磷酸盐振动探测生物分子中的局部电场和水合作用。
Phosphate vibrations probe local electric fields and hydration in biomolecules.
机构信息
Department of Chemistry, Stanford University, Stanford, California 94305-5080, United States.
出版信息
J Am Chem Soc. 2011 Aug 31;133(34):13236-9. doi: 10.1021/ja2042589. Epub 2011 Aug 10.
Abstract
The role of electric fields in important biological processes such as binding and catalysis has been studied almost exclusively by computational methods. Experimental measurements of the local electric field in macromolecules are possible using suitably calibrated vibrational probes. Here we demonstrate that the vibrational transitions of phosphate groups are highly sensitive to an electric field and show how that sensitivity can be quantified, allowing electric field measurements to be made in phosphate-containing biological systems without chemical modification.
摘要
电场在结合和催化等重要生物过程中的作用几乎完全通过计算方法进行了研究。使用经过适当校准的振动探针可以在大分子中测量局部电场。在这里，我们证明了磷酸基团的振动跃迁对电场非常敏感，并展示了如何量化这种敏感性，从而可以在不进行化学修饰的情况下在含磷酸的生物系统中进行电场测量。
相似文献
1
Phosphate vibrations probe local electric fields and hydration in biomolecules.
J Am Chem Soc. 2011 Aug 31;133(34):13236-9. doi: 10.1021/ja2042589. Epub 2011 Aug 10.
2
Phosphate Vibrations Probe Electric Fields in Hydrated Biomolecules: Spectroscopy, Dynamics, and Interactions.
J Phys Chem B. 2021 Apr 22;125(15):3899-3908. doi: 10.1021/acs.jpcb.1c01502. Epub 2021 Apr 9.
3
Computational Study of Phosphate Vibrations as Reporters of DNA Hydration.
J Phys Chem Lett. 2015 Oct 15;6(20):4012-7. doi: 10.1021/acs.jpclett.5b01973. Epub 2015 Sep 24.
4
Ultrafast phosphate hydration dynamics in bulk H2O.
J Chem Phys. 2015 Jun 7;142(21):212406. doi: 10.1063/1.4914152.
5
The mutual interactions of RNA, counterions and water - quantifying the electrostatics at the phosphate-water interface.
Chem Commun (Camb). 2021 Dec 3;57(96):12880-12897. doi: 10.1039/d1cc05367a.
6
Nitrile Probes of Electric Field Agree with Independently Measured Fields in Green Fluorescent Protein Even in the Presence of Hydrogen Bonding.
J Am Chem Soc. 2016 May 25;138(20):6561-70. doi: 10.1021/jacs.6b02156. Epub 2016 May 11.
7
Hofmeister anionic effects on hydration electric fields around water and peptide.
J Chem Phys. 2012 Mar 28;136(12):124501. doi: 10.1063/1.3694036.
8
Vibrational Stark effects calibrate the sensitivity of vibrational probes for electric fields in proteins.
Biochemistry. 2003 Oct 21;42(41):12050-5. doi: 10.1021/bi0352926.
9
Water Dynamics in the Hydration Shells of Biomolecules.
Chem Rev. 2017 Aug 23;117(16):10694-10725. doi: 10.1021/acs.chemrev.6b00765. Epub 2017 Mar 1.
10
Electric fields at the active site of an enzyme: direct comparison of experiment with theory.
Science. 2006 Jul 14;313(5784):200-4. doi: 10.1126/science.1127159.
引用本文的文献
1
Beyond the "spine of hydration": Chiral SFG spectroscopy detects DNA first hydration shell and base pair structures.
J Chem Phys. 2024 Sep 7;161(9). doi: 10.1063/5.0220479.
2
Correlations between the structure and the vibrational spectrum of the phosphate group. Implications for the analysis of an important functional group in phosphoproteins.
RSC Adv. 2020 Jan 29;10(8):4715-4724. doi: 10.1039/c9ra10366j. eCollection 2020 Jan 24.
3
Site-Specific Interrogation of Protein Structure and Stability.
Methods Mol Biol. 2022;2376:65-87. doi: 10.1007/978-1-0716-1716-8_3.
