Vinyldeoxyadenosine in a sarcin-ricin RNA loop and its binding to ricin toxin A-chain

Setu Roday, Suwipa Saen-oon, Vern L. Schramm

Research output: Contribution to journalArticle

3 Citations (Scopus)

Abstract

8-Vinyl-2′-deoxyadenosine (8vdA) is a fluorophore with a quantum yield comparable to that of 2-aminopurine nucleoside. 8vdA was incorporated into a 10-mer stem-tetraloop RNA (8vdA-10) structure for characterization of the properties of the base, 8-vinyladenine (8-vA), with respect to adenine as a substrate or inhibitor for ribosome-inactivating proteins. Ricin toxin A-chain (RTA) and pokeweed antiviral protein (PAP) catalyze the release of adenine from a specific adenosine on a stem-tetraloop (GAGA) sequence at the elongation factor (eEF2) binding site of the 28S subunit of eukaryotic ribosomes, thereby arresting translation. RTA does not catalyze the release of 8-vinyladenine from 8vdA-10. Molecular dynamics simulations implicate a role for Arg180 in oxacarbenium ion destabilization and the lack of catalysis. However, 8vdA-10 is an active site analogue and inhibits RTA with a Ki value of 2.4 μM. Adenine is also released from the second adenosine in the modified tetraloop, demonstrating an alternative mode for the binding of this motif in the RTA active site. The 8vdA analogue defines the specificities of RTA for the two adenylate depurination sites in a RNA substrate with a GAGA tetraloop. The rate of nonenzymatic acid-catalyzed solvolysis of 8-vinyladenine from the stem-loop RNA is described. Unlike RTA, PAP catalyzes the slow release of 8-vinyladenine from 8vdA-10. The isolation of 8-vA and its physicochemical characterization is described.

Original languageEnglish (US)
Pages (from-to)6169-6182
Number of pages14
JournalBiochemistry
Volume46
Issue number21
DOIs
StatePublished - May 29 2007

Fingerprint

Ricin
RNA
Adenine
Adenosine
Catalytic Domain
2-Aminopurine
Ribosome Inactivating Proteins
Peptide Elongation Factors
Ribosome Subunits
Fluorophores
Quantum yield
Substrates
Molecular Dynamics Simulation
2'-deoxyadenosine
Catalysis
Nucleosides
Molecular dynamics
Binding Sites
Ions
Acids

ASJC Scopus subject areas

  • Biochemistry

Cite this

Vinyldeoxyadenosine in a sarcin-ricin RNA loop and its binding to ricin toxin A-chain. / Roday, Setu; Saen-oon, Suwipa; Schramm, Vern L.

In: Biochemistry, Vol. 46, No. 21, 29.05.2007, p. 6169-6182.

Research output: Contribution to journalArticle

Roday, Setu ; Saen-oon, Suwipa ; Schramm, Vern L. / Vinyldeoxyadenosine in a sarcin-ricin RNA loop and its binding to ricin toxin A-chain. In: Biochemistry. 2007 ; Vol. 46, No. 21. pp. 6169-6182.
@article{d20da3f8ef1d400f8d052942a8a30f91,
title = "Vinyldeoxyadenosine in a sarcin-ricin RNA loop and its binding to ricin toxin A-chain",
abstract = "8-Vinyl-2′-deoxyadenosine (8vdA) is a fluorophore with a quantum yield comparable to that of 2-aminopurine nucleoside. 8vdA was incorporated into a 10-mer stem-tetraloop RNA (8vdA-10) structure for characterization of the properties of the base, 8-vinyladenine (8-vA), with respect to adenine as a substrate or inhibitor for ribosome-inactivating proteins. Ricin toxin A-chain (RTA) and pokeweed antiviral protein (PAP) catalyze the release of adenine from a specific adenosine on a stem-tetraloop (GAGA) sequence at the elongation factor (eEF2) binding site of the 28S subunit of eukaryotic ribosomes, thereby arresting translation. RTA does not catalyze the release of 8-vinyladenine from 8vdA-10. Molecular dynamics simulations implicate a role for Arg180 in oxacarbenium ion destabilization and the lack of catalysis. However, 8vdA-10 is an active site analogue and inhibits RTA with a Ki value of 2.4 μM. Adenine is also released from the second adenosine in the modified tetraloop, demonstrating an alternative mode for the binding of this motif in the RTA active site. The 8vdA analogue defines the specificities of RTA for the two adenylate depurination sites in a RNA substrate with a GAGA tetraloop. The rate of nonenzymatic acid-catalyzed solvolysis of 8-vinyladenine from the stem-loop RNA is described. Unlike RTA, PAP catalyzes the slow release of 8-vinyladenine from 8vdA-10. The isolation of 8-vA and its physicochemical characterization is described.",
author = "Setu Roday and Suwipa Saen-oon and Schramm, {Vern L.}",
year = "2007",
month = "5",
day = "29",
doi = "10.1021/bi0621821",
language = "English (US)",
volume = "46",
pages = "6169--6182",
journal = "Biochemistry",
issn = "0006-2960",
publisher = "American Chemical Society",
number = "21",

