Biomedical subjects

Carme Rovira

Publications and source records attributed to Carme Rovira.

13 recordsLinked to original sources

PubMed2007

Protonated heme.

The ions formally corresponding to protonated heme [Fe(II)-hemeH](+) have been obtained by collision-induced dissociation from the electrospray ionization of microperoxidase (MP11) and their gas-phase chemistry has been studied by FTICR mass spectrometry. H/D-exchange reactions, used as a tool to gain information on the protonation sites in polyfunctional molecules, show that labile hydrogens pertain to the propionyl substituents at the periphery of the protoporphyrin IX. Several conceivable isomers for protonated heme have been evaluated by density functional theory. The most stable among the species investigated is the one corresponding to protonation at the beta carbon atom of a vinyl group, yielding a proton affinity (PA) value for [Fe(II)-heme] of 1220 kJ mol(-1). This high PA is consistent with the inertness of the hydrogen atoms at the protonation site towards H/D exchange with ND(3) and CD(3)CO(2)D. Peculiar features of this [Fe(II)-hemeH](+) isomer emerge by analysis of its electronic structure, showing that the vinyl group undergoing formal protonation has gained significant radical character due to electron transfer from the metal center. As a consequence, the iron atom acquires partial iron(III) character and none of the two formal descriptions [Fe(II)-hemeH(+)] and [Fe(III)-hemeH(.)](+) alone may adequately illustrate the protonated heme ion. In agreement with this description, the reactivity of protonated heme presents dual facets, resembling iron(III) in some aspects and iron(II) in others. On the one hand, protonated heme behaves like [Fe(III)-heme](+) ions in H/D-exchange reactions. On the other, it shows markedly decreased reactivity towards the addition of ligands with the notable exception of NO, in line with the high affinity shown by iron(II) complexes towards this molecule, NO, of key biological role.

Computer Simulation↗

PubMed2006

Electronic structure and charge transfer in the ternary intercalated graphite beta-KS0.25C3.

The electronic structure of the ternary intercalated graphite beta-KS(0.25)C3 is studied by means of a first-principles density functional theory approach. The nature of the partially filled bands is analyzed, and the K sublayers of the intercalate are shown to have an important contribution to the Fermi surface. This K-based contribution confers a sizable three-dimensional character to the conductivity even if considerably less than that for the related binary KC8. The electronic structure of beta-KS(0.25)C3 differs noticeably from that of the related ternary compound, KH(x)C4. The charge transfer is analyzed, and a way to evaluate it, which can be used in general for intercalated graphites, is proposed. The charge transfer per C atom in this ternary material is shown to be smaller than that in the KC8 binary compound despite a more favorable stoichiometry ratio between K and C.

Journal Article↗

PubMed2006

Ammonium recruitment and ammonia transport by E. coli ammonia channel AmtB.

To investigate substrate recruitment and transport across the Escherichia coli Ammonia transporter B (AmtB) protein, we performed molecular dynamics simulations of the AmtB trimer. We have identified residues important in recruitment of ammonium and intraluminal binding sites selective of ammonium, which provide a means of cation selectivity. Our results indicate that A162 guides translocation of an extraluminal ammonium into the pore lumen. We propose a mechanism for transporting the intraluminally recruited proton back to periplasm. Our mechanism conforms to net transport of ammonia and can explain why ammonia conduction is lost upon mutation of the conserved residue D160. We unify previous suggestions of D160 having either a structural or an ammonium binding function. Finally, our simulations show that the channel lumen is hydrated from the cytoplasmic side via the formation of single file water, while the F107/F215 stack at the inner-most part of the periplasmic vestibule constitutes a hydrophobic filter preventing AmtB from conducting water.

Ammonia↗

PubMed2006

Structure and dynamics of dioxygen bound to cobalt and iron heme.

