Your browser doesn't support javascript.
loading
Show: 20 | 50 | 100
Results 1 - 20 de 23
Filter
Add more filters










Publication year range
1.
Int J Mol Sci ; 23(7)2022 Mar 26.
Article in English | MEDLINE | ID: mdl-35409016

ABSTRACT

The platinum(II) complexes of general formula [PtCl2(dstp)(S-donor)] were dstp 5,7-dimethyl-1,2,4-triazolo[1,5-a]-pyrimidine (dmtp), 5,7-ditertbutyl-1,2,4-triazolo[1,5-a]pyrimidine (dbtp), 5-methyl-7-isobutyl-1,2,4-triazolo[1,5-a]pyrimidine (ibmtp) or 5,7-diphenyl-1,2,4-triazolo[1,5-a]pyrimidine (dptp), whereas S-tetrahydrothio-phene-1-oxide (TMSO) or diphenyl sulfoxide (DPSO) were synthesized in a one-pot reaction. Here, we present experimental data (1H, 13C, 15N, 195Pt NMR, IR, X-ray) combined with density functional theory (DFT) computations to support and characterize structure-spectra relationships and determine the geometry of dichloride platinum(II) complexes with selected triazolopyrimidines and sulfoxides. Based on the experimental and theoretical data, factors affecting the stability of platinum(II) complexes have been determined.


Subject(s)
Antineoplastic Agents , Platinum , Antineoplastic Agents/chemistry , Benzene Derivatives , Cell Line, Tumor , Oxides , Platinum/chemistry , Pyrimidines , Sulfoxides , Thiophenes , Triazoles/chemistry
2.
ChemMedChem ; 14(11): 1086-1095, 2019 06 05.
Article in English | MEDLINE | ID: mdl-30924298

ABSTRACT

Heterometallic titanocene-based compounds containing gold(I)-phosphane fragments have been extremely successful against renal cancer in vitro and in vivo. The exchange of phosphane by N-heterocyclic carbene ligands to improve or modulate their pharmacological profile afforded bimetallic complexes effective against prostate cancer, but less effective against renal cancer in vitro. Herein we report the synthesis of new bimetallic Ti-Au compounds by the incorporation of two previously reported highly active gold(I)-N-heterocyclic carbene fragments derived from 4,5-diarylimidazoles. The two new compounds [(η5 -C5 H5 )2 TiMe(µ-mba)Au(NHC)] (where NHC=1,3-dibenzyl-4,5-diphenylimidazol-2-ylidene, NHC-Bn 2 a; or 1,3-diethyl-4,5-diphenylimidazol-2-ylidene, NHC-Et 2 b) with the dual linker (-OC(O)-p-C6 H4 -S-) containing both a carboxylate and a thiolate group were evaluated in vitro against renal and prostate cancer cell lines. The compounds were found to be more cytotoxic than previously described Ti-Au compounds containing non-optimized gold(I)-N-heterocyclic fragments. We present studies to evaluate their effects on cell death pathways, migration, inhibition of thioredoxin reductase (TrxR) and vascular endothelial growth factor (VEGF) in the PC3 prostate cancer cell line. The results show that the incorporation of a second metallic fragment such as titanocene into biologically active gold(I) compounds improves their pharmacological profile.


Subject(s)
Antineoplastic Agents/pharmacology , Coordination Complexes/pharmacology , Gold/pharmacology , Heterocyclic Compounds/pharmacology , Methane/analogs & derivatives , Organometallic Compounds/pharmacology , Antineoplastic Agents/chemical synthesis , Antineoplastic Agents/chemistry , Cell Movement/drug effects , Cell Proliferation/drug effects , Cell Survival/drug effects , Cells, Cultured , Coordination Complexes/chemical synthesis , Coordination Complexes/chemistry , Density Functional Theory , Dose-Response Relationship, Drug , Drug Screening Assays, Antitumor , Gold/chemistry , Heterocyclic Compounds/chemical synthesis , Heterocyclic Compounds/chemistry , Humans , Methane/chemical synthesis , Methane/chemistry , Methane/pharmacology , Molecular Structure , Organometallic Compounds/chemistry , Structure-Activity Relationship
3.
ACS Biomater Sci Eng ; 4(2): 463-467, 2018 Feb 12.
Article in English | MEDLINE | ID: mdl-32042890

