Proc Natl Acad Sci U S A 101(48): 16789-16794

Halogen bonds in biological molecules

^{Institut de Biologie Moléculaire et Cellulaire, Centre National de la Recherche Scientifique, Unité Propre de Recherche 9002, Université Louis Pasteur, 15 Rue René Descartes, F-67084 Strasbourg, France; and}^{Department of Biochemistry and Biophysics, Agriculture/Life Sciences Building, Room 2011, Oregon State University, Corvallis, OR 97331-7305}

^{To whom correspondence may be addressed. E-mail:}ude.tsro.dino@spoh or rf.gbsats-u.cmbi@regniffua.p.

Communicated by K. E. van Holde, Oregon State University, Corvallis, OR, October 13, 2004

Received 2004 Aug 17

Freely available online through the PNAS open access option.

Abstract

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 potentially 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 An external file that holds a picture, illustration, etc.
Object name is cjs0807.jpg X···OY interaction (CX is a carbon-bonded chlorine, bromine, or iodine, and OY is a carbonyl, hydroxyl, charged carboxylate, or phosphate group), where the X···O distance is less than or equal to the sums of the respective van der Waals radii (3.27 Å for Cl···O, 3.37Å for Br···O, and 3.50 Å for I···O) and can conform to the geometry seen in small molecules, with the C An external file that holds a picture, illustration, etc.
Object name is cjs0807.jpg X···O angle ≈165° (consistent with a strong directional polarization of the halogen) and the X···OY angle ≈120°. Alternative geometries can be imposed by the more complex 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 π -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.

Keywords: molecular folding, molecular recognition, molecular design

Abstract

Two 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···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···O distances as short as 2.7 Å (≈20% shorter than R_vdW) in crystals of Br₂ with various organic compounds.

These short contacts, originally called charge-transfer bonds, were attributed to the transfer of negative charge from an oxygen, nitrogen, or sulfur (a Lewis base) to a polarizable halogen (a Lewis acid) (5, 6). They are now referred to as halogen bonds (Fig. 1) by analogy to classical hydrogen bonds with which they share numerous properties (6) and are currently being exploited to control the crystallization of organic compounds in the design of new materials (7) as well as in supramolecular chemistry (6). Extensive surveys of structures in the Cambridge Structural Database (8–10) coupled with ab initio calculations (10) have characterized the geometry of halogen bonds in small molecules and show that the interaction is primarily electrostatic, with contributions from polarization, dispersion, and charge transfer. The stabilizing potential of halogen bonds is estimated to range from about half to slightly greater than that of an average hydrogen bond in directing the self-assembly of organic crystals (11, 12).

An external file that holds a picture, illustration, etc.
Object name is zpq0480465480001.jpg

Fig. 1.

Schematic of short halogen (X) interactions to various oxygen-containing functional groups (where O An external file that holds a picture, illustration, etc.
Object name is cjs0807.jpg Y can be a carbonyl, hydroxyl, or carboxylate when Y is a carbon; a phosphate when Y is a phosphorus; or a sulfate when Y is a sulfur). The geometry of the interaction is defined by the normalized R_X_···O distance [R_X_···O = d_X_···O/R_vdW(_X_···O)], the Θ₁ angle of the oxygen relative to the C An external file that holds a picture, illustration, etc.
Object name is cjs0807.jpg X bond, and the Θ₂ angle of the halogen relative to the OY bond.

Similar short halogen–oxygen contacts have rarely been described in biological systems, presumably because of the scarcity of available crystal structures of halogenated biomolecules. As such, their structural and functional roles have been largely ignored in biology. Halogens, however, do play important roles in natural systems. Thyroid hormones represent a class of naturally iodinated molecules for which halogen bonds appear to play a role in their recognition, as evident by the short I···O contacts between tetraiodothyroxine and its transport protein transthyretin (13). In addition, >3,500 halogen-containing metabolites, including the important antibiotics chloramphenicol, 7-chlorotetracyclin, and vancomycin (14), are currently known. Moreover, direct halogenation of proteins and nucleic acids can result from oxidative halogenation by a number of peroxidases involved in inflammatory responses. For example, levels of chlorotyrosines have been correlated with chronic respiratory disease in infants (15), whereas bromotyrosines are associated with allergen-induced asthma (16). In nucleic acids, DNA bases are oxidatively brominated by eosinophil peroxidase (17) and, specifically for brominated cytosines, have been suggested to induce a conformation that may be susceptible to spontaneous transition mutations (18).

Our interest in halogen-induced conformational effects initiated with the observation that the brominated DNA sequence d(CCAGTACbr^UGG) (br^{U, 5-bromouridine) adopts a four-stranded Holliday junction with an associated short Br···O distance (≈3.0 Å). In contrast, standard B-DNA duplexes were seen in the closely related d(CCAGTAC}TGG) (1) and the nonbrominated d(CCAGTACUGG) sequences (unpublished data), where T (a methylated uridine) and U replace br^{U (shown in bold italics). These results could not be explained by the known molecular interactions because of our own ignorance concerning halogen bonds, as is probably true for much of the biochemistry community.}

In the current study, quantum mechanical calculations were used to generate electrostatic potential maps to compare the polarizability of halogen atoms within the context of biological molecules, and a data set of protein and nucleic acid structures with short halogen–oxygen distances was assembled and surveyed to characterize the prevalence and geometry of halogen bonds in biological systems.

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Acknowledgments

We thank Dr. P. A. Karplus for his inquisitiveness, which helped to initiate this study. This work was supported by National Institutes of Health Grant R1GM62957A, National Science Foundation Grant MCB0090615, National Institutes of Environmental Health Sciences Grant ES00210, a Fulbright grant (to P.S.H.), and a grant from the Institut Universitaire de France (to E.W.).

