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Shettar SS, Bagewadi ZK, Alasmary M, Mannasaheb BA, Shaikh IA, Khan AA. Comprehensive biochemical, molecular and structural characterization of subtilisin with fibrinolytic potential in bioprocessing. BIORESOUR BIOPROCESS 2025; 12:21. [PMID: 40117024 PMCID: PMC11928348 DOI: 10.1186/s40643-025-00860-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2024] [Accepted: 02/28/2025] [Indexed: 03/23/2025] Open
Abstract
Enzyme deployment is proliferating extensively in industries owing to their environmentally friendly and easily degradable attributes. This article undertakes an exhaustive examination of wild subtilisin enzyme, covering purification, biochemical delineation, analytical techniques, and practical implementations. The purification methodology involved partial refinement, anionic exchange, and gel filtration chromatography, culminating in a purification factor of 3.406, corroborated by SDS-PAGE showcasing a molecular weight of ~ 42 kDa. Biochemical scrutiny unveiled the enzyme's response, with an optimal pH at 9 and temperature peak at 60 ℃. Various surfactants, metal ions, organic solvents and inhibitors exhibited notable efficacy. Substrate specificity and kinetics showcased the utmost specificity with N-Suc-F-A-A-F-pNA, registering Km and Vmax values of 0.731 ± 0.5 mM and 0.87 ± 9 × 103 U/mg, respectively. Different bioanalytical techniquesproffered insights into structural and biophysical facets. Practical applications encompassed goat skin depilation, feather disintegration, blood clot dissolution, exemplifying the enzyme's multifaceted utility. To embark upon the elucidation of structure-function relationships, a three-dimensional model was devised through homology modelling, leveraging existing subtilisin structures (PDB: 3WHI). Molecular docking score of - 8.8 kcal/mol and dynamic simulations augmented the comprehension of molecular interactions with N-Suc-F-A-A-F-pNA. This research significantly contributes to unravelling the biochemical intricacies of wild subtilisin and underscores potential industrial and biomedical prowess. Subtilisin can be explored for its thrombolytic potential in several cardiovascular diseases. It may aid in the management of thrombosis by dissolving blood clots in conditions like deep pulmonary embolism, myocardial infarction, ischemic strokes, and in atherosclerosis by breaking down fibrin in arterial plaques, thus preventing heart attacks and strokes.
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Affiliation(s)
- Shreya S Shettar
- Department of Biotechnology, KLE Technological University, Vidyanagar, Hubballi, 580031, Karnataka, India
| | - Zabin K Bagewadi
- Department of Biotechnology, KLE Technological University, Vidyanagar, Hubballi, 580031, Karnataka, India.
| | - Mohammed Alasmary
- Department of Medicine, College of Medicine, Najran University, 66462, Najran, Saudi Arabia
| | | | - Ibrahim Ahmed Shaikh
- Department of Pharmacology, College of Pharmacy, Najran University, 66462, Najran, Saudi Arabia
| | - Aejaz Abdullatif Khan
- Department of General Science, Ibn Sina National College for Medical Studies, 21418, Jeddah, Saudi Arabia
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Abdizadeh T, Rezaei S, Emadi Z, Sadeghi R, Saffari-Chaleshtori J, Sadeghi M. Investigation of bioremediation for glyphosate and its metabolite in soil using arbuscular mycorrhizal GmHsp60 protein: a molecular docking and molecular dynamics simulations approach. J Biomol Struct Dyn 2024:1-25. [PMID: 39829398 DOI: 10.1080/07391102.2024.2445767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 06/18/2024] [Indexed: 01/22/2025]
Abstract
The widespread use of glyphosate and the high dependence of the agricultural industry on this herbicide cause environmental pollution and pose a threat to living organisms. One of the appropriate solutions in sustainable agriculture to deal with pollution caused by glyphosate and its metabolites is creating a symbiotic relationship between plants and mycorrhizal fungi. Glomalin-related soil protein is a key protein for the bioremediation of glyphosate and its metabolite aminomethyl phosphonic acid in soil. This study uses homology modeling, molecular docking, and molecular dynamic simulation approaches to investigate the binding mechanism of glomalin-related soil protein from arbuscular mycorrhiza (GmHsp60) with glyphosate and its metabolite and the role of soil protein in the removal and sequestering of common agricultural soil pollutants. GmHsp60 protein structure was predicted by homology modeling, and the quality of the generated model was assessed. Then, the interaction between glyphosate and aminomethyl phosphonic acid and the modeled GmHsp60 protein was explored by molecular docking. Based on docking results, GmHsp60 has an efficient role in the bioremediation of glyphosate and aminomethyl phosphonic acid (-6.03 and -5.34 kcal/mol). Glyphosate forms three hydrogen bonds with Lys258, Gly262, and Glu58 of GmHsp60, and aminomethyl phosphonic acid forms three hydrogen bonds with Lys258, Gly261, and Gly262 of GmHsp60. In addition, the glyphosate's and its metabolite's stability was confirmed by molecular docking simulations and binding free energy calculations using MM/PBSA analysis. This study provides a molecular-level understanding of GmHsp60 expression and function for glyphosate bioremediation.