ABSTRACT

Platinum therapy represents first line of treatment in many malignancies but its high systemic toxicity limits the therapeutic dosage. Herein, we report the synthesis of carboplatin-like complexes with azide and alkyne functional groups and the formation of a platinum (II) - nuclear localization sequence peptide (Pt-NLS) hybrid to improve the import of platinum (II) complexes directly into the cell's nucleus. The Pt-NLS hybrid successfully enters cells and their nuclei, forming Pt-induced nuclear lesions. The in vitro efficacy of Pt-NLS is high, superior to native carboplatin at the same concentration. The methodology used is simple and cost-effective and most importantly can easily be extended to load the Pt (II) onto other supports, opening new possibilities for enhanced delivery of Pt (II) therapy.

4.
J Phys Chem A ; 119(26): 6850-66, 2015 Jul 02.
Article in English | MEDLINE | ID: mdl-26050709

ABSTRACT

Density functional theory was employed for a comprehensive study that provided electronic and structural insights into the KatG catalase reaction that involves oxyheme. The catalytic role of a unique amino acid cofactor Met-Tyr-Trp (MYW) in its radical form found in KatG was thereby elucidated. It was established that the MYW-radical is flexible such that a "hinge-like opening" rotation of the Trp-107 ring with respect to the Tyr-229 ring along their covalent C-C bond is an inherent feature of its catalytic properties. Also, an H-bond between the Tyr-229 and the mobile side chain of Arg-418 further enables the catalytic events. The opening process breaks an H-bond between the N-H of Trp-107 and the inner oxygen of the Fe-O2 (oxyheme) complex present in the closed conformation of the MYW-radical. This motion lowers the spin-crossing energy barrier between the ground state and the catalytically active high-spin states and enables electron transfer from the oxyheme group to the MYW-radical. The release of molecular oxygen is thereby catalyzed and leaves ferric-heme poised for another catalytic cycle. The energy barrier for the oxyheme state to complete the catalytic event, when assisted by the radical opening process, is thereby reduced and estimated to be 5.6 kcal/mol.


Subject(s)
Bacterial Proteins/chemistry , Catalase/chemistry , Heme/chemistry , Methionine/chemistry , Oxygen/chemistry , Tryptophan/chemistry , Tyrosine/chemistry , Carbon/chemistry , Catalysis , Electrons , Hydrogen/chemistry , Hydrogen Bonding , Models, Chemical , Mycobacterium tuberculosis , Nitrogen/chemistry , Quantum Theory
5.
Bioorg Med Chem Lett ; 24(17): 4260-5, 2014 Sep 01.
Article in English | MEDLINE | ID: mdl-25091929

ABSTRACT

Global chemical reactivity descriptors and lipophilicity (logP) were evaluated via density functional theory in order to clarify the structure-cytotoxic activity relationships of substituted chalcones. Stepwise multiple regression was employed to establish correlation between descriptors and cytotoxic activity against three cancer cell lines (HL-60, NALM-6 and WM-115) for 11 compounds. Regression analysis revealed that electrophilicity index and chemical potential significantly contributed in explaining of chalcones cytotoxic potential. Moreover, the established structure-activity relationships based on electronic structure properties allow indicating the substructures responsible for their cytotoxic activity. The study has also been supported by crystallographic data of 2-chloro-2'-hydroxychalcone.


Subject(s)
Antineoplastic Agents/pharmacology , Chalcones/chemistry , Chalcones/toxicity , Electrons , Antineoplastic Agents/chemical synthesis , Antineoplastic Agents/chemistry , Cell Line, Tumor , Cell Proliferation/drug effects , Chalcones/chemical synthesis , Chalcones/pharmacology , Crystallography, X-Ray , Dose-Response Relationship, Drug , Drug Screening Assays, Antitumor , HL-60 Cells , Humans , Models, Molecular , Molecular Structure , Quantum Theory , Regression Analysis , Structure-Activity Relationship
6.
J Inorg Biochem ; 129: 150-61, 2013 Dec.
Article in English | MEDLINE | ID: mdl-24080180

ABSTRACT

A systematic density functional theory study supported by extended X-ray absorption fine structure (EXAFS) and infrared spectroscopic data was conducted to elucidate how structure and vibrational spectra of aqueous desferrioxamine B (DFOB) metal complexes vary with the metal ion identity. Structural parameters derived from EXAFS analyses and trends in metal binding constants are well reproduced and validated by the applied computational model. Vibrational mode analysis guides determination and recognition of crucial structure- and metal-sensitive infrared marker bands. The key marker bands, CO and CN stretching modes, dominate the infrared spectra in the 1400-1650cm(-1) region. The modes are sensitive to the stability and size of the metal core (first coordination shell) and indicative of its deformation from the octahedral symmetry. The results shed light on the fundamental structural and electronic factors that control metal binding by siderophores, and drive their potentially rich and largely unexplored interactions with trace metals.


