Homology modeling and docking studies of a Δ9-fatty acid desaturase from a Cold-tolerant<i>Pseudomonas</i>sp. AMS8

Garba, Lawal; Yussoff, Mohamad Ariff Mohamad; Halim, Khairul Bariyyah Abd; Ishak, Siti Nor Hasmah; Ali, Mohd Shukuri Mohamad; Oslan, Siti Nurbaya; Rahman, Raja Noor Zaliha Raja Abd

doi:10.7717/peerj.4347

Cited by 11 publications

(10 citation statements)

References 43 publications

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“…Currently, only two kinds of three-dimensional structures of the membrane fatty acid desaturases are available, one is the mouse stearoyl-CoA desaturase (Figure 2A, PDB ID: 4YMK), and the other is human integral membrane stearoyl-CoA desaturase (Figure 2B, PDB ID: 4ZYO). Thus, homology modeling and docking are the essential methods to analyze the structure of bacterial membrane fatty acid desaturases and elongase in the current state (21). Herein, we summarized the research approach of homology modeling and docking based on the previous work (21)(22)(23)55).…”

Section: Structure Analysis Methodsmentioning

confidence: 99%

“…Thus, homology modeling and docking are the essential methods to analyze the structure of bacterial membrane fatty acid desaturases and elongase in the current state (21). Herein, we summarized the research approach of homology modeling and docking based on the previous work (21)(22)(23)55). First, after homology analyzes the amino acid sequence, the scientist can determine templates with higher homology and resolution in the protein database (e.g., Protein Data Bank, PDB).…”

Section: Structure Analysis Methodsmentioning

confidence: 99%

“…Scientists also have identified and characterized the various Δ9-fatty acid desaturase gene from Rhodotorula toruloides ( 20 ) and Pseudomonas sp . ( 21 ) ( Table 1 ). These Δ9-desaturases shared three histidine-conserved boxes that would be the catalytic position of Δ9 fatty acid desaturase.…”

Section: Vital Desaturase In ω-6 and ω-3 Pathwaymentioning

confidence: 99%

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Key Enzymes in Fatty Acid Synthesis Pathway for Bioactive Lipids Biosynthesis

et al. 2022

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Dietary bioactive lipids, one of the three primary nutrients, is not only essential for growth and provides nutrients and energy for life's activities but can also help to guard against disease, such as Alzheimer's and cardiovascular diseases, which further strengthen the immune system and maintain many body functions. Many microorganisms, such as yeast, algae, and marine fungi, have been widely developed for dietary bioactive lipids production. These biosynthetic processes were not limited by the climate and ground, which are also responsible for superiority of shorter periods and high conversion rate. However, the production process was also exposed to the challenges of low stability, concentration, and productivity, which was derived from the limited knowledge about the critical enzyme in the metabolic pathway. Fortunately, the development of enzymatic research methods provides powerful tools to understand the catalytic process, including site-specific mutagenesis, protein dynamic simulation, and metabolic engineering technology. Thus, we review the characteristics of critical desaturase and elongase involved in the fatty acids' synthesis metabolic pathway, which aims to not only provide extensive data for enzyme rational design and modification but also provides a more profound and comprehensive understanding of the dietary bioactive lipids' synthetic process.

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Section: Structure Analysis Methodsmentioning

confidence: 99%

Section: Structure Analysis Methodsmentioning

confidence: 99%

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Key Enzymes in Fatty Acid Synthesis Pathway for Bioactive Lipids Biosynthesis

et al. 2022

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“…The target sequence was aligned to the template of Pim3 using the align2d script in Modeller 9.20 (Figure 1A) [12]. The sequence similarity between Pim1 and 3 was very high (78%).…”

Section: Resultsmentioning

confidence: 99%

Insights into the Interaction Mechanisms of the Proviral Integration Site of Moloney Murine Leukemia Virus (Pim) Kinases with Pan-Pim Inhibitors PIM447 and AZD1208: A Molecular Dynamics Simulation and MM/GBSA Calculation Study

Chen¹,

Wang²,

Shi³

et al. 2019

IJMS

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Based on the up-regulation of the proviral integration site of the Moloney murine leukemia virus (Pim) kinase family (Pim1, 2, and 3) observed in several types of leukemias and lymphomas, the development of pan-Pim inhibitors is an attractive therapeutic strategy. While only PIM447 and AZD1208 have entered the clinical stages. To elucidate the interaction mechanisms of three Pim kinases with PIM447 and AZD1208, six Pim/ligand systems were studied by homology modeling, molecular docking, molecular dynamics (MD) simulation and molecular mechanics/generalized Born surface area (MM/GBSA) binding free energy calculation. The residues of the top group (Leu44, Val52, Ala65, Lys67, and Leu120 in Pim1) dominated the pan-Pim inhibitors binding to Pim kinases. The residues of the bottom group (Gln127, Asp128, and Leu174 in Pim1) were crucial for Pims/PIM447 systems, while the contributions of these residues were decreased sharply for Pims/AZD1208 systems. It is likely that the more potent pan-Pim inhibitors should be bound strongly to the top and bottom groups. The residues of the left, right and loop groups were located in the loop regions of the binding pocket, however, the flexibility of these regions triggered the protein interacting with diverse pan-Pim inhibitors efficiently. We hope this work can provide valuable information for the design of novel pan-Pim inhibitors in the future.

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“…AMS8 and Pseudomonas sp. A3 were found to produce large amounts of monounsaturated fatty acids at low temperatures (Garba et al, 2016(Garba et al, , 2018. 9-fatty acid desaturase genes were isolated from each of the strains and were subsequently cloned and successfully expressed in E. coli.…”

Section: Membrane Compositionmentioning

confidence: 99%

Leveraging Pseudomonas Stress Response Mechanisms for Industrial Applications

2021

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Members of the genus Pseudomonas are metabolically versatile and capable of adapting to a wide variety of environments. Stress physiology of Pseudomonas strains has been extensively studied because of their biotechnological potential in agriculture as well as their medical importance with regards to pathogenicity and antibiotic resistance. This versatility and scientific relevance led to a substantial amount of information regarding the stress response of a diverse set of species such as Pseudomonas chlororaphis, P. fluorescens, P. putida, P. aeruginosa, and P. syringae. In this review, environmental and industrial stressors including desiccation, heat, and cold stress, are cataloged along with their corresponding mechanisms of survival in Pseudomonas. Mechanisms of survival are grouped by the type of inducing stress with a focus on adaptations such as synthesis of protective substances, biofilm formation, entering a non-culturable state, enlisting chaperones, transcription and translation regulation, and altering membrane composition. The strategies Pseudomonas strains utilize for survival can be leveraged during the development of beneficial strains to increase viability and product efficacy.

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Homology modeling and docking studies of a Δ9-fatty acid desaturase from a Cold-tolerantPseudomonassp. AMS8

Cited by 11 publications

References 43 publications

Key Enzymes in Fatty Acid Synthesis Pathway for Bioactive Lipids Biosynthesis

Key Enzymes in Fatty Acid Synthesis Pathway for Bioactive Lipids Biosynthesis

Insights into the Interaction Mechanisms of the Proviral Integration Site of Moloney Murine Leukemia Virus (Pim) Kinases with Pan-Pim Inhibitors PIM447 and AZD1208: A Molecular Dynamics Simulation and MM/GBSA Calculation Study

Leveraging Pseudomonas Stress Response Mechanisms for Industrial Applications

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