Coupled Protons and Electrons in Biological Systems
生物系统中的质子和电子耦合
基本信息
- 批准号:10321617
- 负责人:
- 金额:$ 41.88万
- 依托单位:
- 依托单位国家:美国
- 项目类别:
- 财政年份:2021
- 资助国家:美国
- 起止时间:2021-01-01 至 2025-12-31
- 项目状态:未结题
- 来源:
- 关键词:BiochemicalBiochemical ProcessBiologicalBiological ModelsBiological ProcessBiomimeticsCell RespirationComplexCoupledCryoelectron MicroscopyDNA biosynthesisDataDrug DesignElectron TransportElectronsElectrostaticsEnvironmentEnzymesEquilibriumGoalsHydrogenIndividualKineticsLengthMeasurementMethodsModelingMolecular ConformationMotionMovementNuclearNucleotidesOrganismOxidesPathway interactionsPlayProcessProtein ConformationProtein EngineeringProteinsProtonsReactionRibonucleotide ReductaseRoleSeriesSolventsStructureTheoretical StudiesThermodynamicsTimeTryptophanTyrosineWorkalpha helixbiological systemsinsightmolecular dynamicsmulti-scale modelingoptogeneticsprotein complexprototypequantumquantum chemistryrepairedtheories
项目摘要
Project Summary/Abstract
Controlling the movement of electrons and protons is critical for a wide range of biological processes, including
cellular respiration, DNA biosynthesis, and photoreception used for optogenetics. Many of these processes are
driven by the formation of tyrosine or tryptophan radical species via proton-coupled electron transfer (PCET). An
elementary PCET reaction involves the transfer of one electron and one proton, but more complex PCET
processes involve the transfer of multiple electrons and protons. The Hammes-Schiffer group has developed a
general PCET theory enabling the calculation of rate constants and has applied this theory to biomimetic model
systems and to elementary PCET in an enzyme. Simulating more complex biological PCET processes is
challenging because of the significance of hydrogen tunneling and conformational motions, as well as key
contributions from multiple time and length scales. A major goal of this proposal is to develop a multiscale
modeling approach that describes the individual PCET steps, including the electronic and nuclear quantum
effects, as well as the key conformational changes coupled to them. Quantum chemistry and molecular dynamics
methods will be used to compute the input quantities to the PCET theory. The calculated rate constants for
individual PCET reactions and protein conformational changes will serve as input into microkinetic models to
enable the complete description of complex multi-electron, multi-proton biological processes. This multiscale
modeling approach will be closely connected to experimental data, relying on atomic-level structures and
thermodynamic and kinetic measurements. Initially this approach will be applied to PCET in the well-defined,
controlled protein environment of the α3X proteins, which consist of three alpha helices with a single interior
tyrosine or tryptophan that can be oxidized electrochemically. This approach will be expanded to explore multi-
electron, multi-proton reactions in the more complex protein environment of ribonucleotide reductase (RNR).
This enzyme catalyzes the conversion of nucleotides to deoxynucleotides, thereby maintaining the nucleotide
pool balance required for effective DNA synthesis, replication, and repair. In addition to its biochemical
importance, RNR serves as a prototype for multi-step biological PCET. The long-range radical translocation over
~35 Å in RNR is proposed to occur via a series of PCET steps involving tyrosine and tryptophan residues, as
well as significant conformational changes. A recently solved cryo-EM structure of the active complex resolves
the entire PCET pathway and provides an opportunity for theoretical studies. This work will elucidate the impact
of the protein electrostatic environment, solvent accessibility, and conformational motions on PCET. It will also
provide insights into how individual PCET steps are coupled to each other and to protein conformational motions
and what determines the order of the steps and the overall rate. Discovering the factors that impact biological
PCET is vital for understanding and controlling a wide range of essential biochemical processes. These
fundamental insights may also have broader implications for protein design and optogenetics.
