肌红蛋白中色氨酸荧光偏振的分子动力学模拟
Molecular dynamics simulations of fluorescence polarization of tryptophans in myoglobin.
作者信息
Henry E R, Hochstrasser R M
出版信息
Proc Natl Acad Sci U S A. 1987 Sep;84(17):6142-6. doi: 10.1073/pnas.84.17.6142.
Abstract
The fluorescence of heme proteins is influenced by energy transfer from the excited tryptophan to the heme. Molecular dynamics simulations of the tryptophan and heme motions in sperm whale myoglobin were used to calculate the fluorescence intensity and anisotropy decays. The side chains underwent both small rapid orientational fluctuations and large infrequent transitions between conformations. The predicted motions of the tryptophans and the heme produce large fluctuations in the instantaneous rate of energy transfer, but no stable conformations in which energy transfer is suppressed were found. The calculated fluorescence anisotropies exhibited a large subpicosecond decay, corresponding to nondiffusive side-chain motions. The calculations adequately predict the observed fluorescence decay curve for myoglobin and the total anisotropy decay at 16-ps time resolution. The subnanosecond decays of anisotropy for tryptophan-14 in tuna myoglobin are not reproduced by the calculation.
摘要
血红素蛋白的荧光受到从激发态色氨酸到血红素的能量转移的影响。利用抹香鲸肌红蛋白中色氨酸和血红素运动的分子动力学模拟来计算荧光强度和各向异性衰减。侧链经历了小幅度的快速取向波动以及不同构象之间不频繁的大幅度转变。预测的色氨酸和血红素的运动在能量转移的瞬时速率上产生了很大的波动，但未发现能量转移被抑制的稳定构象。计算得到的荧光各向异性表现出很大的亚皮秒衰减，这对应于非扩散性的侧链运动。这些计算充分预测了观察到的肌红蛋白荧光衰减曲线以及在16皮秒时间分辨率下的总各向异性衰减。金枪鱼肌红蛋白中色氨酸-14的亚纳秒各向异性衰减未被该计算重现。
相似文献
1
Molecular dynamics simulations of fluorescence polarization of tryptophans in myoglobin.肌红蛋白中色氨酸荧光偏振的分子动力学模拟
Proc Natl Acad Sci U S A. 1987 Sep;84(17):6142-6. doi: 10.1073/pnas.84.17.6142.
2
Picosecond fluorescence decay of tryptophans in myoglobin.肌红蛋白中色氨酸的皮秒荧光衰减
Proc Natl Acad Sci U S A. 1984 Jul;81(14):4399-403. doi: 10.1073/pnas.81.14.4399.
3
Fluorescence and energy transfer of tryptophans in Aplysia myoglobin.海兔肌红蛋白中色氨酸的荧光和能量转移
Biophys J. 1987 Apr;51(4):653-60. doi: 10.1016/S0006-3495(87)83390-8.
4
Molecular dynamics simulations of heme reorientational motions in myoglobin.肌红蛋白中血红素重排运动的分子动力学模拟
Biophys J. 1993 Mar;64(3):869-85. doi: 10.1016/S0006-3495(93)81447-4.
5
Nanosecond dynamics of tryptophans in different conformational states of apomyoglobin proteins.脱辅基肌红蛋白不同构象状态下色氨酸的纳秒动力学
Biochemistry. 2000 Feb 22;39(7):1879-89. doi: 10.1021/bi992117+.
6
Fluorescence decay kinetics of the tryptophyl residues of myoglobin: effect of heme ligation and evidence for discrete lifetime components.肌红蛋白色氨酸残基的荧光衰减动力学：血红素连接的影响及离散寿命成分的证据。
Biochemistry. 1990 Jun 5;29(22):5270-5. doi: 10.1021/bi00474a008.
7
Oxidation of tryptophans in an interhelical hydrophobic cluster of myoglobin alters the thermodynamics of the denaturation transition.肌红蛋白螺旋间疏水簇中色氨酸的氧化改变了变性转变的热力学。
Biochemistry. 1987 Jun 16;26(12):3530-6. doi: 10.1021/bi00386a042.
8
Solvent accessibility of the heme pocket in tuna myoglobin.金枪鱼肌红蛋白中血红素口袋的溶剂可及性。
Boll Soc Ital Biol Sper. 1984 Mar 30;60(3):459-65.
9
Enhanced resolution of fluorescence anisotropy decays by simultaneous analysis of progressively quenched samples. Applications to anisotropic rotations and to protein dynamics.通过对逐步淬灭样品的同步分析提高荧光各向异性衰减的分辨率。在各向异性旋转和蛋白质动力学中的应用。
Biophys J. 1987 May;51(5):755-68. doi: 10.1016/S0006-3495(87)83402-1.
10
Ultrafast dynamics of nonequilibrium resonance energy transfer and probing globular protein flexibility of myoglobin.研究肌红蛋白中非平衡共振能量转移的超快动力学和探测球状蛋白质柔性。
J Phys Chem A. 2012 Mar 22;116(11):2610-9. doi: 10.1021/jp206106j. Epub 2011 Aug 24.
引用本文的文献
1
Structural Origins of FRET-Observed Nascent Chain Compaction on the Ribosome.核糖体上 FRET 观察到的新生链紧缩的结构起源。
J Phys Chem B. 2018 Nov 1;122(43):9927-9937. doi: 10.1021/acs.jpcb.8b07726. Epub 2018 Oct 18.
