Movatterモバイル変換

[0]ホーム
URL:

Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
Thehttps:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

NIH NLM Logo
Log inShow account info
Access keysNCBI HomepageMyNCBI HomepageMain ContentMain Navigation
pubmed logo
Advanced Clipboard
User Guide

Full text links

Silverchair Information Systems full text link Silverchair Information Systems Free PMC article
Full text links

Actions

Share

.2015 Sep 18;43(16):7731-43.
doi: 10.1093/nar/gkv729. Epub 2015 Jul 21.

Complex long-distance effects of mutations that confer linezolid resistance in the large ribosomal subunit

Affiliations

Complex long-distance effects of mutations that confer linezolid resistance in the large ribosomal subunit

Simone Fulle et al. Nucleic Acids Res..

Abstract

The emergence of multidrug-resistant pathogens will make current antibiotics ineffective. For linezolid, a member of the novel oxazolidinone class of antibiotics, 10 nucleotide mutations in the ribosome have been described conferring resistance. Hypotheses for how these mutations affect antibiotics binding have been derived based on comparative crystallographic studies. However, a detailed description at the atomistic level of how remote mutations exert long-distance effects has remained elusive. Here, we show that the G2032A-C2499A double mutation, located > 10 Å away from the antibiotic, confers linezolid resistance by a complex set of effects that percolate to the binding site. By molecular dynamics simulations and free energy calculations, we identify U2504 and C2452 as spearheads among binding site nucleotides that exert the most immediate effect on linezolid binding. Structural reorganizations within the ribosomal subunit due to the mutations are likely associated with mutually compensating changes in the effective energy. Furthermore, we suggest two main routes of information transfer from the mutation sites to U2504 and C2452. Between these, we observe cross-talk, which suggests that synergistic effects observed for the two mutations arise in an indirect manner. These results should be relevant for the development of oxazolidinone derivatives that are active against linezolid-resistant strains.

© The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

PubMed Disclaimer

Figures

Figure 1.
Figure 1.
Binding region of linezolid in H50S. (A) Structure of the large ribosomal subunit (PDB code 3CPW (8)). The ribosomal RNA is shown in gray and the protein chains are shown in blue; the binding position of linezolid (red) is depicted by a black square. (B andC) Binding mode of linezolid in the PTC of H50S. Nucleotides forming the first (black labels) and second shell (light blue labels) of the binding site are depicted in B and C, respectively; the two mutation sites (G2032A and C2499A) are highlighted in green. The locations of the A- and P-site and of the exit tunnel are indicated.
Figure 2.
Figure 2.
RMSF and per-nucleotide contributions to the effective binding energy. Shown are nucleotides of the first shell of the binding site along with the two mutation sites 2032 and 2499 investigated in this study. The structure with the smallest RMSD to the average structure of the last 20 ns of the respective MD trajectory was used for visualization; linezolid is colored in yellow. (A–C) Per-nucleobase RMSF obtained from MD simulations of linezolid-H50Swt (A), linezolid-H50Smut (B) (deep blue: RMSF 0 Å; white: 1 Å; deep red: RMSF ≥ 2 Å) as well as the difference (linezolid-H50Smut – linezolid-H50Swt; deep blue: ≤ -2 Å; white: 0 Å; deep red: ≥ 2 Å). (D–F) Per-nucleotide contributions as computed by MM-PBSA for linezolid-H50Swt (D), linezolid-H50Smut (E) as well as the difference (linezolid-H50Smut – linezolid-H50Swt) (F) (deep red: ≤ −2 kcal mol−1; white: 0 kcal mol−1; deep blue: ≥ +2 kcal mol−1). Except for the mutated nucleotides, the data for the per-nucleotide decomposition for linezolid-H50Swt has been taken from (14).
Figure 3.
Figure 3.
Interactions of linezolid with nucleotides of the first shell and RMSF of linezolid. (A) Distances monitoring hydrogen bond formation between linezolid's acetamide NH group and the oxygens of the phosphate group of G2505 (linezolid-H50Swt: blue, linezolid-H50Smut: gray; only the smallest distance found in each snapshot is plotted) and between linezolid's acetamide NH group and O2’ of U2504 (linezolid-H50Swt: red). (B andC): Distances monitoring aromatic stacking interactions between the centers of mass of the oxazolidinone core and the nucleobase of U2504 (B), and between the fluorophenyl ring and the nucleobase of C2452 (C). Distances for linezolid-H50Swt and linezolid-H50Smut simulations are depicted with blue and gray lines, respectively. (D) RMSF of linezolid atoms during the linezolid-H50Swt (squares) and linezolid-H50Smut (triangles) simulations. The red line represents the difference between the RMSF of linezolid-H50Smut and linezolid-H50Swt simulations. The data for the linezolid-H50Swt simulation was taken from (14). (E) Chemical structure of linezolid.
Figure 4.
Figure 4.
Summary of interactions, contributions to the effective binding energy, and RMSF as well as proposed signaling pathways from the mutation sites to the binding site. (A) Scheme summarizing non-covalent interactions (Tables 1 and 2), contributions to the effective binding energy (Figure 2), and RMSF (Figure 2) of nucleotides forming the first (white ellipses) and second (light gray ellipses) shell of the PTC binding site and the two mutation sites (dark gray ellipses). Non-covalent interactions are displayed in green for linezolid-H50Swt and in orange for linezolid-H50Smut. Information on contributions to the effective binding energy and RMSF of each nucleotide are depicted on the left side for linezolid-H50Swt and on the right side for linezolid-H50Smut, respectively. See the legend for further details. (B) Routes by which the information of the double mutation is transmitted via second shell nucleotides to U2504 (red arrows) and C2452 (blue arrows), respectively, as well as synergistic effects between these two routes (yellow arrows). The gray arrow depicts a blocking effect of U2504 by U2572 in H50Swt described in (9), but not observed on the time scale of our simulations.
See this image and copyright information in PMC

Similar articles

See all similar articles

Cited by

References

    1. Davies J., Davies D. Origins and evolution of antibiotic resistance. Microbiol. Mol. Biol. Rev. 2010;74:417–433. - PMC - PubMed
    1. Wilson D.N. Ribosome-targeting antibiotics and mechanisms of bacterial resistance. Nat. Rev. Microbiol. 2014;12:35–48. - PubMed
    1. Shaw K.J., Barbachyn M.R. The oxazolidinones: past, present, and future. Ann. N.Y. Acad. Sci. 2011;1241:48–70. - PubMed
    1. Lawrence L., Danese P., DeVito J., Franceschi F., Sutcliffe J. In vitro activities of the Rx-01 oxazolidinones against hospital and community pathogens. Antimicrob. Agents Chemother. 2008;52:1653–1662. - PMC - PubMed
    1. Leach K.L., Brickner S.J., Noe M.C., Miller P.F. Linezolid, the first oxazolidinone antibacterial agent. Ann. N. Y. Acad. Sci. 2011;1222:49–54. - PubMed

Publication types

MeSH terms

Substances

Related information

LinkOut - more resources

Full text links
Silverchair Information Systems full text link Silverchair Information Systems Free PMC article
Cite
Send To

NCBI Literature Resources

MeSHPMCBookshelfDisclaimer

The PubMed wordmark and PubMed logo are registered trademarks of the U.S. Department of Health and Human Services (HHS). Unauthorized use of these marks is strictly prohibited.

[8]ページ先頭
©2009-2025 Movatter.jp