The redox potential of a heme cofactor in Nitrosomonas europaea cytochrome c peroxidase: a polarizable QM/MM study

How Aqueous Solvation Impacts the Frequencies and Intensities of Infrared Absorption Bands in Flavin: The Quest for a Suitable Solvent Model

FTIR spectroscopy accompanied by quantum chemical simulations can reveal important information about molecular structure and intermolecular interactions in the condensed phase. Simulations typically account for the solvent either through cluster quantum mechanical (QM) models, polarizable continuum models (PCM), or hybrid quantum mechanical/molecular mechanical (QM/MM) models. Recently, we studied the effect of aqueous solvent interactions on the vibrational frequencies of lumiflavin, a minimal flavin model, using cluster QM and PCM models. Those models successfully reproduced the relative frequencies of four prominent stretching modes of flavin's isoalloxazine ring in the diagnostic 1450-1750 cm-1 range but poorly reproduced the relative band intensities. Here, we extend our studies on this system and account for solvation through a series of increasingly sophisticated models. Only by combining elements of QM clusters, QM/MM, and PCM approaches do we obtain an improved agreement with the experiment. The study sheds light more generally on factors that can impact the computed frequencies and intensities of IR bands in solution.

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.

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

Helical homopolymers of multiheme cytochromes catalyze biogeochemically significant electron transfers with a reported 10 3 -fold variation in conductivity. Herein, classical molecular dynamics and hybrid quantum/classical molecular mechanics are used to elucidate the structural determinants of the redox potentials and conductivities of the tetra-, hexa-, and octaheme outer-membrane cytochromes E, S, and Z, respectively, from Geobacter sulfurreducens . Second-sphere electrostatic interactions acting on minimally polarized heme centers are found to regulate redox potentials over a computed 0.5-V range. However, the energetics of redox conduction are largely robust to the structural diversity: Single-step electronic couplings (⟨H mn ⟩), reaction free energies , and reorganization energies (λ mn ) are always respectively <|0.026|, <|0.26|, and between 0.5 - 1.0 eV. With these conserved parameter ranges, redox conductivity differed by less than a factor of 10 among the 'nanowires' and is sufficient to meet the demands of cellular respiration if 10 2 - 10 3 'nanowires' are expressed. The 'nanowires' are proposed to be differentiated by the protein packaging to interface with a great variety of environments, and not by conductivity, because the rate-limiting electron transfers are elsewhere in the respiratory process. Conducting-probe atomic force microscopy measurements that find conductivities 10 3 -10 6 -fold more than cellular demands are suggested to report on functionality that is either not used or not accessible under physiological conditions. The experimentally measured difference in conductivity between Omc- S and Z is suggested to not be an intrinsic feature of the CryoEM-resolved structures.

Photomedicine based on heme-derived compounds

Photoimaging and phototherapy have become major platforms for the diagnosis and treatment of various health complications. These applications require a photosensitizer (PS) that is capable of absorbing light from a source and converting it into other energy forms for detection and therapy. While synthetic inorganic materials such as quantum dots and gold nanorods have been widely explored for their medical diagnosis and photodynamic (PDT) and photothermal (PTT) therapy capabilities, translation of these technologies has lagged, primarily owing to potential cytotoxicity and immunogenicity issues. Of the various photoreactive molecules, the naturally occurring endogenous compound heme, a constituent of red blood cells, and its derivatives, porphyrin, biliverdin and bilirubin, have shown immense potential as noteworthy candidates for clinically translatable photoreactive agents, as evidenced by previous reports. While porphyrin-based photomedicines have attracted significant attention and are well documented, research on photomedicines based on two other heme-derived compounds, biliverdin and bilirubin, has been relatively lacking. In this review, we summarize the unique photoproperties of heme-derived compounds and outline recent efforts to use them in biomedical imaging and phototherapy applications.

Theoretical Modeling of Redox Potentials of Biomolecules

The estimation of the redox potentials of biologically relevant systems by means of theoretical-computational approaches still represents a challenge. In fact, the size of these systems typically does not allow a full quantum-mechanical treatment needed to describe electron loss/gain in such a complex environment, where the redox process takes place. Therefore, a number of different theoretical strategies have been developed so far to make the calculation of the redox free energy feasible with current computational resources. In this review, we provide a survey of such theoretical-computational approaches used in this context, highlighting their physical principles and discussing their advantages and limitations. Several examples of these approaches applied to the estimation of the redox potentials of both proteins and nucleic acids are described and critically discussed. Finally, general considerations on the most promising strategies are reported.

Harder, better, faster, stronger: Large-scale QM and QM/MM for predictive modeling in enzymes and proteins

Computational prediction of enzyme mechanism and protein function requires accurate physics-based models and suitable sampling. We discuss recent advances in large-scale quantum mechanical (QM) modeling of biochemical systems that have reduced the cost of high-accuracy models. Tradeoffs between sampling and accuracy have motivated modeling with molecular mechanics (MM) in a multiscale QM/MM or iterative approach. Limitations to both conventional density-functional theory and classical MM force fields remain for describing noncovalent interactions in comparison to experiment or wavefunction theory. Because predictions of enzyme action (i.e. electrostatics), free energy barriers, and mechanisms are sensitive to the protocol and embedding method in QM/MM, convergence tests and systematic methods for quantifying QM-level interactions are a needed, active area of development.