4
The mutual interactions of RNA, counterions and water - quantifying the electrostatics at the phosphate-water interface.
Chem Commun (Camb). 2021 Dec 3;57(96):12880-12897. doi: 10.1039/d1cc05367a.
5
Contact pairs of RNA with magnesium ions-electrostatics beyond the Poisson-Boltzmann equation.
Biophys J. 2021 Dec 7;120(23):5322-5332. doi: 10.1016/j.bpj.2021.10.029. Epub 2021 Oct 27.
6
Phosphate Vibrations Probe Electric Fields in Hydrated Biomolecules: Spectroscopy, Dynamics, and Interactions.
J Phys Chem B. 2021 Apr 22;125(15):3899-3908. doi: 10.1021/acs.jpcb.1c01502. Epub 2021 Apr 9.
7
Vibrational Spectroscopic Map, Vibrational Spectroscopy, and Intermolecular Interaction.
Chem Rev. 2020 Aug 12;120(15):7152-7218. doi: 10.1021/acs.chemrev.9b00813. Epub 2020 Jun 29.
8
Stern-Layer Adsorption of Oligonucleotides on Lamellar Cationic Lipid Bilayer Investigated by Polarization-Resolved SFG-VS.
ACS Omega. 2017 Dec 31;2(12):9241-9249. doi: 10.1021/acsomega.7b01214. Epub 2017 Dec 27.
9
Perspective: Structure and ultrafast dynamics of biomolecular hydration shells.
Struct Dyn. 2017 Apr 20;4(4):044018. doi: 10.1063/1.4981019. eCollection 2017 Jul.
10
Molecular couplings and energy exchange between DNA and water mapped by femtosecond infrared spectroscopy of backbone vibrations.
Struct Dyn. 2017 Apr 7;4(4):044015. doi: 10.1063/1.4980075. eCollection 2017 Jul.
本文引用的文献
1
Nitrile bonds as infrared probes of electrostatics in ribonuclease S.
J Phys Chem B. 2010 Oct 28;114(42):13536-44. doi: 10.1021/jp106406p.
2
Stark realities.
J Phys Chem B. 2009 Mar 12;113(10):2972-83. doi: 10.1021/jp8067393.
3
The GAP arginine finger movement into the catalytic site of Ras increases the activation entropy.
Proc Natl Acad Sci U S A. 2008 Apr 29;105(17):6260-5. doi: 10.1073/pnas.0712095105. Epub 2008 Apr 23.
4
Nitrile and thiocyanate IR probes: quantum chemistry calculation studies and multivariate least-square fitting analysis.
J Chem Phys. 2008 Apr 7;128(13):134506. doi: 10.1063/1.2844787.
5
A phosphoryl transfer intermediate in the GTPase reaction of Ras in complex with its GTPase-activating protein.
Proc Natl Acad Sci U S A. 2006 Sep 19;103(38):13911-6. doi: 10.1073/pnas.0604128103. Epub 2006 Sep 12.
6
Interactions of phosphate groups of ATP and Aspartyl phosphate with the sarcoplasmic reticulum Ca2+-ATPase: an FTIR study.
Biophys J. 2005 Dec;89(6):4352-63. doi: 10.1529/biophysj.105.061689. Epub 2005 Sep 16.
7
Vibrational Stark effects calibrate the sensitivity of vibrational probes for electric fields in proteins.
Biochemistry. 2003 Oct 21;42(41):12050-5. doi: 10.1021/bi0352926.
8
Monitoring the GAP catalyzed H-Ras GTPase reaction at atomic resolution in real time.
Proc Natl Acad Sci U S A. 2001 Jul 3;98(14):7754-9. doi: 10.1073/pnas.131549798.
9
The mechanism of GTP hydrolysis by Ras probed by Fourier transform infrared spectroscopy.
J Biol Chem. 2000 Mar 24;275(12):8492-500. doi: 10.1074/jbc.275.12.8492.
10
Conformational changes generated in GroEL during ATP hydrolysis as seen by time-resolved infrared spectroscopy.
J Biol Chem. 1999 Feb 26;274(9):5508-13. doi: 10.1074/jbc.274.9.5508.
Zotero 插件