| Autor: |
Strelnikov IA; N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 4 Kosygin Street, Moscow 119991, Russia., Kovaleva NA; N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 4 Kosygin Street, Moscow 119991, Russia., Zubova EA; N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 4 Kosygin Street, Moscow 119991, Russia. |
| Jazyk: |
angličtina |
| Zdroj: |
Journal of chemical information and modeling [J Chem Inf Model] 2021 Sep 27; Vol. 61 (9), pp. 4783-4794. Date of Electronic Publication: 2021 Sep 16. |
| DOI: |
10.1021/acs.jcim.1c00506 |
| Abstrakt: |
We have analyzed and compared the available experimental data (PDB) on the backbone geometry of the DNA in solution (NMR), in crystals (X-rays), and in complexes with proteins (X-rays and cryo-electron microscopy). The deoxyribose (pseudorotational angle τ 0 ) and ε/ζ (BI-BII transition in phosphates) flexibilities are practically the same in the four samples. The α/γ mobility is minimal in crystalline DNA: on the histograms, there is one canonical and one noncanonical t / t peak. The α/γ mobility increases in DNA solutions (three more noncanonical peaks) and is maximal in DNA-protein complexes (another additional peak). On a large amount of data, we have confirmed that the three main degrees of freedom of the sugar-phosphate backbone are "orthogonal": changes in any of the angles τ 0 , (ζ-ε), and (γ-α) occur, as a rule, at a constant (usually canonical) value of any other. In the DNA-protein complexes, none of the geometrical parameters commonly used to distinguish the A and B forms of DNA, except for Zp and its simpler analog Zp ', show an unambiguous correlation with τ 0 . Proteins, binding to DNA, in 59% of cases change the local shape of the helix up to the characteristic of the A-form without switching the deoxyribose conformation from south to north. However, we have found simple local characteristics of one nucleotide that correlate with the angles τ 0 and (ζ-ε). These are the angles C3'C1'N* and C4'C3'P(2), respectively. They are orthogonal in DNA-protein complexes exactly as the pair τ 0 and (ζ-ε). Most characteristics of DNA in complexes with proteins are the same in X-ray and in cryo-EM data, except for the histogram for the angle τ 0 . We offer a possible explanation for this difference. We also discuss the artifacts on the ε/ζ histogram for DNA in solutions caused by the currently used NMR refinement protocols. |
| Databáze: |
MEDLINE |
| Externí odkaz: |
|
