RESUMO
Thiol redox chemical reactions play a key role in a variety of physiological processes, mainly due to the presence of low-molecular-weight thiols and cysteine residues in proteins involved in catalysis and regulation. Specifically, the subtle sensitivity of thiol reactivity to the environment makes the use of simulation techniques extremely valuable for obtaining microscopic insights. In this work we review the application of classical and quantum-mechanical atomistic simulation tools to the investigation of selected relevant issues in thiol redox biochemistry, such as investigations on (1) the protonation state of cysteine in protein, (2) two-electron oxidation of thiols by hydroperoxides, chloramines, and hypochlorous acid, (3) mechanistic and kinetics aspects of the de novo formation of disulfide bonds and thiol-disulfide exchange, (4) formation of sulfenamides, (5) formation of nitrosothiols and transnitrosation reactions, and (6) one-electron oxidation pathways.
RESUMO
In this work we review the application of classical and quantum-mechanical atomistic computer simulation tools to the investigation of small ligand interaction with globins. In the first part, studies of ligand migration, with its connection to kinetic association rate constants (kon), are presented. In the second part, we review studies for a variety of ligands such as O2, NO, CO, HS(-), F(-), and NO2(-) showing how the heme structure, proximal effects, and the interactions with the distal amino acids can modulate protein ligand binding. The review presents mainly results derived from our previous works on the subject, in the context of other theoretical and experimental studies performed by others. The variety and extent of the presented data yield a clear example of how computer simulation tools have, in the last decade, contributed to our deeper understanding of small ligand interactions with globins. This article is part of a Special Issue entitled: Oxygen Binding and Sensing Proteins.
Assuntos
Simulação por Computador , Globinas/química , Globinas/metabolismo , Animais , Humanos , Ligantes , Teoria QuânticaRESUMO
The nitroprusside ion [Fe(CN)(5)NO](2-) (NP) reacts with excess HS(-) in the pH range 8.5-12.5, in anaerobic medium ("Gmelin" reaction). The progress of the addition process of HS(-) into the bound NO(+) ligand was monitored by stopped-flow UV/Vis/EPR and FTIR spectroscopy, mass spectrometry, and chemical analysis. Theoretical calculations were employed for the characterization of the initial adducts and reaction intermediates. The shapes of the absorbance-time curves at 535-575 nm depend on the pH and concentration ratio of the reactants, R=[HS(-)]/[NP]. The initial adduct [Fe(CN)(5)N(O)SH](3-) (AH, λ(max) ≈570 nm) forms in the course of a reversible process, with k(ad)=190±20 M(-1)s(-1) , k(-ad)=0.3±0.05 s(-1) . Deprotonation of AH (pK(a)=10.5±0.1, at 25.0 °C, I=1 M), leads to [Fe(CN)(5)N(O)S](4-) (A, λ(max)=535 nm, ε=6000±300 M(-1) cm(-1) ). [Fe(CN)(5)NO](.)(3-) and HS(2)(.)(2-) radicals form through the spontaneous decomposition of AH and A. The minor formation of the [Fe(CN)(5)NO](3-) ion equilibrates with [Fe(CN)(4)NO](2-) through cyanide labilization, and generates the "g=2.03" iron-dinitrosyl, [Fe(NO)(2)(SH)(2)](-) , which is labile toward NO release. Alternative nucleophilic attack of HS(-) on AH and A generates the reactive intermediates [Fe(CN)(5)N(OH)(SH)(2)](3-) and [Fe(CN)(5)N(OH)(S)(SH)](4-) , respectively, which decompose through multielectronic nitrosyl reductions, leading to NH(3) and hydrogen disulfide, HS(2)(-) . N(2)O is also produced at pH≥11. Biological relevance relates to the role of NO, NO(-) , and other bound intermediates, eventually able to be released to the medium and rapidly trapped by substrates. Structure and reactivity comparisons of the new nitrososulfide ligands with free and bound nitrosothiolates are provided.
Assuntos
Compostos Ferrosos/química , Sulfeto de Hidrogênio/química , Óxidos de Nitrogênio/química , Nitroprussiato/química , Concentração de Íons de Hidrogênio , Cinética , Ligantes , Estrutura Molecular , Oxirredução , Espectrofotometria Ultravioleta , EstereoisomerismoRESUMO
There is recent evidence suggesting that nitrite anion (NO 2 (-)) represents the major intravascular NO storage molecule whose transduction to NO is facilitated by a reduction mechanism catalyzed by deoxygenated hemoglobin (deoxy-Hb). In this work, we provide a detailed microscopic study of deoxy-Hb nitrite reductase (NIR) activity by combining classical molecular dynamics and hybrid quantum mechanical-molecular mechanical simulations. Our results point out that two alternative mechanisms could be operative and suggest that the most energetic barriers should stem from either reprotonation of the distal histidine or NO dissociation from the ferric heme. In the first proposed mechanism, which is similar to that proposed for bacterial NIRs, nitrite anion or nitrous acid coordinates to the heme through the N atom. This pathway involves HisE7 in a one or two proton transfer process, depending on whether the active species is nitrite anion or nitrous acid, to yield an intermediate Fe(III)NO species which eventually dissociates leading to NO and methemoglobin. In the second mechanism, the nitrite anion coordinates to the heme through the O atom. This pathway requires only one proton transfer from HisE7 and leads directly to the formation of a hydroxo Fe(III) complex and NO.
