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Träfflista för sökning "WFRF:(Ryde Ulf) srt2:(2000-2004)"

Sökning: WFRF:(Ryde Ulf) > (2000-2004)

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1.
  • Lecerof, David, et al. (författare)
  • Metal binding to Bacillus subtilis ferrochelatase and interaction between metal sites.
  • 2003
  • Ingår i: Journal of Biological Inorganic Chemistry. - : Springer Science and Business Media LLC. - 1432-1327 .- 0949-8257. ; 8:4, s. 452-458
  • Tidskriftsartikel (refereegranskat)abstract
    • Ferrochelatase, the terminal enzyme in heme biosynthesis, catalyses metal insertion into protoporphyrin IX. The location of the metal binding site with respect to the bound porphyrin substrate and the mode of metal binding are of central importance for understanding the mechanism of porphyrin metallation. In this work we demonstrate that Zn2+, which is commonly used as substrate in assays of the ferrochelatase reaction, and Cd2+, an inhibitor of the enzyme, bind to the invariant amino acids His183 and Glu264 and water molecules, all located within the porphyrin binding cleft. On the other hand, Mg2+, which has been shown to bind close to the surface at 7 Å from His183, was largely absent from its site. Activity measurements demonstrate that Mg2+ has a stimulatory effect on the enzyme, lowering KM for Zn2+ from 55 to 24 µM. Changing one of the Mg2+ binding residues, Glu272, to serine abolishes the effect of Mg2+. It is proposed that prior to metal insertion the metal may form a sitting-atop (SAT) complex with the invariant His-Glu couple and the porphyrin. Metal binding to the Mg2+ site may stimulate metal release from the protein ligands and its insertion into the porphyrin.
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2.
  • Gerlach, L O, et al. (författare)
  • Metal ion enhanced binding of amd3100 to asp-262 in the cxcr4 receptor.
  • 2003
  • Ingår i: Biochemistry. - : American Chemical Society (ACS). - 0006-2960 .- 1520-4995. ; 42:3, s. 710-717
  • Tidskriftsartikel (refereegranskat)abstract
    • The affinity of AMD3100, a symmetrical nonpeptide antagonist composed of two 1,4,8,11-tetraazacyclotetradecane (cyclam) rings connected through a 1,4-dimethylene(phenylene) linker to the CXCR4 chemokine receptor was increased 7, 36, and 50-fold, respectively, by incorporation of the following: Cu2+, Zn2+, or Ni2+ into the cyclam rings of the compound. The rank order of the transition metal ions correlated with the calculated binding energy between free acetate and the metal ions coordinated in a cyclam ring. Construction of AMD3100 substituted with only a single Cu2+ or Ni2+ ion demonstrated that the increase in binding affinity of the metal ion substituted bicyclam is achieved through an enhanced interaction of just one of the ring systems. Mutational analysis of potential metal ion binding residues in the main ligand binding crevice of the CXCR4 receptor showed that although binding of the bicyclam is dependent on both Asp171 and Asp262, the enhancing effect of the metal ion was selectively eliminated by substitution of Asp262 located at the extracellular end of TM-VI. It is concluded that the increased binding affinity of the metal ion substituted AMD3100 is obtained through enhanced interaction of one of the cyclam ring systems with the carboxylate group of Asp262. It is suggested that this occurs through a strong concomitant interaction of one of the oxygen's directly with the metal ion and the other oxygen to one of the nitrogens of the cyclam ring through a hydrogen bond.
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3.
  • Jensen, Kasper, et al. (författare)
  • Comparison of the chemical properties of iron and cobalt porphyrins and corrins.
