Staff View: Molecular interactions of trichoderma β-1,4-glucosidase (ThBglT12) with mycelial cell wall components of phytopathogenic macrophomina phaseolina.

Molecular interactions of trichoderma β-1,4-glucosidase (ThBglT12) with mycelial cell wall components of phytopathogenic macrophomina phaseolina.

Efficacy of a β-1,4-glucosidase from Trichoderma harzianum T12 (ThBglT12) in disrupting the cell wall of the phytopathogenic fungus M. phaseolina (Macrophomina phaseolina) was studied, as the underlying molecular mechanisms of cell wall recognition remains elusive. In this study, the binding locatio...

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Main Authors:	Mohammad Hood, Mohammad Hakim, Tengku Abdul Hamid, Tengku Haziyamin, Abdul Wahab, Roswanira, Huyop, Fahrul Zaman, Kaya, Yilmaz, Abdul Hamid, Azzmer Azzar
Format:	Article
Published:	Taylor and Francis Ltd. 2023
Subjects:	QD Chemistry
Online Access:	http://eprints.utm.my/106286/ http://dx.doi.org/10.1080/07391102.2022.2039772
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spelling	my.utm.1062862024-06-29T05:18:25Z http://eprints.utm.my/106286/ Molecular interactions of trichoderma β-1,4-glucosidase (ThBglT12) with mycelial cell wall components of phytopathogenic macrophomina phaseolina. Mohammad Hood, Mohammad Hakim Tengku Abdul Hamid, Tengku Haziyamin Abdul Wahab, Roswanira Huyop, Fahrul Zaman Kaya, Yilmaz Abdul Hamid, Azzmer Azzar QD Chemistry Efficacy of a β-1,4-glucosidase from Trichoderma harzianum T12 (ThBglT12) in disrupting the cell wall of the phytopathogenic fungus M. phaseolina (Macrophomina phaseolina) was studied, as the underlying molecular mechanisms of cell wall recognition remains elusive. In this study, the binding location identified by a consensus of residues predicted by COACH tool, blind docking, and multiple sequence alignment revealed that molecular recognition by ThBglT12 occurred through interactions between the α-1,3-glucan, β-1,3-glucan, β-1,3/1,4-glucan, and chitin components of M. phaseolina, with corresponding binding energies of −7.4, −7.6, −7.5 and −7.8 kcal/mol. The residue consensus verified the participation of Glu172, Tyr304, Trp345, Glu373, Glu430, and Trp431 in the active site pocket of ThBglT12 to bind the ligands, of which Trp345 was the common interacting residue. Root mean square deviation (RMSD), root mean square fluctuation (RMSF), total energy, and minimum distance calculation from molecular dynamics (MD) simulation further confirmed the stability and the closeness of the binding ligands into the ThBglT12 active site pocket. The h-bond occupancy by Glu373 and Trp431 instated the role of the nucleophile for substrate recognition and specificity, crucial for cleaving the β-1,4 linkage. Further investigation showed that the proximity of Glu373 to the anomeric carbon of β-1,3/1,4-glucan (3.5 Å) and chitin (5.5 Å) indicates the nucleophiles’ readiness to form enzyme-substrate intermediates. Plus, the neighboring water molecule appeared to be correctly positioned and oriented towards the anomeric carbon to hydrolyze the β-1,3/1,4-glucan and chitin, in less than 4.0 Å. In a nutshell, the study verified that the ThBglT12 is a good alternative fungicide to inhibit the growth of M. phaseolina. Communicated by Ramaswamy H. Sarma. Taylor and Francis Ltd. 2023 Article PeerReviewed Mohammad Hood, Mohammad Hakim and Tengku Abdul Hamid, Tengku Haziyamin and Abdul Wahab, Roswanira and Huyop, Fahrul Zaman and Kaya, Yilmaz and Abdul Hamid, Azzmer Azzar (2023) Molecular interactions of trichoderma β-1,4-glucosidase (ThBglT12) with mycelial cell wall components of phytopathogenic macrophomina phaseolina. Journal of Biomolecular Structure and Dynamics, 41 (7). pp. 2831-2847. ISSN 0739-1102 http://dx.doi.org/10.1080/07391102.2022.2039772 DOI: 10.1080/07391102.2022.2039772
institution	Universiti Teknologi Malaysia
building	UTM Library
collection	Institutional Repository
continent	Asia
country	Malaysia
content_provider	Universiti Teknologi Malaysia
