RESUMO
In all ThDP-dependent enzymes, the catalytic cycle is initiated with the attack of the C2 atom of the ylide intermediate on the Cα atom of a pyruvate molecule to form the lactyl-ThDP (L-ThDP) intermediate. In this study, the reaction between the ylide intermediate and pyruvate leading to the formation of L-ThDP is addressed from a theoretical point of view. The study includes molecular dynamics, exploration of the potential energy surface by means of QM/MM calculations, and reactivity analysis on key centers. The results show that the reaction occurs via a concerted mechanism in which the carboligation and the proton transfers occur synchronically. It is also observed that during the reaction the protonation state of the N1' atom changes: the reaction starts with the ylide having the N1' atom deprotonated and reaches a transition state showing the N1' atom protonated. This conversion leads to the reaction path of minimum energy, with an activation energy of about 20 kcal mol(-1). On the other hand, it is also observed that the approaching distance between the pyruvate and the ylide, i.e., the Cα-C2 distance, plays a fundamental role in the reaction mechanism since it determines the nucleophilic character of key atoms of the ylide, which in turn trigger the elemental reactions of the mechanism.
Assuntos
Acetolactato Sintase/metabolismo , Ácido Pirúvico/metabolismo , Saccharomyces cerevisiae/enzimologia , Tiamina Pirofosfato/análogos & derivados , Acetolactato Sintase/química , Modelos Moleculares , Ácido Pirúvico/química , Teoria Quântica , Saccharomyces cerevisiae/química , Saccharomyces cerevisiae/metabolismo , Termodinâmica , Tiamina Pirofosfato/química , Tiamina Pirofosfato/metabolismoRESUMO
In this study the formation of the lactyl-thiamin diphosphate intermediate (L-ThDP) is addressed using density functional theory calculations at X3LYP/6-31++G(d,p) level of theory. The study includes potential energy surface scans, transition state search, and intrinsic reaction coordinate calculations. Reactivity is analyzed in terms of Fukui functions. The results allow to conclude that the reaction leading to the formation of L-ThDP occurs via a concerted mechanism, and during the nucleophilic attack on the pyruvate molecule, the ylide is in its AP form. The calculated activation barrier for the reaction is 19.2 kcal/mol, in agreement with the experimental reported value.
Assuntos
Simulação por Computador , Ácido Pirúvico/química , Tiamina Pirofosfato/análogos & derivados , Sítios de Ligação , Catálise , Modelos Químicos , Termodinâmica , Tiamina Pirofosfato/químicaRESUMO
The equilibria among the various ionization and tautomeric states involved in the activation of ThDP is addressed using high level density functional theory calculations, X3LYP/6-311++G(d,p)//X3LYP(PB)/6-31++G(d,p). This study provides the first theoretically derived thermodynamic data for the internal equilibria in the activation of ThDP. The role of the medium polarity on the geometry and thermodynamics of the diverse equilibria of ThDP is addressed. The media chosen are cyclohexane and water, as paradigms of apolar and polar media. The results suggest that all ionization and tautomeric states are accessible during the catalytic cycle, even in the absence of substrate, being APH(+) the form required to interconvert the AP and IP tautomers; and the generation of the ylide proceeds via the formation of the IP form. Additionally, the calculated ΔG° values allow to calculate all the equilibrium constants, including the pK(C2) for the thiazolium C2 atom whose ionization is believed to initiate the catalytic cycle.
Assuntos
Modelos Químicos , Termodinâmica , Tiamina Pirofosfato/química , CatáliseRESUMO
Acetohydroxyacid synthase (AHAS) is a thiamin diphosphate dependent enzyme that catalyses the decarboxylation of pyruvate to yield the hydroxyethyl-thiamin diphosphate (ThDP) anion/enamine intermediate (HEThDP(-)). This intermediate reacts with a second ketoacid to form acetolactate or acetohydroxybutyrate as products. Whereas the mechanism involved in the formation of HEThDP(-) from pyruvate is well understood, the role of the enzyme in controlling the carboligation reaction of HEThDP(-) has not been determined yet. In this work, molecular dynamics (MD) simulations were employed to identify the aminoacids involved in the carboligation stage. These MD studies were carried out over the catalytic subunit of yeast AHAS containing the reaction intermediate (HEThDP(-)) and a second pyruvate molecule. Our results suggest that additional acid-base ionizable groups are not required to promote the catalytic cycle, in contrast with earlier proposals. This finding leads us to postulate that the formation of acetolactate relies on the acid-base properties of the HEThDP(-) intermediate itself. PM3 semiempirical calculations were employed to obtain the energy profile of the proposed mechanism on a reduced model of the active site. These calculations confirm the role of HEThDP(-) intermediate as the ionizable group that promotes the carboligation and product formation steps of the catalytic cycle.
Assuntos
Acetolactato Sintase/química , Acetolactato Sintase/metabolismo , Tiamina Pirofosfato/análogos & derivados , Aminoácidos/química , Domínio Catalítico , Proteínas Fúngicas/química , Proteínas Fúngicas/metabolismo , Lactatos/metabolismo , Simulação de Dinâmica Molecular , Ácido Pirúvico/química , Ácido Pirúvico/metabolismo , Termodinâmica , Tiamina Pirofosfato/química , Tiamina Pirofosfato/metabolismo , Leveduras/enzimologiaRESUMO
Thiamin pyrophosphate is an essential coenzyme in all organisms that depend on fermentation, respiration or photosynthesis to produce ATP. It is synthesized through two independent biosynthetic routes: one for the synthesis of 2-methyl-4-amino-5-hydroxymethylpyrimidine pyrophosphate (pyrimidine moiety) and another for the synthesis of 4-methyl-5-(beta-hydroxyethyl) thiazole phosphate (thiazole moiety). Herein, we will describe the three-dimensional structure of THI1 protein from Arabidopsis thaliana determined by single wavelength anomalous diffraction to 1.6A resolution. The protein was produced using heterologous expression in bacteria, unexpectedly bound to 2-carboxylate-4-methyl-5-beta-(ethyl adenosine 5-diphosphate) thiazole, a potential intermediate of the thiazole biosynthesis in Eukaryotes. THI1 has a topology similar to dinucleotide binding domains and although details concerning its function are unknown, this work provides new clues about the thiazole biosynthesis in Eukaryotes.
Assuntos
Proteínas de Arabidopsis/química , Arabidopsis/enzimologia , Trifosfato de Adenosina/química , Sequência de Aminoácidos , Proteínas de Arabidopsis/metabolismo , Sítios de Ligação , Escherichia coli/metabolismo , Modelos Moleculares , Dados de Sequência Molecular , Conformação Proteica , Estrutura Secundária de Proteína , Estrutura Terciária de Proteína , Homologia de Sequência de Aminoácidos , Tiamina Pirofosfato/química , Tiazóis/químicaRESUMO
We present an easy and sensitive method for measuring thiamine and its phosphate esters in small biological samples of microalgae (Amphidinium carterae Hulburt and Nitzschia microcephala Grun). The method consists of extraction of thiamine and its derivatives in acid solution, followed by liquid chromatography with fluorescence detection. The detection limit is as low as 15 fmol of thiamine. For comparison to microalgae, the method has been applied to evaluate thiamine levels in the crustacean Artemia salina Leach and is suitable for nutritional studies of the food web of the Baltic salmon, which suffers from thiamine deficiency. This method of HPLC analysis can be readily utilized to follow uptake and interconversion of thiamine and its phosphate esters in many micro- and macroalgae.