Binding and Docking Interactions of NO, CO and O2 in Heme Proteins as Probed by Density Functional Theory

Dynamics and reactivity in heme proteins include direct and indirect interactions of the ligands/substrates like CO, NO and O2 with the environment. Direct electrostatic interactions result from amino acid side chains in the inner cavities and/or metal coordination in the active site, whereas indirect interactions result by ligands in the same coordination sphere. Interactions play a crucial role in stabilizing transition states in catalysis or altering ligation chemistry. We have probed, by Density Functional Theory (DFT), the perturbation degree in the stretching vibrational frequencies of CO, NO and O2 molecules in the presence of electrostatic interactions or hydrogen bonds, under conditions simulating the inner cavities. Moreover, we have studied the vibrational characteristics of the heme bound form of the CO and NO ligands by altering the chemistry of the proximal to the heme ligand. CO, NO and O2 molecules are highly polarizable exerting vibrational shifts up to 80, 200 and 120 cm−1, respectively, compared to the non-interacting ligand. The importance of Density Functional Theory (DFT) methodology in the investigation of the heme-ligand-protein interactions is also addressed

The origin of the FeIV=O intermediates in cytochrome aa3 oxidase

AbstractThe dioxygen reduction mechanism in cytochrome oxidases relies on proton control of the electron transfer events that drive the process. Proton delivery and proton channels in the protein that are relevant to substrate reduction and proton pumping are considered, and the current status of this area is summarized. We propose a mechanism in which the coupling of the oxygen reduction chemistry to proton translocation (P→F transition) is related to the properties of two groups of highly conserved residues, namely, His411/G386-T389 and the heme a3–propionateA–D399–H403 chain. This article is part of a Special Issue entitled: Respiratory Oxidases

Fouille des terrains Karmoyannis-Nannopoulos (agora d’Argos)

Chroniques de l’EfA :Argos, Terrain Nannopoulos 2005Argos, Terrain Nannopoulos 2006Argos, Terrain Nannopoulos 2007Argos, Terrain Nannopoulos 2008Argos, Terrain Nannopoulos 2009 Les fouilles successives des terrains Karmoyannis et Nannopoulos, situés dans le secteur nord-ouest de l’agora antique dans son extension accessible à l’exploration archéologique, ont mis au jour les vestiges de plusieurs bâtiments et structures qui n’ont malheureusement pas retenu l’attention de Pausanias, ainsi qu’un..

Reductive N–N coupling of NO molecules on transition metal complexes leading to N2O

Nitric oxide reductase (NOR) type reactions (2NO + 2e- + 2H+ → N2O + H2O) on transition metal complexes not involving NO disproportionation (3NO → N2O + NO2) are reviewed. The former has little reported, although the latter is very common reaction. The formation of N2O indicates that N-N coupling of two NO molecules is an essential step. A few examples of N-N coupling on transition metal complexes have been structurally characterized, including several examples of hyponitrite (O-N{double bond, long}N-O)2- complexes and only one diruthenium complex bearing neutral (O{double bond, long}N-N{double bond, long}O) binding mode. Protonation or heating their complexes led to elimination of N2O. In the examination of the NOR-type reaction, only a few functional model complexes for the active site of the metalloenzyme have been developed. These complexes also showed NOR activity. Finally, an NO reduction cycle in the diruthenium system is described

Structural dynamics of heme-copper oxidases and nitric oxide reductases: time-resolved step-scan Fourier transform infrared and time-resolved resonance Raman studies

Of the spectroscopic methods available for the characterization of the dynamics of heme protein active sites, time-resolved resonance Raman spectroscopy (TR 3) is a powerful technique because excitation within the heme π-π* electronic absorption transitions selectively enhances vibrational modes of the heme and bound-proximal/distal ligands without the interference from the modes associated with the protein matrix. On the other hand, time-resolved step-scan (TRS 2) Fourier transform infrared (FTIR) spectroscopy has the sensitivity and resolution to detect, in addition to ligands bound to metal centers and the kinetics of ligand photodissociation, transient changes at the level of individual amino acids during protein action. This review outlines the application of both TR 3 and TRS 2-FTIR to heme-copper oxidases and nitric oxide reductase

Probing the environment of Cu B in heme-copper oxidases

Time-resolved step-scan FTIR (TRS 2-FTIR) and density functional theory have been applied to probe the structural dynamics of Cu B in heme-copper oxidases at room temperature. The TRS 2-FTIR data of cbb 3 from Pseudomonas stutzen indicate a small variation in the frequency of the transient CO bound to Cu B in the pH/pD 7-9 range. This observation in conjunction with density functional theory calculations, in which significant frequency shifts of the v(CO) are observed upon deprotonation and/or detachment of the Cu B ligands, demonstrates that the properties of the CU B ligands including the cross-linked tyrosine, in contrast to previous reports, remain unchanged in the pH 7-9 range. We attribute the small variations in the v(CO) of CUB to protein conformational changes in the vicinity of Cu B. Consequently, the split of the heme Fe-CO vibrations (a-, β-, and γ-forms) is not due to changes in the ligation and/or protonation states of the Cu B ligands or to the presence of one or more ionizable groups, as previously suggested, but the result of global protein conformational changes in the vicinity of Cu B which, in turn, affect the position of Cu B with respect to the heme F