@article{,
title = {Brownian-dynamics simulations of metal-ion binding to four-way junctions},
author = {B N van Buuren and T Hermann and S S Wijmenga and E Westhof},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11788713},
isbn = {11788713},
year = {2002},
date = {2002-01-01},
journal = {Nucleic Acids Res},
volume = {30},
number = {2},
pages = {507-514},
abstract = {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 degrees or around -70 to -80 degrees. 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.},
note = {1362-4962
Journal Article},
keywords = {Base Pair Mismatch Base Sequence Binding Sites Cations/*metabolism *Computer Simulation DNA/*chemistry/genetics/*metabolism Diffusion Electrostatics Metals/*metabolism Models, Biomolecular *Nucleic Acid Conformation Nucleic Acid Hybridization RNA/chemistry/genetics/metabolism Recombination, Genetic/*genetics Support, Molecular Nuclear Magnetic Resonance, Non-U.S. Gov't, Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
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 degrees or around -70 to -80 degrees. 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.