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. 2016 Jan;13(1):55-8.
doi: 10.1038/nmeth.3658. Epub 2015 Nov 16.

Parmbsc1: a refined force field for DNA simulations

Ivan Ivani  1   2 , Pablo D Dans  1   2 , Agnes Noy  3 , Alberto Pérez  4 , Ignacio Faustino  1   2 , Adam Hospital  1   2 , Jürgen Walther  1   2 , Pau Andrio  2   5 , Ramon Goñi  2   5 , Alexandra Balaceanu  1   2 , Guillem Portella  1   2   6 , Federica Battistini  1   2 , Josep Lluis Gelpí  2   7 , Carlos González  8 , Michele Vendruscolo  6 , Charles A Laughton  9   10 , Sarah A Harris  3 , David A Case  11 , Modesto Orozco  1   2   7
Affiliations

Parmbsc1: a refined force field for DNA simulations

Ivan Ivani et al. Nat Methods. 2016 Jan.

Abstract

We present parmbsc1, a force field for DNA atomistic simulation, which has been parameterized from high-level quantum mechanical data and tested for nearly 100 systems (representing a total simulation time of ∼ 140 μs) covering most of DNA structural space. Parmbsc1 provides high-quality results in diverse systems. Parameters and trajectories are available at http://mmb.irbbarcelona.org/ParmBSC1/.

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Figures

Figure 1
Figure 1. Analysis of the Drew-Dickerson dodecamer
(a) Visual comparison of MD average structure (brown) and NMR structure (PDB id: 1NAJ) (light blue) and X-ray structure (PDB id: 1BNA) (green). (b) RMSd of 1.2 μs trajectory of DDD compared with BDNA (blue) and A-DNA (green) form (coming from Fiber). (c) RMSd compared to experimental structures (with (dark) and without (light) ending base-pairs): X-ray (green) and NMR (blue). Linear fits of all RMSd curves are plotted on top. (d) Evolution of total number of hydrogen bonds formed between base pairs in the whole duplex. (e) Helical rotational parameters (twist, roll, and tilt) comparison of average values per base-pair step (standard deviations are shown by error bars) coming from NMR (cyan), X-ray (dark green), 1 μs parmbsc0 trajectory (black) and 1.2 μs parmbsc1 trajectory (violet).
Figure 2
Figure 2. Analysis of non-canonical DNA structures
(a) Comparison of Z-DNA (PDB id: 1I0T) simulations in neutralized conditions (green) and in 4 M solution of Na+Cl− (blue). Structural comparisons at given time points are shown above the RMSd curves. (b) Simulation of anti-parallel H-DNA (PDB id: 2AF1) showing deviation of the structure over time (highlighted in red). RMSd of (c) parallel d(T-A•T)10, (d) parallel d(G-G•C)10, and (e) antiparallel d(G-G•C)10 triplexes. (f) Parallel (PDB id: 352D) and (g) anti-parallel (PDB id: 156D) quadruplex showing stable structures over time. (h) Structural stability of d(GCGAAGC) hairpin (PDB id: 1PQT) and (i) OxyQ quadruplex (PDB id: 1JRN) with ions, over time. (j) Human Telomeric Quadruplex (PDB id: 1KF1) with highlighted loops. RMSd of HTQ backbone, loop 1, loop 2 and loop 3 regions are shown below. In all panels, parmbsc1 (final, averaged or at a given trajectory point) structures (light blue; also green for Z-DNA) are overlapped over experimental structure (grey) for comparison. See Supplementary Table 1 for information on the PDB structures.
Figure 3
Figure 3. Analysis of DNA-protein complexes
Structural details of microsecond trajectories of four complexes with PDB id: 1TRO (a), 2DGC (b), 3JXC (c) and 1KX5 (d) (500 ns trajectory). Each plot shows overlap of the MD starting (red) and final (blue) structures, time dependent mass-weighted root mean square deviation (RMSD in Å) of all DNA (red) and protein (cyan) heavy atoms, and comparison of the values of rotational helical parameter roll (in degrees) at each base pair step calculated from the X-ray crystal structure (cyan) and averaged along the MD simulation (red line with the standard deviation envelope in light red). For clarity, in the 1KX5 plot of the roll value, the base pair steps are defined by the number of the position along the DNA strand and not by the base pair step name.
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References

    1. Pérez A, Luque FJ, Orozco M. Acc. Chem. Res. 2011;45:196–205. - PubMed
    1. Pérez A, Luque FJ, Orozco M. J. Am. Chem. Soc. 2007;129:14739–14745. - PubMed
    1. Varnai P, Zakrzewska K. Nucleic Acids Res. 2004;32:4269–4280. - PMC - PubMed
    1. Pérez A, et al. Biophys. J. 2007;92:3817–3829. - PMC - PubMed
    1. Zgarbová M, et al. J. Chem. Theory Comput. 2013;9:2339–2354. - PMC - PubMed

Online Methods references

    1. Krishnan R, Binkley JS, Seeger R, Pople JA. J. Chem. Phys. 1980;72:650–654.
    1. Woon DE, Dunning TH., Jr J. Chem. Phys. 1993;98:1358–1371.
    1. Becke AD. J. Chem. Phys. 1993;98:5648–5652.
    1. Head–Gordon M, Pople JA, Frisch MJ. Chemical Physics Letters. 1988;153:503–506.
    1. Halkier A, Helgaker T, Jørgensen P, Klopper W, Olsen J. Chem. Phys. Lett. 1999;302:437–446.

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