Browsing by Subject "Enzymes"
Now showing items 1-20 of 20
-
Conference Object
Abduction and induction for learning models of inhibition in metabolic networks
(2005)This paper describes the use of a mixture of abduction and induction for the temporal modelling of the effects of toxins in metabolic networks. Background knowledge is used which describes network topology and functional ...
-
Article
The Active Site Structure of Heme a3 3+-C≡N-CuB2+ of Cytochrome aa 3 Oxidase as Revealed from Resonance Raman Scattering
(2003)Resonance Raman and FTIR spectroscopies have been employed to investigate the structure of the heme a3-C≡N-CuB complex of oxidized cytochrome aa3 oxidase. The characterization of this complex is essential since a central ...
-
Article
Addressing the Functional Determinants of FAK during Ciliogenesis in Multiciliated Cells
(2017)We previously identified focal adhesion kinase (FAK) as an important regulator of ciliogenesis in multiciliated cells. FAK and other focal adhesion (FA) proteins associate with the basal bodies and their striated rootlets ...
-
Article
Continuum treatment of long-range interactions in free energy calculations. Application to protein-ligand binding
(1997)A method is proposed to include long-range electrostatic interactions in free energy calculations that involve the creation or deletion of net charges in a macromolecule. The vicinity of the mutation site is treated ...
-
Article
Detection of a photostable five-coordinate heme a3-Fe-Co species and functional implications of His384/α10 in CO-bound ba 3-cytochrome c oxidase from Thermus thermophilus
(2004)Resonance Raman (RR) spectra are reported for the fully reduced carbon monoxy derivative of ba3-cytochrome c oxidase from Thermus thermophilus. The RR spectra show the formation of a photolabile six-coordinate heme-CO and ...
-
Article
Detection of the His-heme Fe2+-NO species in the reduction of NO to N2O by ba3-oxidase from thermus thermophilus
(2005)Reaction pathways in the enzymatic formation and cleavage of the N-N and N-O bonds, respectively, are difficult to verify without the structure of the intermediates, but we now have such information on the heme a3 2+-NO ...
-
Article
Dielectric relaxation in an enzyme active site: Molecular dynamics simulations interpreted with a macroscopic continuum model
(2001)Dielectric relaxation plays an important role in many chemical processes in proteins, including acid-base titration, ligand binding, and charge transfer reactions. Its complexity makes experimental characterization difficult, ...
-
Doctoral Thesis Open Access
Dissecting the role of histone N-Terminal acetyltransferase NAA40 in gene regulation, metabolism and cancer
(Πανεπιστήμιο Κύπρου, Σχολή Θετικών και Εφαρμοσμένων Επιστημών / University of Cyprus, Faculty of Pure and Applied Sciences, 2021-11)Η Ν-άλφα-ακετυλτρανσφεράση 40 (ΝΑΑ40) καταλύει τη μεταφορά μιας ακετυλομάδας στο άλφα αμινοτελικό άκρο της σερίνης 1 (S1) στις ιστόνες Η4 και Η2Α. Παρόλο που προηγούμενες μελέτες έχουν συνδέσει την ΝΑΑ40 με τον καρκίνο, η ...
-
Article
Evidence for the presence of two conformations of the heme a 3-CuB pocket of cytochrome caa 3 from Thermus thermophilus
(2011)Resonance Raman (RR) and "light" minus "dark" Fourier transform infrared (FTIR) difference spectra are reported for the CO-bound caa3 oxidase from Thermus thermophilus. Two Fe-CO stretching modes at 518 and 507 cm-1, the ...
-
Article
Fourier transform infrared (FTIR) and step-scan time-resolved FTIR spectroscopies reveal a unique active site in cytochrome caa3 oxidase from Thermus thermophilus
(2002)Fourier transform infrared (FTIR) and step-scan time-resolved FTIR difference spectra are reported for the [carbonmonoxy]cytochrome caa3 from Thermus thermophilus. A major C-O mode of heme a3 at 1958 cm-1 and two minor ...