In this study we use ab initio molecular dynamics simulations to analyze the structure and dynamics of the oxygen ligand in models of the oxymyoglobin active site and its cobalt-substituted analog. Our calculations are performed for iron-porphyrin and cobalt-porphyrin complexes with imidazole and oxygen as axial ligands, and we investigate the effect of the distal histidine in the structure and dynamics of the metal-oxygen unit (MeO(2), Me = Fe, Co). We find that the interaction between the distal histidine and the oxygen ligand is stronger for the cobalt complex than for the iron one, consistent with the superoxide ion character of the bound O(2). The dynamics of the O(2) ligand can be described as oscillations of the O-O axis projection on the porphyrin plane within a porphyrin quadrant combined with frequent jumps from one quadrant to another. However, the ligand motion is significantly faster for CoO(2) compared to FeO(2). As a result, the iron complex shows localized ligand sites, whereas for cobalt several configurations are possible. This gives support to the highly dynamic motion of the oxygen ligand found in several experiments on cobalt oxymyoglobin and model complexes and underlines the higher mobility of the CoO(2) fragment compared to FeO(2).

Binding Sites↗

PubMed2005

Substrate distortion in the Michaelis complex of Bacillus 1,3-1,4-beta-glucanase. Insight from first principles molecular dynamics simulations.

The structure and dynamics of the enzyme-substrate complex of Bacillus 1,3-1,4-beta-glucanase, one of the most active glycoside hydrolases, is investigated by means of Car-Parrinello molecular dynamics simulations (CPMD) combined with force field molecular dynamics (QM/MM CPMD). It is found that the substrate sugar ring located at the -1 subsite adopts a distorted 1S3 skew-boat conformation upon binding to the enzyme. With respect to the undistorted 4C1 chair conformation, the 1S3 skew-boat conformation is characterized by: (a) an increase of charge at the anomeric carbon (C1), (b) an increase of the distance between C1 and the leaving group, and (c) a decrease of the intraring O5-C1 distance. Therefore, our results clearly show that the distorted conformation resembles both structurally and electronically the transition state of the reaction in which the substrate acquires oxocarbenium ion character, and the glycosidic bond is partially broken. Together with analysis of the substrate conformational dynamics, it is concluded that the main determinants of substrate distortion have a structural origin. To fit into the binding pocket, it is necessary that the aglycon leaving group is oriented toward the beta region, and the skew-boat conformation naturally fulfills this premise. Only when the aglycon is removed from the calculation the substrate recovers the all-chair conformation, in agreement with the recent determination of the enzyme product structure. The QM/MM protocol developed here is able to predict the conformational distortion of substrate binding in glycoside hydrolases because it accounts for polarization and charge reorganization at the -1 sugar ring. It thus provides a powerful tool to model E.S complexes for which experimental information is not yet available.

Bacillus↗

PubMed2005

Structure, protonation state and dynamics of catalase compound II.

Density functional calculations are performed to investigate the protonation state of the compound II intermediate (Cpd II) of the catalase reaction cycle. Several scenarios are considered, depending on the protonation state of the active center (heme) and the catalytic His residue. Only the form with a protonated Fe==O unit (i.e. Fe--OH) is in agreement with the recent high-resolution crystal structure, while the traditional description of Cpd II as an oxoferryl species corresponds to a configuration slightly higher in energy. The computed Fe--O stretch frequency is in agreement with the available experimental data. Molecular dynamics simulations show that the pocket water remains in the region between the His61 and Asn133 catalytic residues, but it occasionally tries to escape towards the main channel in a concerted motion with the Asn133 residue. A possible role for this residue in the process of ligand entry/escape from the binding pocket is proposed.

Catalase↗

PubMed2005

Hydroxide and proton migration in aquaporins.

