Aminoglycoside binding in the major groove of duplex RNA: the thermodynamic and electrostatic forces that govern recognition

Jin, Emily; Katritch, Vsevolod; Olson, Wilma K.; Kharatisvili, Malkhaz; Abagyan, Ruben; Pilch, Daniel S.

doi:10.1006/jmbi.2000.3639

Cited by 64 publications

(61 citation statements)

References 75 publications

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“…28,34,35 In this connection, we have shown that pH modulates the extent to which aminoglycosides thermally stabilize the host RNA (⌬T m ) as well as the observed binding energetics. 28,35 Specifically,…”

Section: Ph Dependence Of Aminoglycoside-rrna Recognitionmentioning

confidence: 95%

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Thermodynamics of aminoglycoside–rRNA recognition

Pilch¹,

Kaul²,

Barbieri³

et al. 2003

Biopolymers

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2-Deoxystreptamine (2-DOS) aminoglycosides are a family of structurally related broad-spectrum antibiotics that are used widely in the treatment of infections caused by aerobic Gram-negative bacilli. Their antibiotic activities are ascribed to their abilities to bind a highly conserved A site in the 16 S rRNA of the 30 S ribosomal subunit and interfere with protein synthesis. The abilities of the 2-DOS aminoglycosides to recognize a specific subdomain of a large RNA molecule make these compounds archetypical models for RNA-targeting drugs. This article presents a series of calorimetric, spectroscopic, osmotic stress, and computational studies designed to evaluate the thermodynamics (DeltaG, DeltaH, DeltaS, DeltaCp) of aminoglycoside-rRNA interactions, as well as the hydration changes that accompany these interactions. In conjunction with the current structural database, the results of these studies provide important insights into the molecular forces that dictate and control the rRNA binding affinities and specificities of the aminoglycosides. Significantly, identification of these molecular driving forces [which include binding-linked drug protonation reactions, polyelectrolyte contributions from counterion release, conformational changes, hydration effects, and molecular interactions (e.g., hydrogen bonds and van der Waals interactions)], as well as the relative magnitudes of their contributions to the binding free energy, could not be achieved by consideration of structural data alone, highlighting the importance of acquiring both thermodynamic and structural information for developing a complete understanding of the drug-RNA binding process. The results presented here begin to establish a database that can be used to predict, over a range of conditions, the relative affinity of a given aminoglycoside or aminoglycoside mimetic for a targeted RNA site vs binding to potential competing secondary sites. This type of predictive capability is essential for establishment of a rational design approach to the development of new RNA-targeted drugs.

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Section: Ph Dependence Of Aminoglycoside-rrna Recognitionmentioning

confidence: 95%

“…28,34,35 It is therefore important to understand the pH-dependent chemical properties of the aminoglycosides, as well as the nature of the relationship between these properties and the RNA binding affinity and specificity exhibited by the drugs. Such information would be difficult to obtain from structural studies alone.…”

Section: Summary and Concluding Remarksmentioning

confidence: 99%

Thermodynamics of aminoglycoside–rRNA recognition

Pilch¹,

Kaul²,

Barbieri³

et al. 2003

Biopolymers

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“…ITC is the only technique that allows the direct thermodynamic analysis of biomolecular interactions, providing the binding constant and stoichiometry in addition to the enthalpy and entropy of binding. Several ITC studies showed that electrostatic binding is usually driven by enthalpy (3,26,31,41,50). However, it is important to point out that the calorimetric enthalpy is actually a sum of all the heat effects, endothermic and exothermic, taking place during the interaction.…”

Section: Vol 76 2002 Membrane Recognition By Vsv G Protein 3761mentioning

confidence: 99%

Membrane Recognition by Vesicular Stomatitis Virus Involves Enthalpy-Driven Protein-Lipid Interactions

Carneiro¹,

Bianconi²,

Weissmüller

et al. 2002

J Virol

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Vesicular stomatitis virus (VSV) infection depends on the fusion of viral and cellular membranes, which is mediated by virus spike glycoprotein G at the acidic environment of the endosomal compartment. VSV G protein does not contain a hydrophobic amino acid sequence similar to the fusion peptides found among other viral glycoproteins, suggesting that membrane recognition occurs through an alternative mechanism. Here we studied the interaction between VSV G protein and liposomes of different phospholipid composition by force spectroscopy, isothermal titration calorimetry (ITC), and fluorescence spectroscopy. Force spectroscopy experiments revealed the requirement for negatively charged phospholipids for VSV binding to membranes, suggesting that this interaction is electrostatic in nature. In addition, ITC experiments showed that VSV binding to liposomes is an enthalpically driven process. Fluorescence data also showed the lack of VSV interaction with the vesicles as well as inhibition of VSV-induced membrane fusion at high ionic strength. Intrinsic fluorescence measurements showed that the extent of G protein conformational changes depends on the presence of phosphatidylserine (PS) on the target membrane. Although the increase in PS content did not change the binding profile, the rate of the fusion reaction was remarkably increased when the PS content was increased from 25 to 75%. On the basis of these data, we suggest that G protein binding to the target membrane essentially depends on electrostatic interactions, probably between positive charges on the protein surface and negatively charged phospholipids in the cellular membrane. In addition, the fusion is exothermic, indicating no entropic constraints to this process.

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“…RNA function has been inhibited by small molecules (Fourmy et al 1996;Cho et al 1998;Carter et al 2000;Jin et al 2000;Lynch and Puglisi 2001a,b;Kaul and Pilch 2002; ODMiR inhibition of E. coli RNase P www.rnajournal.org Vicens and Westhof 2002;Lynch et al 2003) and oligonucleotide-based therapeutics (Galderisi et al 1999;Stein 2001;Disney et al 2003). Oligonucleotide-based therapeutics can be rapidly designed and screened because much is known about molecular recognition between oligonucleotides and RNA, analogs are synthetically accessible (Freier and Altmann 1997), and their pharmacokinetic properties are likely to be similar (Crooke et al 1996).…”

Section: Discussionmentioning

confidence: 99%

Inhibition of Escherichia coli RNase P by oligonucleotide directed misfolding of RNA

Childs

Poole²,

Turner³

2003

RNA

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Oligonucleotide directed misfolding of RNA (ODMiR) uses short oligonucleotides to inhibit RNA function by exploiting the ability of RNA to fold into different structures with similar free energies. It is shown that the 2 -O-methyl oligonucleotide, m(CAGCCUACCCGG), can trap Escherichia coli RNase P RNA (M1 RNA) in a nonfunctional structure in a transcription mixture containing RNase P protein (C5 protein). At about 200 nM, the 12-mer thus inhibits 50% of pre-tRNA processing by RNase P. Roughly 10-fold more 12-mer is required to inhibit RNase P containing full-length, renatured RNase P RNA. Diethyl pyrocarbonate modification in the presence of 12-mer reveals increased modification of sites in and interacting with P4, suggesting a structural rearrangement of a large pseudoknot important for catalytic activity. Thus, the ODMiR method can be applied to RNAs even when folding is facilitated by a cognate protein.

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Aminoglycoside binding in the major groove of duplex RNA: the thermodynamic and electrostatic forces that govern recognition

Cited by 64 publications

References 75 publications

Thermodynamics of aminoglycoside–rRNA recognition

Thermodynamics of aminoglycoside–rRNA recognition

Membrane Recognition by Vesicular Stomatitis Virus Involves Enthalpy-Driven Protein-Lipid Interactions

Inhibition of Escherichia coli RNase P by oligonucleotide directed misfolding of RNA

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