-
Conference Object
Modelling inhibition in metabolic pathways through abduction and induction
(2004)In this paper, we study how a logical form of scientific modelling that integrates together abduction and induction can be used to understand the functional class of unknown enzymes or inhibitors. We show how we can model, ...
-
Article
Near-monodisperse, catalytically active, imidazole-containing homooligomers: Synthesis by group transfer polymerization and solution characterization
(1999)Oligomers covering degrees of polymerization up to 23 of 2-(1-imidazolyl)-ethyl methacrylate (ImEMA) were synthesized by group transfer polymerization (GTP) in propylene carbonate and tetrahydrofuran (THF). While GTP ...
-
Article
Nitric-oxide reductase: Structure and properties of the catalytic site from resonance Raman scattering
(2002)We have applied resonance Raman spectroscopy to investigate the properties of the dinuclear center of oxidized, reduced, and NO-bound nitric-oxide reductase from Paracoccus denitrificans. The spectra of the oxidized enzyme ...
-
Article
Precipitation of a water-soluble ABC triblock methacrylic polyampholyte: effects of time, pH, polymer concentration, salt type and concentration, and presence of a protein
(1999)The solution behavior of a low molecular weight ABC triblock methacrylic polyampholyte with the structure (dimethylaminoethyl methacrylate)8-(methyl methacrylate)12-(methacrylic acid)16 was investigated by turbidimetry. ...
-
Article
The protein effect in the structure of two ferryl-oxo intermediates at the same oxidation level in the heme copper binuclear center of cytochrome c oxidase
(2013)Identification of the intermediates and determination of their structures in the reduction of dioxygen to water by cytochrome c oxidase (CcO) are particularly important to understanding both O2 activation and proton pumping ...
-
Article
Resonance raman spectroscopy of nitric oxide reductase and cbb3 Heme-Copper oxidase
(2008)Elucidating the structure and properties of the active sites in cbf 3 heme-copper oxidase and in nitric oxide reductase (Nor) is crucial in understanding the reaction mechanisms of oxygen and nitric oxide reduction by both ...
-
Article
The role of the cross-link His-Tyr in the functional properties of the binuclear center in cytochrome c oxidase
(2002)Resonance Raman and Fourier transform infrared spectroscopies have been used to study the aa3-type cytochrome c oxidase and the Y280H mutant from Paracoccus denitrificans. The stability of the binuclear center in the absence ...
-
Article
The structure of the hyponitrite species in a heme Fe-Cu binuclear center
(2007)NO laughing matter: The enzymatic production of laughing gas (N 2O) from two molecules of NO requires the formation of the N-N bond and the subsequent cleavage of the N-OH bond. Resonance Raman spectroscopic studies have ...
-
Article
Time-Resolved Resonance Raman and Time-Resolved Step-Scan FTIR Studies of Nitric Oxide Reductase from Paracoccus denitrificans: Comparison of the Heme b3-FeB Site to That of the Heme-CuB in Oxidases
(2003)Time-resolved resonance Raman (TR3) and time-resolved step-scan (TRS2) FTIR spectroscopies have been used to probe the structural dynamics at the heme b3 proximal and distal sites after carbon monoxide photolysis from fully ...
-
Doctoral Thesis Open Access
Μελέτη των αντιδράσεων οξειδασών του κυτοχρώματος c με CN, N3 και NO2 με τη χρήση φασματοσκοπίας υπερύθρου και συντονισμού Raman
(Πανεπιστήμιο Κύπρου, Σχολή Θετικών και Εφαρμοσμένων Επιστημών / University of Cyprus, Faculty of Pure and Applied Sciences, 2015-12)Η κυτταρική αναπνοή είναι μια από τις σημαντικότερες λειτουργίες των ζώντων οργανισμών, καθώς οδηγεί στην παραγωγή ATP. H οξειδάση του κυτοχρώματος c αποτελεί το τελικό ένζυμο της αναπνευστικής αλυσίδας, καταλύοντας την ...