Ribonuclease S dynamics measured using a nitrile label with 2D IR vibrational echo spectroscopy.
Ribonuclease S dynamics measured using a nitrile label with 2D IR vibrational echo spectroscopy.
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DOI：
10.1021/jp2122856
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发表时间：
2012-04-05
影响因子：
3.3
通讯作者：
Fayer, Michael D.
中科院分区：
文献类型：
--
作者：
Bagchi, Sayan;Boxer, Steven G.;Fayer, Michael D.
在半合成酶核糖核酸酶 S 的活性位点附近引入腈标记的氨基酸，对氰基苯丙氨酸，作为蛋白质动力学和波动的探针。核糖核酸酶 S 是枯草杆菌蛋白酶作用于核糖核酸酶 A 的有限蛋白水解产物，由包含氨基酸 1-20 的小片段（S 肽）和包含残基 21-124 的较大片段（S 蛋白）组成。描述了对腈标记的 S 肽和 RNase S 进行的一系列二维振动回波实验。使用中心线斜率法分析二维红外振动回波线形状随时间的变化，以获得频频相关函数（FFCF）。观察结果表明，S 肽中的腈探针具有与水中的单个氨基酸对氰基苯丙氨酸相似但更快的动力学。相比之下，当肽结合形成核糖核酸酶 S 时，腈标记的动力学主要由均质相移（运动变窄）贡献主导，而非常快的非均质结构动力学贡献很小。这些结果提供了对核糖核酸酶 S 复合物结构动力学性质的深入了解。还通过分子动力学模拟研究了腈标记的 S 肽和核糖核酸酶 S 复合物的平衡动力学。将实验确定的 FFCF 与分子动力学模拟获得的 FFCF 进行比较，从而测试模拟确定热平衡条件下快速时间尺度上蛋白质结构波动的幅度和时间尺度的能力。
A nitrile labeled amino acid, p-cyanophenylalanine, is introduced near the active site of the semisynthetic enzyme ribonuclease S to serve as a probe of protein dynamics and fluctuations. Ribonuclease S is the limited proteolysis product of subtilisin acting on ribonuclease A, and consists of a small fragment including amino acids 1–20, the S-peptide, and a larger fragment including residues 21–124, the S-protein. A series of two-dimensional vibrational echo experiments performed on the nitrile labeled S-peptide and the RNase S are described. The time-dependent changes in the two-dimensional infrared vibrational echo line shapes are analyzed using the center line slope method to obtain the frequency-frequency correlation function (FFCF). The observations show that the nitrile probe in the S-peptide has dynamics that are similar to, but faster than, those of the single amino acid p-cyanophenylalanine in water. In contrast, the dynamics of the nitrile label when the peptide is bound to form ribonuclease S are dominated by homogeneous dephasing (motionally narrowed) contributions with only a small contribution from very fast inhomogeneous structural dynamics. The results provide insights into the nature of the structural dynamics of the ribonuclease S complex. The equilibrium dynamics of the nitrile labeled S-peptide and the ribonuclease S complex are also investigated by molecular dynamics simulations. The experimentally determined FFCFs are compared to the FFCFs obtained from the molecular dynamics simulations, thereby testing the capacity of simulations to determine the amplitudes and time scales of protein structural fluctuations on fast time scales under thermal equilibrium conditions.
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影响因子：
3.3
作者：
Finkelstein, IJ;Goj, A;Fayer, MD
通讯作者：
Fayer, MD
影响因子：
4.4
作者：
Asbury, JB;Steinel, T;Fayer, MD
通讯作者：
Fayer, MD
DOI：
10.1039/f19888402181
发表时间：
1988-01-01
期刊：
JOURNAL OF THE CHEMICAL SOCIETY-FARADAY TRANSACTIONS I
影响因子：
--
作者：
EATON, G;PENANUNEZ, AS;SYMONS, MCR
通讯作者：
SYMONS, MCR
影响因子：
56.9
作者：
FRAUENFELDER, H;SLIGAR, SG;WOLYNES, PG
通讯作者：
WOLYNES, PG
影响因子：
15
作者：
Bagchi, Sayan;Nebgen, Benjamin T.;Fayer, M. D.
通讯作者：
Fayer, M. D.