The thermodynamic origin of the stability of a thermophilic ribozyme

被引:56
作者
Fang, XW
Golden, BL
Littrell, K
Shelton, V
Thiyagarajan, P
Pan, T
Sosnick, TR
机构
[1] Univ Chicago, Dept Biochem & Mol Biol, Chicago, IL 60637 USA
[2] Purdue Univ, Dept Biochem, W Lafayette, IN 47907 USA
[3] Argonne Natl Lab, Argonne, IL 60439 USA
[4] Univ Chicago, Dept Chem, Chicago, IL 60637 USA
[5] Univ Chicago, Inst Biophys Dynam, Chicago, IL 60637 USA
关键词
D O I
10.1073/pnas.071050698
中图分类号
O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];
学科分类号
07 ; 0710 ; 09 ;
摘要
Understanding the mechanism of thermodynamic stability of an RNA structure has significant implications for the function and design of RNA. We investigated the equilibrium folding of a thermophilic ribozyme and its mesophilic homologue by using hydroxyl radical protection, small-angle x-ray scattering, and circular dichroism. Both RNAs require Mg2+ to fold to their native structures that are very similar. The stability is measured as a function of Mg2+ and urea concentrations at different temperatures. The enhanced stability of the thermophilic ribozyme primarily is derived from a tremendous increase in the amount of structure formed in the ultimate folding transition. This increase in structure formation and cooperativity arises because the penultimate and the ultimate folding transitions in the mesophilic ribozyme become linked into a single transition in the folding of the thermophilic ribozyme. Therefore, the starting point, or reference state, for the transition to the native, functional thermophilic ribozyme is significantly less structured. The shift in the reference state, and the resulting increase in folding cooperativity, is likely due to the stabilization of selected native interactions that only form in the ultimate transition. This mechanism of using a less structured intermediate and increased cooperativity to achieve higher functional stability for tertiary RNAs is fundamentally different from that commonly proposed to explain the increased stability of thermophilic proteins.
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页码:4355 / 4360
页数:6
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共 35 条
[1]   The complete atomic structure of the large ribosomal subunit at 2.4 Å resolution [J].
Ban, N ;
Nissen, P ;
Hansen, J ;
Moore, PB ;
Steitz, TA .
SCIENCE, 2000, 289 (5481) :905-920
[2]   Crystal structure of the ribonucleoprotein core of the signal recognition particle [J].
Batey, RT ;
Rambo, RP ;
Lucast, L ;
Rha, B ;
Doudna, JA .
SCIENCE, 2000, 287 (5456) :1232-+
[3]   CHARACTERIZATION OF RIBONUCLEASE-P RNAS FROM THERMOPHILIC BACTERIA [J].
BROWN, JW ;
HAAS, ES ;
PACE, NR .
NUCLEIC ACIDS RESEARCH, 1993, 21 (03) :671-679
[4]   X-ray crystal structures of 70S ribosome functional complexes [J].
Cate, JH ;
Yusupov, MM ;
Yusupova, GZ ;
Earnest, TN ;
Noller, HF .
SCIENCE, 1999, 285 (5436) :2095-2104
[5]   Crystal structure of a group I ribozyme domain: Principles of RNA packing [J].
Cate, JH ;
Gooding, AR ;
Podell, E ;
Zhou, KH ;
Golden, BL ;
Kundrot, CE ;
Cech, TR ;
Doudna, JA .
SCIENCE, 1996, 273 (5282) :1678-1685
[6]   VISUALIZING THE HIGHER-ORDER FOLDING OF A CATALYTIC RNA MOLECULE [J].
CELANDER, DW ;
CECH, TR .
SCIENCE, 1991, 251 (4992) :401-407
[7]   The two faces of the Escherichia coli 23 S rRNA sarcin/ricin domain:: The structure at 1.11 Å resolution [J].
Correll, CC ;
Wool, IG ;
Munishkin, A .
JOURNAL OF MOLECULAR BIOLOGY, 1999, 292 (02) :275-287
[8]   Mg2+-dependent compaction and folding of yeast tRNAPhe and the catalytic domain of the B-subtilis RNase P RNA determined by small-angle X-ray scattering [J].
Fang, XW ;
Littrell, K ;
Yang, X ;
Henderson, SJ ;
Siefert, S ;
Thiyagarajan, P ;
Pan, T ;
Sosnick, TR .
BIOCHEMISTRY, 2000, 39 (36) :11107-11113
[9]   A thermodynamic framework and cooperativity in the tertiary folding of a Mg2+-dependent ribozyme [J].
Fang, XW ;
Pan, T ;
Sosnick, TR .
BIOCHEMISTRY, 1999, 38 (51) :16840-16846
[10]   Crystal structure of a hepatitis delta virus ribozyme [J].
Ferré-D'Amaré, AR ;
Zhou, KH ;
Doudna, JA .
NATURE, 1998, 395 (6702) :567-574