Comparative modeling and enzymatic affinity of novel haloacid dehalogenase from Bacillus megaterium strain BHS1 isolated from alkaline Blue Lake in Turkey.

This study presents the initial structural model of L-haloacid dehalogenase (DehLBHS1) from Bacillus megaterium BHS1, an alkalotolerant bacterium known for its ability to degrade halogenated environmental pollutants. The model provides insights into the structural features of DehLBHS1 and expands our understanding of the enzymatic mechanisms involved in the degradation of these hazardous pollutants. Key amino acid residues (Arg40, Phe59, Asn118, Asn176, and Trp178) in DehLBHS1 were identified to play critical roles in catalysis and molecular recognition of haloalkanoic acid, essential for efficient binding and transformation of haloalkanoic acid molecules. DehLBHS1 was modeled using I-TASSER, yielding a best TM-score of 0.986 and an RMSD of 0.53 Å. Validation of the model using PROCHECK revealed that 89.2% of the residues were located in the most favored region, providing confidence in its structural accuracy. Molecular docking simulations showed that the non-simulated DehLBHS1 preferred 2,2DCP over other substrates, forming one hydrogen bond with Arg40 and exhibiting a minimum energy of -2.5 kJ/mol. The simulated DehLBHS1 exhibited a minimum energy of -4.3 kJ/mol and formed four hydrogen bonds with Arg40, Asn176, Asp9, and Tyr11, further confirming the preference for 2,2DCP. Molecular dynamics simulations supported this preference, based on various metrics, including RMSD, RMSF, gyration, hydrogen bonding, and molecular distance. MM-PBSA calculations showed that the DehLBHS1-2,2-DCP complex had a markedly lower binding energy (-21.363 ± 1.26 kcal/mol) than the DehLBHS1-3CP complex (-14.327 ± 1.738 kcal/mol). This finding has important implications for the substrate specificity and catalytic function of DehLBHS1, particularly in the bioremediation of 2,2-DCP in contaminated alkaline environments. These results provide a detailed view of the molecular interactions between the enzyme and its substrate and may aid in the development of more efficient biocatalytic strategies for the degradation of halogenated compounds.Communicated by Ramaswamy H. Sarma.

Antibacterial activity of Calendula officinalis and Echinacea purpurea extracts against the causal agent of tomatoes' bacterial canker: Clavibacter michiganensis subsp. michiganensis / Actividad antibacteriana de los extractos de Calendula officinalis y Echinacea purpurea contra el agente causal del cancro bacteriano del tomate: Clavibacter michiganensis subsp. Michiganensis

We aimed to investigate the effects of Calendula officinalis and Echinacea purpurea extracts in terms of growth parameters, antibacterial activity and phenolic profile in tomato infected by Clavibacter michiganensis subsp. michiganensis (CmmT7). A significant difference was observed in E. purpuraextract, indicating the highest effects on plant height (27.25 cm), fresh plant weight (28.45 cm), root length (24.42 cm), and root weight (6.74 g) (p<0.05). Moreover, Calendula officinalis and Echinacea purpurea extracts showed significant inhibitory activity against CmmT7 (p<0.05). Among phenolic compounds, the only chlorogenic acid amounts were varied in the tomato seedlings leaves with C. officinalis extract (K3) + CmmT7, E. purpurea extract (E3) + CmmT7 and CmmT7 (p<0.01). Moreover, chlorogenic acid amount was approximately 9 times higher than in CmmT7-treated leaves when compared to control. The results showed that application of the extracts of these plants had a significant influence on bacterial canker and growth parameters.

Nuestro objetivo fue investigar los efectos de los extractos de Calendula officinalis y Echinacea purpurea en términos de parámetros de crecimiento, actividad antibacteriana y perfil fenólico en tomate infectado por Clavibacter michiganensis subsp. michiganensis (CmmT7). Se observó una diferencia significativa en el extracto de E. purpura, que indica los mayores efectos sobre la altura de la planta (27,25 cm), el peso de la planta fresca(28,45 cm), la longitud de la raíz (24,42 cm) y el peso de la raíz (6,74 g) (p<0,05). Además, los extractos de Calendula officinalis y Echinacea purpurea mostraron una actividad inhibidora significativa contra CmmT7 (p<0,05). Entre los compuestos fenólicos, las únicas cantidades de ácido clorogénico se variaron en las hojas de las plántulas de tomate con extracto de C. officinalis (K3) CmmT7, extracto de E. purpurea(E3) CmmT7 y CmmT7 (p<0.01). Además, la cantidad de ácido clorogénico fue aproximadamente 9 veces mayor que en las hojas tratadas con CmmT7 en comparación con el control. Los resultados mostraron que la aplicación de los extractos de estas plantas tuvo una influencia significativa sobre el cancro bacteriano y los parámetros de crecimiento.

Substrate docking and molecular dynamic simulation for prediction of fungal enzymes from Trichoderma species-assisted extraction of nanocellulose from oil palm leaves.

