| Literature DB >> 33238710 |
Denis Lacabanne1, Julien Boudet2, Alexander A Malär1, Pengzhi Wu2,3, Riccardo Cadalbert1, Loic Salmon2, Frédéric H-T Allain2,3, Beat H Meier1, Thomas Wiegand1.
Abstract
Protein-nucleic acid interactions are essential in a variety of biological events ranging from the replication of genomic DNA to the synthesis of proteins. Noncovalent interactions guide such molecular recognition events, and protons are often at the center of them, particularly due to their capability of forming hydrogen bonds to the nucleicEntities:
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Year: 2020 PMID: 33238710 PMCID: PMC7734624 DOI: 10.1021/acs.jpcb.0c08150
Source DB: PubMed Journal: J Phys Chem B ISSN: 1520-5207 Impact factor: 2.991
Figure 1Solid-state NMR experiments to probe protein–nucleic acid interactions. Representation of correlations observed in a combination of solid-state NMR experiments to detect protein–nucleic acid contacts. Lysine, arginine, and tryptophan side-chains are shown as illustrative residues coordinating to a DNA strand. In this work, hnCδ1Hδ1, hNH, hCH, and hNεCε2 were used.
Figure 2Protein resonance assignment by 1H-detected solid-state NMR spectroscopy. (A) Representative 2D planes of 3D hCANH spectra (blue) and hNH spectrum (light green) of pRN1:ATP:DNA recorded at a MAS frequency of 100 kHz. (B) Strip plots illustrating the 3D sequential resonance assignment with four experiments: hCANH (blue), hNCAH (red), hNcoCAH (green), and hCAcoNH (purple).
Figure 3Arginine side-chains detected in solid-state NMR hNH spectra. Comparison of hNH spectra showing the arginine side-chain region for the pRN1:DNA (A Nη–Hη correlations and C Nε–Hε correlations) and pRN1:ATP:DNA complexes (B Nη–Hη correlations and D Nε–Hε correlations). Upon ATP-binding, R309 and R311 become detectable in the spectra, the first one at high proton chemical-shift values compatible with hydrogen-bond formation. Structures (E and F) are prepared from the PDB files 6GVU and 6GVT using pymol.[64] The carbon atoms of DNA and ATP are shown in yellow and green, respectively.
Figure 4Lysine side-chains detected in solid-state NMR hNH spectra. Comparison of hNH spectra (A and B) showing the lysine side-chain region for the pRN1:DNA (A) and pRN1:ATP:DNA (B). Structures (C and D) are prepared from the PDB files 6GVU and 6GVT using pymol.[64] The red circle highlights a missing lysine correlation for the pRN1:ATP:DNA compared to the pRN1:DNA complex. The carbon atoms of DNA and ATP are shown in yellow and green, respectively.
Figure 5Aromatic side-chain region detected by 1H fast MAS solid-state NMR. (A) hCH solid-state NMR spectrum of pRN1:DNA and (B) pRN1:ATP:DNA. (C) Overlay of the assigned spectra. (D) Superimposition of hNH spectra for the Trp side-chain region. The structures in E and F were drawn from the PDB files 6GVU and 6GVT using pymol.[64] Carbon atoms of DNA and ATP are shown in yellow and green, respectively.
Figure 6Solid-state NMR spectroscopic approaches to detect tryptophan side-chains. (A) SPECIFIC 15N, 13C spectra recorded at a MAS frequency of 17 kHz showing Trp side-chains for pRN1:DNA (shown in red) and pRN1:ATP:DNA (shown in green). Assignments are shown on the spectrum. (B) 13C,1H 2D hnCH spectrum recorded at a MAS frequency of 100 kHz of the binary complex selectively exciting only NC pairs of Trp side-chains (for the overlay with the hCH spectrum see part C). (D) 13C,1H 2D hnCH spectrum of pRN1:ATP:DNA selectively exciting only N–C pairs of Trp side-chains (for the overlay with the hCH spectrum see part E).