Subject(s)
Deferoxamine/chemistry , Metals/chemistry , Models, Molecular , Molecular Structure , Spectrophotometry, Infrared
7.
J Biol Chem ; 287(44): 37057-65, 2012 Oct 26.
Article in English | MEDLINE | ID: mdl-22918833

ABSTRACT

Catalase activity of the dual-function heme enzyme catalase-peroxidase (KatG) depends on several structural elements, including a unique adduct formed from covalently linked side chains of three conserved amino acids (Met-255, Tyr-229, and Trp-107, Mycobacterium tuberculosis KatG numbering) (MYW). Mutagenesis, electron paramagnetic resonance, and optical stopped-flow experiments, along with calculations using density functional theory (DFT) methods revealed the basis of the requirement for a radical on the MYW-adduct, for oxyferrous heme, and for conserved residues Arg-418 and Asp-137 in the rapid catalase reaction. The participation of an oxyferrous heme intermediate (dioxyheme) throughout the pH range of catalase activity is suggested from our finding that carbon monoxide inhibits the activity at both acidic and alkaline pH. In the presence of H(2)O(2), the MYW-adduct radical is formed normally in KatG[D137S] but this mutant is defective in forming dioxyheme and lacks catalase activity. KatG[R418L] is also catalase deficient but exhibits normal formation of the adduct radical and dioxyheme. Both mutants exhibit a coincidence between MYW-adduct radical persistence and H(2)O(2) consumption as a function of time, and enhanced subunit oligomerization during turnover, suggesting that the two mutations disrupting catalase turnover allow increased migration of the MYW-adduct radical to protein surface residues. DFT calculations showed that an interaction between the side chain of residue Arg-418 and Tyr-229 in the MYW-adduct radical favors reaction of the radical with the adjacent dioxyheme intermediate present throughout turnover in WT KatG. Release of molecular oxygen and regeneration of resting enzyme are thereby catalyzed in the last step of a proposed catalase reaction.


Subject(s)
Bacterial Proteins/chemistry , Catalase/chemistry , Free Radicals/chemistry , Mycobacterium tuberculosis/enzymology , Amino Acid Motifs , Amino Acid Substitution , Bacterial Proteins/antagonists & inhibitors , Bacterial Proteins/genetics , Carbon Monoxide/chemistry , Catalase/antagonists & inhibitors , Catalase/genetics , Catalytic Domain , Heme/chemistry , Hydrogen-Ion Concentration , Kinetics , Models, Chemical , Mutagenesis, Site-Directed , Oxygen/chemistry , Protein Multimerization , Quantum Theory
8.
J Phys Chem B ; 116(31): 9387-95, 2012 Aug 09.
Article in English | MEDLINE | ID: mdl-22779777

ABSTRACT

The imidazole side-chains of histidine residues perform key roles in proteins, and spectroscopic markers are of great interest. The imidazole Raman spectrum is subject to resonance enhancement at UV wavelengths, and a number of UVRR markers of structure have been investigated. We report a systematic experimental and computational study of imidazole UVRR spectra, which elucidates the band pattern, and the effects of protonation and deprotonation, of H/D exchange, of metal complexation, and of addition of a methyl substituent, modeling histidine itself. A consistent assignment scheme is proposed, which permits tracking of the bands through these chemical variations. The intensities are dominated by normal mode contributions from stretching of the strongest ring bonds, C(2)N and C(4)C(5), consistent with enhancement via resonance with a dominant imidazole π-π* transition.