  • 2003
  • Ingår i: ChemBioChem. - : Wiley. - 1439-4227. ; 4:5, s. 413-424
  • Tidskriftsartikel (refereegranskat)abstract
    • Density functional calculations have been used to compare various geometric, electronic and functional properties of iron and cobalt porphyrin (Por) and corrin (Cor) species. The investigation is focussed on octahedral MII/III complexes (where M is the metal) with two axial imidazole ligands (as a model of b and c type cytochromes) or with one imidazole and one methyl ligand (as a model of methylcobalamin). However, we have also studied some five-coordinate MII complexes with an imidazole ligand and four-coordinate MI/II complexes without any axial ligands as models of other intermediates in the reaction cycle of coenzyme B12. The central cavity of the corrin ring is smaller than that of porphine. We show that the cavity of corrin is close to ideal for low-spin CoIII, CoII, and CoI with the axial ligands encountered in biology, whereas the cavity in porphine is better suited for intermediate-spin states. Therefore, the low-spin state of Co is strongly favoured in complexes with corrins, whereas there is a small energy difference between the various spin states in iron porphyrin species. There are no clear differences for the reduction potentials of the octahedral complexes, but [CoICor] is more easily formed (by at least 40 kJ mole-1) than [FeIPor]. Cobalt and corrin form a strong CoC bond that is more stable against hydrolysis than iron and porphine. Finally, FeII/III gives a much lower reorganisation energy than CoII/III; this is owing to the occupied dz2 orbital in CoII. Altogether, these results give some clues about how nature has chosen the tetrapyrrole rings and their central metal ion.
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4.
  • Jensen, Kasper, et al. (författare)
  • Conversion of homocysteine to methionine by methionine synthase: a density functional study.
  • 2003
  • Ingår i: Journal of the American Chemical Society. - : American Chemical Society (ACS). - 1520-5126 .- 0002-7863. ; 125:46, s. 13970-13971
  • Tidskriftsartikel (refereegranskat)abstract
    • This communication reports a theoretical study of the conversion of homocysteine to methionine by methionine synthase. The reaction pathway is based on density functional calculations with large basis sets, including thermodynamic, relativistic, and solvent effects. We find that the suggested SN2 mechanism explains well the experimentally observed reaction rate. The results show that the reaction is highly polar, as reflected in the change of charge density along the reaction coordinate. It is enhanced in the protein by two effects: deprotonation of the bound substrate and desolvation of substrate and cofactor in the rate-determining step.
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5.
  • Jensen, Kasper, et al. (författare)
  • How O-2 binds to heme - Reasons for rapid binding and spin inversion
  • 2004
  • Ingår i: Journal of Biological Chemistry. - 1083-351X. ; 279:15, s. 14561-14569
  • Tidskriftsartikel (refereegranskat)abstract
    • We have used density functional methods to calculate fully relaxed potential energy curves of the seven lowest electronic states during the binding of O-2 to a realistic model of ferrous deoxyheme. Beyond a Fe-O distance of similar to 2.5 Angstrom, we find a broad crossing region with five electronic states within 15 kJ/mol. The almost parallel surfaces strongly facilitate spin inversion, which is necessary in the reaction of O-2 with heme ( deoxyheme is a quintet and O-2 a triplet, whereas oxyheme is a singlet). Thus, despite a small spin-orbit coupling in heme, the transition probability approaches unity. Using reasonable parameters, we estimate a transition probability of 0.06-1, which is at least 15 times larger than for the nonbiological Fe-O+ system. Spin crossing is anticipated between the singlet ground state of bound oxyheme, the triplet and septet dissociation states, and a quintet intermediate state. The fact that the quintet state is close in energy to the dissociation couple is of biological importance, because it explains how both spin states of O-2 may bind to heme, thereby increasing the overall efficiency of oxygen binding. The activation barrier is estimated to be < 15 kJ/mol based on our results and Mossbauer experiments. Our results indicate that both the activation energy and the spin-transition probability are tuned by the porphyrin as well as by the choice of the proximal heme ligand, which is a histidine in the globins. Together, they may accelerate O-2 binding to iron by &SIM;10(11) compared with the Fe-O+ system. A similar near degeneracy between spin states is observed in a ferric deoxyheme model with the histidine ligand hydrogen bonded to a carboxylate group, i.e. a model of heme peroxidases, which bind H2O2 in this oxidation state.
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6.
  • Jensen, Kasper, et al. (författare)
  • Importance of proximal hydrogen bonds in haem proteins.
