Catalytic Mechanism of the Serine Hydroxymethyltransferase: A Computational ONIOM QM/MM Study

Abstract

Serine hydroxymethyltransferase (SHMT) is an important drug target to fight malaria, which is one of the most devastating infectious diseases, with 216 million cases cited and accounting for ∼450 000 deaths in 2016. In this paper, computational studies were performed to unveil the catalytic mechanism of SHMT using quantum mechanics/molecular mechanics (QM/ MM) methodologies. This enzyme is responsible for the extraordinary cyclization of a tetrahydrofolate (THF) into 5,10methylene−THF. This process is catalyzed by a pyridoxal-5′phosphate (PLP) cofactor that binds L-serine and, from this, one molecule of L-glycine is produced. The results show that the catalytic process occurs in eight sequential steps that involve an αelimination, the cyclization of the 5-hydroxymethyl−THF intermediate into 5,10-methylene−THF, and the protonation of the quinonoid intermediate. According to the calculated energetic profile, the rate-limiting step of the full mechanism is the elimination of the hydroxymethyl group, from which results a formaldehyde intermediate that then becomes covalently bonded to the THF cofactor. The calculated barrier (DLPNO−CCSD(T)/CBS:ff99SB) for the rate-limiting step (18.0 kcal/mol) agrees very well with the experimental kinetic results (15.7−16.2 kcal/mol). The results also highlight the key role played by Glu57 during the full catalytic process and particularly in the first step of the mechanism that requires an anionic Glu57, contrasting with some proposals available in the literature for this step. It was also concluded that the cyclization of THF must occur in the enzyme, rather than in solution, as it has been proposed also in the past. Together, all of these results provide knowledge and insight on the catalytic mechanism of SHMT, which can now be used to develop inhibitors targeting SHMT and, therefore, antimalaria drugs.

Cations in motion: QM/MM studies of the dynamic and electrostatic roles of H+ and Mg2+ ions in enzyme reactions

“…Alternative, more affordable methods use bespoke semiempirical algorithms such as DFTB [26][27][28] where standard semiempirical methods fail. In an effort to optimize accuracy and costs, mixed QM algorithms can also be used such as ONIOM [7,18,29]. Cluster QM calculations offer another approach, simplifying the problem by eliminating the MM degrees of freedom [30].…”

“…Describing both the quantum chemistry required for accurate description of reactions as well as the complex structural/dynamical aspects of the protein/nucleic acid environment, hybrid quantum/classical QM/MM methods have a unique, unprecedented capability to examine reaction mechanisms at sub-atomic details. An extensive amount of work has been done toward understanding various enzymatic systems such as lipoxygenases [1,2], cofactor-free oxidases [3,4], Kemp eliminase [5,6], serine hydroxymethyltransferase [7] and many others [8][9][10][11][12][13]. Here we focus on phosphate catalytic reactions, which contribute probably the most important catalytic reactions in living organisms [14][15][16][17][18][19].…”

A QM/MM simulation study of transamination reaction at the active site of aspartate aminotransferase: Free energy landscape and proton transfer pathways

“…We note that the proton transfer at the active site of We note that the method of QM/MM calculations have been used rather extensively to study the mechanism and energetics of many enzymatic reactions in the past. [44][45][46][47][48][49][50][51][52][53] However, to the best of our knowledge, such a study of the mechanism and free energies of transamination reaction considering full structural details of the enzyme, PLP, substrate and the surrounding environment is presented here for the first time. Specifically, we have used the Car-Parrinello method [54] for ab initio MD and AMBER [55] force fields for the classical MD to perform QM/MM [44,45] simulations of the transamination reaction at active site of the aspartate transaminase enzyme.…”

Formation of Unstable and very Reactive Chemical Species Catalyzed by Metalloenzymes: A Mechanistic Overview

“…Before the cobalt-containing cobalamin (vitamin B 12 ) cofactor can react with the activated substrate, it needs to be activated by 5-methyl-tetrahydrofolate (5-methyl-THF) [166,167]. In this process, the methyl group from the 5-methyl-THF becomes coordinated directly to the metal ion and THF is released to the solvent.…”