Yılmaz KAYA

Article | 2020 | Journal of Biomolecular Structure and Dynamics39 ( 7 )

Literature has shown that oil palm leaves (OPL) can be transformed into nanocellulose (NC) by fungal lignocellulosic enzymes, particularly those produced by the Trichoderma species. However, mechanism of beta-glucosidase and xylanase selectivity to degrade lignin, hemicellulose and cellulose in OPL for NC production remains relatively vague. The study aimed to comprehend this aspect by an in silico approach of molecular docking, molecular dynamics (MD) simulation and Molecular-mechanics Poisson-Boltzmann surface area (MM-PBSA) analysis, to compare interactions between the beta-glucosidase- and xylanase from Trichoderma asperellum UC . . .1 in complex with each substrate. Molecular docking of the enzyme-substrate complex showed residues Glu165-Asp226-Glu423 and Arg155-Glu210-Ser160 being the likely catalytic residues of beta-glucosidase and xylanase, respectively. The binding affinity of beta-glucosidase for the substrates are as follows: cellulose (-8.1 kcal mol(-1)) > lignin (-7.9 kcal mol(-1)) > hemicellulose (-7.8 kcal mol(-1)), whereas, xylanase showed a corresponding preference for; hemicellulose (-6.7 kcal mol(-1)) > cellulose (-5.8 kcal mol(-1)) > lignin (-5.7 kcal mol(-1)). Selectivity of both enzymes was reiterated by MD simulations where interactions between beta-glucosidase-cellulose and xylanase-hemicellulose were the strongest. Notably low free-binding energy (Delta G(bind)) of beta-glucosidase and xylanase in complex with cellulose (-207.23 +/- 47.13 kJ/mol) and hemicellulose (-131.48 +/- 24.57 kJ/mol) were observed, respectively. The findings thus successfully identified the cellulose component selectivity of the polymer-acting beta-glucosidase and xylanase of T. asperellum UC1. Communicated by Ramaswamy H. Sarm More less

Yılmaz KAYA

Article | 2019 | Journal of Biomolecular Structure and Dynamics38 ( 14 )

Fungi of the Trichoderma species are valued industrial enzymes in support of the

Yılmaz KAYA

Article | 2019 | Journal of Biomolecular Structure and Dynamics38 ( 12 )

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 alpha-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. Sarm More less

Yılmaz KAYA

Letter | 2019 | Journal of Biomolecular Structure and Dynamics38 ( 11 )

KeyWords Plus:ALPHA-HALOALKANOIC ACID; DEHALOGENASE; DEGRADATION

Yılmaz KAYA

Article | 2023 | Journal of Biomolecular Structure and Dynamics42 ( 3 )

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 halo . . .alkanoic 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. Keywords: DehLBHS1; dehalogenase; alkalotolerant; dichloropropionate; haloalkanoic acid; homology modellin More less