A Multi-Scale Computational Study on the Mechanism of Streptococcus pneumoniae Nicotinamidase (SpNic)

Ion, Bogdan; Kazim, Erum; Gauld, James W.

doi:10.3390/molecules191015735

Cited by 9 publications

(17 citation statements)

References 45 publications

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“…Inter lies 2.4 kcal mol −1 higher in energy than TS1 and is able to reversibly rearrange back to the reactive complex essentially without a barrier. That TS’s relative energy is lower than Inter’s is a common artifact of the use of zero-point vibrational energy (ZPVE) correction and/or empirical corrections on flat potential energy surface313233. Interestingly, in our specific system, the stabilization effect on TS1 from ZPVE correction happens to be more significant than that of Inter.…”

Section: Resultsmentioning

confidence: 79%

Insights into the Phosphoryl Transfer Mechanism of Human Ubiquitous Mitochondrial Creatine Kinase

Fan

et al. 2016

Sci Rep

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Human ubiquitous mitochondrial creatine kinase (uMtCK) is responsible for the regulation of cellular energy metabolism. To investigate the phosphoryl-transfer mechanism catalyzed by human uMtCK, in this work, molecular dynamic simulations of uMtCK∙ATP-Mg2+∙creatine complex and quantum mechanism calculations were performed to make clear the puzzle. The theoretical studies hereof revealed that human uMtCK utilizes a two-step dissociative mechanism, in which the E227 residue of uMtCK acts as the catalytic base to accept the creatine guanidinium proton. This catalytic role of E227 was further confirmed by our assay on the phosphatase activity. Moreover, the roles of active site residues in phosphoryl transfer reaction were also identified by site directed mutagenesis. This study reveals the structural basis of biochemical activity of uMtCK and gets insights into its phosphoryl transfer mechanism.

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Section: Resultsmentioning

confidence: 79%

Insights into the Phosphoryl Transfer Mechanism of Human Ubiquitous Mitochondrial Creatine Kinase

Fan

et al. 2016

Sci Rep

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“…It can be noted that the reaction likely occurred without an energy barrier, since the IM1 was slightly higher than that of the TS1. This is a common result of using single-point calculations or empirical corrections on potential energy surfaces (PESs), which can be avoided at a higher level of theory calculation, without the inclusion of the environment’s electrostatic charge [36].…”

Section: Resultsmentioning

confidence: 99%

A Density Functional Theory (DFT) Study of the Acyl Migration Occurring during Lipase-Catalyzed Transesterifications

Mao

et al. 2019

IJMS

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Acyl migration (AM) is the main side reaction in the large-scale, regio-specific lipase catalyzed production of structural triglycerides (STs). A detailed understanding of the mechanism of AM was obtained during the process of lipase-catalyzed schemes (LCSs), which play a vital role in improving the quality and total yield of STs. However, currently, the mechanism of AM remains controversial. Herein, the two mechanisms (non-catalyzed (NCM) and lipase-catalyzed (LCM)) of AM have been analyzed in detail by the density functional theory (DFT) at the molecular level. Based on the computational results, we concluded that the energy barrier of the rate-limiting step in the LCM was 18.8 kcal/mol, which is more in agreement with the available experimental value (17.8 kcal/mol), indicating that LCM could significantly accelerate the rate of AM, because it has an energy barrier ~2 times lower than that of the NCM. Interestingly, we also found that the catalytic triad (Asp-His-Ser) of the lipase and water could effectively drop the reaction barrier, which served as the general acid or base, or shuttle of the proton.

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“…The alignment also revealed that PolyNic contained all the conserved catalytic triad residues of the cysteine-hydrolases family ( Figure 5 , filled circles): a catalytic cysteine at position 150 (C150, PolyNic numbering), an aspartate at position 25 (D25) and a lysine at position 111 (K111) (French et al, 2010b; Sanchez-Carron et al, 2013; Ion et al, 2014; Sheng and Liu, 2014). Furthermore, PolyNic showed the characteristic cis -peptide bond ( Figure 5 , positions L145 and A146, filled squares), which is invariably preceded by a conserved glycine (G144), and the conserved specific metal ion binding, which includes one aspartate (D67) and two histidines (H69 and H86) ( Figure 5 , filled triangles).…”

Section: Resultsmentioning

confidence: 99%

Combined Whole-Cell High-Throughput Functional Screening for Identification of New Nicotinamidases/Pyrazinamidases in Metagenomic/Polygenomic Libraries

et al. 2016

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Nicotinamidases catalyze the hydrolysis of the amide bond in nicotinamide (NAM) to produce ammonia and nicotinic acid (NA). These enzymes are an essential component of the NAD+ salvage pathway and are implicated in the viability of several pathogenic organisms. Its absence in humans makes them a promising drug target. In addition, although they are key analytical biocatalysts for screening modulators in relevant biomedical enzymes, such as sirtuins and poly-ADP-ribosyltransferases, no commercial sources are available. Surprisingly, the finding of an affordable source of nicotinamidase from metagenomic libraries is hindered by the absence of a suitable and fast screening method. In this manuscript, we describe the development of two new whole-cell methods using the chemical property of one of the products formed in the enzymatic reaction (pyrazinoic or NA) to form colored complexes with stable iron salts, such as ammonium ferrous sulfate or sodium nitroprusside (SNP). After optimization of the assay conditions, a fosmid polygenomic expression library obtained from deep-sea mesophilic bacteria was screened, discovering several positive clones with the ammonium ferrous sulfate method. Their quantitative rescreening with the SNP method allowed the finding of the first nicotinamidase with balanced catalytic efficiency toward NAM (nicotinamidase activity) and pyrazinamide (pyrazinamidase activity). Its biochemical characterization has also made possible the development of the first high-throughput whole-cell method for prescreening of new nicotinamidase inhibitors by the naked eye, saving time and costs in the design of future antimicrobial and antiparasitic agents.

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A Multi-Scale Computational Study on the Mechanism of Streptococcus pneumoniae Nicotinamidase (SpNic)

Cited by 9 publications

References 45 publications

Insights into the Phosphoryl Transfer Mechanism of Human Ubiquitous Mitochondrial Creatine Kinase

Insights into the Phosphoryl Transfer Mechanism of Human Ubiquitous Mitochondrial Creatine Kinase

A Density Functional Theory (DFT) Study of the Acyl Migration Occurring during Lipase-Catalyzed Transesterifications

Combined Whole-Cell High-Throughput Functional Screening for Identification of New Nicotinamidases/Pyrazinamidases in Metagenomic/Polygenomic Libraries

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