Does the DFT Self-Interaction Error Affect Energies Calculated in Proteins with Large QM Systems?

Structural Determinants of Redox Conduction Favor Robustness over Tunability in Microbial Cytochrome Nanowires

Structural determinants of a 103-fold variation in electrical conductivity for helical homopolymers of tetra-, hexa-, and octa-heme cytochromes (named Omc- E, S, and Z, respectively) from Geobacter sulfurreducens are investigated with the Pathways model for electron tunneling, classical molecular dynamics, and hybrid quantum/classical molecular mechanics. Thermally averaged electronic couplings for through-space heme-to-heme electron transfer in the "nanowires" computed with density functional theory are ≤0.015 eV. Pathways analyses also indicate that couplings match within a factor of 5 for all "nanowires", but some alternative tunneling routes are found involving covalent protein backbone bonds (Omc- S and Z) or propionic acid-ligating His H-bonds on adjacent hemes (OmcZ). Reorganization energies computed from electrostatic vertical energy gaps or a version of the Marcus continuum expression parameterized on the total (donor + acceptor) solvent-accessible surface area typically agree within 20% and fall within the range 0.48-0.98 eV. Reaction free energies in all three "nanowires" are ≤|0.28| eV, even though Coulombic interactions primarily tune the site redox energies by 0.7-1.2 eV. Given the conserved energetic parameters, redox conductivity differs by < 103-fold among the cytochrome "nanowires". Redox currents do not exceed 3.0 × 10-3 pA at a physiologically relevant 0.1 V bias, with the slowest electron transfers being on a (μs) timescale much faster than typical (ms) enzymatic turnovers. Thus, the "nanowires" are proposed to be functionally robust to variations in structure that provide a habitat-customized protein interface. The 30 pA to 30 nA variation in conductivity previously reported from atomic force microscopy experiments is not intrinsic to the structures and/or does not result from the physiologically relevant redox conduction mechanism.

Is breaking of a hydrogen bond enough to lead to drug resistance?

Drug resistance is a serious problem in cancer, viral, bacterial, fungal and parasitic diseases. Examination of crystal structures of protein-drug complexes is often not enough to explain why a certain mutation leads to drug resistance. As an example, the crystal structure of the kinase inhibitor dasatinib bound to the Abl1 kinase shows a hydrogen bond between the drug and residue Thr315 and very few contacts between the drug and residues Val299 and Phe317, yet mutations in those residues lead to drug resistance. In the first case, it is tempting to suggest that the loss of a hydrogen bond leads to drug resistance, whereas in the other two cases it is not known why mutations lead to drug resistance in the first place. We carried out extensive molecular dynamics (MD) simulations and free energy calculations to explain drug resistance to dasatinib from a molecular point of view and show that resistance is due to a multitude of subtle effects. Importantly, our calculations could reproduce the experimental values for the binding energies upon mutations in all three cases and shed light on their origin.

Xanthine oxidoreductase inhibition – A review of computational aspect

Xanthine Oxidoreductase (XOR) exists in a variety of organisms from bacteria to humans and catalyzes the oxidation of hypoxanthine to xanthine and from xanthine to uric acid. Excessive uric acid could lead to gout and hyperuricemia. In this paper, we have reviewed the recent computational studies on xanthine oxidase inhibition. Computational methods, such as molecular dynamics (molecular mechanics), quantum mechanics, and quantum mechanics/molecular mechanics (QM/MM), have been employed to investigate the binding affinity of xanthine oxidase with synthesized and isolated nature inhibitors. The limitations of different computational methods for xanthine oxidase inhibition studies were also discussed. Implications of the computational approach could be used to help to understand the existing arguments on substrate/product orientation in xanthine oxidase inhibition, which allows designing new inhibitors with higher efficacy.

Reassessment of the Mechanisms of Thermal C-H Bond Activation of Methane by Cationic Magnesium Oxides: A Critical Evaluation of the Suitability of Different Density Functionals

The mechanisms of the thermal reactions of the two iconic magnesium oxide cations MgO^.+ and Mg₂ O₂ ^.+ with methane have been re-evaluated at the CCSD(T)/CBS//CCSD/def2-TZVP level of theory. For the reaction of MgO^.+ with CH₄ , only the classical hydrogen-atom transfer (HAT) was found; in contrast, for the Mg₂ O₂ ^.+ /CH₄ couple, both HAT and proton-coupled electron-transfer (PCET) exist as mechanistic variants. In order to evaluate the suitability of density functional theory (DFT) methods, the reactions were computed by using 27 density functionals. The results obtained demonstrate that the various DFT methods often deliver rather different results for both geometric and energetic features. As to the prediction of the apparent barriers, pure functionals give the largest mean absolute errors. BMK, ωB97XD, and the double-hybrid functional mPW2PLYP were confirmed to come closest to the results provided by CCSD(T)/CBS. Thus, mechanistic conclusions based on a single DFT method should be viewed with great caution. In summary, this study may assist in the selection of a suitable quantum chemical method to unravel the mechanistic details of C-H bond activation by charged metal oxides.