  • 2003
  • Ingår i: Molecular Physics. - : Informa UK Limited. - 1362-3028 .- 0026-8976. ; 101:13, s. 2003-2018
  • Tidskriftsartikel (refereegranskat)abstract
    • We have used the density functional B3LYP method to study the effect of hydrogen bonds from the histidine ligand in various haem proteins to carboxyl groups or to the carbonyl backbone. Hydrogen bonds to carbonyl groups (encountered in globins and cytochromes, for example) have a small influence on the geometry and properties of the haem site. However, hydrogen bonds to a carboxyl group (encountered in peroxidases and haem oxidase) may have a profound effect. The results indicate that in the Fe3+ state, this leads to a deprotonation of the histidine ligand, whereas in the Fe2+ state, the proton involved in the hydrogen bond may reside on either histidine or the carboxylate group, depending on the detailed structure of the surroundings. If the histidine is deprotonated, the axial Fe-N bond length decreases by 0.15 Å, whereas the equatorial bond lengths increase. Moreover, the charge on iron and histidine is reduced, as is the spin density on iron. Most importantly, the energy difference between the high and intermediate spin states changes so that whereas the two spin states are degenerate in the Fe2+ state for the protonated histidine, they are degenerate for the Fe3+ state when it is deprotonated. This may facilitate the spin-forbidden binding of dioxygen and peroxide substrates, which takes place for the Fe2+ state in globins but in the Fe3+ state in peroxidases. The reduction potential of the haem group decreases when it hydrogen-bonds to a negatively charged group. The inner-sphere reorganization energy of the Fe2+/Fe3+ transition in a five-coordinate haem complex is ˜30 kJ mol−1, except when the histidine ligand is deprotonated without any hydrogen-bond interaction.
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7.
  • Jensen, Kasper, et al. (författare)
  • The axial N-base has minor influence on Co-C bond cleavage in cobalamins
  • 2002
  • Ingår i: Journal of molecular structure. Theochem. - 0166-1280. ; 585:1, s. 239-255
  • Tidskriftsartikel (refereegranskat)abstract
    • We have investigated the properties of cobalamin complexes with imidazolate using the density functional B3LYP method, In particular, we have compared imidazolate (Imm) with imidazole and 5,6-dimethylbenzimidazole (DMB), and studied how constraints in the axial Co-N bond length may affect the strength of the Co-C bond. The results show that the optimum Co-N-Imm bond is similar to0.2 Angstrom shorter than that of imidazole. There is no indication from crystal structures that the histidine ligand would be deprotonated in the enzymes. However, it is likely that it attains some imidazolate character through its hydrogen bond to a conserved aspartate residue. The Co-N bond with imidazolate is three times more rigid than that with imidazole or DMB, but twice as flexible as the Co-C bond. Constraints in the Co-N-Imm bond length give rise to a larger change in the corrin conformation than imidazole, but smaller than for DMB. The resulting effect for the Co-C bond dissociation energy is larger for imidazolate than for imidazole or DMB. However, even the largest reasonable distortion can only enhance catalysis by 15 kJ mol(-1). Therefore, we conclude that, irrespective of the nature of the N-base, constraints in the axial Co-N bond lengths cannot be the main reason for the catalytic power of cobalamin enzymes.
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8.
  • Jensen, Kasper, et al. (författare)
  • Theoretical prediction of the co-c bond strength in cobalamins.