项目摘要/摘要
控制电子和质子的运动对于广泛的生物过程至关重要,包括
细胞呼吸,DNA生物合成和用于光遗传学的光感受。这些过程中有许多是
由酪氨酸或色氨酸自由基通过质子偶联电子转移(PCET)驱动。一个
基本PCET反应涉及一个电子和一个质子的转移,但更复杂的PCET
过程涉及多个电子和质子的转移。 Hammes-Schiffer组已开发
一般的PCET理论实现了速率常数的计算,并将该理论应用于仿生模型
系统和酶中的基本PCET。模拟更复杂的生物PCET过程是
具有挑战性,因为氢隧穿和构象运动的重要性以及关键
来自多个时间和长度尺度的贡献。该提案的主要目标是开发多尺度
描述各个PCET步骤的建模方法,包括电子和核量子
效果以及关键的会议变化与它们结合。量子化学和分子动力学
方法将用于计算PCET理论的输入量。计算的费率常数
单个PCET反应和蛋白质构象变化将作为对微动模型的输入
启用复杂的多电子,多原子生物学过程的完整描述。这个多尺度
建模方法将与实验数据紧密连接,依靠原子级结构和
热力学和动力学测量。最初,此方法将应用于定义明确的PCET
α3X蛋白的受控蛋白质环境,该蛋白质由三个α螺旋组成
可以用电化学氧化的酪氨酸或色氨酸。该方法将扩展以探索多
电子,核糖核苷酸还原(RNR)中更复杂的蛋白质环境中的多质子反应。
这种酶催化了核苷酸向脱氧核苷酸的转化,从而维持核苷酸
有效的DNA合成,复制和修复所需的池平衡。除了生化
重要的是,RNR是多步生物PCET的原型。远程激进的易位
提议在RNR中〜35Å通过一系列涉及酪氨酸和色氨酸残留物的PCET步骤,如
以及重大构象变化。活跃复合物的最近解决的冷冻EM结构解决了
整个PCET途径,为理论研究提供了机会。这项工作将阐明影响
蛋白质静电环境,溶剂可及性和PCET上的构象运动。它也会
提供有关如何相互耦合和蛋白质构象运动的见解
以及决定步骤顺序和整体速率的是什么。发现影响生物学的因素
PCET对于理解和控制广泛的基本生化过程至关重要。这些
基本见解也可能对蛋白质设计和光遗传学具有更广泛的影响。
项目成果
期刊论文数量(0)
专著数量(0)
科研奖励数量(0)
会议论文数量(0)
专利数量(0)
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SHARON HAMMES-SCHIFFER其他文献
SHARON HAMMES-SCHIFFER的其他文献
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{{ truncateString('SHARON HAMMES-SCHIFFER', 18)}}的其他基金
Coupled Protons and Electrons in Biological Systems
生物系统中的质子和电子耦合
- 批准号:
10543740 - 财政年份:2021
- 资助金额:
$ 41.88万 - 项目类别:
Simulation of Proton and Hydride Transfer in Enzymes
酶中质子和氢化物转移的模拟
- 批准号:
7941376 - 财政年份:2009
- 资助金额:
$ 41.88万 - 项目类别:
SIMULATION OF PROTON AND HYDRIDE TRANSFER IN ENZYMES
酶中质子和氢化物转移的模拟
- 批准号:
6340282 - 财政年份:2000
- 资助金额:
$ 41.88万 - 项目类别:
SIMULATION OF PROTON AND HYDRIDE TRANSFER IN ENZYMES
酶中质子和氢化物转移的模拟
- 批准号:
6386717 - 财政年份:2000
- 资助金额:
$ 41.88万 - 项目类别:
Simulation of Proton and Hydride Transfer in Enzymes
酶中质子和氢化物转移的模拟
- 批准号:
8247720 - 财政年份:1998
- 资助金额:
$ 41.88万 - 项目类别:
SIMULATION OF PROTON AND HYDRIDE TRANSFER IN ENZYMES
酶中质子和氢化物转移的模拟
- 批准号:
2910352 - 财政年份:1998
- 资助金额:
$ 41.88万 - 项目类别:
Simulation of Protein and Hydride Transfer in Enzymes
酶中蛋白质和氢化物转移的模拟
- 批准号:
6579729 - 财政年份:1998
- 资助金额:
$ 41.88万 - 项目类别:
Simulation of Proton and Hydride Transfer in Enzymes
酶中质子和氢化物转移的模拟
- 批准号:
7385038 - 财政年份:1998
- 资助金额:
$ 41.88万 - 项目类别:
SIMULATION OF PROTON AND HYDRIDE TRANSFER IN ENZYMES
酶中质子和氢化物转移的模拟
- 批准号:
2608983 - 财政年份:1998
- 资助金额:
$ 41.88万 - 项目类别:
SIMULATION OF PROTON AND HYDRIDE TRANSFER IN ENZYMES
酶中质子和氢化物转移的模拟
- 批准号:
6519829 - 财政年份:1998
- 资助金额:
$ 41.88万 - 项目类别:
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