2
Resolution of Two Sub-Populations of Conformers and Their Individual Dynamics by Time Resolved Ensemble Level FRET Measurements.通过时间分辨整体水平荧光共振能量转移测量解析构象异构体的两个亚群及其个体动力学
PLoS One. 2015 Dec 23;10(12):e0143732. doi: 10.1371/journal.pone.0143732. eCollection 2015.
3
Determination of the polarization states of an arbitrary polarized terahertz beam: vectorial vortex analysis.任意偏振太赫兹光束偏振态的测定：矢量涡旋分析
Sci Rep. 2015 Mar 24;5:9416. doi: 10.1038/srep09416.
4
Multiphoton absorption of myoglobin-nitric oxide complex: relaxation by D-NEMD of a stationary state.肌红蛋白-一氧化氮复合物的多光子吸收：通过 D-NEMD 弛豫来达到稳定态。
J Phys Chem B. 2012 Mar 15;116(10):3397-410. doi: 10.1021/jp212148x. Epub 2012 Mar 6.
5
Mutagenesis of tryptophan199 suggests that hopping is required for MauG-dependent tryptophan tryptophylquinone biosynthesis.色氨酸 199 的突变表明， hopping 是 MauG 依赖的色氨酸色氨酸醌生物合成所必需的。
Proc Natl Acad Sci U S A. 2011 Oct 11;108(41):16956-61. doi: 10.1073/pnas.1109423108. Epub 2011 Oct 3.
6
Structural heterogeneity and quantitative FRET efficiency distributions of polyprolines through a hybrid atomistic simulation and Monte Carlo approach.通过混合原子模拟和蒙特卡罗方法研究多聚脯氨酸的结构异质性和定量 FRET 效率分布。
PLoS One. 2011;6(5):e19791. doi: 10.1371/journal.pone.0019791. Epub 2011 May 24.
7
Origin of slow relaxation following photoexcitation of W7 in myoglobin and the dynamics of its hydration layer.肌红蛋白中W7光激发后缓慢弛豫的起源及其水化层的动力学
J Phys Chem B. 2008 Dec 18;112(50):16121-34. doi: 10.1021/jp803042u.
8
Effect of flexibility and cis residues in single-molecule FRET studies of polyproline.多聚脯氨酸单分子荧光共振能量转移研究中柔性和顺式残基的影响。
Proc Natl Acad Sci U S A. 2007 Nov 27;104(48):18964-9. doi: 10.1073/pnas.0709567104. Epub 2007 Nov 20.
9
Characterizing the unfolded states of proteins using single-molecule FRET spectroscopy and molecular simulations.利用单分子荧光共振能量转移光谱和分子模拟对蛋白质的未折叠状态进行表征。
Proc Natl Acad Sci U S A. 2007 Jan 30;104(5):1528-33. doi: 10.1073/pnas.0607097104. Epub 2007 Jan 24.
10
Simulation of fluorescence anisotropy experiments: probing protein dynamics.荧光各向异性实验的模拟：探究蛋白质动力学
Biophys J. 2005 Dec;89(6):3757-70. doi: 10.1529/biophysj.105.069500. Epub 2005 Sep 16.
本文引用的文献
1
The internal dynamics of globular proteins.球状蛋白质的内部动力学。
CRC Crit Rev Biochem. 1981;9(4):293-349. doi: 10.3109/10409238109105437.
2
Fluorescence depolarization of tryptophan residues in proteins: a molecular dynamics study.蛋白质中色氨酸残基的荧光去极化：一项分子动力学研究。
Biochemistry. 1983 Jun 7;22(12):2884-93. doi: 10.1021/bi00281a017.
3
Picosecond fluorescence decay of tryptophans in myoglobin.肌红蛋白中色氨酸的皮秒荧光衰减
Proc Natl Acad Sci U S A. 1984 Jul;81(14):4399-403. doi: 10.1073/pnas.81.14.4399.
4
Dynamics of proteins: elements and function.蛋白质动力学：要素与功能
Annu Rev Biochem. 1983;52:263-300. doi: 10.1146/annurev.bi.52.070183.001403.
5
Integrating the equations of motion.对运动方程进行积分。
J Mol Biol. 1983 Aug 15;168(3):617-20. doi: 10.1016/s0022-2836(83)80305-2.
6
Molecular dynamics simulation of photodissociation of carbon monoxide from hemoglobin.血红蛋白中一氧化碳光解离的分子动力学模拟
Proc Natl Acad Sci U S A. 1985 Apr;82(7):2034-8. doi: 10.1073/pnas.82.7.2034.
7
Fluorescence and energy transfer of tryptophans in Aplysia myoglobin.海兔肌红蛋白中色氨酸的荧光和能量转移
Biophys J. 1987 Apr;51(4):653-60. doi: 10.1016/S0006-3495(87)83390-8.
8
Resolution of the fluorescence excitation spectrum of indole into the 1La and 1Lb excitation bands.吲哚荧光激发光谱分解为1La和1Lb激发带。
Photochem Photobiol. 1977 May;25(5):441-4. doi: 10.1111/j.1751-1097.1977.tb09168.x.
9
Structure of myoglobin refined at 2-0 A resolution. I. Crystallographic refinement of metmyoglobin from sperm whale.以2.0埃分辨率精修的肌红蛋白结构。I. 抹香鲸高铁肌红蛋白的晶体学精修。
J Mol Biol. 1977 Mar 5;110(3):537-68. doi: 10.1016/s0022-2836(77)80111-3.
10
Picosecond dynamics of tyrosine side chains in proteins.蛋白质中酪氨酸侧链的皮秒动力学
Biochemistry. 1979 Mar 20;18(6):927-42. doi: 10.1021/bi00573a001.
Zotero 插件