Linkage of monovalent and divalent ion binding in the folding of the P4-P6 domain of the Tetrahymena ribozyme.
We have explored the linkage of monovalent and divalent ion binding in the folding of the P4-P6 domain of Tetrahymena thermophila ribozyme by examining the Mg2+-induced folding and the urea-induced denaturation of the folded state as a function of Na+ under equilibrium folding conditions using hydroxyl radical footprinting. These studies allowed a thermodynamic examination of eight discrete protection sites within P4-P6 that are involved in several tertiary structure contacts. Monovalent ions compete with Mg2+ ions in mediating P4-P6 folding. The urea denaturation isotherms demonstrated DeltaDeltaG values of >2 kcal x mol(-1) in experiments conducted in 10 versus 200 mM NaCl at a constant 10 mM MgCl2. However, the individual-site isotherms reported by footprinting revealed that larger than average changes in DeltaG values were localized to specific sites within the Mg2+-rich A-bulge. The competitive effects of monovalent ions were less when K+ rather than Na+ was the monovalent cation present. This result indicates the importance of the specific K+ binding sites that are associated with AA-platform structures to P4-P6 folding and stability. These site-specific footprinting data provide quantitative and site-specific measurements of the ion-linked stability for P4-P6 that are interpreted with respect to crystallographic data.
Uchida
Takeshi
T
Center for Synchrotron Biosciences, Department of Physiology and Biophysics, Albert Einstein College of Medicine of Yeshiva University, 1300 Morris Park Avenue, Bronx, New York 10461, USA.
He
Qin
Q
Ralston
Corie Y
CY
Brenowitz
Michael
M
Chance
Mark R
MR
D000818:Animals; D001483:Base Sequence; D002384:Catalysis; D002413:Cations, Divalent / Q000378:metabolism* / Q000494:pharmacology; D002414:Cations, Monovalent / Q000378:metabolism* / Q000494:pharmacology; D008274:Magnesium / Q000378:metabolism / Q000494:pharmacology; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation / Q000187:drug effects; D011188:Potassium / Q000378:metabolism / Q000494:pharmacology; D016337:RNA, Catalytic / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D012343:RNA, Transfer / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D012964:Sodium / Q000378:metabolism / Q000494:pharmacology; D013768:Tetrahymena / Q000201:enzymology* / Q000235:genetics*; D013816:Thermodynamics; D014508:Urea / Q000494:pharmacology
D002413:Cations, Divalent; D002414:Cations, Monovalent; D016337:RNA, Catalytic; D014508:Urea; D012343:RNA, Transfer; D012964:Sodium; D008274:Magnesium; D011188:Potassium