content_source	UTM Institutional Repository
url_provider	http://eprints.utm.my/
topic	QD Chemistry
spellingShingle	QD Chemistry Mohammad Hood, Mohammad Hakim Tengku Abdul Hamid, Tengku Haziyamin Abdul Wahab, Roswanira Huyop, Fahrul Zaman Kaya, Yilmaz Abdul Hamid, Azzmer Azzar Molecular interactions of trichoderma β-1,4-glucosidase (ThBglT12) with mycelial cell wall components of phytopathogenic macrophomina phaseolina.
description	Efficacy of a β-1,4-glucosidase from Trichoderma harzianum T12 (ThBglT12) in disrupting the cell wall of the phytopathogenic fungus M. phaseolina (Macrophomina phaseolina) was studied, as the underlying molecular mechanisms of cell wall recognition remains elusive. In this study, the binding location identified by a consensus of residues predicted by COACH tool, blind docking, and multiple sequence alignment revealed that molecular recognition by ThBglT12 occurred through interactions between the α-1,3-glucan, β-1,3-glucan, β-1,3/1,4-glucan, and chitin components of M. phaseolina, with corresponding binding energies of −7.4, −7.6, −7.5 and −7.8 kcal/mol. The residue consensus verified the participation of Glu172, Tyr304, Trp345, Glu373, Glu430, and Trp431 in the active site pocket of ThBglT12 to bind the ligands, of which Trp345 was the common interacting residue. Root mean square deviation (RMSD), root mean square fluctuation (RMSF), total energy, and minimum distance calculation from molecular dynamics (MD) simulation further confirmed the stability and the closeness of the binding ligands into the ThBglT12 active site pocket. The h-bond occupancy by Glu373 and Trp431 instated the role of the nucleophile for substrate recognition and specificity, crucial for cleaving the β-1,4 linkage. Further investigation showed that the proximity of Glu373 to the anomeric carbon of β-1,3/1,4-glucan (3.5 Å) and chitin (5.5 Å) indicates the nucleophiles’ readiness to form enzyme-substrate intermediates. Plus, the neighboring water molecule appeared to be correctly positioned and oriented towards the anomeric carbon to hydrolyze the β-1,3/1,4-glucan and chitin, in less than 4.0 Å. In a nutshell, the study verified that the ThBglT12 is a good alternative fungicide to inhibit the growth of M. phaseolina. Communicated by Ramaswamy H. Sarma.
format	Article
author	Mohammad Hood, Mohammad Hakim Tengku Abdul Hamid, Tengku Haziyamin Abdul Wahab, Roswanira Huyop, Fahrul Zaman Kaya, Yilmaz Abdul Hamid, Azzmer Azzar
author_facet	Mohammad Hood, Mohammad Hakim Tengku Abdul Hamid, Tengku Haziyamin Abdul Wahab, Roswanira Huyop, Fahrul Zaman Kaya, Yilmaz Abdul Hamid, Azzmer Azzar
author_sort	Mohammad Hood, Mohammad Hakim
title	Molecular interactions of trichoderma β-1,4-glucosidase (ThBglT12) with mycelial cell wall components of phytopathogenic macrophomina phaseolina.
title_short	Molecular interactions of trichoderma β-1,4-glucosidase (ThBglT12) with mycelial cell wall components of phytopathogenic macrophomina phaseolina.
title_full	Molecular interactions of trichoderma β-1,4-glucosidase (ThBglT12) with mycelial cell wall components of phytopathogenic macrophomina phaseolina.
title_fullStr	Molecular interactions of trichoderma β-1,4-glucosidase (ThBglT12) with mycelial cell wall components of phytopathogenic macrophomina phaseolina.
title_full_unstemmed	Molecular interactions of trichoderma β-1,4-glucosidase (ThBglT12) with mycelial cell wall components of phytopathogenic macrophomina phaseolina.
title_sort	molecular interactions of trichoderma β-1,4-glucosidase (thbglt12) with mycelial cell wall components of phytopathogenic macrophomina phaseolina.
publisher	Taylor and Francis Ltd.
publishDate	2023
url	http://eprints.utm.my/106286/ http://dx.doi.org/10.1080/07391102.2022.2039772
_version_	1803334986639605760
score	13.211869

Molecular interactions of trichoderma β-1,4-glucosidase (ThBglT12) with mycelial cell wall components of phytopathogenic macrophomina phaseolina.

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