Experimental Evidence for the Existence of Non-exo-Anomeric Conformations in Branched Oligosaccharides: NMR Analysis of the Structure and Dynamics of Aminoglycosides of the Neomycin Family

Asensio, Juan Luis; Hidalgo, Antonio Vásquez; Cuesta, Igor; González, Carlos; Cañada, F. Javier; Vicent, Cristina; Chiara, José Luis; Cuevas, Gabriel; Jiménez‐Barbero, Jesús

doi:10.1002/1521-3765(20021115)8:22<5228::aid-chem5228>3.0.co;2-l

Cited by 23 publications

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“…Similarly, rotamer populations around ϕ and ψ are more widely scattered in the unbound than in the bound state. The increased flexibility of free paromomycin is consistent with both theoretical and experimental observations46 for other aminoglycosides of the neomycin family. Rotamer populations in the bound state are clustered around ϕ values (ϕ ∼±60°) that correspond to the exoanomeric conformation (Figure 9D).…”

Section: Resultssupporting

confidence: 86%

“…The three‐dimensional structure of oligosaccharides plays a critical role in their interaction with nucleic acids 46, 47. It has been argued that RNA recognizes and binds the “native” solution conformers of aminoglycosides and that the binding event does not produce major changes in drug conformation 46, 47. To compare the dynamic behavior of paromomycin in its bound and unbound states, a 3‐ns simulation of unbound paromomycin in explicit water solvent was performed.…”

Section: Resultsmentioning

confidence: 99%

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Erratum

2010

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We have recently introduced a computational methodology that combines molecular dynamics (MD) simulations, free‐energy calculations, and in vitro binding assays to predict the minimum RNA structural requirements for selective, high‐affinity RNA binding to small‐molecule ligands. Here, we show that this methodology can be applied to the conformationally flexible aminoglycoside antibiotic paromomycin. A RNA consisting of an 11‐mer:10‐mer duplex that contains one 16S ribosome RNA decoding A‐site bound to paromomycin was simulated for 4 ns. The methodology predicts that the 11‐mer:10‐mer duplex binds to paromomycin with high affinity, whereas smaller RNA duplexes lose complex stability and the ability to bind paromomycin. The predicted high‐affinity binding to paromomycin of the 11‐mer:10‐mer duplex was confirmed experimentally (EC50 = 0.28 μM), as well as the inability of smaller complexes to bind. Our simulations show good agreement with experiment for dynamic and structural properties of the isolated A‐site, including hydrogen‐bonding networks and RNA structural rearrangements upon ligand binding. The results suggest that MD simulations can supplement in vitro methods as a tool for predicting minimum RNA‐binding motifs for both small, rigid ligands, and large, flexible ligands when structural information is available. © 2007 Wiley Periodicals, Inc. Biopolymers 86: 95–111, 2007. This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com

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Section: Resultssupporting

confidence: 86%

Section: Resultsmentioning

confidence: 99%

Erratum

2010

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“…The partial atomic charges were determined on the basis of QM calculations, performed with the use of Gaussian29. The validity of the parameters was evaluated by comparing several inter-proton distances obtained during MD simulation of paromomycin in explicit solvent with the NMR data30 (for simulation details and parameters see Supporting Information). …”

Section: Methodsmentioning

confidence: 99%

Molecular Dynamics Study of the Ribosomal A-Site

2008

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Many aminoglycosidic antibiotics target the A-site of 16S RNA in the small ribosomal subunit and affect the fidelity of protein translation in bacteria. Upon binding aminoglycosides displace two adenines (A1492 and A1493 for E. coli numbering) that are involved in tRNA anticodon loop recognition. The major difference in the aminoglycosidic binding site between the prokaryota and eukaryota is an adenine into guanine substitution in the position 1408. This mutation likely affects the dynamics of near A1492 and A1493 and hinders the binding of aminoglycosides to eukaryotic ribosomes. With multiple 20 ns long all-atom molecular dynamics simulations we study the flexibility of a 22-nucleotide RNA fragment which mimics the aminoglycosidic binding site. Simulations are carried out for both, native and A1408G mutated RNA, as well as for their complexes with aminoglycosidic representative -paromomycin. We observe intra-and extrahelical configurations of A1492 and A1493, which differ between the prokaryotic and the mutated structure. We obtained configurations of the A-site that were also observed in the NMR and crystal structures. Our studies show the differences in the internal mobility of the A-site, as well as in ion and water density distributions inside the binding cleft, between the prokaryotic and mutated RNA. We also compare the performance of two force field parameters for RNA -Amber and Charmm.

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“…The syn-Ψ geometry also constitutes the most populated minimum for the free antibiotics, according to NMR data. 8 In contrast, the analogous glycosidic linkage of kanamycin bound to ANT4 is defined by an anti-ψ geometry (φ/ψ ) -21/152). This conformation represents a high-energy minimum that must be stabilized by specific aminoglycoside-ANT4 interactions.…”

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A Simple Structural-Based Approach to Prevent Aminoglycoside Inactivation by Bacterial Defense Proteins. Conformational Restriction Provides Effective Protection against Neomycin-B Nucleotidylation by ANT4

et al. 2005

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Herein, we describe how the conformational differences exhibited by aminoglycosides in the binding pockets of the ribosome and those enzymes involved in bacterial resistance can be exploited in the design of new antibiotic derivatives with improved activity in resistant strains. The simple modification shown in the figure, leading to the conformationally restricted 5, provides an effective protection against aminoglycoside inactivation by Staphylococcus aureus ANT4, both in vivo and in vitro.

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Experimental Evidence for the Existence of Non-exo-Anomeric Conformations in Branched Oligosaccharides: NMR Analysis of the Structure and Dynamics of Aminoglycosides of the Neomycin Family

Cited by 23 publications

References 13 publications

Erratum

Erratum

Molecular Dynamics Study of the Ribosomal A-Site

A Simple Structural-Based Approach to Prevent Aminoglycoside Inactivation by Bacterial Defense Proteins. Conformational Restriction Provides Effective Protection against Neomycin-B Nucleotidylation by ANT4

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