低温下确定蛋白质赖氨酸侧链NH₃⁺基团¹H-¹⁵N异核相关核磁共振信号的有效策略。
Effective strategy to assign ¹H- ¹⁵N heteronuclear correlation NMR signals from lysine side-chain NH3₃⁺ groups of proteins at low temperature.
作者信息
Esadze Alexandre, Zandarashvili Levani, Iwahara Junji
机构信息
Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, 77555-1068, USA.
出版信息
J Biomol NMR. 2014 Sep;60(1):23-7. doi: 10.1007/s10858-014-9854-y. Epub 2014 Aug 17.
Abstract
Recent studies have shown that lysine side-chain NH3(+) groups are excellent probes for NMR investigations of dynamics involving hydrogen bonds and ion pairs relevant to protein function. However, due to rapid hydrogen exchange, observation of (1)H-(15)N NMR cross peaks from lysine NH3(+) groups often requires use of a relatively low temperature, which renders difficulty in resonance assignment. Here we present an effective strategy to assign (1)H and (15)N resonances of NH3(+) groups at low temperatures. This strategy involves two new (1)H/(13)C/(15)N triple-resonance experiments for lysine side chains. Application to a protein-DNA complex is demonstrated.
摘要
最近的研究表明，赖氨酸侧链的NH3(+)基团是用于核磁共振研究与蛋白质功能相关的氢键和离子对动力学的优秀探针。然而，由于氢的快速交换，观察赖氨酸NH3(+)基团的(1)H-(15)N核磁共振交叉峰通常需要使用相对较低的温度，这给共振归属带来了困难。在此，我们提出了一种在低温下归属NH3(+)基团的(1)H和(15)N共振的有效策略。该策略涉及针对赖氨酸侧链的两个新的(1)H/(13)C/(15)N三共振实验。并展示了其在蛋白质-DNA复合物中的应用。
相似文献
1
Effective strategy to assign ¹H- ¹⁵N heteronuclear correlation NMR signals from lysine side-chain NH3₃⁺ groups of proteins at low temperature.
J Biomol NMR. 2014 Sep;60(1):23-7. doi: 10.1007/s10858-014-9854-y. Epub 2014 Aug 17.
2
Heteronuclear NMR spectroscopy for lysine NH(3) groups in proteins: unique effect of water exchange on (15)N transverse relaxation.
J Am Chem Soc. 2007 Mar 14;129(10):2971-80. doi: 10.1021/ja0683436. Epub 2007 Feb 15.
3
A Unique and Simple Approach to Improve Sensitivity in N-NMR Relaxation Measurements for NH₃⁺ Groups: Application to a Protein-DNA Complex.
Molecules. 2017 Aug 15;22(8):1355. doi: 10.3390/molecules22081355.
4
Dynamics of lysine side-chain amino groups in a protein studied by heteronuclear 1H−15N NMR spectroscopy.
J Am Chem Soc. 2011 Feb 2;133(4):909-19. doi: 10.1021/ja107847d.
5
NMR studies on the dynamics of hydrogen bonds and ion pairs involving lysine side chains of proteins.
Adv Protein Chem Struct Biol. 2013;93:37-80. doi: 10.1016/B978-0-12-416596-0.00002-6.
6
Temperature dependence of internal motions of protein side-chain NH3(+) groups: insight into energy barriers for transient breakage of hydrogen bonds.
Biochemistry. 2015 Jan 20;54(2):538-45. doi: 10.1021/bi5012749. Epub 2014 Dec 22.
7
A general strategy for the assignment of aliphatic side-chain resonances of uniformly 13C,15N-labeled large proteins.
J Am Chem Soc. 2005 Aug 31;127(34):11920-1. doi: 10.1021/ja053539b.
8
Hydrogen-exchange kinetics studied through analysis of self-decoupling of nuclear magnetic resonance.
J Magn Reson. 2020 Mar;312:106687. doi: 10.1016/j.jmr.2020.106687. Epub 2020 Jan 16.
9
Automated amino acid side-chain NMR assignment of proteins using (13)C- and (15)N-resolved 3D [ (1)H, (1)H]-NOESY.
J Biomol NMR. 2008 Sep;42(1):23-33. doi: 10.1007/s10858-008-9259-x. Epub 2008 Aug 16.
10
Residue-specific pKa determination of lysine and arginine side chains by indirect 15N and 13C NMR spectroscopy: application to apo calmodulin.
J Am Chem Soc. 2007 Dec 26;129(51):15805-13. doi: 10.1021/ja0721824. Epub 2007 Nov 29.
引用本文的文献
1
Site-Specific Detection and Characterization of Ubiquitin Carbamylation.
Biochemistry. 2022 Apr 19;61(8):712-721. doi: 10.1021/acs.biochem.2c00085. Epub 2022 Apr 5.