Acknowledgments

Notes

Abbreviations: br^{U, 5-bromouridine; X}^{U, 5-halouridine; X}^{C, 5-halocytosine;}R_vdW, sum of van der Waals radii; PDB, Protein Data Bank; O_W, oxygen atom of a water molecule.

Notes

Abbreviations: br^{U, 5-bromouridine; X}^{U, 5-halouridine; X}^{C, 5-halocytosine;}R_vdW, sum of van der Waals radii; PDB, Protein Data Bank; O_W, oxygen atom of a water molecule.

References

1. Hays, F. A., Vargason, J. M. & Ho, P. S. (2003) Biochemistry42, 9586–9597. [[PubMed]
2. Howard, E. I., Sanishvili, R., Cachau, R. E., Mitschler, A., Chevrier, B., Barth, P., Lamour, V., Van Zandt, M., Sibley, E., Bon, C., et al. (2004) Proteins55, 792–804. [[PubMed]
3. Muzet, N., Guillot, B., Jelsch, C., Howard, E. & Lecomte, C. (2003) Proc. Natl. Acad. Sci. USA100, 8742–8747.
4. Hassel, O(1972) in Nobel Lectures, Chemistry 1963–1970 (Elsevier, Amsterdam).[Google Scholar]
5. Foster, R(1969) Organic Charge-Tranfer Complexes (Academic, London).[Google Scholar]
6. Metrangolo, P. & Resnati, G. (2001) Chem. Eur. J.7, 2511–2519. [[PubMed]
7. Brisdon, A(2002) Annu. Rep. Prog. Chem.98, 107–114. [PubMed][Google Scholar]
8. Cody, V. & Murray-Rust, P. (1984) J. Mol. Struct.112, 189–199. [PubMed]
9. Ouvrard, C., Le Questel, J. Y., Berthelot, M. & Laurence, C. (2003) Acta Crystallogr. B59, 512–526. [[PubMed]
10. Lommerse, J. P. M., Stone, A. J., Taylor, R. & Allen, F. H. (1996) J. Am. Chem. Soc.118, 3108–3116. [PubMed]
11. Corradi, E., Meille, S. V., Messina, M. T., Metrangolo, P. & Resnati, G. (2000) Angew. Chem. Int. Ed.112, 1852–1856. [PubMed]
12. Lommerse, J. P. M., Price, S. L. & Taylor, R. (1997) J. Comput. Chem.18, 757–774. [PubMed]
13. Wojtczak, A., Cody, V., Luft, J. R. & Pangborn, W. (2001) Acta Crystallogr. D57, 1061–1070. [[PubMed]
14. van Pee, K. H. & Unversucht, S. (2003) Chemosphere52, 299–312. [[PubMed]
15. Buss, I. H., Senthilmohan, R., Darlow, B. A., Mogridge, N., Kettle, A. J. & Winterbourn, C. C. (2003) Pediatr. Res.53, 455–462. [[PubMed]
16. Wu, W., Samoszuk, M. K., Comhair, S. A., Thomassen, M. J., Farver, C. F., Dweik, R. A., Kavuru, M. S., Erzurum, S. C. & Hazen, S. L. (2000) J. Clin. Invest.105, 1455–1463.
17. Shen, Z., Mitra, S. N., Wu, W., Chen, Y., Yang, Y., Qin, J. & Hazen, S. L. (2001) Biochemistry40, 2041–2051. [[PubMed]
18. Vargason, J. M., Eichman, B. F. & Ho, P. S. (2000) Nat. Struct. Biol.7, 758–761. [[PubMed]
19. Mecozzi, S., West, A. P., Jr, & Dougherty, D. A. (1996) Proc. Natl. Acad. Sci. USA93, 10566–10571.
20. Berman, H. M., Battistuz, T., Bhat, T. N., Bluhm, W. F., Bourne, P. E., Burkhardt, K., Feng, Z., Gilliland, G. L., Iype, L., Jain, S., et al. (2002) Acta Crystallogr. D58, 899–907. [[PubMed]
21. Bondi, A(1964) J. Chem. Phys.68, 441–451. [PubMed][Google Scholar]
22. Brünger, A. T., Adams, P. D., Clore, G. M., DeLano, W. L., Gros, P., Grosse-Kunstleve, R. W., Jiang, J. S., Kuszewski, J., Nilges, M., Pannu, N. S., et al. (1998) Acta Crystallogr. D54, 905–921. [[PubMed]
23. Collaborative Computational Project Number 4(1994) Acta Crystallogr. D50, 760–763. [[PubMed][Google Scholar]
24. Karplus, P. A. (1996) Protein Sci.5, 1406–1420.
25. Allen, F. H., Baalham, C. A., Lommerse, J. P. M. & Raithby, P. R. (1998) Acta Crystallogr. B54, 320–329. [PubMed]
26. Sarkhel, S. & Desiraju, G. R. (2004) Proteins54, 247–259. [[PubMed]
27. De Moliner, E., Brown, N. R. & Johnson, L. N. (2003) Eur. J. Biochem.270, 3174–3181. [[PubMed]
28. Sunami, T., Kondo, J., Hirao, I., Watanabe, K., Miura, K. I. & Takenaka, A. (2004) Acta Crystallogr. D60, 90–96. [[PubMed]
29. Sunami, T., Kondo, J., Kobuna, T., Hirao, I., Watanabe, K., Miura, K. & Takenaka, A. (2002) Nucleic Acids Res.30, 5253–5260.
30. Seeman, N. C. (2004) Sci. Am.290, 71–75. [PubMed]
31. Wang, J., Wolf, R. M., Caldwell, J. W., Kollman, P. A. & Case, D. A. (2004) J. Comput. Chem.25, 1157–1174. [[PubMed]