细胞视黄酸结合蛋白II定点突变体的结构分析揭示了结构完整性与配体结合之间的关系。
Structural analysis of site-directed mutants of cellular retinoic acid-binding protein II addresses the relationship between structural integrity and ligand binding.
作者信息
Vaezeslami Soheila, Jia Xiaofei, Vasileiou Chrysoula, Borhan Babak, Geiger James H
机构信息
Rigaku Americas Corporation, 9009 New Trails Drive, The Woodlands, TX 77381, USA.
出版信息
Acta Crystallogr D Biol Crystallogr. 2008 Dec;64(Pt 12):1228-39. doi: 10.1107/S0907444908032216. Epub 2008 Nov 18.
Abstract
The structural integrity of cellular retinoic acid-binding protein II (CRABPII) has been investigated using the crystal structures of CRABPII mutants. The overall fold was well maintained by these CRABPII mutants, each of which carried multiple different mutations. A water-mediated network is found to be present across the large binding cavity, extending from Arg111 deep inside the cavity to the alpha2 helix at its entrance. This chain of interactions acts as a ;pillar' that maintains the integrity of the protein. The disruption of the water network upon loss of Arg111 leads to decreased structural integrity of the protein. A water-mediated network can be re-established by introducing the hydrophilic Glu121 inside the cavity, which results in a rigid protein with the alpha2 helix adopting an altered conformation compared with wild-type CRABPII.
摘要
利用细胞视黄酸结合蛋白II（CRABPII）突变体的晶体结构，对其结构完整性进行了研究。这些CRABPII突变体均携带多个不同的突变，但整体折叠结构保持良好。发现一个由水介导的网络贯穿于大的结合腔，从腔内部深处的精氨酸111延伸至其入口处的α2螺旋。这条相互作用链起到了维持蛋白质完整性的“支柱”作用。精氨酸111缺失导致水网络破坏，进而使蛋白质的结构完整性降低。通过在腔内引入亲水性的谷氨酸121，可以重新建立水介导的网络，这会使蛋白质变得刚性，且α2螺旋与野生型CRABPII相比呈现出改变的构象。
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本文引用的文献
1
Processing of X-ray diffraction data collected in oscillation mode.
Methods Enzymol. 1997;276:307-26. doi: 10.1016/S0076-6879(97)76066-X.
2
Protein design: reengineering cellular retinoic acid binding protein II into a rhodopsin protein mimic.
J Am Chem Soc. 2007 May 16;129(19):6140-8. doi: 10.1021/ja067546r. Epub 2007 Apr 21.
3
The structure of Apo-wild-type cellular retinoic acid binding protein II at 1.4 A and its relationship to ligand binding and nuclear translocation.
J Mol Biol. 2006 Oct 27;363(3):687-701. doi: 10.1016/j.jmb.2006.08.059. Epub 2006 Aug 26.
4
Engineering a rhodopsin protein mimic.
J Am Chem Soc. 2006 Apr 12;128(14):4522-3. doi: 10.1021/ja058591m.
5
Refinement of macromolecular structures by the maximum-likelihood method.
Acta Crystallogr D Biol Crystallogr. 1997 May 1;53(Pt 3):240-55. doi: 10.1107/S0907444996012255.
6
Assessment of phase accuracy by cross validation: the free R value. Methods and applications.
Acta Crystallogr D Biol Crystallogr. 1993 Jan 1;49(Pt 1):24-36. doi: 10.1107/S0907444992007352.
7
Experimental pK(a) values of buried residues: analysis with continuum methods and role of water penetration.
Biophys J. 2002 Jun;82(6):3289-304. doi: 10.1016/s0006-3495(02)75670-1.
8
Direct channeling of retinoic acid between cellular retinoic acid-binding protein II and retinoic acid receptor sensitizes mammary carcinoma cells to retinoic acid-induced growth arrest.
Mol Cell Biol. 2002 Apr;22(8):2632-41. doi: 10.1128/MCB.22.8.2632-2641.2002.
9
The novel co-activator CRABPII binds to RARalpha and RXRalpha via two nuclear receptor interacting domains and does not require the AF-2 'core'.
FEBS Lett. 2001 Oct 19;507(1):67-73. doi: 10.1016/s0014-5793(01)02938-6.
10
Localization of the RAR interaction domain of cellular retinoic acid binding protein-II.
J Mol Biol. 2001 Jan 26;305(4):939-49. doi: 10.1006/jmbi.2000.4340.
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