Can Second Coordination Sphere and Long-Range Interactions Modulate Hydrogen Atom Transfer in a Non-Heme Fe(II)-Dependent Histone Demethylase?

Abstract

Fe(II)-dependent oxygenases employ hydrogen atom transfer (HAT) to produce a myriad of products. Understanding how such enzymes use dynamic processes beyond the immediate vicinity of the active site to control the selectivity and efficiency of HAT is important for metalloenzyme engineering; however, obtaining such knowledge by experiments is challenging. This study develops a computational framework for identifying second coordination sphere (SCS) and especially long-range (LR) residues relevant for catalysis through dynamic cross-correlation analysis (DCCA) using the human histone demethylase PHF8 (KDM7B) as a model oxygenase. Furthermore, the study explores the mechanistic pathways of influence of the SCS and LR residues on the HAT reaction. To demonstrate the plausibility of the approach, we investigated the effect of a PHF8 F279S clinical mutation associated with X-linked intellectual disability, which has been experimentally shown to ablate PHF8-catalyzed demethylation. In agreement, the molecular dynamics (MD) and quantum mechanics/molecular mechanics (QM/MM) studies showed a change in the H3 1–14 K9me2 substrate orientation and an increased HAT barrier. We systematically analyzed the pathways by which the identified SCS and LR residues may influence HAT by exploring changes in H3K9me2 substrate orientation, interdomain correlated motions, HAT transition state stabilization, reaction energetics, electron transfer mechanism, and alterations in the intrinsic electric field of PHF8. Importantly, SCS and LR variations decrease key motions of α9−α12 of the JmjC domain toward the Fe(IV)-center that are associated with tighter binding of the H3 1–14 K9me2 substrate. SCS and LR residues alter the intrinsic electric field of the enzyme along the reaction coordinate and change the individual energetic contributions of residues toward TS stabilization. The overall results suggest that DCCA can indeed identify non-active-site residues relevant for catalysis. The substitutions of such dynamically correlated residues might be used as a tool to tune HAT in non-heme Fe(II)- and 2OG-dependent enzymes.

Mutational Study of the Tryptophan Tetrad Important for Electron Transfer in European Robin Cryptochrome 4a

“…The hydrogen bonds have been estimated through a Python script . Quite surprisingly, it is observed that certain hydrogen bonds are preserved among the different mutations, which contrasts earlier studies that reported notable deviations in the presence of hydrogen bonds among different mutations , …”

“…The hydrogen bonds have been estimated through a Python script. 71 Quite surprisingly, it is observed that certain hydrogen bonds are preserved among the different mutations, which contrasts earlier studies that reported notable deviations in the presence of hydrogen bonds among different mutations 72,73 The influence of the mutations on the intermolecular distances relevant for the cascade of electron transfers (d 1−4 ) (see Figure 1) has been summarized in Figure 8. Figure 8 shows that the introduced mutations do not significantly affect the intermolecular distances between the tryptophans.…”

Dioxygen Binding Is Controlled by the Protein Environment in Non‐heme FeII and 2‐Oxoglutarate Oxygenases: A Study on Histone Demethylase PHF8 and an Ethylene‐Forming Enzyme

“…The second coordination sphere (SCS) and protein environment in general are largely involved in enzyme catalysis [25,28–32] . The focus of this study is to explore the specific interactions in the SCS and beyond that control the dioxygen transport and binding in two Fe II /2OG enzymes – PHF8, which uses the in‐line mode, and EFE, which implements exclusively the off‐line mode.…”

“…The second coordination sphere (SCS) and protein environment in general are largely involved in enzyme catalysis. [25,[28][29][30][31][32] The focus of this study is to explore the specific interactions in the SCS and beyond that control the dioxygen transport and binding in two Fe II /2OG enzymes -PHF8, which uses the in-line mode, and EFE, which implements exclusively the off-line mode. Here, we use computational methods to investigate whether the dioxygen binding and interactions with SCS residues in Fe II / 2OG oxygenases to determine the formation of either an in-line or off-line Fe III -OO *À Intermediate, which further influences their reaction mechanisms.…”

Multiscale QM/MM modelling of catalytic systems with ChemShell

“…74 The 2-oxoglutarate (2OG) dependent non-haem iron oxygenases catalyse a wide variety of oxidative processes and have been the target of multiple recent studies. [75][76][77][78][79][80][81][82][83][84][85][86] Chaturvedi et al used ChemShell QM/MM calculations to investigate the reaction mechanism of PHF8, which catalyses demethylation of methylated lysine in histones, and is a target for cancer treatments. 87 The simulations revealed that rearrangement of 2OG at the iron centre is an important part of the mechanism, which may help inform the design of inhibitors.…”