通过二维红外测量和模拟对淀粉样纤维中按残基排序的酰胺 I 振动的频率分布。
Frequency distribution of the amide-I vibration sorted by residues in amyloid fibrils revealed by 2D-IR measurements and simulations.
机构信息
Institut des Sciences Moléculaires d'Orsay, UMR CNRS 8214, Université Paris-Sud 11, 91405 Orsay, France.
出版信息
J Phys Chem B. 2012 Mar 15;116(10):3322-30. doi: 10.1021/jp2096423. Epub 2012 Mar 6.
Abstract
The infrared optical response of amyloid fibrils Aβ(1-40) is investigated. Simulations of two models corresponding to different protonation states are compared with experiment. The simulations reveal that vibrational frequency distributions inside the fibrils are dominated by side chain fluctuations. We further confirm earlier suggestions based on 2D-IR measurements that water molecules can be trapped inside the fibrils.
摘要
研究了淀粉样纤维 Aβ(1-40)的红外光学响应。比较了对应于不同质子化状态的两种模型的模拟与实验结果。模拟表明，纤维内部的振动频率分布主要由侧链波动决定。我们进一步证实了基于 2D-IR 测量的早期建议，即水分子可以被困在纤维内部。
相似文献
1
Frequency distribution of the amide-I vibration sorted by residues in amyloid fibrils revealed by 2D-IR measurements and simulations.
J Phys Chem B. 2012 Mar 15;116(10):3322-30. doi: 10.1021/jp2096423. Epub 2012 Mar 6.
2
2D IR provides evidence for mobile water molecules in beta-amyloid fibrils.
Proc Natl Acad Sci U S A. 2009 Oct 20;106(42):17751-6. doi: 10.1073/pnas.0909888106. Epub 2009 Oct 8.
3
Two-dimensional infrared spectra of isotopically diluted amyloid fibrils from Abeta40.
Proc Natl Acad Sci U S A. 2008 Jun 3;105(22):7720-5. doi: 10.1073/pnas.0802993105. Epub 2008 May 22.
4
Spectroscopic Signature for Stable β-Amyloid Fibrils versus β-Sheet-Rich Oligomers.
J Phys Chem B. 2018 Jan 11;122(1):144-153. doi: 10.1021/acs.jpcb.7b10765. Epub 2017 Dec 27.
5
Mapping the amide-I vibrations of model dipeptides with secondary structure sensitivity and amino acid residue specificity, and its application to amyloid β-peptide in aqueous solution.
Spectrochim Acta A Mol Biomol Spectrosc. 2019 Aug 5;219:391-400. doi: 10.1016/j.saa.2019.04.070. Epub 2019 Apr 26.
6
Molecular dynamics study of water channels in natural and synthetic amyloid-β fibrils.
J Chem Phys. 2021 Jun 21;154(23):235102. doi: 10.1063/5.0049250.
7
Infrared Probe Technique Reveals a Millipede-like Structure for Aβ(8-28) Amyloid Fibril.
Langmuir. 2016 Feb 2;32(4):937-46. doi: 10.1021/acs.langmuir.5b03616. Epub 2016 Jan 21.
8
Structural analyses of experimental 13C edited amide I' IR and VCD for peptide β-sheet aggregates and fibrils using DFT-based spectral simulations.
J Phys Chem B. 2013 Sep 12;117(36):10359-69. doi: 10.1021/jp405613r. Epub 2013 Aug 27.
9
Parallel β-sheet vibrational couplings revealed by 2D IR spectroscopy of an isotopically labeled macrocycle: quantitative benchmark for the interpretation of amyloid and protein infrared spectra.
J Am Chem Soc. 2012 Nov 21;134(46):19118-28. doi: 10.1021/ja3074962. Epub 2012 Nov 9.
10
Conformational preferences and vibrational frequency distributions of short peptides in relation to multidimensional infrared spectroscopy.
J Am Chem Soc. 2001 Dec 26;123(51):12886-98. doi: 10.1021/ja011088z.
引用本文的文献
1
Tautomeric Effect of Histidine on β-Sheet Formation of Amyloid Beta 1-40: 2D-IR Simulations.
Biophys J. 2020 Aug 18;119(4):831-842. doi: 10.1016/j.bpj.2020.07.009. Epub 2020 Jul 18.
2
Vibrational Approach to the Dynamics and Structure of Protein Amyloids.