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Affiliation(s)
- Tooba Abdizadeh
- Clinical Biochemistry Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Somayeh Rezaei
- Department of Environmental Health Engineering, School of Health, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Zahra Emadi
- Department of Environmental Health Engineering, School of Health, Shahrekord University of Medical Sciences, Shahrekord, Iran
- Student Research Committee, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Ramin Sadeghi
- Chemical Engineering Department, Iran University of Science & Technology, Narmak, Tehran, Iran
| | - Javad Saffari-Chaleshtori
- Clinical Biochemistry Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Mehraban Sadeghi
- Clinical Biochemistry Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran
- Department of Environmental Health Engineering, School of Health, Shahrekord University of Medical Sciences, Shahrekord, Iran
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Bhattacharjee N, Alonso-Cotchico L, Lucas MF. Enzyme immobilization studied through molecular dynamic simulations. Front Bioeng Biotechnol 2023; 11:1200293. [PMID: 37362217 PMCID: PMC10285225 DOI: 10.3389/fbioe.2023.1200293] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 05/30/2023] [Indexed: 06/28/2023] Open
Abstract
In recent years, simulations have been used to great advantage to understand the structural and dynamic aspects of distinct enzyme immobilization strategies, as experimental techniques have limitations in establishing their impact at the molecular level. In this review, we discuss how molecular dynamic simulations have been employed to characterize the surface phenomenon in the enzyme immobilization procedure, in an attempt to decipher its impact on the enzyme features, such as activity and stability. In particular, computational studies on the immobilization of enzymes using i) nanoparticles, ii) self-assembled monolayers, iii) graphene and carbon nanotubes, and iv) other surfaces are covered. Importantly, this thorough literature survey reveals that, while simulations have been primarily performed to rationalize the molecular aspects of the immobilization event, their use to predict adequate protocols that can control its impact on the enzyme properties is, up to date, mostly missing.
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Bhatt P, Joshi T, Bhatt K, Zhang W, Huang Y, Chen S. Binding interaction of glyphosate with glyphosate oxidoreductase and C-P lyase: Molecular docking and molecular dynamics simulation studies. JOURNAL OF HAZARDOUS MATERIALS 2021; 409:124927. [PMID: 33450511 DOI: 10.1016/j.jhazmat.2020.124927] [Citation(s) in RCA: 86] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 12/14/2020] [Accepted: 12/20/2020] [Indexed: 05/12/2023]
Abstract
Widespread application of glyphosate poses a threat to living organisms. Microbial strains are able to degrade glyphosate via contrasting metabolic pathways with the help of enzymes. Glyphosate oxidoreductase (GOX) and C-P lyase are the key enzymes for the biodegradation of glyphosate and its intermediate metabolite aminomethylphosphonic acid (AMPA) in microbes. The microbial degradation of glyphosate has been reported, but the underlying molecular mechanism is still unclear. Therefore, in this study, the interaction mechanism of GOX and C-P lyase with glyphosate and AMPA were investigated by using molecular docking and molecular dynamics (MD) simulations. The results indicate that glyphosate contacts with the active site of GOX and C-P lyase by hydrogen bonds as well as hydrophobic and van der Waals interactions in aqueous solution to maintain its stability. The presence of glyphosate and AMPA in the active site significantly changes the conformation of GOX and C-P lyase. The results of the MD simulations confirm that GOX and C-P lyase complexes are stable during the catalytic reaction. This study offers a molecular level of understanding of the expression and function of GOX and C-P lyase for the bioremediation of glyphosate.
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Affiliation(s)
- Pankaj Bhatt
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Tushar Joshi
- Department of Biotechnology, Kumaun University, Bhimtal Campus, Bhimtal, Uttarakhand 263136, India
| | - Kalpana Bhatt
- Department of Botany and Microbiology, Gurukul Kangri University, Haridwar, Uttarakhand 249404, India
| | - Wenping Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Yaohua Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Shaohua Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China.
