大的有利的焓变驱动 RNA 识别基序蛋白对特定 RNA 的识别。
Large favorable enthalpy changes drive specific RNA recognition by RNA recognition motif proteins.
机构信息
Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642, United States.
出版信息
Biochemistry. 2011 Mar 8;50(9):1429-31. doi: 10.1021/bi102057m. Epub 2011 Feb 2.
Abstract
The RNA recognition motif (RRM) is a prevalent class of RNA binding domains. Although a number of RRM/RNA structures have been determined, thermodynamic analyses are relatively uncommon. Here, we use isothermal titration calorimetry to characterize single-stranded (ss)RNA binding by four representative RRM-containing proteins: (i) U2AF(65), (ii) SXL, (iii) TIA-1, and (iv) PAB. In all cases, ssRNA binding is accompanied by remarkably large favorable enthalpy changes (-30 to -60 kcal mol(-1)) and unfavorable entropy changes. Alterations of key RRM residues and binding sites indicate that under the nearly physiological conditions of these studies, large thermodynamic changes represent a signature of specific ssRNA recognition by RRMs.
摘要
RNA 识别基序（RRM）是一类普遍存在的 RNA 结合结构域。尽管已经确定了许多 RRM/RNA 结构，但热力学分析相对较少。在这里，我们使用等温滴定量热法来表征四个代表性的含有 RRM 的蛋白质与单链（ss）RNA 的结合：（i）U2AF（65），（ii）SXL，（iii）TIA-1，和（iv）PAB。在所有情况下，ssRNA 结合伴随着非常大的有利焓变（-30 至-60 kcal mol（-1））和不利的熵变。关键 RRM 残基和结合位点的改变表明，在这些研究的几乎生理条件下，大的热力学变化代表了 RRMs 特异性识别 ssRNA 的特征。
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本文引用的文献
1
Solution conformation and thermodynamic characteristics of RNA binding by the splicing factor U2AF65.
J Biol Chem. 2008 Nov 28;283(48):33641-9. doi: 10.1074/jbc.M806297200. Epub 2008 Oct 8.
2
Structure and function of KH domains.
FEBS J. 2008 Jun;275(11):2712-26. doi: 10.1111/j.1742-4658.2008.06411.x. Epub 2008 Apr 15.
3
Structural basis for polypyrimidine tract recognition by the essential pre-mRNA splicing factor U2AF65.
Mol Cell. 2006 Jul 7;23(1):49-59. doi: 10.1016/j.molcel.2006.05.025.
4
The RNA recognition motif, a plastic RNA-binding platform to regulate post-transcriptional gene expression.
FEBS J. 2005 May;272(9):2118-31. doi: 10.1111/j.1742-4658.2005.04653.x.
5
Escherichia coli Hfq has distinct interaction surfaces for DsrA, rpoS and poly(A) RNAs.
Nat Struct Mol Biol. 2004 Dec;11(12):1206-14. doi: 10.1038/nsmb858. Epub 2004 Nov 7.
6
U2AF homology motifs: protein recognition in the RRM world.
Genes Dev. 2004 Jul 1;18(13):1513-26. doi: 10.1101/gad.1206204.
7
RNA sequence elements required for high affinity binding by the zinc finger domain of tristetraprolin: conformational changes coupled to the bipartite nature of Au-rich MRNA-destabilizing motifs.
J Biol Chem. 2004 Jul 2;279(27):27870-7. doi: 10.1074/jbc.M402551200. Epub 2004 Apr 26.
8
Recognition of the mRNA AU-rich element by the zinc finger domain of TIS11d.
Nat Struct Mol Biol. 2004 Mar;11(3):257-64. doi: 10.1038/nsmb738. Epub 2004 Feb 8.
9
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Nat Struct Mol Biol. 2004 Jan;11(1):20-8. doi: 10.1038/nsmb706. Epub 2003 Dec 29.
10
Ionization constants and heats of tris(hydroxymethyl)aminomethane and phosphate buffers.
J Biol Chem. 1956 Feb;218(2):961-9.
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