Correlating enzymatic reactivity for different substrates using transferable data-driven collective variables.

Machine learning (ML) is transforming the investigation of complex biological processes. In enzymatic catalysis, one significant challenge is identifying the reactive conformations (RC) of the enzyme:substrate complex where the substrate assumes a precise arrangement in the active site necessary to initiate a reaction. Traditional methods are hindered by the complexity of the multidimensional free energy landscape involved in the transition from nonreactive to reactive conformations.

Engineering DszC Mutants from Transition State Macrodipole Considerations and Evolutionary Sequence Analysis.

We describe an approach to identify enzyme mutants with increased turnover using the enzyme DszC as a case study. Our approach is based on recalculating the barriers of alanine mutants through single-point energy calculations at the hybrid QM/MM level in the wild-type reactant and transition state geometries. We analyze the difference in the electron density between the reactant and transition state to identify sites/residues where electrostatic interactions stabilize the transition state over the reactants.

QM/MM Study of the Reaction Mechanism of Thermophilic Glucuronoyl Esterase for Biomass Treatment.

Hydrolysis of lignocellulosic biomass, composed of a lignin-carbohydrate-complex (LCC) matrix, is critical for producing bioethanol from glucose. However, current methods for LCC processing require costly and polluting processes. The fungal Thermothelomyces thermophila glucuronoyl esterase (TtGE) is a promising thermophilic enzyme that hydrolyses LCC ester bonds.

Role of Enzyme and Active Site Conformational Dynamics in the Catalysis by α-Amylase Explored with QM/MM Molecular Dynamics.

We assessed enzyme:substrate conformational dynamics and the rate-limiting glycosylation step of a human pancreatic α-amylase:maltopentose complex. Microsecond molecular dynamics simulations suggested that the distance of the catalytic Asp197 nucleophile to the anomeric carbon of the buried glucoside is responsible for most of the enzyme active site fluctuations and that both Asp197 and Asp300 interact the most with the buried glucoside unit. The buried glucoside binds either in a chair or skew conformations, both of which can change to TS-like conformations characteristic of retaining glucosidases.

Different Enzyme Conformations Induce Different Mechanistic Traits in HIV-1 Protease.

The influence of the dynamical flexibility of enzymes on reaction mechanisms is a cornerstone in biological sciences. In this study, we aim to 1) study the convergence of the activation free energy by using the first step of the reaction catalysed by HIV-1 protease as a case study, and 2) provide further evidence for a mechanistic divergence in this enzyme, as two different reaction pathways were seen to contribute to this step. We used quantum mechanics/molecular mechanics molecular dynamics simulations, on four different initial conformations that led to different barriers in a previous study.

Towards the Accurate Thermodynamic Characterization of Enzyme Reaction Mechanisms.

We employed QM/MM molecular dynamics (MD) simulations to characterize the rate-limiting step of the glycosylation reaction of pancreatic α-amylase with combined DFT/molecular dynamics methods (PBE/def2-SVP : AMBER). Upon careful choice of four starting active site conformations based on thorough reactivity criteria, Gibbs energy profiles were calculated with umbrella sampling simulations within a statistical convergence of 1-2 kcal ⋅ mol . Nevertheless, Gibbs activation barriers and reaction energies still varied from 11.

Animal Fatty Acid Synthase: A Chemical Nanofactory.

Fatty acids are crucial molecules for most living beings, very well spread and conserved across species. These molecules play a role in energy storage, cell membrane architecture, and cell signaling, the latter through their derivative metabolites. synthesis of fatty acids is a complex chemical process that can be achieved either by a metabolic pathway built by a sequence of individual enzymes, such as in most bacteria, or by a single, large multi-enzyme, which incorporates all the chemical capabilities of the metabolic pathway, such as in animals and fungi, and in some bacteria.

Combined in silico and in vitro studies to identify novel antidiabetic flavonoids targeting glycogen phosphorylase.

Novel pharmacological strategies for the treatment of diabetic patients are now focusing on inhibiting glycogenolysis steps. In this regard, glycogen phosphorylase (GP) is a validated target for the discovery of innovative antihyperglycemic molecules. Natural products, and in particular flavonoids, have been reported as potent inhibitors of GP at the cellular level.

Structural and mechanistic aspects of S-S bonds in the thioredoxin-like family of proteins.

