Kinetic pathway analysis of an α-helix in two protonation states: Direct observation and optimal dimensionality reduction
Kinetic pathway analysis of an α-helix in two protonation states: Direct observation and optimal dimensionality reduction
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DOI：
10.1063/1.5082192
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发表时间：
2019-02-21
影响因子：
4.4
通讯作者：
Kuczera, Krzysztof
中科院分区：
文献类型：
--
作者：
Jas, Gouri S.;Childs, Ed W.;Kuczera, Krzysztof
二级结构元件的热力学稳定构象形成稳定的三级/四级结构，有效地执行其适当的生物功能。二级和三级/四级结构元件从一级结构的形成机制是由各自系统的动力学性质驱动的。在这里，我们已经进行了热力学和动力学表征的α螺旋杂肽在两个质子化状态，创建一级结构中涉及一个单一的组氨酸残基的质子的添加和删除。应用远紫外圆二色谱法，观察到α螺旋在去质子化状态下显着更稳定。纳秒激光温度跳跃光谱监测质子化构象的时间分辨色氨酸荧光进行测量该系统的动力学。在296 K和314 K之间的最终温度下测量的弛豫速率产生20 ns-11 ns的较快分量和314 ns-198 ns的较慢分量。基于两种构象的全原子分子动力学轨迹，对螺旋-线圈动力学途径进行了原子详细表征。应用聚类和动力学粗粒化与最佳降维产生的动力学模型与两个到五个国家的轨迹的描述。这些模型包括对应于螺旋、卷曲和中间体的聚集态。“线圈”状态涉及最大数量的构象，与预期的高熵的结构合奏。“螺旋”聚集态被发现是混合的完整的螺旋和部分折叠的形式。实验观察到的α螺旋杂肽的去质子化形式的较高螺旋稳定性反映在动力学模型产生的“螺旋”聚集状态的性质中。在质子化形式中，“卷曲”状态表现出最低的自由能和最长的寿命，而在去质子化形式中，“螺旋”状态被发现是最稳定的。总的来说，粗粒度的模型表明，一级结构中的单个组氨酸残基的质子化诱导所研究的螺旋形成杂肽的自由能景观和动力学网络的显着变化。由AIP Publishing授权出版。
Thermodynamically stable conformers of secondary structural elements make a stable tertiary/quaternary structure that performs its proper biological function efficiently. Formation mechanisms of secondary and tertiary/quaternary structural elements from the primary structure are driven by the kinetic properties of the respective systems. Here we have carried out thermodynamic and kinetic characterization of an alpha helical heteropeptide in two protonation states, created with the addition and removal of a proton involving a single histidine residue in the primary structure. Applying far-UV circular dichroism spectroscopy, the alpha helix is observed to be significantly more stable in the deprotonated state. Nanosecond laser temperature jump spectroscopy monitoring time-resolved tryptophan fluorescence on the protonated conformer is carried out to measure the kinetics of this system. The measured relaxation rates at a final temperature between 296K and 314 K generated a faster component of 20 ns-11 ns and a slower component of 314 ns-198 ns. Atomically detailed characterization of the helix-coil kinetic pathways is performed based on all-atom molecular dynamics trajectories of the two conformers. Application of clustering and kinetic coarse-graining with optimum dimensionality reduction produced description of the trajectories in terms of kinetic models with two to five states. These models include aggregate states corresponding to helix, coil, and intermediates. The "coil" state involves the largest number of conformations, consistent with the expected high entropy of this structural ensemble. The "helix" aggregate states are found to be mixed with the full helix and partially folded forms. The experimentally observed higher helix stability in the deprotonated form of the alpha helical heteropeptide is reflected in the nature of the "helix" aggregate state arising from the kinetic model. In the protonated form, the "coil" state exhibits the lowest free energy and longest lifetime, while in the deprotonated form, it is the "helix" that is found to be most stable. Overall, the coarse grained models suggest that the protonation of a single histidine residue in the primary structure induces significant changes in the free energy landscape and kinetic network of the studied helix-forming heteropeptide. Published under license by AIP Publishing.