The authorial delusion: counting lady Macbeth’s children

In 1933, literary critic L. C. Knights published a caustic essay against the notion cultivated by certain of his colleagues, predominantly A. C. Bradley, that Shakespeare is a ‘great creator of characters’. Knights (1973) regarded the examination of isolated particles such as ‘character’ as disorientating, alleging that an analysis of this sort obscures the greater merit of language. Knight’s polemic essentially stands in the threshold of the dissention between formalists and realists: the former consider the examination of the fictional narrative as anything but a textual construct a scholarly faux pas; the latter regard the referential relationship between text and the world as a foundation for the creation of fiction. This is a pseudo-dilemma. The notion that literature is denuded of its artistic merit once it is defined by its constituent artefacts is disorienting, for it completely bypasses the dynamics of its creation. Put differently, a post-event analysis can exist as a standalone act, albeit it cannot challenge or dismiss the foundational principles of the event’s creation process

Tuning Heme Functionality: The Cases of Cytochrome c Oxidase and Myoglobin Oxidation

The (Fe-O) moiety of Cytochrome c oxidase ferryl intermediate of the dioxygen activation reaction and the oxy-myoglobin (Mb-O2) structure have been probed by QM/MM (hybrid quantum mechanical/ molecular mechanical) calculations using Density Functional Theory (DFT)/MM to elucidate the effect of the heme propionates and the protein matrix on the chemistry of heme Fe-O moieties. On this line, we have probed the role of His97 in various protonation states of the heme propionate-6 in Mb and compared the results to that of the Cytochrome c oxidase chemistry

Assigning vibrational spectra of ferryl-oxo intermediates of cytochrome c oxidase by periodic orbits and molecular dynamics

Presented at 10th Congress in Chemistry Greece – Cyprus, 2009, Heraklion, Greece, 2-4 JulyComplexity is inherent in biological molecules not only because of the large number of atoms but also because of their nonlinear interactions responsible for chaotic behaviours, localized motions, and bifurcation phenomena. Thus, versatile spectroscopic techniques have been invented to achieve temporal and spacial resolution to minimize the uncertainties in assigning the spectra of complex molecules. Can we associate spectral lines to specific chemical bonds or species in a large molecule? Can energy stay localized in a bond for a substantial period of time to leave its spectroscopic signature? These longstanding problems are investigated by studying the resonance Raman spectra of ferryl-oxo intermediates of cytochrome c oxidase. The difference spectra of isotopically substituted ferryl oxygen (16O minus 18O) in the cytochrome c oxidase recorded in several laboratories show one or two prominent positive peaks which have not been completely elucidated yet. By applying the hierarchical methods of nonlinear mechanics, and particularly the study of periodic orbits in the active site of the enzyme, in conjunction with molecular dynamics calculations of larger systems which include the embraced active site by the protein and selected protonated/deprotonated conformations of amino acids, we translate the spectral lines to molecular motions. It is demonstrated that for the active site stable periodic orbits exist for a substantial energy range. Families of periodic orbits which are associated with the vibrations of FeIV=O bond mark the regions of phase space where nearby trajectories remain localized, as well as assign the spectral bands of the active site in the protein matrix. We demonstrate that proton movement adjacent to active site, which occurs during the P → F transition, can lead to significant perturbations of the Fe IV=O isotopic difference vibrational spectra in cytochrome c oxidase, without a change in oxidation state of the metal sites. This finding links spectroscopic characteristics to protonation events occurring during enzymatic turnove

Assigning vibrational spectra of ferryl-oxo intermediates of cytochrome c oxidase by periodic orbits and molecular dynamics

Presented at 10th Congress in Chemistry Greece – Cyprus, 2009, Heraklion, Greece, 2-4 JulyComplexity is inherent in biological molecules not only because of the large number of atoms but also because of their nonlinear interactions responsible for chaotic behaviours, localized motions, and bifurcation phenomena. Thus, versatile spectroscopic techniques have been invented to achieve temporal and spacial resolution to minimize the uncertainties in assigning the spectra of complex molecules. Can we associate spectral lines to specific chemical bonds or species in a large molecule? Can energy stay localized in a bond for a substantial period of time to leave its spectroscopic signature? These longstanding problems are investigated by studying the resonance Raman spectra of ferryl-oxo intermediates of cytochrome c oxidase. The difference spectra of isotopically substituted ferryl oxygen (16O minus 18O) in the cytochrome c oxidase recorded in several laboratories show one or two prominent positive peaks which have not been completely elucidated yet. By applying the hierarchical methods of nonlinear mechanics, and particularly the study of periodic orbits in the active site of the enzyme, in conjunction with molecular dynamics calculations of larger systems which include the embraced active site by the protein and selected protonated/deprotonated conformations of amino acids, we translate the spectral lines to molecular motions. It is demonstrated that for the active site stable periodic orbits exist for a substantial energy range. Families of periodic orbits which are associated with the vibrations of FeIV=O bond mark the regions of phase space where nearby trajectories remain localized, as well as assign the spectral bands of the active site in the protein matrix. We demonstrate that proton movement adjacent to active site, which occurs during the P → F transition, can lead to significant perturbations of the Fe IV=O isotopic difference vibrational spectra in cytochrome c oxidase, without a change in oxidation state of the metal sites. This finding links spectroscopic characteristics to protonation events occurring during enzymatic turnove

Protein dynamics and spectroscopy for ferryl intermediate of cytochrome c oxidase: a molecular dynamics approach

Cytochrome c oxidase is the membrane bound terminal enzyme in the respiratory chain. Molecular oxygen is reduced to water in its heme Fe/Cu B active site. The O-O bond cleavage produces the ferryl-oxo (Fe IV=O) intermediate. Molecular Dynamics calculations for a part of the protein containing over 8600 atoms are employed to probe the frequencies of vibrational modes which involve the stretching of Fe-O during protonation/deprotonation events near the active site. The role of protein frame for the spectroscopic properties of the ferryl intermediate is proved to be significant, as the intensity of the oxygen sensitive bands is controlled by conformational changes. In addition, the mechanism of the release of the produced water molecules is examined by changing the protonation state of a residue in the entrance of a proton pathway in the enzym

Dioxygen reduction by cytochrome oxidase: a proton transfer limited reaction

The kinetic constraints that are imposed on cytochrome oxidase in its dual function as the terminal oxidant in the respiratory process and as a redox-linked proton pump provide a unique opportunity to investigate the molecular details of biological O2 activation. By using flow/flash techniques, it is possible to visualize individual steps in the O2-binding and reduction process, and results from a number of spectroscopic investigations on the oxidation of reduced cytochrome oxidase by O2 are now available. In this article, we use these results to synthesize a reaction mechanism for O2 activation in the enzyme and to simulate time-concentration profiles for a number of intermediates that have been observed experimentally. Kinetic manifestations of the consequences of coupling exergonic electron transfer to endergonic proton translocation emerge from this analysis. An important conclusion is that, in achieving efficiency in this redox-coupled proton translocation mechanism, rate limitation in dioxygen activation in cytochrome oxidase is transferred to protonation reactions that occur late in the reduction reaction. As a consequence, potentially toxic intermediate oxidation states of dioxygen accumulate to substantial concentration during the reduction reaction, which allows us to detect and characterize these species