3DNA: a versatile, integrated software system for the analysis, rebuilding and visualization of three-dimensional nucleic-acid structures

Lu, Xiang‐Jun; Olson, Wilma K.

doi:10.1038/nprot.2008.104

Cited by 591 publications

(655 citation statements)

References 71 publications

(86 reference statements)

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“…Refinement and stereochemical quality statistics of the final model are shown in Table 1. The analysis of DNA structural parameters was carried out using the program 3DNA (36). Chimera was used to calculate structural alignments and root mean square deviations (r.m.s.d.)…”

Section: Methodsmentioning

confidence: 99%

Crystal Structures of the DNA-binding Domain Tetramer of the p53 Tumor Suppressor Family Member p73 Bound to Different Full-site Response Elements

Ethayathulla

Nguyen

Viadiu

2013

Journal of Biological Chemistry

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Background: Members of the p53 protein family bind to full-site response elements (REs) to trigger specific cellular pathways. Results: We solved two crystal structures of the p73 DNA-binding domain in complex with full-site REs. Conclusion: Lys-138 in loop L1 distinguishes between consensus REs. Significance: Conformational changes in Lys-138 might explain specificity between cell arrest and apoptosis target genes.

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Section: Methodsmentioning

confidence: 99%

Crystal Structures of the DNA-binding Domain Tetramer of the p53 Tumor Suppressor Family Member p73 Bound to Different Full-site Response Elements

Ethayathulla

Nguyen

Viadiu

2013

Journal of Biological Chemistry

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“…S1. Analysis of DNA parameters was carried out using the programs Curvesϩ (49), 3DNA (50), and Entanlge (51).…”

Section: Methodsmentioning

confidence: 99%

Structure of the Escherichia coli Antitoxin MqsA (YgiT/b3021) Bound to Its Gene Promoter Reveals Extensive Domain Rearrangements and the Specificity of Transcriptional Regulation

Brown¹,

Wood

Peti³

et al. 2011

Journal of Biological Chemistry

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Bacterial cultures, especially biofilms, produce a small number of persister cells, a genetically identical subpopulation of wild type cells that are metabolically dormant, exhibit multidrug tolerance, and are highly enriched in bacterial toxins. The gene most highly up-regulated in Escherichia coli persisters is mqsR, a ribonuclease toxin that, along with mqsA, forms a novel toxin⅐antitoxin (TA) system. Like all known TA systems, both the MqsR⅐MqsA complex and MqsA alone regulate their own transcription. Despite the importance of TA systems in persistence and biofilms, very little is known about how TA modules, and antitoxins in particular, bind and recognize DNA at a molecular level. Here, we report the crystal structure of MqsA bound to a 26-bp fragment from the mqsRA promoter. We show that MqsA binds DNA predominantly via its C-terminal helix-turn-helix domain, with direct binding of recognition helix residues Asn 97 and Arg 101 to the DNA major groove. Unexpectedly, the structure also revealed that the MqsA N-terminal domain interacts with the DNA phosphate backbone. This results in a more than 105°rotation of the Nterminal domains between the free and complexed states, an unprecedented rearrangement for an antitoxin. The structure also shows that MqsA bends the DNA by more than 55°in order to achieve symmetrical binding. Finally, using a combination of biochemical and NMR studies, we show that the DNA sequence specificity of MqsA is mediated by direct readout.

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“…Hydrogen atoms were added to the system according to expected protonation states at physiological pH using the Molecular Operating Environment (MOE) software package, and Na + were added manually in the vicinity of each phosphate group to produce an overall neutral structure. Where relevant, the central cytosine was also manually modified, and the results of all simulations were analysed using the X3DNA software package 21, 22 . Atomic coordinates of wild-type, methylated and hydroxymethylated DNA dodecamers were obtained from X-ray structures deposited in the Protein Data Bank (PDB IDs: 1BNA, 4GJU, 4GLG, 4GLH and 4GLC) 23 , and truncated to 5´-ATTCGCG-3´ heptamers containing a single modification on the central C. All DNA termini were capped with methyl groups for simplicity.…”

Section: Computational Methodologymentioning

confidence: 99%

Theoretical modelling of epigenetically modified DNA sequences

et al. 2015

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We report herein a set of calculations designed to examine the effects of epigenetic modifications on the structure of DNA. The incorporation of methyl, hydroxymethyl, formyl and carboxy substituents at the 5-position of cytosine is shown to hardly affect the geometry of CG base pairs, but to result in rather larger changes to hydrogen-bond and stacking binding energies, as predicted by dispersion-corrected density functional theory (DFT) methods. The same modifications within double-stranded GCG and ACA trimers exhibit rather larger structural effects, when including the sugar-phosphate backbone as well as sodium counterions and implicit aqueous solvation. In particular, changes are observed in the buckle and propeller angles within base pairs and the slide and roll values of base pair steps, but these leave the overall helical shape of DNA essentially intact. The structures so obtained are useful as a benchmark of faster methods, including molecular mechanics (MM) and hybrid quantum mechanics/molecular mechanics (QM/MM) methods. We show that previously developed MM parameters satisfactorily reproduce the trimer structures, as do QM/MM calculations which treat bases with dispersion-corrected DFT and the sugar-phosphate backbone with AMBER. The latter are improved by inclusion of all six bases in the QM region, since a truncated model including only the central CG base pair in the QM region is considerably further from the DFT structure. This QM/MM method is then applied to a set of double-stranded DNA heptamers derived from a recent X-ray crystallographic study, whose size puts a DFT study beyond our current computational resources. These data show that still larger structural changes are observed than in base pairs or trimers, leading us to conclude that it is important to model epigenetic modifications within realistic molecular contexts.

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3DNA: a versatile, integrated software system for the analysis, rebuilding and visualization of three-dimensional nucleic-acid structures

Cited by 591 publications

References 71 publications

Crystal Structures of the DNA-binding Domain Tetramer of the p53 Tumor Suppressor Family Member p73 Bound to Different Full-site Response Elements

Crystal Structures of the DNA-binding Domain Tetramer of the p53 Tumor Suppressor Family Member p73 Bound to Different Full-site Response Elements

Structure of the Escherichia coli Antitoxin MqsA (YgiT/b3021) Bound to Its Gene Promoter Reveals Extensive Domain Rearrangements and the Specificity of Transcriptional Regulation

Theoretical modelling of epigenetically modified DNA sequences

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