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Nucleic Acids Research, 2002, Vol. 30, No. 2 507-514
© 2002 Oxford University Press

Brownian-dynamics simulations of metal-ion binding to four-way junctions

Bernd N. M. van Buuren*, Thomas Hermann1, Sybren S. Wijmenga and Eric Westhof2

Department of Medical Biosciences, Medical Biophysics, Umeå University, S-90187 Umeå, Sweden, 1Computational Chemistry and Structure, Anadys Pharmaceuticals, Inc., 9050 Camino Santa Fe, San Diego, CA 92121, USA and 2Institut de Biologie Moleculaire et Cellulaire du CNRS, UPR 9002, 15 rue Rene Descartes, F-67084 Strasbourg, France

Four-way junctions (4Hs) are important intermediates in DNA rearrangements such as genetic recombination. Under the influence of multivalent cations these molecules undergo a conformational change, from an extended planar form to a quasi-continuous stacked X-structure. Recently, a number of X-ray structures and a nuclear magnetic resonance (NMR) structure of 4Hs have been reported and in three of these the position of multivalent cations is revealed. These structures belong to two main families, characterized by the angle between the two co-axial stacked helices, which is either around +40 to +55° or around –70 to –80°. To investigate the role of metal-ion binding on the conformation of folded 4Hs we performed Brownian-dynamics simulations on the set of available structures. The simulations confirm the proposed metal-ion binding sites in the NMR structure and in one of the X-ray structures. Furthermore, the calculations suggest positions for metal-ion binding in the other X-ray structures. The results show a striking dependence of the ion density on the helical environment (B-helix or A-helix) and the structural family.

* To whom correspondence should be addressed at present address: Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands. Tel: +31 30 253 9929; Fax: +31 30 253 7623; Email: bernd{at}nmr.chem.uu.nl


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