Effects of Mg2+, K+, and H+ on an equilibrium between alternative conformations of an RNA pseudoknot
Effects of Mg2+, K+, and H+ on an equilibrium between alternative conformations of an RNA pseudoknot
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DOI：
10.1006/jmbi.1997.1119
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发表时间：
1997-07-18
影响因子：
5.6
通讯作者：
Draper, DE
中科院分区：
文献类型：
--
作者：
Gluick, TC;Gerstner, RB;Draper, DE
一个复杂的假结结构围绕着第一个核糖体起始位点在土方iclia大肠杆菌α mRNA和介导其调节核糖体蛋白S4。含有该假结的112 nt RNA片段存在于两种构象中，其在室温以下通过凝胶电泳可分辨。在30 ° C和45 ° C之间，构象异构体在1小时到1分钟的时间范围内达到热力学平衡，并且构象异构体之间的相互转化与H+、K+和Mg 2+浓度有关。Mg 2+有利于形成“快速"电泳形式：在限速步骤中结合单个Mg 2+，然后协同结合类似于1.7个其他离子。后者离子的结合为反应提供了大部分有利的自由能。然而，“慢”形式结合大约相同数量的Mg离子，尽管更弱，使得饱和Mg 2+浓度将平衡驱动到仅类似于70%的快形式。一个单一的H+被吸收到“慢”构象的转换中，其具有约5.9的表观pK;低pH值也稳定了部分假结结构，其在类似于62摄氏度的温度下熔化。Mg 2+和H+似乎通过相对较小（10至100倍）的差异指导α mRNA折叠，其对替代构象异构体的亲和力。K+对构象平衡的影响很小，但在高浓度下会加速构象异构体之间的相互转换。α mRNA构象转换的动力学缓慢，活化能大，平衡常数依赖于tRNA，I组内含子和RNase P RNA三级结构折叠的缓慢步骤，尽管它与这些不同之处在于单一Mg 2+与限速步骤的关联。(C)出版社：Academic Press Limited。
A complex pseudoknot structure surrounds the first ribosome initiation site in the Eschericlia coli alpha mRNA and mediates its regulation by ribosomal protein S4. A 112 nt RNA fragment containing this pseudoknot exists in two conformations that are resolvable by gel electrophoresis below room temperature. Between 30 degrees C and 45 degrees C the conformers reach thermodynamic equilibrium on a time scale ranging from one hour to one minute, and the interconversion between conformers is Linked to H+, K+ and Mg2+ concentrations. Mg2+ favors formation of the ''fast'' electrophoretic form: a single Mg2+ is bound in the rate-Limiting step, followed by cooperative binding of similar to 1.7 additional ions. Binding of the latter ions provides most of the favorable free energy for the reaction. However, the ''slow'' form binds about the same number of Mg ions, albeit more weakly, so that saturating Mg2+ concentrations drive the equilibrium to only similar to 70% fast form. A single H+ is taken up in the switch to the ''slow'' conformer, which has apparent pK approximate to 5.9; low pH also stabilizes part of the pseudoknot structure melting at similar to 62 degrees C. Mg2+ and H+ appear to direct alpha mRNA folding by relatively small (10 to 100-fold) differences in their affinities for alternative conformers. K+ has very Little effect on the conformational equilibrium, but at high concentrations accelerates interconversion between the conformers.The alpha mRNA conformational switch is similar in its slow kinetics, large activation energy, and Mg2+ dependence of the equilibrium constant to slow steps in the folding of tRNA, group I introns, and RNase P RNA tertiary structures, though it differs from these in the association of a single Mg2+ with the rate-limiting step. (C) 1997 Academic Press Limited.