}

TY - JOUR

T1 - Vinyldeoxyadenosine in a sarcin-ricin RNA loop and its binding to ricin toxin A-chain

AU - Roday, Setu

AU - Saen-oon, Suwipa

AU - Schramm, Vern L.

PY - 2007/5/29

Y1 - 2007/5/29

N2 - 8-Vinyl-2′-deoxyadenosine (8vdA) is a fluorophore with a quantum yield comparable to that of 2-aminopurine nucleoside. 8vdA was incorporated into a 10-mer stem-tetraloop RNA (8vdA-10) structure for characterization of the properties of the base, 8-vinyladenine (8-vA), with respect to adenine as a substrate or inhibitor for ribosome-inactivating proteins. Ricin toxin A-chain (RTA) and pokeweed antiviral protein (PAP) catalyze the release of adenine from a specific adenosine on a stem-tetraloop (GAGA) sequence at the elongation factor (eEF2) binding site of the 28S subunit of eukaryotic ribosomes, thereby arresting translation. RTA does not catalyze the release of 8-vinyladenine from 8vdA-10. Molecular dynamics simulations implicate a role for Arg180 in oxacarbenium ion destabilization and the lack of catalysis. However, 8vdA-10 is an active site analogue and inhibits RTA with a Ki value of 2.4 μM. Adenine is also released from the second adenosine in the modified tetraloop, demonstrating an alternative mode for the binding of this motif in the RTA active site. The 8vdA analogue defines the specificities of RTA for the two adenylate depurination sites in a RNA substrate with a GAGA tetraloop. The rate of nonenzymatic acid-catalyzed solvolysis of 8-vinyladenine from the stem-loop RNA is described. Unlike RTA, PAP catalyzes the slow release of 8-vinyladenine from 8vdA-10. The isolation of 8-vA and its physicochemical characterization is described.

AB - 8-Vinyl-2′-deoxyadenosine (8vdA) is a fluorophore with a quantum yield comparable to that of 2-aminopurine nucleoside. 8vdA was incorporated into a 10-mer stem-tetraloop RNA (8vdA-10) structure for characterization of the properties of the base, 8-vinyladenine (8-vA), with respect to adenine as a substrate or inhibitor for ribosome-inactivating proteins. Ricin toxin A-chain (RTA) and pokeweed antiviral protein (PAP) catalyze the release of adenine from a specific adenosine on a stem-tetraloop (GAGA) sequence at the elongation factor (eEF2) binding site of the 28S subunit of eukaryotic ribosomes, thereby arresting translation. RTA does not catalyze the release of 8-vinyladenine from 8vdA-10. Molecular dynamics simulations implicate a role for Arg180 in oxacarbenium ion destabilization and the lack of catalysis. However, 8vdA-10 is an active site analogue and inhibits RTA with a Ki value of 2.4 μM. Adenine is also released from the second adenosine in the modified tetraloop, demonstrating an alternative mode for the binding of this motif in the RTA active site. The 8vdA analogue defines the specificities of RTA for the two adenylate depurination sites in a RNA substrate with a GAGA tetraloop. The rate of nonenzymatic acid-catalyzed solvolysis of 8-vinyladenine from the stem-loop RNA is described. Unlike RTA, PAP catalyzes the slow release of 8-vinyladenine from 8vdA-10. The isolation of 8-vA and its physicochemical characterization is described.

UR - http://www.scopus.com/inward/record.url?scp=34249778366&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=34249778366&partnerID=8YFLogxK

U2 - 10.1021/bi0621821

DO - 10.1021/bi0621821

M3 - Article

VL - 46

SP - 6169

EP - 6182

JO - Biochemistry

JF - Biochemistry

SN - 0006-2960

IS - 21

ER -