Subject(s)
Histidine/analysis , Imidazoles/analysis , Proteins/chemistry , Spectrum Analysis, Raman/methods , Binding Sites , Coordination Complexes/chemistry , Metals/chemistry , Models, Molecular , Protons
9.
J Phys Chem A ; 116(1): 571-81, 2012 Jan 12.
Article in English | MEDLINE | ID: mdl-22117527

ABSTRACT

Resonance Raman spectra are computed applying the weighted gradient methodology with CIS and DFT gradients to determine the characteristic spectral patterns for Hg(II) and Pb(II) loaded sulfur-rich proteins while excited to a characteristic LMCT electronic transition band. A framework of structure-spectrum relationships is established to assess lead coordination modes via vibrational spectroscopy. Illustrative calculations on Hg(II) complexes agree with experimental data demonstrating reliability and accuracy of the applied methodology. In contrast to Hg(II) complexes, a unique 3-center-4-electron hypervalent C(ß)H···S interaction present in lead-sulfur complexes was established and suggested to play a key role in the strong preference for lead versus other metal ions in lead specific proteins such as PbrR691. The characteristic Pb-S symmetric stretching bands, predicted without additional refinements such as scaling of a force field or frequencies, are found around 238 cm(-1) for 3-coordinated lead-sulfur domains and around 228 cm(-1) for 4-coordinated lead-sulfur domains. These results present an experimental challenge for clear detection of lead coordination via solely UVRR spectroscopy. In addition to predicted UVRR spectra, UVRR excitation profiles for relevant vibrational bands of lead-sulfur domains are presented.


Subject(s)
Coordination Complexes/chemistry , Lead/chemistry , Mercury/chemistry , Proteins/chemistry , Sulfur/chemistry , Models, Molecular , Quantum Theory , Spectrum Analysis , Spectrum Analysis, Raman , Thermodynamics , Vibration
10.
Biometals ; 25(2): 393-412, 2012 Apr.
Article in English | MEDLINE | ID: mdl-22187125

ABSTRACT

Although siderophores are generally viewed as biological iron uptake agents, recent evidence has shown that they may play significant roles in the biogeochemical cycling and biological uptake of other metals. One such siderophore that is produced by A. vinelandii is the triscatecholate protochelin. In this study, we probe the solution chemistry of protochelin and its complexes with environmentally relevant trace metals to better understand its effect on metal uptake and cycling. Protochelin exhibits low solubility below pH 7.5 and degrades gradually in solution. Electrochemical measurements of protochelin and metal-protochelin complexes reveal a ligand half-wave potential of 200 mV. The Fe(III)Proto(3-) complex exhibits a salicylate shift in coordination mode at circumneutral to acidic pH. Coordination of Mn(II) by protochelin above pH 8.0 promotes gradual air oxidation of the metal center to Mn(III), which accelerates at higher pH values. The Mn(III)Proto(3-) complex was found to have a stability constant of log ß(110) = 41.6. Structural parameters derived from spectroscopic measurements and quantum mechanical calculations provide insights into the stability of the Fe(III)Proto(3-), Fe(III)H(3)Proto, and Mn(III)Proto(3-) complexes. Complexation of Co(II) by protochelin results in redox cycling of Co, accompanied by accelerated degradation of the ligand at all solution pH values. These results are discussed in terms of the role of catecholate siderophores in environmental trace metal cycling and intracellular metal release.


Subject(s)
Coordination Complexes/chemistry , Siderophores/chemistry , Trace Elements/chemistry , Hydrogen-Ion Concentration , Oxidation-Reduction , Solubility , Trace Elements/metabolism
11.
Inorg Chem ; 50(21): 11099-110, 2011 Nov 07.
Article in English | MEDLINE | ID: mdl-21958150