Disulfide bonds play a critical role in a variety of structural and mechanistic processes associated with proteins inside the cells and in the extracellular environment. The thioredoxin family of proteins like thioredoxin (Trx), glutaredoxin (Grx) and protein disulfide isomerase, are involved in the formation, transfer or isomerization of disulfide bonds through a characteristic thiol-disulfide exchange reaction. Here, we review the structural and mechanistic determinants behind the thiol-disulfide exchange reactions for the different enzyme types within this family, rationalizing the known experimental data in light of the results from computational studies.

Properties that rank protein:protein docking poses with high accuracy.

The development of docking algorithms to predict near-native structures of protein:protein complexes from the structure of the isolated monomers is of paramount importance for molecular biology and drug discovery. In this study, we assessed the capacity of the interfacial area of protein:protein complexes and of Molecular Mechanics-Poisson Boltzmann Surface Area (MM-PBSA)-derived properties, to rank docking poses. We used a set of 48 protein:protein complexes, and a total of 67 docking experiments distributed among bound:bound, bound:unbound, and unbound:unbound test cases.

Modeling of Human Fatty Acid Synthase and in Silico Docking of Acyl Carrier Protein Domain and Its Partner Catalytic Domains.

Human fatty acid synthase (hFAS) is a megasynthase whose main function is de novo biosynthesis of saturated fatty acids. Interest has been drawn to this enzyme beyond its physiological role due to the association between high levels of hFAS and clinical conditions such as obesity, diabetes, and cancer. Thus, it has become an undeniably attractive pharmacological target.

Mechanistic insights on the reduction of glutathione disulfide by protein disulfide isomerase.

We explore the enzymatic mechanism of the reduction of glutathione disulfide (GSSG) by the reduced domain of human protein disulfide isomerase (hPDI) with atomistic resolution. We use classical molecular dynamics and hybrid quantum mechanics/molecular mechanics calculations at the mPW1N/6-311+G(2d,2p):FF99SB//mPW1N/6-31G(d):FF99SB level. The reaction proceeds in two stages: () a thiol-disulfide exchange through nucleophilic attack of the Cys53-thiolate to the GSSG-disulfide followed by the deprotonation of Cys56-thiol by Glu47-carboxylate and () a second thiol-disulfide exchange between the Cys56-thiolate and the mixed disulfide intermediate formed in the first step.

A QM/MM study of the reaction mechanism of human β-ketoacyl reductase.

Human fatty acid synthase (hFAS) is a multifunctional enzyme involved in a wide diversity of biological functions. For instance, it is a precursor of phospholipids and other complex processes such as the de novo synthesis of long chain fatty acid. Human FAS is also a component of biological membranes and it is implicated in the overexpression of several types of cancers.

Improving the Biodesulfurization of Crude Oil and Derivatives: A QM/MM Investigation of the Catalytic Mechanism of NADH-FMN Oxidoreductase (DszD).

The development of biocatalytic desulfurization strategies of petroleum and its derivatives could result in more economic alternatives than the widely used chemical desulfurization. The organism Rhodococcus erythropolis IGTS8 has been shown to metabolize organic sulfur compounds through a mechanism known as 4S pathway, which involves four enzymes (DszA, DszB, DszC, and DszD) and has been explored in biodesulfurization. Here we have applied QM/MM methods to study the catalytic mechanism of the enzyme DszD, a NADH-FMN oxidoreductase that occupies a central place on the 4S pathway by catalyzing the formation of the FMNH2 that is used by the two monooxynases in the cycle: DszA and DszC.

Benchmarking of Density Functionals for the Accurate Description of Thiol-Disulfide Exchange.

A set of 92 density functionals was employed to accurately characterize thiol-disulfide exchange. The properties we have benchmarked throughout the study include the geometry of a 15 atoms model system, the potential energy surface, the activation barrier, and the energy of reaction for thiol-disulfide exchange. Reference energies were determined at the CCSD(T)/CBS//MP2/aug-cc-pVDZ level of theory, and reference geometries were calculated at the MP2/aug-cc-pVTZ level.

Parameters for Molecular Dynamics Simulations of Manganese-Containing Metalloproteins.

A set of geometrical parameters has been determined for single manganese metalloproteins for the AMBER force field, and ultimately to other force fields with a similar philosophy. Twelve (12) models from 9 different single-cluster manganese proteins were optimized and parametrized, using a bonded model approach. Mn-ligand bonds, Mn-ligand angles, and Restrained Electrostatic Potential charges for all the 74 residues in the first metal coordination sphere of each Mn metalloprotein were parametrized.