Dihedral-Based Segment Identification and Classification of Biopolymers II: Polynucleotides

Abstract

In an accompanying paper (Nagy, G.; Oostenbrink, C. Dihedral-based segment identification and classification of biopolymers I: Proteins. J. Chem. Inf. Model. 2013, DOI: 10.1021/ci400541d), we introduce a new algorithm for structure classification of biopolymeric structures based on main-chain dihedral angles. The DISICL algorithm (short for DIhedral-based Segment Identification and CLassification) classifies segments of structures containing two central residues. Here, we introduce the DISICL library for polynucleotides, which is based on the dihedral angles ε, ζ, and χ for the two central residues of a three-nucleotide segment of a single strand. Seventeen distinct structural classes are defined for nucleotide structures, some of which—to our knowledge—were not described previously in other structure classification algorithms. In particular, DISICL also classifies noncanonical single-stranded structural elements. DISICL is applied to databases of DNA and RNA structures containing 80,000 and 180,000 segments, respectively. The classifications according to DISICL are compared to those of another popular classification scheme in terms of the amount of classified nucleotides, average occurrence and length of structural elements, and pairwise matches of the classifications. While the detailed classification of DISICL adds sensitivity to a structure analysis, it can be readily reduced to eight simplified classes providing a more general overview of the secondary structure in polynucleotides.

Cellular levels and molecular dynamics simulations of estragole DNA adducts point at inefficient repair resulting from limited distortion of the double-stranded DNA helix

“…In the first strand of the DNA duplex, the simulation starting from the E_1 conformation showed obvious changes with respect to the reference DNA simulations, where the sharp turn (ST) type gave a 3.5% increase at the expense of the AB transition class. The ST type defines segments where the backbone turns more than 90° (Nagy and Oostenbrink 2014), which is consistent with the observation of the DNA backbone connecting C17 and G18 bases, accompanied by the base extrusion (Fig. 7).…”

“…The stability of the MD simulation for the reference double-stranded DNA helix and the modified DNA helix (with DNA adduct) was tested by monitoring RMSD, which represent the deviations in each trajectory snapshot relative to the respective starting structure. The form of the DNA helix was classified by the DISICL algorithm (Nagy and Oostenbrink 2014). The hydrogen bonding occupancy was analyzed using a geometric criterion.…”

“…A slight rise of the BL class (B-Loop) occupancy was observed in both simulations starting from the E_1 and E_3 conformations. Although the B-Loop cannot form the perfect B-helix, the increased percentage of B-Loop induces the structure shifting to become more like B-type helix (Nagy and Oostenbrink 2014). In the second strand, values of the unclassified (UC) and ST fractions in the simulation starting from the E_1 conformation increased with 5.2% and 0.9%, respectively, compared to the unmodified DNA, followed by a slight increase of the UC class (2.6%) in the E_2 simulation.…”

StreaMD: Advanced analysis of molecular dynamics using R

“…The xtc file used here contains only the atom coordinates of the riboswitch. In addition, we have the possibility to take other coarse‐graining schemes, e.g., reduced tree representation (structure element as a vertex), use of SPQR – SPlit and conQueR (one nucleotide as two vertices) or even the use of entire structural segments as vertex xtc.file <‐ “xtc.trajectory” stream.ofile <‐ tempfile() for (i in seq(1.1,1.5,0.1)){ } …”

MDplot: Visualise Molecular Dynamics

“…Automated figure generation is likely to aid in the understanding of results at the first glance and may be used in presentations and publications. Planned extensions include both the integration of new functionalities such as a DISICL (secondary structure classification (Nagy and Oostenbrink, 2014a,b)) as well as the provision of loading interfaces for additional molecular dynamics engines. Further developments will be published on the projects′ GitHub page and on CRAN.…”