Gaponenko V, Howarth J W, Columbus L, Gasmi-Seabrook G, Yuan J, Hubbell W L, Rosevear P R
Department of Molecular Genetics, Biochemistry, and Microbiology, University of Cincinnati, College of Medicine, Ohio 45267, USA.
Protein Sci. 2000 Feb;9(2):302-9. doi: 10.1110/ps.9.2.302.
We describe a simple experimental approach for the rapid determination of protein global folds. This strategy utilizes site-directed spin labeling (SDSL) in combination with isotope enrichment to determine long-range distance restraints between amide protons and the unpaired electron of a nitroxide spin label using the paramagnetic effect on relaxation rates. The precision and accuracy of calculating a protein global fold from only paramagnetic effects have been demonstrated on barnase, a well-characterized protein. Two monocysteine derivatives of barnase, (H102C) and (H102A/Q15C), were 15N enriched, and the paramagnetic nitroxide spin label, MTSSL, attached to the single Cys residue of each. Measurement of amide 1H longitudinal relaxation times, in both the oxidized and reduced states, allowed the determination of the paramagnetic contribution to the relaxation processes. Correlation times were obtained from the frequency dependence of these relaxation processes at 800, 600, and 500 MHz. Distances in the range of 8 to 35 A were calculated from the magnitude of the paramagnetic contribution to the relaxation processes and individual amide 1H correlation times. Distance restraints from the nitroxide spin to amide protons were used as restraints in structure calculations. Using nitroxide to amide 1H distances as long-range restraints and known secondary structure restraints, barnase global folds were calculated having backbone RMSDs <3 A from the crystal structure. This approach makes it possible to rapidly obtain the overall topology of a protein using a limited number of paramagnetic distance restraints.
我们描述了一种用于快速确定蛋白质整体折叠的简单实验方法。该策略利用定点自旋标记(SDSL)结合同位素富集,通过顺磁对弛豫速率的影响来确定酰胺质子与氮氧化物自旋标记的未配对电子之间的长程距离限制。仅基于顺磁效应计算蛋白质整体折叠的精度和准确性已在巴那斯酶(一种特征明确的蛋白质)上得到证明。巴那斯酶的两种单半胱氨酸衍生物(H102C)和(H102A/Q15C)进行了15N富集,并将顺磁氮氧化物自旋标记MTSSL连接到每个衍生物的单个半胱氨酸残基上。测量氧化态和还原态下酰胺1H纵向弛豫时间,可确定顺磁对弛豫过程的贡献。通过这些弛豫过程在800、600和500 MHz频率下的频率依赖性获得相关时间。根据顺磁对弛豫过程的贡献大小和各个酰胺1H相关时间计算出8至35埃范围内的距离。从氮氧化物自旋到酰胺质子的距离限制被用作结构计算中的限制条件。使用从氮氧化物到酰胺1H的距离作为长程限制以及已知的二级结构限制,计算出的巴那斯酶整体折叠与晶体结构相比,主链均方根偏差小于3埃。这种方法使得使用有限数量的顺磁距离限制就能快速获得蛋白质的整体拓扑结构。