Computational Treatment of Metalloproteins

The nucleotide excision repair proteins through the lens of molecular dynamics simulations

Mutations that affect the proteins responsible for the nucleotide excision repair (NER) pathway can lead to diseases such as xeroderma pigmentosum, trichothiodystrophy, Cockayne syndrome, and Cerebro-oculo-facio-skeletal syndrome. Hence, understanding their molecular behavior is needed to elucidate these diseases' phenotypes and how the NER pathway is organized and coordinated. Molecular dynamics techniques enable the study of different protein conformations, adaptable to any research question, shedding light on the dynamics of biomolecules. However, as important as they are, molecular dynamics studies focused on DNA repair pathways are still becoming more widespread. Currently, there are no review articles compiling the advancements made in molecular dynamics approaches applied to NER and discussing: (i) how this technique is currently employed in the field of DNA repair, focusing on NER proteins; (ii) which technical setups are being employed, their strengths and limitations; (iii) which insights or information are they providing to understand the NER pathway or NER-associated proteins; (iv) which open questions would be suited for this technique to answer; and (v) where can we go from here. These questions become even more crucial considering the numerous 3D structures published regarding the NER pathway's proteins in recent years. In this work, we tackle each one of these questions, revising and critically discussing the results published in the context of the NER pathway.

A modified bonded model approach for molecular dynamics simulations of New Delhi Metallo-β-lactamase

Modelling metalloproteins using the classical force fields is challenging. Several methods have been devised to model metalloproteins in force fields. Of these methods, the bonded model, combined with Restrained Electrostatic Potential (RESP) charge fitting, proved its superiority. The latter method was facilitated by the development of the python-based Metal Centre Parameter Builder (MCPB.py) AmberTool. However, the standard bonded model method offered by the MCPB.py tool may not be appropriate for validating and refining the binding modes predicted by docking when crystal structures are lacking. That is because the representation of coordination interactions between any bound ligand and metal ions by covalent bonds can hinder the flexibility of the ligand. Therefore, a new modification to the standard bonded model approach is proposed here. Molecular dynamics (MD) simulations based on the new modified bonded model (MBM) approach avoid the bias caused by coordination bonds and, unlike hybrid QM/MM MD, allow for sufficient sampling of the binding mode given the currently available computational power. The MBM MD approach reproduced the studied crystal structure conformations of New Delhi Metallo-β-lactamase 1 (NDM-1). Furthermore, the MBM approach described the binding interactions of intact β-lactams with NDM-1 reasonably, and predicted a non-productive binding mode for the poor NDM-1 substrate aztreonam whilst predicting productive binding modes for known good substrates. This study presents a useful MD method for metallo-β-lactamases and provides better understanding of β-lactam substrates recognition by NDM-1. The proposed MBM approach might also be useful in the investigation of other metal-containing protein targets.

Schiff base compounds as artificial metalloenzymes

Much research has been done on traditional homogeneous metal catalysts and enzymatic catalysts, but recently a new class of hybrid catalysts called synthetic (artificial) metalloenzymes has been considered by researchers. Metalloenzymes as hybrid catalysts (host-guest systems) have been shown that combine the properties of a homogeneous and also enzymatic catalyst. The hybrid catalyst will have added value such as enantioselectivity or chemo-selectivity. This review focuses on Schiff base complexes that either act as homogeneous artificial enzymes or contribute to the structure of a host in the preparation of hybrid metalloenzymes. Because this approach can virtually be applied to any bio- or synthetic host or guest coordination complex, the details of hybrid catalysts seem important for advance in catalysis.

Review on the QM/MM Methodologies and Their Application to Metalloproteins

The multiscaling quantum mechanics/molecular mechanics (QM/MM) approach was introduced in 1976, while the extensive acceptance of this methodology started in the 1990s. The combination of QM/MM approach with molecular dynamics (MD) simulation, otherwise known as the QM/MM/MD approach, is a powerful and promising tool for the investigation of chemical reactions’ mechanism of complex molecular systems, drug delivery, properties of molecular devices, organic electronics, etc. In the present review, the main methodologies in the multiscaling approaches, i.e., density functional theory (DFT), semiempirical methodologies (SE), MD simulations, MM, and their new advances are discussed in short. Then, a review on calculations and reactions on metalloproteins is presented, where particular attention is given to nitrogenase that catalyzes the conversion of atmospheric nitrogen molecules N₂ into NH₃ through the process known as nitrogen fixation and the FeMo-cofactor.

Radical SAM Enzymes and Metallocofactor Assembly: A Structural Point of View

This Review focuses on the structure-function relationship of radical S-adenosyl-l-methionine (SAM) enzymes involved in the assembly of metallocofactors corresponding to the active sites of [FeFe]-hydrogenase and nitrogenase [MoFe]-protein. It does not claim to correspond to an extensive review on the assembly machineries of these enzyme active sites, for which many good reviews are already available, but instead deals with the contribution of structural data to the understanding of their chemical mechanism (Buren et al. Chem. Rev.2020, 142 ( (25), ) 11006-11012; Britt et al. Chem. Sci.2020, 11 ( (38), ), 10313-10323). Hence, we will present the history and current knowledge about the radical SAM maturases HydE, HydG, and NifB as well as what, in our opinion, should be done in the near future to overcome the existing barriers in our understanding of this fascinating chemistry that intertwine organic radicals and organometallic complexes.