ABSTRACT

A series of tri- and bimetallic titanium-gold, titanium-palladium, and titanium-platinum derivatives of the general formulas [Ti{η(5)-C(5)H(4)(CH(2))(n)PPh(2)(AuCl)}(2)]·2THF [n = 0 (1); n = 2 (2); n = 3 (3)] and [TiCl(2){η(5)-C(5)H(4)κ-(CH(2))(n)PPh(2)}(2)(MCl(2))]·2THF [M = Pd, n = 0 (4); n = 2 (5); n = 3 (6) ; M = Pt, n = 0 (7); n = 2 (8); n = 3 (9)] have been synthesized and characterized by different spectroscopic techniques and mass spectrometry. The molecular structures of compounds 1-9 have been investigated by means of density functional theory calculations. The calculated IR spectra of the optimized structures fit well with the experimental IR data obtained for 1-9. The stability of the heterometallic compounds in deuterated solvents [CDCl(3), dimethyl sulfoxide (DMSO)-d(6), and mixtures 50:50 DMSO-d(6)/D(2)O and 1:99 DMSO-d(6)/D(2)O at acidic and neutral pH] has been evaluated by (31)P and (1)H NMR spectroscopy showing a higher stability for these compounds than for Cp(2)TiCl(2) or precursors [Ti{η(5)-C(5)H(4)(CH(2))(n)PPh(2)}(2)]. The new compounds display a lower acidity (1-2 units) than Cp(2)TiCl(2). The decomposition products have been identified over time. Complexes 1-9 have been tested as potential anticancer agents, and their cytotoxicity properties were evaluated in vitro against HeLa human cervical carcinoma and DU-145 human prostate cancer cells. TiAu(2) and TiPd compounds were highly cytotoxic for these two cell lines. The interactions of the compounds with calf thymus DNA have been evaluated by thermal denaturation (1-9) and by circular dichroism (1, 3, 4, and 7) spectroscopic methods. All of these complexes show a stronger interaction with DNA than that displayed by Cp(2)TiCl(2) at neutral pH. The data are consistent with electrostatic interactions with DNA for TiAu(2) compounds and for a covalent binding mode for TiM (M = Pd, Pt) complexes.


Subject(s)
Antineoplastic Agents/chemical synthesis , Chemistry, Pharmaceutical/methods , Organometallic Compounds/chemical synthesis , Palladium/chemistry , Phosphines/chemical synthesis , Platinum/chemistry , Titanium/chemistry , Animals , Antineoplastic Agents/metabolism , Antineoplastic Agents/pharmacology , Cattle , Cell Line, Tumor , Cell Survival/drug effects , Circular Dichroism , DNA/analysis , DNA/chemistry , Female , Humans , Inhibitory Concentration 50 , Magnetic Resonance Spectroscopy , Male , Models, Molecular , Nucleic Acid Conformation/drug effects , Organometallic Compounds/metabolism , Organometallic Compounds/pharmacology , Phosphines/metabolism , Phosphines/pharmacology , Prostatic Neoplasms/drug therapy , Prostatic Neoplasms/pathology , Spectrophotometry, Infrared , Structure-Activity Relationship , Uterine Cervical Neoplasms/drug therapy , Uterine Cervical Neoplasms/pathology
12.
J Phys Chem A ; 113(12): 2926-34, 2009 Mar 26.
Article in English | MEDLINE | ID: mdl-19260673

ABSTRACT

A framework of the weighted-gradient approach is developed for effective quantum-mechanical modeling of resonance Raman (RR) intensities with a view toward rationalizing enhancement patterns observed for histidine and tryptophan side chains. Unlike the single-state gradient approach, this new procedure utilizes the vertical gradients obtained for all computed excited states to produce an effective gradient and the RR intensity patterns for a particular frequency of the excitation photon. The dramatic spectral changes observed for the histidine ring upon its protonation, deprotonation, or deuterium substitution of exchangeable protons is well reproduced by this model. Spectral comparison for the tryptophan ring clearly demonstrated improved quality of the weighted-gradient over the single-state gradient approach. Computed spectra exemplify the potential application of this model to support vibrational studies of electronic and structural interactions of chromophores in proteins.


Subject(s)
Quantum Theory , Spectrum Analysis, Raman , Histidine , Tryptophan
13.
Inorg Chem ; 48(3): 1122-31, 2009 Feb 02.
Article in English | MEDLINE | ID: mdl-19119867