  • 2003
  • Ingår i: The Journal of Physical Chemistry Part A: Molecules, Spectroscopy, Kinetics, Environment and General Theory. - : American Chemical Society (ACS). - 1520-5215. ; 107:38, s. 7539-7545
  • Tidskriftsartikel (refereegranskat)abstract
    • The homolytic Co-C bond dissociation energy (BDE) is central to the understanding of the function of vitamin B12, an important coenzyme of many proteins. We investigate why earlier density functional (B3LYP) estimations of the BDE in methylcobalamin have given so poor results (91-117 kJ/mol) compared to the experimental estimate (155 ± 13 kJ/mol). Improving the basis set increases the discrepancy, as does a proper treatment of basis set superposition error (~3 kJ/mol) and inclusion of zero-point energy corrections (-21 kJ/mol). On the other hand, relativistic (+6 kJ/mol), solvation (+7 kJ/mol in water), and thermal corrections (+6 kJ/mol) increase the BDE. However, neither of these corrections can explain the discrepancy. Instead, the problem seems to be the B3LYP density functional, which gives a corrected BDE of 78 kJ/mol, whereas the density functional Becke-Perdew-86 method and second-order perturbation theory (MP2) give BDEs of 134-139 kJ/mol. A comparison with other methods indicates that the error comes from the Hartree-Fock exchange (~40 kJ/mol) and the LYP functional (~15 kJ/mol). The problem is not restricted to methylcobalamin but seems to be general for homolytic metal-carbon BDEs of transition metals in tetra-pyrrole-like systems.
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9.
  • Karlström, Gunnar, et al. (författare)
  • MOLCAS : a program package for computational chemistry
  • 2003
  • Ingår i: Computational materials science. - 0927-0256 .- 1879-0801. ; 28:2, s. 222-239
  • Tidskriftsartikel (refereegranskat)abstract
    • The program system MOLCAS is a package for calculations of electronic and structural properties of molecular systems in gas, liquid, or solid phase. It contains a number of modern quantum chemical methods for studies of the electronic structure in ground and excited electronic states. A macromolecular environment can be modeled by a combination of quantum chemistry and molecular mechanics. It is further possible to describe a crystalline material using model potentials. Solvent effects can be treated using continuum models or by combining quantum chemical calculations with molecular dynamics or Monte-Carlo simulations. MOLCAS is especially adapted to treat systems with a complex electronic structure, where the simplest quantum chemical models do not work. These features together with the inclusion of relativistic effects makes it possible to treat with good accuracy systems including atoms from the entire periodic system. MOLCAS has effective methods for geometry optimization of equilibria, transition states, conical intersections, etc. This facilitates studies of excited state energy surfaces, spectroscopy, and photochemical processes.
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10.
  • Llano, Jorge, 1968- (författare)
  • Modern Computational Physical Chemistry : An Introduction to Biomolecular Radiation Damage and Phototoxicity
  • 2004
  • Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
    • The realm of molecular physical chemistry ranges from the structure of matter and the fundamental atomic and molecular interactions to the macroscopic properties and processes arising from the average microscopic behaviour.Herein, the conventional electrodic problem is recast into the simpler molecular problem of finding the electrochemical, real chemical, and chemical potentials of the species involved in redox half-reactions. This molecular approach is followed to define the three types of absolute chemical potentials of species in solution and to estimate their standard values. This is achieved by applying the scaling laws of statistical mechanics to the collective behaviour of atoms and molecules, whose motion, interactions, and properties are described by first principles quantum chemistry. For atomic and molecular species, calculation of these quantities is within the computational implementations of wave function, density functional, and self-consistent reaction field theories. Since electrons and nuclei are the elementary particles in the realm of chemistry, an internally consistent set of absolute standard values within chemical accuracy is supplied for all three chemical potentials of electrons and protons in aqueous solution. As a result, problems in referencing chemical data are circumvented, and a uniform thermochemical treatment of electron, proton, and proton-coupled electron transfer reactions in solution is enabled.The formalism is applied to the primary and secondary radiation damage to DNA bases, e.g., absorption of UV light to yield electronically excited states, formation of radical ions, and transformation of nucleobases into mutagenic lesions as OH radical adducts and 8-oxoguanine. Based on serine phosphate as a model compound, some insight into the direct DNA strand break mechanism is given.Psoralens, also called furocoumarins, are a family of sensitizers exhibiting cytostatic and photodynamic actions, and hence, they are used in photochemotherapy. Molecular design of more efficient photosensitizers can contribute to enhance the photophysical and photochemical properties of psoralens and to reduce the phototoxic reactions. The mechanisms of photosensitization of furocoumarins connected to their dark toxicity are examined quantum chemically.
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  • Resultat 1-10 av 33

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