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微生物细胞色素纳米线中氧化还原传导的结构决定因素有利于稳健性而非可调性。

Structural Determinants of Redox Conduction Favor Robustness over Tunability in Microbial Cytochrome Nanowires.

作者信息

Guberman-Pfeffer Matthew J

机构信息

Department of Molecular Biophysics and Biochemistry, Yale University, 333 Cedar St., New Haven, CT, 06510.

Microbial Sciences Institute, Yale University, 840 West Campus Drive, West Haven, CT, 06516.

出版信息

bioRxiv. 2023 Jan 22:2023.01.21.525004. doi: 10.1101/2023.01.21.525004.

Abstract

Helical homopolymers of multiheme cytochromes catalyze biogeochemically significant electron transfers with a reported 10 -fold variation in conductivity. Herein, classical molecular dynamics and hybrid quantum/classical molecular mechanics are used to elucidate the structural determinants of the redox potentials and conductivities of the tetra-, hexa-, and octaheme outer-membrane cytochromes E, S, and Z, respectively, from . Second-sphere electrostatic interactions acting on minimally polarized heme centers are found to regulate redox potentials over a computed 0.5-V range. However, the energetics of redox conduction are largely robust to the structural diversity: Single-step electronic couplings (⟨H ⟩), reaction free energies , and reorganization energies (λ ) are always respectively <|0.026|, <|0.26|, and between 0.5 - 1.0 eV. With these conserved parameter ranges, redox conductivity differed by less than a factor of 10 among the 'nanowires' and is sufficient to meet the demands of cellular respiration if 10 - 10 'nanowires' are expressed. The 'nanowires' are proposed to be differentiated by the protein packaging to interface with a great variety of environments, and not by conductivity, because the rate-limiting electron transfers are elsewhere in the respiratory process. Conducting-probe atomic force microscopy measurements that find conductivities 10 -10 -fold more than cellular demands are suggested to report on functionality that is either not used or not accessible under physiological conditions. The experimentally measured difference in conductivity between Omc- S and Z is suggested to not be an intrinsic feature of the CryoEM-resolved structures.

摘要

多血红素细胞色素的螺旋同聚物催化具有生物地球化学意义的电子转移,据报道其电导率变化达10倍。在此,我们分别使用经典分子动力学和混合量子/经典分子力学来阐明来自[具体来源未给出]的四血红素、六血红素和八血红素外膜细胞色素E、S和Z的氧化还原电位和电导率的结构决定因素。发现作用于极化程度最低的血红素中心的二级静电相互作用在计算得到的0.5伏范围内调节氧化还原电位。然而,氧化还原传导的能量学在很大程度上对结构多样性具有鲁棒性:单步电子耦合(⟨H⟩)、反应自由能和重组能(λ)始终分别<|0.026|、<|0.26|且在0.5 - 1.0电子伏特之间。在这些保守的参数范围内,“纳米线”之间的氧化还原电导率差异小于10倍,如果表达10 - 10“纳米线”,则足以满足细胞呼吸的需求。“纳米线”被认为是通过蛋白质包装来区分,以便与各种环境相互作用,而不是通过电导率,因为限速电子转移发生在呼吸过程的其他地方。进行探针原子力显微镜测量发现电导率比细胞需求高10 - 10倍,这表明报告的是在生理条件下未被使用或无法获得的功能。实验测量的Omc - S和Z之间的电导率差异被认为不是低温电子显微镜解析结构的固有特征。

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