , Eric Westhof † , and P. Shing Ho ‡§ † Institut de Biologie Mole ´culaire et Cellulaire, Centre National de la Recherche Scientifique, Unite ´ Propre de Recherche 9002, Universite ´ Louis Pasteur, 15 Rue Rene ´ Descartes, F-67084 Strasbourg, France; and § Department of Biochemistry and Biophysics, Agriculture y Life Sciences Building, Room 2011, Oregon State University, Corvallis, OR 97331-7305 Communicated by K. E. van Holde, Oregon State University, Corvallis, OR, October 13, 2004 (received for review August 17, 2004) Short oxygen–halogen interactions have been known in organic chemistry since the 1950s and recently have been exploited in the design of supramolecular assemblies. The present survey of protein and nucleic acid structures reveals similar halogen bonds as po- tentially stabilizing inter- and intramolecular interactions that can affect ligand binding and molecular folding. A halogen bond in biomolecules can be defined as a short C O X z O O Y interaction (C O X is a carbon-bonded chlorine, bromine, or iodine, and O O Y is a carbonyl, hydroxyl, charged carboxylate, or phosphate group), where the X z O distance is less than or equal to the sums of the respective van der Waals radii (3.27 Å for Cl z O, 3.37Å for Br z O, and 3.50 Å for I z O) and can conform to the geometry seen in small molecules, with the C O X z O angle ' 165° (consistent with a strong directional polarization of the halogen) and the X z O O Y angle ' 120°. Alternative geometries can be imposed by the more com- plex environment found in biomolecules, depending on which of the two types of donor systems are involved in the interaction: ( i ) the lone pair electrons of oxygen (and, to a lesser extent, nitrogen and sulfur) atoms or ( ii ) the delocalized p-electrons of peptide bonds or carboxylate or amide groups. Thus, the specific geometry and diversity of the interacting partners of halogen bonds offer new and versatile tools for the design of ligands as drugs and materials in nanotechnology. molecular folding u molecular recognition u molecular design T wo recent biomolecular single-crystal structures, a four- stranded DNA Holliday junction (1) and an ultrahigh- resolution structure (0.66 Å) of the enzyme aldose reductase complex with a halogenated inhibitor (2), revealed unusually short Br z O contacts [ ' 3.0 Å, or ' 12% shorter than the sum of their van der Waals radii ( R vdW )]. The atypical contact in the enzyme complex was attributed to an electrostatic interaction between the polarized bromine and the lone pair electrons of the oxygen atom of a neighboring threonine side chain (3). Short halogen–oxygen interactions are not in themselves new: The chemist Odd Hassel (4) had earlier described Br z O distances as short as 2.7 Å ( ' 20% shorter than R vdW ) in crystals of Br 2 with various organic compounds....
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This note was uploaded on 05/28/2010 for the course WE BIBI010000 taught by Professor Marnikvuylsteke during the Spring '10 term at Ghent University.
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