Assuntos
Ânions/metabolismo , Hemoglobinas/química , Hemoglobinas/metabolismo , Óxido Nítrico/metabolismo , Nitritos/química , Nitritos/metabolismo , Ânions/química , Sítios de Ligação , Catálise , Histidina/química , Histidina/metabolismo , Humanos , Ligantes , Modelos Moleculares , Óxido Nítrico/química , Nitrito Redutases/química , Nitrito Redutases/metabolismo , Conformação ProteicaRESUMO
In this work, we present a complete and detailed experimental characterization and theoretical study of a variety of coordinated S-nitrosothiols (RSNOs), such as cysteine derivatives, mercaptosuccinic acid, benzyl thiol, and phenyl thiol. Some of them are extremely unstable and sensitive in free form. Strikingly, in contrast with free S-nitrosothiols, we found that, upon coordination to iridium, they become very stable even in aqueous solutions. The study of these coordinated complexes provides further insight on the elucidation of structural aspects dealing with the nature of the S-N bond in RSNOs, a fact which still remains a matter of controversy.
Assuntos
S-Nitrosotióis/química , Água/química , Cristalografia por Raios X , Cisteína/química , Ésteres/química , Espectroscopia de Ressonância Magnética , Compostos de Potássio/química , Solubilidade , Espectrometria de Massas por Ionização por Electrospray , Espectrofotometria Ultravioleta , Espectroscopia de Infravermelho com Transformada de Fourier , Tiomalatos/químicaRESUMO
Heme proteins are found in all living organisms, and perform a wide variety of tasks ranging from electron transport, to the oxidation of organic compounds, to the sensing and transport of small molecules. In this work we review the application of classical and quantum-mechanical atomistic simulation tools to the investigation of several relevant issues in heme proteins chemistry: (i) conformational analysis, ligand migration, and solvation effects studied using classical molecular dynamics simulations; (ii) electronic structure and spin state energetics of the active sites explored using quantum-mechanics (QM) methods; (iii) the interaction of heme proteins with small ligands studied through hybrid quantum mechanics-molecular mechanics (QM-MM) techniques; (iv) and finally chemical reactivity and catalysis tackled by a combination of quantum and classical tools.
Assuntos
Simulação por Computador , Hemeproteínas/química , Modelos Químicos , Teoria Quântica , Ligação de Hidrogênio , Ligantes , Conformação ProteicaRESUMO
In this work we present for the first time an X-ray structure of a coordinated S-nitrosothiol obtained by reaction of the extremely reactive K[IrCl5NO] with benzylmercaptan in acetonitrile. This surprisingly stable compound, trans-K[IrCl4(CH3CN)N(O)SCH2Ph], was isolated in high yield (80%) and fully characterized by FTIR, 1H NMR, and ESI-MS. To our knowledge this is the first example of a coordinated S-nitrosothiol that has been isolated.
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We report an investigation of the reaction between (S)-nitroso-l-cysteine ethyl ester and l-cysteine ethyl ester as a model of physiologically relevant transnitrosation processes. Our theoretical and experimental evidence clearly supports the existence of a nitroxyl disulfide intermediate in solution.
Assuntos
Cisteína/análogos & derivados , Cisteína/química , Compostos Nitrosos/química , Cinética , Espectroscopia de Ressonância Magnética , Modelos Moleculares , Nitrosação , TermodinâmicaRESUMO
We have investigated the structure and the vibrational spectrum of peroxynitrite anion in aqueous solution by means of combined quantum-classical (QM/MM) molecular dynamics simulations. In our QM/MM scheme, the reactant was modeled using density functional theory with a Gaussian basis set and the solvent was described using the mean-field TIP4P and the polarizable TIP4P-FQ force fields. The choice of basis sets, functionals and force field parameters has been validated by performing calculations on isolated peroxynitrite and on small peroxynitrite-water complexes. Poor values for isolated peroxynitrite structural properties and vibrational frequencies are found for most ab initio methods, particularly regarding the ON-OO(-) bond distance and the harmonic stretching frequency, probably due to the singlet-triplet instability found in the HF wave function. On the other hand, DFT methods yield results in better agreement with high level CCSD(T) ab initio calculations. We have computed the vibrational spectrum for aqueous peroxynitrite by calculating the Fourier transform of the velocity autocorrelation function extracted from the QM-MM molecular dynamics simulations. Our computational scheme, which allows for the inclusion of both anharmonicity and solvent effects, is able to clarify previous discrepancies regarding the experimental spectra assignments and to shed light on the subtle interplay between solvation and peroxynitrite structure and properties.