Fungi of the Trichoderma species are valued industrial enzymes in support of the 'zero-waste' technology to convert agro-industrial biomass into valuable products, i.e. nanocellulose (NC). In this study, an in silico approach using substrate docking and molecular dynamic (MD) simulation was used to predict the order of which the multilayers of cellulosic polymers, i.e. lignin, hemicellulose and cellulose in oil palm leaves (OPL) are degraded by fungal enzymes, endocellulase and exocellulase. The study aimed to establish the catalytic tendencies of the enzymes to optimally degrade the cellulosic components of OPL for high yield production of NC. Energy minimized endocellulase and exocellulase models revealed satisfactory scores of PROCHECK (90.0% and 91.2%), Verify3D (97.23% and 98.85%) and ERRAT (95.24% and 91.00%) assessments. Active site prediction by blind docking, COACH meta-server and multiple sequence alignment indicated the catalytic triads for endocellulase and exocellulase were Ser116-His205-Glu249 and Ser382-Arg124-Asp385, respectively. Binding energy of endocellulase docked with hemicellulose (-6.0 kcal mol-1) was the most favourable followed by lignin (-5.6 kcal mol-1) and cellulose (-4.4 kcal mol-1). Exocellulase, contrarily, bonded favorably with lignin (-8.7 kcal mol-1), closely followed by cellulose (-8.5 kcal mol-1) and hemicellulose (-8.4 kcal mol-1). MDs simulations showed that interactions of complexes, endocellulase-hemicellulose and the exocellulase-cellulose being the most stable. Thus, the findings of the study successfully identified the specific actions of sugar-acting enzymes for NC production. Communicated by Ramaswamy H. Sarma.

Haloadaptation: insights from comparative modeling studies between halotolerant and non-halotolerant dehalogenases.

Halophiles are extremophilic microorganisms that grow optimally at high salt concentrations by producing a myriad of equally halotolerant enzymes. Structural haloadaptation of these enzymes adept to thriving under high-salt environments, though are not fully understood. Herein, the study attempts an in silico investigation to identify and comprehend the evolutionary structural adaptation of a halotolerant dehalogenase, DehHX (GenBank accession number: KR297065) of the halotolerant Pseudomonas halophila, over its non-halotolerant counterpart, DehMX1 (GenBank accession number KY129692) produced by Pseudomonas aeruginosa. GC content of the halotolerant DehHX DNA sequence was distinctively higher (58.9%) than the non-halotolerant dehalogenases (55% average GC). Its acidic residues, Asp and Glu were 8.27% and 12.06%, respectively, compared to an average 5.5% Asp and 7% Glu, in the latter; but lower contents of basic and hydrophobic residues in the DehHX. The secondary structure of DehHX interestingly revealed a lower incidence of α-helix forming regions (29%) and a higher percentage of coils (57%), compared to 49% and 29% in the non-halotolerant homologues, respectively. Simulation models showed the DehHX is stable under a highly saline environment (25% w/v) by adopting a highly negative-charged surface with a concomitant weakly interacting hydrophobic core. The study thus, established that a halotolerant dehalogenase undergoes notable evolutionary structural changes related to GC content over its non-halotolerant counterpart, in order to adapt and thrive under highly saline environments.Communicated by Ramaswamy H. Sarma.

In silico and empirical approaches toward understanding the structural adaptation of the alkaline-stable lipase KV1 from Acinetobacter haemolyticus.

Interests in Acinetobacter haemolyticus lipases are showing an increasing trend concomitant with growth of the enzyme industry and the widening search for novel enzymes and applications. Here, we present a structural model that reveals the key catalytic residues of lipase KV1 from A. haemolyticus. Homology modeling of the lipase structure was based on the structure of a carboxylesterase from the archaeon Archaeoglobus fulgidus as the template, which has a sequence that is 58% identical to that of lipase KV1. The lipase KV1 model is comprised of a single compact domain consisting of seven parallel and one anti-parallel ß-strand surrounded by nine α-helices. Three structurally conserved active-site residues, Ser165, Asp259, and His289, and a tunnel through which substrates access the binding site were identified. Docking of the substrates tributyrin and palmitic acid into the pH 8 modeled lipase KV1 active sites revealed an aromatic platform responsible for the substrate recognition and preference toward tributyrin. The resulting binding modes from the docking simulation correlated well with the experimentally determined hydrolysis pattern, for which pH 8 and tributyrin being the optimum pH and preferred substrate. The results reported herein provide useful insights into future structure-based tailoring of lipase KV1 to modulate its catalytic activity.

Halophiles: biology, adaptation, and their role in decontamination of hypersaline environments.

The unique cellular enzymatic machinery of halophilic microbes allows them to thrive in extreme saline environments. That these microorganisms can prosper in hypersaline environments has been correlated with the elevated acidic amino acid content in their proteins, which increase the negative protein surface potential. Because these microorganisms effectively use hydrocarbons as their sole carbon and energy sources, they may prove to be valuable bioremediation agents for the treatment of saline effluents and hypersaline waters contaminated with toxic compounds that are resistant to degradation. This review highlights the various strategies adopted by halophiles to compensate for their saline surroundings and includes descriptions of recent studies that have used these microorganisms for bioremediation of environments contaminated by petroleum hydrocarbons. The known halotolerant dehalogenase-producing microbes, their dehalogenation mechanisms, and how their proteins are stabilized is also reviewed. In view of their robustness in saline environments, efforts to document their full potential regarding remediation of contaminated hypersaline ecosystems merits further exploration.