Hypothetical hydroxide and proton migration along the linear water chain in Aquaporin GlpF from Escherichia coli are studied by ab initio Car-Parrinello molecular dynamics simulations. It is found that the protein stabilizes a bipolar single file of water. The single file features a contiguous set of water-water hydrogen bonds in which polarization of the water molecules vary with position along the channel axis. Deprotonation of the water chain promotes the reorientation of water molecules while the hydroxide ion rapidly migrates by sequentially accepting protons from the neighboring water molecules. The hydroxide ion is not attracted by a conserved, channel-lining arginine residue, but is immobilized at two centrally located, conserved Asparagine-Proline-Alanine motifs where fourfold coordination stabilizes the ion. Hydroxide transition from the channel vestibules into the channel lumen is strongly influenced by electrostatic coupling to two conserved oppositely aligned macrodipoles. This suggests that the macrodipole's negative poles play a role in preventing hydroxide ions from entering into the channel's inner vestibules. Water protonation within the lumen facilitates water reorientation and subsequent proton expelling occurs. In the periplasmic half-channel, expelling occurs via the Grotthuss mechanism. Protonation within the cytoplasmic half-channel implies wire-breakage at the Asn-Pro-Ala motifs. The proton is here diffusively rejected as (H(5)O(2))(+).

Alanine↗

PubMed2005

Study of ligand-protein interactions by means of density functional theory and first-principles molecular dynamics.

Density Functional Theory (DFT) is a promising technique to study protein-ligand interactions from an atomistic-electronic point of view. It provides information on the electronic rearrangements upon ligand binding, the structure and the relative energy of the ligand in the binding pocket, among other properties. In addition, DFT-based techniques such as first-principles molecular dynamics (FPMD) (e.g., the Car-Parrinello [CP] method) are used to simulate the short-time dynamics of ligand-protein interactions. These techniques are emerging as a useful tool to decipher complex protein-ligand interactions in which chemical bonds are formed and/or broken during the binding process. In this chapter, the basis of DFT, its limitations, and current developments of the theory are discussed, focusing on its applications in the area of ligand-protein interactions. The performance of the method is illustrated with three examples in which the ligand binding process induces changes in the spin state or in the protonation state of the active species. The first two examples deal with the binding of oxygen to the active center of myoglobin, whereas the third one describes the binding of a formic acid inhibitor in the active center of catalase.

Binding Sites↗

PubMed2004

Structure-energy relations in methylcobalamin with and without bound axial base.

The properties of the Co-C bond in methylcobalamin (MeCbl) are analyzed by means of first-principles molecular dynamics. The optimized structure is in very good agreement with experiments, reproducing the bent-up deformation of the corrin ring as well as the metal-ligand bond distances. The analysis of the binding energies, bond orders, and vibrational stretching frequencies shows that the axial base slightly weakens the Co-C bond (by 4%), while the alkyl ligand substantially reinforces the Co-axial base bond (by 90%). These findings support several experiments and provide insight into the conversion between the base-on and base-off forms of the MeCbl cofactor.

Chemical Phenomena↗

PubMed2004

Structure of Helicobacter pylori catalase, with and without formic acid bound, at 1.6 A resolution.

Helicobacter pylori produces one monofunctional catalase, encoded by katA (hp0875). The crystal structure of H. pylori catalase (HPC) has been determined and refined at 1.6 A with crystallographic agreement factors R and R(free) of 17.4 and 21.9%, respectively. The crystal exhibits P2(1)2(1)2 space group symmetry and contains two protein subunits in the asymmetric unit. The core structure of the HPC subunit, including the disposition of a heme b prosthetic group, is closely related to those of other catalases, although it appears to be the only clade III catalase that has been characterized that does not bind NADPH. The heme iron in one subunit of the native enzyme appears to be covalently modified, possibly with a perhydroxy or dioxygen group in a compound III-like structure. Formic acid is known to bind in the active site of catalases, promoting the breakdown of reaction intermediates compound I and compound II. The structure of an HPC crystal soaked with sodium formate at pH 5.6 has also been determined to 1.6 A (with R and R(free) values of 18.1 and 20.7%, respectively), revealing at least 36 separate formate or formic acid residues in the HPC dimer. In turn, the number of water molecules refined into the models decreased from 1016 in the native enzyme to 938 in the formate-treated enzyme. Extra density, interpreted as azide, is found in a location of both structures that involves interaction with all four subunits in the tetramer. Electron paramagnetic resonance spectra confirm that azide does not bind as a ligand of the iron and that formate does bind in the heme pocket. The stability of the formate or formic acid molecule found inside the heme distal pocket has been investigated by calculations based on density functional theory.