ABSTRACT

The new Ru(II) chloroquine complexes [Ru(eta(6)-arene)(CQ)Cl2] (CQ = chloroquine; arene = p-cymene 1, benzene 2), [Ru(eta(6)-p-cymene)(CQ)(H2O)2][BF4]2 (3), [Ru(eta(6)-p-cymene)(CQ)(en)][PF6]2 (en = ethylenediamine) (4), and [Ru(eta(6)-p-cymene)(eta(6)-CQDP)][BF4]2 (5, CQDP = chloroquine diphosphate) have been synthesized and characterized by use of a combination of NMR and FTIR spectroscopy with DFT calculations. Each complex is formed as a single coordination isomer: In 1-4, chloroquine binds to ruthenium in the eta(1)-N mode through the quinoline nitrogen atom, whereas in 5 an unprecedented eta(6) bonding through the carbocyclic ring is observed. 1, 2, 3, and 5 are active against CQ-resistant (Dd2, K1, and W2) and CQ-sensitive (FcB1, PFB, F32, and 3D7) malaria parasites (Plasmodium falciparum); importantly, the potency of these complexes against resistant parasites is consistently higher than that of the standard drug chloroquine diphosphate. 1 and 5 also inhibit the growth of colon cancer cells, independently of the p53 status and of liposarcoma tumor cell lines with the latter showing increased sensitivity, especially to 1 (IC50 8 microM); this is significant because this type of tumor does not respond to currently employed chemotherapies.


Subject(s)
Antimalarials/chemical synthesis , Antimalarials/pharmacology , Antineoplastic Agents/chemical synthesis , Antineoplastic Agents/pharmacology , Chloroquine/chemistry , Ruthenium Compounds/chemical synthesis , Ruthenium Compounds/pharmacology , Animals , Antimalarials/chemistry , Antineoplastic Agents/chemistry , Cell Line, Tumor , Cell Proliferation/drug effects , Humans , Magnetic Resonance Spectroscopy , Models, Molecular , Molecular Structure , Plasmodium falciparum/drug effects , Ruthenium Compounds/chemistry , Spectrophotometry, Infrared
14.
J Biol Chem ; 284(11): 7017-29, 2009 Mar 13.
Article in English | MEDLINE | ID: mdl-19139099

ABSTRACT

A mechanism accounting for the robust catalase activity in catalase-peroxidases (KatG) presents a new challenge in heme protein enzymology. In Mycobacterium tuberculosis, KatG is the sole catalase and is also responsible for peroxidative activation of isoniazid, an anti-tuberculosis pro-drug. Here, optical stopped-flow spectrophotometry, rapid freeze-quench EPR spectroscopy both at the X-band and at the D-band, and mutagenesis are used to identify catalase reaction intermediates in M. tuberculosis KatG. In the presence of millimolar H2O2 at neutral pH, oxyferrous heme is formed within milliseconds from ferric (resting) KatG, whereas at pH 8.5, low spin ferric heme is formed. Using rapid freeze-quench EPR at X-band under both of these conditions, a narrow doublet radical signal with an 11 G principal hyperfine splitting was detected within the first milliseconds of turnover. The radical and the unique heme intermediates persist in wild-type KatG only during the time course of turnover of excess H2O2 (1000-fold or more). Mutation of Met255, Tyr229, or Trp107, which have covalently linked side chains in a unique distal side adduct (MYW) in wild-type KatG, abolishes this radical and the catalase activity. The D-band EPR spectrum of the radical exhibits a rhombic g tensor with dual gx values (2.00550 and 2.00606) and unique gy (2.00344) and gz values (2.00186) similar to but not typical of native tyrosyl radicals. Density functional theory calculations based on a model of an MYW adduct radical built from x-ray coordinates predict experimentally observed hyperfine interactions and a shift in g values away from the native tyrosyl radical. A catalytic role for an MYW adduct radical in the catalase mechanism of KatG is proposed.


Subject(s)
Bacterial Proteins/chemistry , Catalase/chemistry , Heme/chemistry , Hydrogen Peroxide/chemistry , Models, Chemical , Mycobacterium tuberculosis/enzymology , Peroxidase/chemistry , Bacterial Proteins/genetics , Catalase/genetics , Catalysis , Heme/genetics , Hydrogen Peroxide/metabolism , Hydrogen-Ion Concentration , Mycobacterium tuberculosis/genetics , Peroxidase/genetics , Protein Structure, Tertiary/physiology
15.
J Phys Chem A ; 112(50): 12781-8, 2008 Dec 18.
Article in English | MEDLINE | ID: mdl-18754605

