Role of counterion condensation in folding of the Tetrahymena ribozyme II.: Counterion-dependence of folding kinetics

被引:92
作者
Heilman-Miller, SL
Pan, J
Thirumalai, D
Woodson, SA [1 ]
机构
[1] Univ Maryland, Dept Chem, College Pk, MD 20742 USA
[2] Univ Maryland, Inst Phys Sci & Technol, College Pk, MD 20742 USA
[3] Univ Maryland, Ctr Biomol Struct & Org, College Pk, MD 20742 USA
[4] Johns Hopkins Univ, TC Jenkins Dept Biophys, Baltimore, MD 21218 USA
关键词
RNA folding; group I ribozyme; counterion condensation; polyamines;
D O I
10.1006/jmbi.2001.4660
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
Condensed counterions contribute to the stability of compact structures in RNA, largely by reducing electrostatic repulsion among phosphate groups. Varieties of cations induce a collapsed state in the Tetrahymena ribozyme that is readily transformed to the catalytically active structure in the presence of Mg2+. Native gel electrophoresis was used to compare the effects of the valence and size of the counterion on the kinetics of this transition. The rate of folding was found to decrease with the charge of the counterion. Transitions in monovalent ions occur 20- to 40-fold faster than transitions induced by multivalent metal ions. These results suggest that multivalent cations yield stable compact structures, which are slower to reorganize to the native conformation than those induced by monovalent ions. The folding kinetics are 12-fold faster in the presence of spermidine(3+) than [Co(NH3)(6)](3+), consistent with less effective stabilization of long-range RNA interactions by polyamines. Under most conditions, the observed folding rate decreases with increasing counterion concentration. In saturating amounts of counterion, folding is accelerated by addition of urea. These observations indicate that reorganization of compact intermediates involves partial unfolding of the RNA. We find that folding of the ribozyme is most efficient in a mixture of monovalent salt and Mg2+. This is attributed to competition among counterions for binding to the RNA. The counterion dependence of the folding kinetics is discussed in terms of the ability of condensed ions to stabilize compact structures in RNA. (C) 2001 Academic Press.
引用
收藏
页码:57 / 68
页数:12
相关论文
共 57 条
[1]  
Bloomfield V. A., 2000, NUCL ACIDS STRUCTURE
[2]  
Bloomfield VA, 1997, BIOPOLYMERS, V44, P269, DOI 10.1002/(SICI)1097-0282(1997)44:3<269::AID-BIP6>3.0.CO
[3]  
2-T
[4]  
Buchmueller KL, 2000, NAT STRUCT BIOL, V7, P362
[5]  
BURKARD ME, 1999, RNA WORLD, P233
[6]   Denaturants can accelerate folding rates in a class of globular proteins [J].
Camacho, CJ ;
Thirumalai, D .
PROTEIN SCIENCE, 1996, 5 (09) :1826-1832
[7]   Metal-binding sites in the major groove of a large ribozyme domain [J].
Cate, JH ;
Doudna, JA .
STRUCTURE, 1996, 4 (10) :1221-1229
[8]   A magnesium ion core at the heart of a ribozyme domain [J].
Cate, JH ;
Hanna, RL ;
Doudna, JA .
NATURE STRUCTURAL BIOLOGY, 1997, 4 (07) :553-558
[9]   CONFORMATIONAL-CHANGES OF TRANSFER RIBONUCLEIC-ACID - RELAXATION KINETICS OF EARLY MELTING TRANSITION OF METHIONINE TRANSFER RIBONUCLEIC-ACID (ESCHERICHIA-COLI) [J].
COLE, PE ;
CROTHERS, DM .
BIOCHEMISTRY, 1972, 11 (23) :4368-&
[10]   CONFORMATIONAL-CHANGES OF TRANSFER RIBONUCLEIC-ACID - EQUILIBRIUM PHASE-DIAGRAMS [J].
COLE, PE ;
CROTHERS, DM ;
YANG, SK .
BIOCHEMISTRY, 1972, 11 (23) :4358-&