What can be learned from the electrostatic environments within nitrogenase enzymes?

15 May 2025, Version 3
This content is a preprint and has not undergone peer review at the time of posting.

Abstract

Nitrogen fixation is a fundamental, and yet challenging, chemical transformation due to the intrinsic inertness of dinitrogen. Whereas industrial ammonia synthesis relies on the energy-intensive Haber–Bosch process, nitrogenase enzymes achieve this transformation under ambient conditions—yet at the expense of a remarkably high ATP demand. Understanding their mode of operation could inspire the development of more efficient synthetic catalysts. In this study, we scrutinize the electrostatic environment surrounding nitrogenase’s active site, the so-called M-cluster. Strikingly, we observe that all types of M-clusters exhibit similar trends, with distinct patterns around the individual metal sites that have been proposed as potential N2-coordination sites. Specifically, a strong local electric field pointing away from the Fe2 site is identified, as well as a minor field pointing towards the Fe6 sites. Furthermore, a significant oriented long-range field along the Fe2–Fe6 axis is computed across the entire family of nitrogenases. In the final part of the manuscript, we discuss how the observed electrostatic patterns may impact chemical reactivity, and how they can be connected to previously made mechanistic hypotheses. Overall, this study provides further evidence for the ubiquitousness of local electric fields in enzyme catalysis, even when substrates that seemingly have only limited electrostatic susceptibility are involved.

Keywords

nitrogenase
oriented local electric fields
electrostatics
enzymes

Supplementary materials

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Supporting Information
Description
Electric field quantification from AMOEBA force field output, OLEF patterns around Fe2 and Fe6 for the FeMoco unit of 3U7Q determined with polarizable force field parameters, OLEF patterns around the different metal sites of the FeMoco unit of 3U7Q, OLEF patterns when removing residues in an increasing radius around the FeMoco unit of 3U7Q.
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