ABSTRACT

Density functional theory has been applied to a series of unsubstituted planar metalloporphyrins (MPs) to elucidate how geometry and frequencies correlate with the metal-nitrogen distance, referred to as the core size. Different transition metals can invoke expansion or contraction of the porphyrin core due to electronic effects resulting from the amount of d-electron pairing as well as occupancy of the d(x(2)(-y(2))) orbital. A full vibrational analysis consisting of all in-plane and out-of-plane frequencies was carried out, and the resulting modes were plotted against core size for a linear analysis and grouped within symmetry blocks. The modes were separated according to planarity, and all modes with a large slope and best fit greater than 0.8 were considered sensitive to metal-nitrogen distances. All planar skeletal modes above 1450 cm(-1), including the pyrolle ring deformations, are found to be core-size sensitive. The most significant out-of-plane modes sensitive to core size are gamma(8) and gamma(9), which are infrared active and grouped within the A(2u) symmetry block. The present work also opens possible quantitative applications for the correlation of spectroscopic properties of MPs and heme proteins with actual structural parameters.


Subject(s)
Metalloporphyrins/chemistry , Crystallography, X-Ray/methods , Kinetics , Metals/chemistry , Models, Molecular , Nitrogen/chemistry , Normal Distribution , Porphyrins/chemistry , Protein Conformation , Protoporphyrins/chemistry , Vibration
16.
Inorg Chem ; 46(18): 7509-21, 2007 Sep 03.
Article in English | MEDLINE | ID: mdl-17676837

ABSTRACT

Density functional theory (DFT) structure calculations and time-dependent DFT electronic excitation calculations on simple mononuclear lead structures confirm recent reports on the stabilization of tricoordinated structural domains in poisoned proteins. However, the possibility of the formation of tetracoordinated lead complexes should not be disregarded in studies on mechanisms of lead toxicity because structures with both coordination modes are plausible and might contribute to observed UV spectra. Reported calculations along with detailed molecular orbital analysis confirm that the intense UV signal at around 260 nm is an indicator of the ligand-to-metal charge transfer (LMCT) band where the electrons are transferred from the sulfur 3p orbital to the lead 6p orbital. The composition of the LMCT band reveals significant excitations not only from the Pb-S bonding orbitals but also from sulfur lone-pair orbitals to the Pb-S antibonding orbitals for which the electron density is largely localized on the Pb "6p-like" molecular orbitals. There is a solid indication that the stereochemically active pair orbital of lead is not strongly hybridized and remains largely of the 6s character in tricoordinated lead structures and is minimally hybridized in tetracoordinated lead structures. Computed UV spectra of lead model complexes are compared to experimental UV spectra of model lead peptides. The comparison shows a good agreement with the major spectral trends and changes observed in these experiments.


Subject(s)
Electrons , Lead Poisoning , Lead/chemistry , Ligands , Models, Molecular , Molecular Conformation , Spectrophotometry , Zinc Fingers
17.
Inorg Chem ; 45(14): 5585-90, 2006 Jul 10.
Article in English | MEDLINE | ID: mdl-16813422

ABSTRACT

Density functional theory (DFT)-based normal mode calculations have been carried out on models for B12-cofactors to assign reported isotope-edited resonance Raman spectra, which isolate vibrations of the organo-Co group. Interpretation is straightforward for alkyl-Co derivatives, which display prominent Co-C stretching vibrational bands. DFT correctly reproduces Co-C distances and frequencies for the methyl and ethyl derivatives. However, spectra are complex for adenosyl derivatives, due to mixing of Co-C stretching with a ribose deformation coordinate and to activation of modes involving Co-C-C bending and Co-adenosyl torsion. Despite this complexity, the computed spectra provide a satisfactory re-assignment of the experimental data. Reported trends in adenosyl-cobalamin spectra upon binding to the methylmalonyl CoA mutase enzyme, as well as on subsequent binding of substrates and inhibitors, provide support for an activation mechanism involving substrate-induced deformation of the adenosyl ligand.


Subject(s)
Cobamides/chemistry , Methylmalonyl-CoA Mutase/chemistry , Cobamides/metabolism , Enzyme Activation , Methylmalonyl-CoA Mutase/metabolism , Quantum Theory , Spectrum Analysis, Raman
18.
J Am Chem Soc ; 128(16): 5427-35, 2006 Apr 26.
Article in English | MEDLINE | ID: mdl-16620114