Amino Acid Sequence↗

PubMed2003

Interdependence of redox state, hydrogen bonding, anion recognition and charge partition in crystals of (EDT-TTF-CONHMe)6 [Re6Se8(CN)6] (CH3CN)2(CH2Cl2)2.

Neutral pi-conjugated molecules and their radical cations co-exist in [(EDT-TTF-CONHMe+*)4(EDT-TTF-CONHMe0)2] [Re6Se8(CN)6]4- (CH3CN)2(CH2Cl2)2 whose crystal structure reveals that, upon one-electron oxidation, an activation of the N-H and C-H hydrogen bond donor ability is coupled to a deactivation of the hydrogen bond acceptor character of the carbonyl oxygen atom: this is expressed in the supramolecular hydrogen bond pattern and, ultimately, into charge localisation and partition in the solid state.

Journal Article↗

PubMed2002

Protonation state of the equatorial ligands and dynamics of the OH...O units in a cobaloxime biomimetic.

The protonation state of the dimethylglyoxime ligands in the B(12) coenzyme biomimetic [Co(CCl=CHCl)(dmgH)(2)(py)].CHCl(3) was investigated by using first-principles molecular dynamics. Our simulations at 173 and 300 K reveal that one of the oxime protons remains bonded to a nitroxyl group, while the proton of the second NO...H-ON unit is essentially shared with similar probability between the two oxygen atoms. This reconciles the results of the experimental determination (Jones, P. G.; Yang, L.; Steinborn, D. Acta Cryst. 1996, C52, 2399), showing all N-O distances as equivalent, with the commonly accepted rule that the protonation state of the dimethylglyoxime ligands can be identified by the different N-O distances. Further aspects of the dynamics of the OH...O units, in relation to the occurrence of weak CH...O intermolecular interactions, are analyzed.

Journal Article↗

PubMed1996

Metal Complexes of Dithiolate Ligands: 5,6-Dihydro-1,4-dithiin-2,3-dithiolato (dddt(2-)), 5,7-Dihydro-1,4,6-trithiin-2,3-dithiolato (dtdt(2-)), and 2-Thioxo-1,3-dithiole-4,5-dithiolato (dmit(2-)). Synthesis, Electrochemical Studies, Crystal and Electronic Structures, and Conducting Properties.

