Structural alphabets for conformational analysis of nucleic acids available at dnatco.datmos.org

Černý, Jiří; Božíková, Paulína; Malý, Michal; Tykač, Michal; Biedermannová, Lada; Schneider, Bohdan

doi:10.1107/s2059798320009389

Cited by 18 publications

(12 citation statements)

References 40 publications

(33 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…We do not discuss quantitative values that depend on the method used and consider the superposition areas qualitatively, i.e., small superposition (less than 1 Å 2 , frequently negligible ring overlap) or substantial overlap (more than 2 Å 2 ). The assignment of NtCs to optimized dDMPs and cdDMPs uses DNATCO software [28].…”

Section: Methodsmentioning

confidence: 99%

Understanding the Origin of Structural Diversity of DNA Double Helix

et al. 2021

View full text Add to dashboard Cite

Deciphering the contribution of DNA subunits to the variability of its 3D structure represents an important step toward the elucidation of DNA functions at the atomic level. In the pursuit of that goal, our previous studies revealed that the essential conformational characteristics of the most populated “canonic” BI and AI conformational families of Watson–Crick duplexes, including the sequence dependence of their 3D structure, preexist in the local energy minima of the elemental single-chain fragments, deoxydinucleoside monophosphates (dDMPs). Those computations have uncovered important sequence-dependent regularity in the superposition of neighbor bases. The present work expands our studies to new minimal fragments of DNA with Watson–Crick nucleoside pairs that differ from canonic families in the torsion angles of the sugar-phosphate backbone (SPB). To address this objective, computations have been performed on dDMPs, cdDMPs (complementary dDMPs), and minimal fragments of SPBs of respective systems by using methods of molecular and quantum mechanics. These computations reveal that the conformations of dDMPs and cdDMPs having torsion angles of SPB corresponding to the local energy minima of separate minimal units of SPB exhibit sequence-dependent characteristics representative of canonic families. In contrast, conformations of dDMP and cdDMP with SPB torsions being far from the local minima of separate SPB units exhibit more complex sequence dependence.

show abstract

Section: Methodsmentioning

confidence: 99%

Understanding the Origin of Structural Diversity of DNA Double Helix

et al. 2021

View full text Add to dashboard Cite

show abstract

“…The homology model of the FOXO4/IRE complex was based on the available crystal structure 3l2c, extending the 3l2c template DNA sequence “–CTATGTAAACAAC–” to the IRE “GACTATCAAAACAACGC” sequence. The necessary nucleotide substitutions as well as residues missing at the 5′ and 3′ termini were modeled using the MMB program. , The backbone conformation of the newly built termini was set to the canonical B form DNA using dinucleotide conformation class (NtC) BB00. , The geometry of the initial model was further equilibrated during a 200 ns molecular dynamics simulation in GROMACS 2021.4 using the ff14SB force field for FOXO4 and the tumuc1 force field for DNA. The model was placed in a rectangular box with the 10 Å shortest distance from the walls.…”

Section: Experimental Sectionmentioning

confidence: 99%

Isotopic Depletion Increases the Spatial Resolution of FPOP Top-Down Mass Spectrometry Analysis

Polák,

Černý,

Novák

2024

Anal. Chem.

Self Cite

View full text Add to dashboard Cite

Protein radical labeling, like fast photochemical oxidation of proteins (FPOP), coupled to a top-down mass spectrometry (MS) analysis offers an alternative analytical method for probing protein structure or protein interaction with other biomolecules, for instance, proteins and DNA. However, with the increasing mass of studied analytes, the MS/MS spectra become complex and exhibit a low signal-to-noise ratio. Nevertheless, these difficulties may be overcome by protein isotope depletion. Thus, we aimed to use protein isotope depletion to analyze FPOP-oxidized samples by top-down MS analysis. For this purpose, we prepared isotopically natural (IN) and depleted (ID) forms of the FOXO4 DNA binding domain (FOXO4-DBD) and studied the protein–DNA interaction interface with double-stranded DNA, the insulin response element (IRE), after exposing the complex to hydroxyl radicals. As shown by comparing tandem mass spectra of natural and depleted proteins, the ID form increased the signal-to-noise ratio of useful fragment ions, thereby enhancing the sequence coverage by more than 19%. This improvement in the detection of fragment ions enabled us to detect 22 more oxidized residues in the ID samples than in the IN sample. Moreover, less common modifications were detected in the ID sample, including the formation of ketones and lysine carbonylation. Given the higher quality of ID top-down MSMS data set, these results provide more detailed information on the complex formation between transcription factors and DNA-response elements. Therefore, our study highlights the benefits of isotopic depletion for quantitative top-down proteomics. Data are available via ProteomeXchange with the identifier PXD044447.

show abstract

“…All this information provides a goldmine for comparative studies on these factors, enabling trends in structure (and in other features such as DNA hydration) to be statistically assessed for large groups of structures (see, for example, refs. ( 101 , 102 , 103 , 104 )). Such data-mining studies have revealed for example that in duplex DNA sequences, the d(TA) step is the most flexible in terms of base step morphology parameters such as roll and tilt and thus can contribute to DNA helix bending ( 21 , 26 , 27 , 28 , 29 , 30 , 31 ).…”

Section: The Importance Of the Pdb And Ndb For Studies On Dna Structure Flexibility And Functionmentioning

confidence: 99%

Beyond the double helix: DNA structural diversity and the PDB

Neidle

2021

Journal of Biological Chemistry

View full text Add to dashboard Cite

This is a PDF file of an article that has undergone enhancements after acceptance, such as the addition of a cover page and metadata, and formatting for readability, but it is not yet the definitive version of record. This version will undergo additional copyediting, typesetting and review before it is published in its final form, but we are providing this version to give early visibility of the article. Please note that, during the production process, errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain.

show abstract

Structural alphabets for conformational analysis of nucleic acids available at dnatco.datmos.org

Cited by 18 publications

References 40 publications

Understanding the Origin of Structural Diversity of DNA Double Helix

Understanding the Origin of Structural Diversity of DNA Double Helix

Isotopic Depletion Increases the Spatial Resolution of FPOP Top-Down Mass Spectrometry Analysis

Beyond the double helix: DNA structural diversity and the PDB

Contact Info

Product

Resources

About