Metalloproteins/metalloenzymes for the synthesis of acetyl-CoA in the Wood-Ljungdahl pathway

This paper focuses on the group of metalloproteins/metalloenzymes in the acetyl-coenzyme A synthesis pathway of anaerobic microbes called Wood-Ljungdahl pathway, including formate dehydrogenase (FDH), corrinoid iron sulfur protein (CoFeSP), acetyl-CoA synthase (ACS) and CO dehydrogenase (CODH). FDH, a key metalloenzyme involved in the conversion of carbon dioxide to methyltetrahydrofolate, catalyzes the reversible oxidation of formate to carbon dioxide. CoFeSP, as a methyl group transformer, accepts the methyl group from CH₃-H₄ folate and then transfers it to ACS. CODH reversibly catalyzes the reduction of CO₂ to CO and ACS functions for acetyl-coenzyme A synthesis through condensation of the methyl group, CO and coenzyme A, to finish the whole pathway. This paper introduces the structure, function and reaction mechanisms of these enzymes.     

Electrochemical Studies of CO2-Reducing Metalloenzymes

Only two enzymes are capable of directly reducing CO₂: CO dehydrogenase, which produces CO at a [NiFe₄S₄] active site, and formate dehydrogenase, which produces formate at a mononuclear W or Mo active site. Both metalloenzymes are very rapid, energy-efficient and specific in terms of product. They have been connected to electrodes with two different objectives. A series of studies used protein film electrochemistry to learn about different aspects of the mechanism of these enzymes (reactivity with substrates, inhibitors…). Another series focused on taking advantage of the catalytic performance of these enzymes to build biotechnological devices, from CO₂-reducing electrodes to full photochemical devices performing artificial photosynthesis. Here, we review all these works.     

MCAT is not required for in vitro polyketide synthesis in a minimal actinorhodin polyketide synthase from Streptomyces coelicolor

Background: It has been proposed that Streptomyces malonyl CoA:holo acyl carrier protein transacylases (MCATs) provide a link between fatty acid and polyketide biosynthesis. Two recent studies have provided evidence that the presence of MCAT is essential for polyketide synthesis to proceed in reconstituted minimal polyketide synthases (PKSs). In contrast to this, we previously showed that the holo acyl carrier proteins (ACPs) from type II PKSs are capable of catalytic self -malonylation in the presence of malonyl CoA, which suggests that MCAT might not be necessary for polyketide biosynthesis.Results: We reconstituted a homologous actinorhodin (act) type II minimal PKS in vitro, When act holo-ACP is present in limiting concentrations, MCAT is required by the synthase complex in order for polyketide biosynthesis to proceed. When holo-ACP is present in excess, however, efficient polyketide synthesis proceeds without MCAT, The rate of polyketide production increases with holo-ACP concentration, but at low ACP concentration or equimolar ACP:KS:CLF (KS, ketosynthase; CLF, chain length determining factor) concentrations this rate is significantly lower than expected, indicating that free holo-ACP is sequestered by the KS/CLF complex.Conclusions: The rate of polyketide biosynthesis is dictated by the ratio of holo-ACP to KS and CLF, as well as by the total protein concentration, There is no absolute requirement for MCAT in polyketide biosynthesis in vitro, although the role of MCAT during polyketide synthesis in vivo remains an open question. MCAT might be responsible for the rate enhancement of malonyl transfer at very low free holo-ACP concentrations or it could be required to catalyse the transfer of malonyl groups from malonyl CoA to sequestered holo-ACP.     

Applications of domain-domain interactions in pathway study

The domain combination pair approach is employed to derive putative protein domain–domain interactions (DDI) from the protein–protein interactions (PPI) database DIP. The results of putative DDI are computed for seven species. To determine the prediction performance, putative DDI results are compared with that of the database InterDom, where an average matching ratio of about 76% can be achieved.

Several real PPI pathways are reconstructed based on the predicted DDI results. It is found that the pathways could be reconstructed with reasonable accuracy. Furthermore, a novel quantity, so called AP-order index, is introduced to predict the regulatory order for six PPI pathways. It is found that the AP-order index is a very reliable parameter to determine the regulatory order of PPI.     

Environmentally benign process for the synthesis of N-formyl amino acid esters

Several amino acid ester hydrochlorides were reacted with ammonium formate to give N-formyl amino acid esters in good yields.     

Dynamic folding pathway models of the villin headpiece subdomain (HP‐36) structure

We have investigated the folding pathway of the 36‐residue villin headpiece subdomain (HP‐36) by action‐derived molecular dynamics simulations. The folding is initiated by hydrophobic collapse, after which the concurrent formation of full tertiary structure and α‐helical secondary structure is observed. The collapse is observed to be associated with a couple of specific native contacts contrary to the conventional nonspecific hydrophobic collapse model. Stable secondary structure formation after the collapse suggests that the folding of HP‐36 follows neither the framework model nor the diffusion‐collision model. The C‐terminal helix forms first, followed by the N‐terminal helix positioned in its native orientation. The short middle helix is shown to form last. Signs for multiple folding pathways are also observed. © 2009 Wiley Periodicals, Inc. J Comput Chem 2010     

Pt电极上甲酸电催化氧化机理研究进展

本文综述了甲酸在铂电极上电催化氧化机理的实验和理论研究进展. 铂电极甲酸的电化学氧化主要有两种途径：1）间接途径,甲酸经由CO中间物氧化为最终产物CO₂,室温下该途径对总电流贡献不超过1%;2）直接途径,甲酸直接氧化生成CO₂. 作者课题组对文献中桥式吸附甲酸根是否是甲酸氧化反应直接途径的反应中间物的争论进行了详细的分析和探讨,认为桥式吸附的甲酸根不是间接途径中生成CO的前驱体,也不是甲酸直接氧化途径的中间物. 作者课题组还指出了支持甲酸根是甲酸直接氧化途径的反应中间物的推论的问题所在.     

Application of nano-scale zero-valent iron adsorbed on magnetite nanoparticles for removal of carbon tetrachloride: Products and degradation pathway

Nano-scale zero-valent iron (nZVI) attached to Fe₃O₄ nanoparticles (Fe⁰@Fe₃O₄), which has better dispersibility and a larger specific surface area than the nanoparticles alone, were prepared and applied to the reductive dechlorination of carbon tetrachloride (CT). CT removal efficiencies by Fe⁰@Fe₃O₄ composites with different ratios of the two components were compared. Under optimum conditions, when the Fe⁰/Fe₃O₄ ratio was 1:2, almost no CT was detected after 50 min and it took only about 30 min to reach a removal efficiency of 90%, compared with 120 min for an Fe⁰/Fe₃O₄ ratio of 1:4. An increase in the amount of nZVI in the catalyst effectively improved the removal of CT and accelerated the reaction rate. Chloroform was the main product. Compared with Fe₃O₄ alone, a significant increase in the solution concentrations of ferrous and ferric ions occurred in the Fe⁰@Fe₃O₄ system: both Fe²⁺ and Fe³⁺ reached their maximum concentrations at 60 min and then tended to decline over the next 60 min. The increase in Fe²⁺ concentration was attributed to the reaction between nZVI and CT, which produces ferrous ions when electrons transfer from Fe⁰ to organic chlorides. Synergistic effects between the composite constituents promoted the relative rates of mass transfer to reactive sites and Fe²⁺ generated in solution facilitated the reduction of chlorinated organic pollutants by magnetite. Thus, Fe⁰@Fe₃O₄ nanoparticles effectively achieved reductive dechlorination of CT and provide an improved nZVI catalyst for the remediation of chlorinated organic compounds.