2
NMR Spectroscopy of supramolecular chemistry on protein surfaces.
Beilstein J Org Chem. 2020 Oct 9;16:2505-2522. doi: 10.3762/bjoc.16.203. eCollection 2020.
3
NMR Methods for Characterizing the Basic Side Chains of Proteins: Electrostatic Interactions, Hydrogen Bonds, and Conformational Dynamics.
Methods Enzymol. 2019;615:285-332. doi: 10.1016/bs.mie.2018.08.017. Epub 2018 Sep 27.
4
Direct detection of lysine side chain NH in protein-heparin complexes using NMR spectroscopy.
Analyst. 2018 Feb 7;143(3):635-638. doi: 10.1039/c7an01406f. Epub 2018 Jan 2.
5
A Unique and Simple Approach to Improve Sensitivity in N-NMR Relaxation Measurements for NH₃⁺ Groups: Application to a Protein-DNA Complex.
Molecules. 2017 Aug 15;22(8):1355. doi: 10.3390/molecules22081355.
6
Conformational Dynamics and the Binding of Specific and Nonspecific DNA by the Autoinhibited Transcription Factor Ets-1.
Biochemistry. 2016 Jul 26;55(29):4105-18. doi: 10.1021/acs.biochem.6b00460. Epub 2016 Jul 15.
7
Changes in conformational dynamics of basic side chains upon protein-DNA association.
Nucleic Acids Res. 2016 Aug 19;44(14):6961-70. doi: 10.1093/nar/gkw531. Epub 2016 Jun 10.
8
Physicochemical Properties of Ion Pairs of Biological Macromolecules.
Biomolecules. 2015 Sep 30;5(4):2435-63. doi: 10.3390/biom5042435.
9
Entropic Enhancement of Protein-DNA Affinity by Oxygen-to-Sulfur Substitution in DNA Phosphate.
Biophys J. 2015 Sep 1;109(5):1026-37. doi: 10.1016/j.bpj.2015.07.032.
10
Balancing between affinity and speed in target DNA search by zinc-finger proteins via modulation of dynamic conformational ensemble.
Proc Natl Acad Sci U S A. 2015 Sep 15;112(37):E5142-9. doi: 10.1073/pnas.1507726112. Epub 2015 Aug 31.
本文引用的文献
1
Positive and negative impacts of nonspecific sites during target location by a sequence-specific DNA-binding protein: origin of the optimal search at physiological ionic strength.
Nucleic Acids Res. 2014 Jun;42(11):7039-46. doi: 10.1093/nar/gku418. Epub 2014 May 16.
2
Stopped-flow fluorescence kinetic study of protein sliding and intersegment transfer in the target DNA search process.
J Mol Biol. 2014 Jan 9;426(1):230-44. doi: 10.1016/j.jmb.2013.09.019. Epub 2013 Sep 25.
3
Detection of salt bridges to lysines in solution in barnase.
Chem Commun (Camb). 2013 Oct 28;49(84):9824-6. doi: 10.1039/c3cc45602a.
4
NMR studies on the dynamics of hydrogen bonds and ion pairs involving lysine side chains of proteins.
Adv Protein Chem Struct Biol. 2013;93:37-80. doi: 10.1016/B978-0-12-416596-0.00002-6.
5
CHARMM36 all-atom additive protein force field: validation based on comparison to NMR data.
J Comput Chem. 2013 Sep 30;34(25):2135-45. doi: 10.1002/jcc.23354. Epub 2013 Jul 6.
6
Direct observation of the ion-pair dynamics at a protein-DNA interface by NMR spectroscopy.
J Am Chem Soc. 2013 Mar 6;135(9):3613-9. doi: 10.1021/ja312314b. Epub 2013 Feb 25.
7
Asymmetrical roles of zinc fingers in dynamic DNA-scanning process by the inducible transcription factor Egr-1.
Proc Natl Acad Sci U S A. 2012 Jun 26;109(26):E1724-32. doi: 10.1073/pnas.1121500109. Epub 2012 Jun 6.
8
Signature of mobile hydrogen bonding of lysine side chains from long-range 15N-13C scalar J-couplings and computation.
J Am Chem Soc. 2011 Jun 22;133(24):9192-5. doi: 10.1021/ja202219n. Epub 2011 May 27.
9
Dynamics of lysine side-chain amino groups in a protein studied by heteronuclear 1H−15N NMR spectroscopy.
J Am Chem Soc. 2011 Feb 2;133(4):909-19. doi: 10.1021/ja107847d.
10
NMR studies of translocation of the Zif268 protein between its target DNA Sites.
Biochemistry. 2010 Sep 21;49(37):7998-8005. doi: 10.1021/bi100962h.
Zotero 插件