ABSTRACT

Combining quantum and molecular mechanics (QM/MM) methods and protein structure prediction algorithms, helix and loop movements are computed along the pathway of CO dissociation from myoglobin (Mb). The results are compared with high-resolution crystallographic data using sequence-displacement graphs. These graphs provide an unbiased method for evaluating main-chain segmental motions; they resolve an apparent disagreement between two sets of high-resolution crystal structures for MbCO and deoxyMb. The QM/MM modeling of the CO deligation reproduces the experimentally observed spin states and photodissociated crystal structure. The principal effect of CO dissociation is shown to be a concerted rotation of the E and F helices, which hold the heme like a clamshell. The rotation is a response to deligation forces, which impel the F helix away from the heme because of the Fe spin conversion, and which allow the E helix to collapse toward the heme as nonbonded contacts on the distal side are relieved. Additional helix and loop displacements stem from these primary events. In particular, the CD loop is found to be repositioned as a result of steric interactions with the water molecule that becomes H-bonded to the distal histidine in deoxyMb. A similar EF rotation and CD loop displacement are proposed to be the first steps along the allosteric pathway from the R to the T state in hemoglobin.


Subject(s)
Hemoglobins/chemistry , Models, Molecular , Myoglobin/chemistry , Allosteric Regulation , Crystallography , Quantum Theory
19.
Inorg Chem ; 45(4): 1424-6, 2006 Feb 20.
Article in English | MEDLINE | ID: mdl-16471949

ABSTRACT

Density functional theory (DFT) has been applied to the analysis of interligand vibrations in two chiral isomers of hydroperoxo complex of cobalt bleomycin (BLM-Co(III)-OOH, BLM = bleomycin). The DFT-based normal coordinate analysis reveals that 16O/18O isotope-sensitive modes associated with the Co-OOH moiety uniquely reflect the chiral organization of ligands around the cobalt atom. This study provides an independent probe of cobalt chirality coordinated to BLM and shows that interligand modes associated with the Co-OOH moiety could be used as a structural marker of the chiral isomers.


Subject(s)
Bleomycin/analogs & derivatives , Hydrogen Peroxide/chemistry , Bleomycin/chemistry , Ligands , Models, Molecular , Spectrum Analysis, Raman , X-Ray Diffraction
20.
J Am Chem Soc ; 127(48): 16882-91, 2005 Dec 07.
Article in English | MEDLINE | ID: mdl-16316234

ABSTRACT

The basis of the respective regiospecificities of intradiol and extradiol dioxygenase is poorly understood and may be linked to the protonation state of the bidentate-bound catechol in the enzyme/substrate complex. Previous ultraviolet resonance Raman (UVRR) and UV-visible (UV-vis) difference spectroscopic studies demonstrated that, in extradiol dioxygenases, the catechol is bound to the Fe(II) as a monoanion. In this study, we use the same approaches to demonstrate that, in catechol 1,2-dioxygenase (C12O), an intradiol enzyme, the catechol binds to the Fe(III) as a dianion. Specifically, features at 290 nm and 1550 cm(-1) in the UV-vis and UVRR difference spectra, respectively, are assigned to dianionic catechol based on spectra of the model compound, ferric tris(catecholate). The UVRR spectroscopic band assignments are corroborated by density functional theory (DFT) calculations. In addition, negative features at 240 nm in UV-vis difference spectra and at 1600, 1210, and 1175 cm(-1) in UVRR difference spectra match those of a tyrosinate model compound, consistent with protonation of the axial tyrosinate ligand when it is displaced from the ferric ion coordination sphere upon substrate binding. The DFT calculations ascribe the asymmetry of the bound dianionic substrate to the trans donor effect of an equatorially ligated tyrosinate ligand. In addition, the computations suggest that trans donation from the tyrosinate ligand may facilitate charge transfer from the substrate to yield the iron-bound semiquinone transition state, which is capable of reacting with dioxygen. In illustrating the importance of ligand trans effects in a biological system, the current study demonstrates the power of combining difference UVRR and optical spectroscopies to probe metal ligation in solution.


Subject(s)
Catechol 1,2-Dioxygenase/chemistry , Anaerobiosis , Catechol 1,2-Dioxygenase/metabolism , Catechols/chemistry , Ferric Compounds/chemistry , Kinetics , Models, Molecular , Pyridines/chemistry , Spectrophotometry, Ultraviolet , Spectrum Analysis, Raman , Substrate Specificity , Tyrosine/analogs & derivatives , Tyrosine/chemistry
SELECTION OF CITATIONS
SEARCH DETAIL
...