New precursors to potentially conductive noninteger oxidation state (NIOS) compounds based on metal complexes [ML(2)](n)()(-) [M = Ni, Pd, Pt; L = 5,6-dihydro-1,4-dithiin-2,3-dithiolato (dddt(2)(-)), 5,7-dihydro-1,4,6-trithiin-2,3-dithiolato (dtdt(2)(-)), and 2-thioxo-1,3-dithiole-4,5-dithiolato (dmit(2)(-)); n = 2, 1, 0] have been investigated. Complexes of the series (NR(4))[ML(2)] (R = Me, Et, Bu; L = dddt(2)(-), dtdt(2)(-)) have been isolated and characterized, and the crystal structure of (NBu(4))[Pt(dtdt)(2)] (1) has been determined {1 = C(24)H(44)NPtS(10), a = 12.064(2) Å, b = 17.201(3) Å, c = 16.878(2) Å, beta = 102.22(2) degrees, V = 3423(1) Å(3), monoclinic, P2(1)/n, Z = 4}. Oxidation of these complexes affords the corresponding neutral species [ML(2)](0). Another series of general formula (cation)(n)()[M(dmit)(2)] [cation = PPN(+), BTP(+), and (SMe(y)()Et(3)(-)(y)())(+) with y = 0, 1, 2, and 3, n = 2, 1, M = Ni, Pd] has also been studied. All of these (cation)(n)()[M(dmit)(2)] complexes have been isolated and characterized [with the exception of (cation)[Pd(dmit)(2)] for cation = (SMe(y)()Et(3)(-)(y)())(+)]. The crystal structures of (PPN)[Ni(dmit)(2)].(CH(3))(2)CO (2) and (SMeEt(2))[Ni(dmit)(2)] (3) have been determined {2 = C(45)H(36)NNiS(10)P(2)O, a = 12.310(2) Å, b = 13.328(3) Å, c = 15.850(3) Å, alpha = 108.19(3) degrees, beta = 96.64(2) degrees, gamma = 99.67(2) degrees, V = 2373(1) Å(3), triclinic, P&onemacr;, Z = 2; 3 = C(11)H(13)NiS(11), a = 7.171(9) Å, b = 17.802(3) Å, c = 16.251(3) Å, beta = 94.39(4) degrees, V = 2068(2) Å(3), monoclinic, P2(1)/n, Z = 4} NIOS salts derived from the preceding precursors were obtained by electrochemical oxidation. Electrochemical studies of the [M(dddt)(2)] complexes show that they may be used for the preparation of NIOS radical cation salts and [M(dddt)(2)][M'(dmit)(2)](x)() compounds, but not for the preparation of (cation)[M(dddt)(2)](z)() NIOS radical anion salts. The electrochemical oxidation of the [M(dtdt)(2)](-) complexes always yields the neutral [M(dtdt)(2)](0) species. The crystal structure of [Pt(dddt)(2)][Ni(dmit)(2)](2) (4) has been determined and is consistent with the low compaction powder conductivity (5 x 10(-)(5) S cm(-)(1) at room temperature) {4 = C(20)H(8)Ni(2)PtS(28), a = 20.336(4) Å, b = 7.189(2) Å, c = 14.181(2) Å, beta = 97.16(2) degrees, V = 2057(1) Å(3), monoclinic, C2/m, Z = 2}. The crystal structures of the semiconducting NIOS compounds (BTP)[Ni(dmit)(2)](3) (5) and (SMe(3))[Ni(dmit)(2)](2) (6) have been determined {5 = C(43)H(22)PNi(3)S(30), a = 11.927(2) Å, b = 24.919(2) Å, c = 11.829(3) Å, alpha = 93.11(1) degrees, beta = 110.22(1) degrees, gamma = 83.94(1) degrees, V = 3284(1) Å(3), triclinic, P&onemacr;, Z = 2; 6 = C(15)H(9)Ni(2)S(21), a = 7.882(1) Å, b = 11.603(2) Å, c = 17.731(2) Å, alpha = 77.44(1) degrees, beta = 94.39(1) degrees, gamma = 81.27(1) degrees, V = 1563(1) Å(3), triclinic, P&onemacr;, Z = 2}. The parent compound (SEt(3))[Ni(dmit)(2)](z) (unknown stoichiometry) is also a semiconductor with a single-crystal conductivity at room temperature of 10 S cm(-)(1). By contrast, the single-crystal conductivity at room temperature of (SMeEt(2))[Pd(dmit)(2)](2) (7) is rather high (100 S cm(-)(1)). 7 behaves as a pseudometal down to 150 K and undergoes an irreversible metal-insulator transition below this temperature. The crystal structure of 7 has been determined {7 = C(17)H(13)NPd(2)S(21), a = 7.804(4) Å, b = 36.171(18) Å, c = 6.284(2) Å, alpha = 91.68(4) degrees, beta = 112.08(4) degrees, gamma = 88.79(5) degrees, V = 1643(1) Å(3), triclinic, P&onemacr;, Z = 2}. The electronic structure of (SMeEt(2))[Pd(dmit)(2)](2) (7) and the possible origin of the metal-insulator transition at 150 K are discussed on the basis of tight-binding band structure calculations.

Journal Article↗