Predicting Effects of Site-Directed Mutagenesis on Enzyme Kinetics by QM/MM and QM Calculations: A Case of Glutamate Carboxypeptidase II

Quantum and molecular mechanics (QM/MM) and QM-only (cluster model) modeling techniques represent the two workhorses in mechanistic understanding of enzyme catalysis. One of the stringent tests for QM/MM and/or QM approaches is to provide quantitative answers to real-world biochemical questions, such as the effect of single-point mutations on enzyme kinetics. This translates into predicting the relative activation energies to 1-2 kcal·mol^-1 accuracy; such predictions can be used for the rational design of novel enzyme variants with desired/improved characteristics. Herein, we employ glutamate carboxypeptidase II (GCPII), a dizinc metallopeptidase, also known as the prostate specific membrane antigen, as a model system. The structure and activity of this major cancer antigen have been thoroughly studied, both experimentally and computationally, which makes it an ideal model system for method development. Its reaction mechanism is quite well understood: the reaction coordinate comprises a "tetrahedral intermediate" and two transition states and experimental activation Gibbs free energy of ∼17.5 kcal·mol^-1 can be inferred for the known k_cat ≈ 1 s^-1. We correlate experimental kinetic data (including the E424H variant, newly characterized in this work) for various GCPII mutants (k_cat = 8.6 × 10^-5 s^-1 to 2.7 s^-1) with the energy profiles calculated by QM/MM and QM-only (cluster model) approaches. We show that the near-quantitative agreement between the experimental values and the calculated activation energies (ΔH^⧧) can be obtained and recommend the combination of the two protocols: QM/MM optimized structures and cluster model (QM) energetics. The trend in relative activation energies is mostly independent of the QM method (DFT functional) used. Last but not least, a satisfactory correlation between experimental and theoretical data allows us to provide qualitative and fairly simple explanations of the observed kinetic effects which are thus based on a rigorous footing.

A High Coordination of Cross-Links Is Beneficial for the Strength of Cross-Linked Fibers

The influence of the coordination of (reversible) cross-links on the mechanical properties of aligned fiber bundles is investigated. Two polymeric systems containing cross-links of different coordination (two- and three-fold coordination) but having the same binding energy are investigated. In particular, the response to loading of these systems is compared. Mechanical parameters (strength, stiffness and work-to-fracture) are obtained by computational loading tests. The influence of coordination is studied for simple test systems with pre-defined topologies that maximize strength as well as for more realistic fiber bundles containing nine chains. The results show that a higher coordination of cross-links has a beneficial effect on the strength and the stiffness of the systems, while the work-to-fracture was found larger for the system having a smaller coordination of cross-links. It can be concluded that controlling the coordination of cross-links is a versatile tool to specifically tailor the mechanical properties of polymeric structures.

The shielding effect of metal complexes on the binding affinities of ligands to metalloproteins

The contributions of metal–ligand interactions to the ligand binding affinities are largely reduced by the shielding effects of metal complexes.

Accurate Quantum Mechanical/Molecular Mechanical Calculations of Reduction Potentials in Azurin Variants

Understanding the regulation mechanism and molecular determinants of the reduction potential of metalloprotein is a major challenge. An ab initio quantum mechanical/molecular mechanical (QM/MM) method combining the minimum free energy path (MFEP) and fractional number of electron (FNE) approaches has been developed in our group to simulate the redox processes of large systems. The FNE scheme provides an efficient unique description for the redox process, while the MFEP method provides improved conformational sampling on complex environments such as protein in the QM/MM calculations. The reduction potentials of wild-type and seven mutants of azurin, a type 1 copper metalloprotein, were simulated with the QM/MM-MFEP+FNE approach in this paper. A range of 350 mV for the variations of the reduction potentials of these azurin proteins was reproduced faithfully with relative errors around 20 mV. The correlation between structural interactions and reduction potentials observed in simulations provides in-depth insight into the regulation of reduction potentials, which potentially can also be very useful to the engineering of metalloprotein-based electrocatalysts in artificial photosynthesis. The excellent accuracy and efficiency of the QM/MM-MFEP+FNE approach demonstrate the potential for simulations of many electron transfer processes in condensed phases and biochemical systems.

Metal Ion Modeling Using Classical Mechanics

Metal ions play significant roles in numerous fields including chemistry, geochemistry, biochemistry, and materials science. With computational tools increasingly becoming important in chemical research, methods have emerged to effectively face the challenge of modeling metal ions in the gas, aqueous, and solid phases. Herein, we review both quantum and classical modeling strategies for metal ion-containing systems that have been developed over the past few decades. This Review focuses on classical metal ion modeling based on unpolarized models (including the nonbonded, bonded, cationic dummy atom, and combined models), polarizable models (e.g., the fluctuating charge, Drude oscillator, and the induced dipole models), the angular overlap model, and valence bond-based models. Quantum mechanical studies of metal ion-containing systems at the semiempirical, ab initio, and density functional levels of theory are reviewed as well with a particular focus on how these methods inform classical modeling efforts. Finally, conclusions and future prospects and directions are offered that will further enhance the classical modeling of metal ion-containing systems.