Electronic Structure Benchmark Calculations of CO2 Fixing Elementary Chemical Steps in RuBisCO Using the Projector-Based Embedding Approach

Abstract

<jats:p>&lt;div&gt;Ribulose 1,5-bisphosphate carboxylase-oxygenase (RuBisCO) is the main enzyme involved in atmospheric carbon dioxide (CO&lt;sub&gt;2&lt;/sub&gt;) fixation in the biosphere. This enzyme catalyses a set of five chemical steps that take place in the same active-site within magnesium (II) coordination sphere. Here, a set of electronic structure benchmark calculations have been carried out on a reaction path proposed by Gready &lt;i&gt;et al.&lt;/i&gt; by means of the projector-based embedding approach. Activation and reaction energies for all main steps catalyzed by RuBisCO have been calculated at the MP2, SCS-MP2, CCSD and CCSD(T)/aug-cc-pVDZ and cc-pVDZ levels of theory. &lt;/div&gt;&lt;div&gt;&lt;br&gt;&lt;/div&gt;&lt;div&gt;The treatment of the magnesium cation with post-HF methods is explored to determine the nature of its involvement in the mechanism. With the high-level ab initio values as a reference, we tested the performance of a set of density functional theory (DFT) exchange-correlation (xc) functionals in reproducing the reaction energetics of RuBisCO carboxylase activity on a set of model fragments. Different DFT xc-functionals show large variation in activation and reaction energies. Activation and reaction energies computed at the B3LYP level are close to the reference SCS-MP2 results for carboxylation, hydration and protonation reactions.&lt;/div&gt;&lt;div&gt;&lt;br&gt;&lt;/div&gt;&lt;div&gt;However, for the carbon-carbon bond dissociation reaction, B3LYP and other functionals give results that differ significantly from the ab initio reference values. The results show the applicability of the projector-based embedding approach to metalloenzymes. This technique removes the uncertainty associated with the selection of different DFT xc-functionals and so can overcome some of inherent limitations of DFT calculations, complementing and potentially adding to modelling of enzyme reaction mechanisms with DFT methods.&lt;/div&gt;</jats:p>

Carbon dioxide fixation in RuBisCO is protonation state dependent and irreversible

“…In the final step, we benchmark the obtained activation barrier and reaction free energy with high level ab-initio electronic structure methods using a projector-embedding approach. 17,[38][39][40][41] Enzyme assisted proton exchange between hydroxyl oxygen atoms in the substrate creates reactive species for the carboxylation reaction To activate RuBisCO for catalysis, first Lys201 is carbamylated (Kcx201) and the magnesium (II) cation and substrate bind to the active site accompanied with the closure of loop 6 (activated enzymatic form). 7,47 The CO 2 fixation reaction starts with the proton abstraction from the C3 carbon atom creating a reactive enolate (blue proton in Figure 2), named here as Enolate 2.…”

“…35,36 Projector-embedding approach with post-HF electronic structure calculations Activation barriers and reaction energies were also calculated using several high level ab-initio electronic structure methods embedded into a DFT environment by a projector-embedding approach. 17,[38][39][40][41] With this technique, it is possible to obtain activation and reaction energies at a high-level of theory with accuracy and at a low computational cost. This approach reduces errors from DFT xc-functional and allows a post-HF treatment of the reactive core of the catalyzed reaction describing the surrounding atoms with DFT xc-functional.…”

“…RuBisCO fragment model was reported by us employing the projector embedding approach on this relevant metallo enzyme. 17 Boltzmann Weighted Reactivity Descriptors from conceptual DFT…”

“…11 The elementary chemical steps associated with this comparable slow conversion of CO 2 are still not completely understood giving rise to several theoretical and experimental studies focused on its molecular mechanisms. 7,8,[12][13][14][15][16][17] RuBisCO is composed of eight large and eight small sub-units (L 8 S 8 ) in its form I that is mainly found in plants, algae and the majority of photosynthetic organisms. 7,8,18,19 The large sub-units are catalytic active and form a toroid around a four-fold symmetry axis (Figure 1A).…”

“…7,13,14 The sequence of elementary steps in the reaction mechanism were studied computationally with Density Functional Theory (DFT) calculations using different fragment models and compared to measured rate constants and deuterium or carbon isotope effects. 7,13,15,17,22 After Clealand and collaborators first proposed the mechanism, 23 Cummins, Gready and coworkers have provided a potential energy profile of the elementary steps using DFT calculations and optimized structures of fragments of the active site with increasing number of Figure 1: Quaternary structure of RuBisCO (form I) hexa-decamer complex with the catalytic active dimer composed of two large sub-units containing the active site associated with CO 2 fixation through the elementary steps shown at the bottom. (A) Schematic representation of the whole enzymatic complex highlighting the eight large sub-units in orange-blue and the eight small sub-units in yellow below and above of the toroid.…”