Molecules. 2019 Jan 6;24(1):186. doi: 10.3390/molecules24010186.
3
Spectroscopic Signature for Stable β-Amyloid Fibrils versus β-Sheet-Rich Oligomers.
J Phys Chem B. 2018 Jan 11;122(1):144-153. doi: 10.1021/acs.jpcb.7b10765. Epub 2017 Dec 27.
4
Not All β-Sheets Are the Same: Amyloid Infrared Spectra, Transition Dipole Strengths, and Couplings Investigated by 2D IR Spectroscopy.
J Phys Chem B. 2017 Sep 28;121(38):8935-8945. doi: 10.1021/acs.jpcb.7b06826. Epub 2017 Sep 19.
5
Watching Proteins Wiggle: Mapping Structures with Two-Dimensional Infrared Spectroscopy.
Chem Rev. 2017 Aug 23;117(16):10726-10759. doi: 10.1021/acs.chemrev.6b00582. Epub 2017 Jan 6.
6
Isotope-Labeled Amyloids via Synthesis, Expression, and Chemical Ligation for Use in FTIR, 2D IR, and NMR Studies.
Methods Mol Biol. 2016;1345:21-41. doi: 10.1007/978-1-4939-2978-8_2.
7
Transition Dipoles from 1D and 2D Infrared Spectroscopy Help Reveal the Secondary Structures of Proteins: Application to Amyloids.
J Phys Chem B. 2015 Nov 5;119(44):14065-75. doi: 10.1021/acs.jpcb.5b07706. Epub 2015 Oct 16.
8
2D IR spectroscopy of histidine: probing side-chain structure and dynamics via backbone amide vibrations.
J Phys Chem B. 2014 Jul 17;118(28):7799-805. doi: 10.1021/jp411901m. Epub 2014 Apr 18.
9
Thermally induced protein unfolding probed by isotope-edited IR spectroscopy.
J Phys Chem B. 2012 Aug 16;116(32):9627-34. doi: 10.1021/jp304613b. Epub 2012 Aug 1.
本文引用的文献
1
All-atom empirical potential for molecular modeling and dynamics studies of proteins.
J Phys Chem B. 1998 Apr 30;102(18):3586-616. doi: 10.1021/jp973084f.
2
Utilizing Lifetimes to Suppress Random Coil Features in 2D IR Spectra of Peptides.
J Phys Chem Lett. 2011 Aug 25;2(18):2357-2361. doi: 10.1021/jz201024m.
3
2DIR spectroscopy of human amylin fibrils reflects stable β-sheet structure.
J Am Chem Soc. 2011 Oct 12;133(40):16062-71. doi: 10.1021/ja204035k. Epub 2011 Sep 15.
4
Proton transport in biological systems can be probed by two-dimensional infrared spectroscopy.
J Chem Phys. 2011 Jan 28;134(4):044502. doi: 10.1063/1.3522770.
5
Dry amyloid fibril assembly in a yeast prion peptide is mediated by long-lived structures containing water wires.
Proc Natl Acad Sci U S A. 2010 Dec 14;107(50):21459-64. doi: 10.1073/pnas.1008616107. Epub 2010 Nov 22.
6
Structural classification of the amide I sites of a beta-hairpin with isotope label 2DIR spectroscopy.
Phys Chem Chem Phys. 2010 Aug 28;12(32):9347-57. doi: 10.1039/b925645h. Epub 2010 Jul 1.
7
2D IR line shapes probe ovispirin peptide conformation and depth in lipid bilayers.
J Am Chem Soc. 2010 Mar 3;132(8):2832-8. doi: 10.1021/ja9101776.
8
2D IR provides evidence for mobile water molecules in beta-amyloid fibrils.
Proc Natl Acad Sci U S A. 2009 Oct 20;106(42):17751-6. doi: 10.1073/pnas.0909888106. Epub 2009 Oct 8.
9
2D-IR experiments and simulations of the coupling between amide-I and ionizable side chains in proteins: application to the Villin headpiece.
J Phys Chem B. 2009 Aug 13;113(32):11260-73. doi: 10.1021/jp900245s.
10
Coherent infrared multidimensional spectra of the OH stretching band in liquid water simulated by direct nonlinear exciton propagation.
J Chem Phys. 2009 May 14;130(18):184501. doi: 10.1063/1.3120771.
Zotero 插件