Conformational and Reaction Dynamic Coupling in Histidine Kinases: Insights from Hybrid QM/MM Simulations

Abstract

Histidine kinases (HK) of bacterial two-component systems represent a hallmark of allosterism in proteins, being able to detect a signal through the sensor domain and transmit this information through the protein matrix to the kinase domain which, once active, autophosphorylates a specific histidine residue. Inactive-to-active transition results in a large conformational change that moves the kinase on top of the histidine. In the present work, we use several molecular simulation techniques (Molecular Dynamics, Hybrid QM/MM, and constant pH molecular dynamics) to study the activation and autophosphorylation reactions in L. plantarum WalK, a cis-acting HK. In agreement with previous results, we show that the chemical step requires tight coupling with the conformational step in order to maintain the histidine phosphoacceptor in the correct tautomeric state, with a reactive δ-nitrogen. During the conformational transition, the kinase domain is never released and walks along the HK helix axis, breaking and forming several conserved residue-based contacts. The phosphate transfer reaction is concerted in the transition state region and is catalyzed through the stabilization of the negative developing charge of transferring phosphate along the reaction.

Atomistic Simulations of the Mechanisms of the Poorly Catalytic Mitochondrial Chaperone Trap1: Insights into the Effects of Structural Asymmetry on Reactivity

“…To build our model, we have relied on distinct in silico approaches. Methodological choices are closely based on the rationale adopted in a similar study by one of the authors on enzymatic stereoselectivity and are in line with options suggested in several reviews referenced earlier. − , In the Supporting Information, we evaluate the reliability of our choices, focusing on the following aspects: (1) the suitability of both chosen MD approaches to evaluate % reac and Δ F ⧧ and their statistical validity, (2) the suitability of the semiempirical QM method DFTB3/O-Phyd in evaluating Δ F ⧧ , especially in relation to other methodological options ,,− ,,,,,,,, and whether benchmarking is satisfactory, and (3) how well sampling along the relatively simple RC Enz and RC Sub still manages to capture chemical changes involving other QM atoms.…”

“…In silico case studies (e.g. refs and − to mention only a few recent studies) point to a plethora of accessible reaction pathways, for which it is exceedingly difficult to predetermine a suitably descriptive reaction coordinate − (cf. Results and Discussion).…”

“…Regardless of Buc ’s and Str ’s similar active sites (Figure a), some common traits that could catalyze ATP cleavage are identifiable through chemical intuition, studies on related enzymes, ,,,− and mutagenesis experiments. ,,− Namely (cf. Figure b, depicting Str ’s active site in a “reactive” state during one of our simulations; vide infra), Glu130, with its hydrogen bond to the nucleophilic water ( Wat Nuc ) and conformational links to the rest of the chaperone through its vicinal Arg129 ( vide infra ), stands out as the general base in an enzyme-assisted hydrolytic pathway (RC Enz ; Scheme , top).…”

Molecular basis of unidirectional information transmission in two-component systems: lessons from the DesK-DesR thermosensor

“…To study both the phosphotransfer and the phosphatase reaction mechanisms, we used a multiple steered molecular dynamics (MSMD) strategy, combined with Jarzynski's relationship to determine the corresponding Free Energy Profiles. This strategy has already been shown to be useful in previous works from our group for phosphoryl transfer reactions 35,53,54 . Briefly, in MSMD the system is driven "multiple" times along the selected reaction coordinate under nonequilibrium conditions, by applying an external force, and for each individual trajectory, the work performed by the external force is computed.…”

“…The copyright holder for this preprint this version posted November 12, 2021. ; https://doi.org/10.1101/2021.11.12.468217 doi: bioRxiv preprint strategy has already been shown to be useful in previous works from our group for phosphoryl transfer reactions 35,53,54 . Briefly, in MSMD the system is driven "multiple" times along the selected reaction coordinate under nonequilibrium conditions, by applying an external force, and for each individual trajectory, the work performed by the external force is computed.…”