Structural insights on binding mechanism of CAD complexes (CPSase, ATCase and DHOase)

Kanagarajan, Surekha; Prabhu, Dhamodharan; Nachiappan, Mutharasappan; Choubey, Sanjay Kumar; Jayaprakash, Prajisha; Biswal, Jayashree; Jeyakanthan, Jeyaraman

doi:10.1080/07391102.2020.1761877

Cited by 3 publications

(3 citation statements)

References 29 publications

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“…In the alanine, aspartate, and glutamate metabolism, two DEGs ( carBA , KQ76_05770 and KQ76_05765 ) encoding carbamoyl phosphate synthase were significantly up-regulated (2.154-fold and 3.084-fold) in S. aureus ATCC25923 ( p < 0.05). The interface residues located near the CarB region of carboxy phosphate synthetic domain plays a key role in carbamoyl phosphate synthetase, aspartate transcarbamoylase, and dihydroorotase (CAD) complex regulation in the pyrimidine biosynthesis [ 63 ]. Correspondingly, in the pyrimidine metabolism, four DEGs ( pyrBCR , KQ76_05755 , KQ76_05760 , and KQ76_05745 ) were also significantly up-regulated (2.968-fold to 3.213-fold) ( p < 0.05), and encoded an aspartate carbamoyltransferase, a dihydroorotase, and a phosphoribosyl transferase, respectively.…”

Section: Resultsmentioning

confidence: 99%

Identification of Antibacterial Components and Modes in the Methanol-Phase Extract from a Herbal Plant Potentilla kleiniana Wight et Arn

Tang

Pan

Chen

2023

Foods

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The increase in bacterial resistance and the decline in the effectiveness of antimicrobial agents are challenging issues for the control of infectious diseases. Traditional Chinese herbal plants are potential sources of new or alternative medicine. Here, we identified antimicrobial components and action modes of the methanol-phase extract from an edible herb Potentilla kleiniana Wight et Arn, which had a 68.18% inhibition rate against 22 species of common pathogenic bacteria. The extract was purified using preparative high-performance liquid chromatography (Prep-HPLC), and three separated fragments (Fragments 1–3) were obtained. Fragment 1 significantly elevated cell surface hydrophobicity and membrane permeability but reduced membrane fluidity, disrupting the cell integrity of the Gram-negative and Gram-positive pathogens tested (p < 0.05). Sixty-six compounds in Fragment 1 were identified using Ultra-HPLC and mass spectrometry (UHPLC-MS). The identified oxymorphone (6.29%) and rutin (6.29%) were predominant in Fragment 1. Multiple cellular metabolic pathways were altered by Fragment 1, such as the repressed ABC transporters, protein translation, and energy supply in two representative Gram-negative and Gram-positive strains (p < 0.05). Overall, this study demonstrates that Fragment 1 from P. kleiniana Wight et Arn is a promising candidate for antibacterial medicine and food preservatives.

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Section: Resultsmentioning

confidence: 99%

Identification of Antibacterial Components and Modes in the Methanol-Phase Extract from a Herbal Plant Potentilla kleiniana Wight et Arn

Tang

Pan

Chen

2023

Foods

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“…First, it computed ΔG and mutated one of the interface residues to alanine, and then calculated the ΔG MUT (mutant type), which allows subsequent calculation of ΔΔG (change in binding free energy) by subtracting the ΔGWT of ΔG MUT . This procedure is employed for all the interface residues to calculate ΔG values [23] …”

Section: Methodsmentioning

confidence: 99%

“…This procedure is employed for all the interface residues to calculate ΔG values. [23] Molecular dynamics simulation MD simulation was carried out by Desmond (v3.8) module embedded in Schrödinger suite software to inspect the stability of binding mode as well as the consistency. [24] Two complexes formed by the highly active inhibitor T6 with TLR4 were chosen for MD simulation to investigate their stability.…”

Section: Alanine Scanning Mutagenesismentioning

confidence: 99%

Exploration of the Binding Modes of Toll‐Like Receptor 4 Competitive Inhibitors: A Combined Ligand‐Based and Target‐Based Approach

et al. 2023

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The interactions of Toll‐like receptor 4 (TLR4) with competitive inhibitors were investigated by a combined ligand‐based and target‐based approach. Firstly, the ligand‐based pharmacophore model of the reported TLR4 inhibitors was constructed by utilizing the common feature method, which included three hydrophobic groups and a hydrogen bond receptor. The Schrödinger software suite glide module was used to dock inhibitors with proteins and verify the importance of these four interaction points from the target level. Then, molecular dynamics, alanine scanning mutagenesis, and binding free energy calculation were used to identify the key amino acids in the binding mode. In addition, blind docking proved that the TLR4 inhibitor does not bind to TLR4 itself like other TLR family proteins. Based on this, we also screened a class of sesquiterpene coumarins which possibly have TLR4 inhibitory activity and will conduct a detailed study later. Together, this study revealed the interactions between TLR4 protein and its competitive inhibitors, which shed light on better access for developing its novel inhibitors.

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Modeling and monitoring the effects of three partly conserved Ile residues in the dimerization domain of a Mip-like virulence factor from Escherichia coli

Seal,

Chakraborty,

Polley

et al. 2023

Journal of Biomolecular Structure and Dynamics

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Structural insights on binding mechanism of CAD complexes (CPSase, ATCase and DHOase)

Cited by 3 publications

References 29 publications

Identification of Antibacterial Components and Modes in the Methanol-Phase Extract from a Herbal Plant Potentilla kleiniana Wight et Arn

Identification of Antibacterial Components and Modes in the Methanol-Phase Extract from a Herbal Plant Potentilla kleiniana Wight et Arn

Exploration of the Binding Modes of Toll‐Like Receptor 4 Competitive Inhibitors: A Combined Ligand‐Based and Target‐Based Approach

Modeling and monitoring the effects of three partly conserved Ile residues in the dimerization domain of a Mip-like virulence factor from Escherichia coli

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