The thermodynamics of charge transfer in DNA photolyase: using thermodynamic integration calculations to analyse the kinetics of electron transfer reactions.
The thermodynamics of charge transfer in DNA photolyase: using thermodynamic integration calculations to analyse the kinetics of electron transfer reactions.
复制标题
DNA光裂合酶中电荷转移的热力学：利用热力学积分计算来分析电子转移反应的动力学。
DOI：
10.1039/c000876a
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发表时间：
2010
期刊：
影响因子：
--
通讯作者：
T. Steinbrecher
中科院分区：
文献类型：
--
作者：
S. Krapf;Thorsten Koslowski;T. Steinbrecher
DNA光解酶是一种光敏氧化还原酶，存在于许多生物体中，参与光损伤DNA的修复。它们能够在结合的辅因子和色氨酸氨基酸残基的链之间进行电子转移。由于其独特的机制和重要的功能，光解酶近年来得到了广泛的研究，无论是实验还是计算都是如此。在这项工作中，我们提出了一种基于经典分子动力学的自由能计算与量子力学计算相结合的新应用，用于生物分子的电荷转移。我们的方法允许确定马库斯电荷输运理论中的所有反应参数。我们能够计算出正电荷沿参与生物分子功能的蛋白质侧链移动的自由能分布，以及电荷转移速率，这与实验结果很好地一致。我们模拟电荷转移反应的方法明确地包括了蛋白质柔性和溶剂动力学对电荷转移能量学的影响。通过将该方法应用于生物分子体系，我们相信该方法很容易适用于生物化学和其他领域中电荷转移现象的研究。
DNA Photolyases are light sensitive oxidoreductases present in many organisms that participate in the repair of photodamaged DNA. They are capable of electron transfer between a bound cofactor and a chain of tryptophan amino acid residues. Due to their unique mechanism and important function, photolyases have been subject to intense study in recent times, with both experimental and computational efforts. In this work, we present a novel application of classical molecular dynamics based free energy calculations, combined with quantum mechanical computations, to biomolecular charge transfer. Our approach allows for the determination of all reaction parameters in Marcus' theory of charge transport. We were able to calculate the free energy profile for the movement of a positive charge along protein sidechains involved in the biomolecule's function as well as charge-transfer rates that are in good agreement with experimental results. Our approach to simulate charge-transfer reactions explicitly includes the influence of protein flexibility and solvent dynamics on charge-transfer energetics. As applied here to a biomolecular system of considerable scientific interest, we believe the method to be easily adaptable to the study of charge-transfer phenomena in biochemistry and other fields.
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影响因子：
16.6
作者：
Biskup, Till;Schleicher, Erik;Okafuji, Asako;Link, Gerhard;Hitomi, Kenichi;Getzoff, Elizabeth D.;Weber, Stefan
通讯作者：
Weber, Stefan
影响因子：
56.9
作者：
PARK, HW;KIM, ST;DEISENHOFER, J
通讯作者：
DEISENHOFER, J
大肠杆菌 DNA 光裂合酶中的电子转移途径：Trp306 至 FADH。
影响因子：
3.4
作者：
Cheung,MS;Daizadeh,I;Stuchebrukhov,AA;Heelis,PF
通讯作者：
Heelis,PF
影响因子：
3.4
作者：
Ritz, T;Adem, S;Schulten, K
通讯作者：
Schulten, K
影响因子：
7.3
作者：
T. Steinbrecher;D. Case;A. Labahn
通讯作者：
T. Steinbrecher;D. Case;A. Labahn