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Di Giosia M, Marforio TD, Cantelli A, Valle F, Zerbetto F, Su Q, Wang H, Calvaresi M. Inhibition of α-chymotrypsin by pristine single-wall carbon nanotubes: Clogging up the active site. J Colloid Interface Sci 2020; 571:174-184. [DOI: 10.1016/j.jcis.2020.03.034] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Revised: 02/26/2020] [Accepted: 03/08/2020] [Indexed: 10/24/2022]
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Insights into the binding mechanism of a model protein with fomesafen: Spectroscopic studies, thermodynamics and molecular modeling exploration. J Mol Struct 2019. [DOI: 10.1016/j.molstruc.2019.05.128] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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Zaboli M, Raissi H, Zaboli M, Farzad F, Torkzadeh-Mahani M. Stabilization of d-lactate dehydrogenase diagnostic enzyme via immobilization on pristine and carboxyl-functionalized carbon nanotubes, a combined experimental and molecular dynamics simulation study. Arch Biochem Biophys 2019; 661:178-186. [DOI: 10.1016/j.abb.2018.11.019] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 11/18/2018] [Accepted: 11/19/2018] [Indexed: 12/29/2022]
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Bologna F, Mattioli EJ, Bottoni A, Zerbetto F, Calvaresi M. Interactions between Endohedral Metallofullerenes and Proteins: The Gd@C 60-Lysozyme Model. ACS OMEGA 2018; 3:13782-13789. [PMID: 31458078 PMCID: PMC6644377 DOI: 10.1021/acsomega.8b01888] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 10/09/2018] [Indexed: 06/10/2023]
Abstract
Endohedral metallofullerenes (EMFs) have great potential as radioisotope carriers for nuclear medicine and as contrast agents for X-ray and magnetic resonance imaging. EMFs have still important restrictions for their use due to low solubility in physiological environments, low biocompatibility, nonspecific cellular uptake, and a strong dependence of their peculiar properties on physiological parameters, such as pH and salt content. Conjugation of the EMFs with proteins can overcome many of these limitations. Here we investigated the thermodynamics of binding of a model EMF (Gd@C60) with a protein (lysozyme) that is known to act as a host for the empty fullerene. As a rule, even if the shape of an EMF is exactly the same as that of the related fullerene, the interactions with a protein are significantly different. The estimated interaction energy (ΔG binding) between Gd@C60 and lysozyme is -18.7 kcal mol-1, suggesting the possibility of using proteins as supramolecular carriers for EMFs. π-π stacking, hydrophobic interactions, surfactant-like interactions, and electrostatic interactions govern the formation of the hybrid between Gd@C60 and lysozyme. The comparison of the energy contributions to the binding between C60 or Gd@C60 and lysozyme suggests that, although shape complementarity remains the driving force of the binding, the presence of electron transfer from the gadolinium atom to the carbon cage induces a charge distribution on the fullerene cage that strongly affects its interaction with the protein.
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Affiliation(s)
- Fabio Bologna
- Dipartimento di Chimica “Giacomo
Ciamician”, Alma Mater Studiorum—Università
di Bologna, via F. Selmi 2, 40126 Bologna, Italy
| | - Edoardo Jun Mattioli
- Dipartimento di Chimica “Giacomo
Ciamician”, Alma Mater Studiorum—Università
di Bologna, via F. Selmi 2, 40126 Bologna, Italy
| | - Andrea Bottoni
- Dipartimento di Chimica “Giacomo
Ciamician”, Alma Mater Studiorum—Università
di Bologna, via F. Selmi 2, 40126 Bologna, Italy
| | - Francesco Zerbetto
- Dipartimento di Chimica “Giacomo
Ciamician”, Alma Mater Studiorum—Università
di Bologna, via F. Selmi 2, 40126 Bologna, Italy
| | - Matteo Calvaresi
- Dipartimento di Chimica “Giacomo
Ciamician”, Alma Mater Studiorum—Università
di Bologna, via F. Selmi 2, 40126 Bologna, Italy
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Liu Y, Liu Z, Zeng G, Chen M, Jiang Y, Shao B, Li Z, Liu Y. Effect of surfactants on the interaction of phenol with laccase: Molecular docking and molecular dynamics simulation studies. JOURNAL OF HAZARDOUS MATERIALS 2018; 357:10-18. [PMID: 29859460 DOI: 10.1016/j.jhazmat.2018.05.042] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 05/01/2018] [Accepted: 05/21/2018] [Indexed: 06/08/2023]
Abstract
Some surfactants can enhance the removal of phenol by laccase (Lac) in various industrial effluents. Their behavior and function in the biodegradation of phenolic wastewater have been experimentally reported by many researchers, but the underlying molecular mechanism is still unclear. Therefore, the interaction mechanisms of phenol with Lac from Trametes versicolor were investigated in the presence or absence of Triton X-100 (TX100) or rhamnolipid (RL) by molecular docking and molecular dynamics (MD) simulations. The results indicate that phenol contacts with an active site of Lac by hydrogen bonds (HBs) and van der Waals (vdW) interactions in aqueous solution for maintaining its stability. The presence of TX100 or RL results in the significant changes of enzymatic conformations. Meanwhile, the hydrophobic parts of surfactants contact with the outside surface of Lac. These changes lead to the decrease of binding energy between phenol and Lac. The migration behavior of water molecules within hydration shell is also inevitably affected. Therefore, the amphipathic TX100 or RL may influence the phenol degradation ability of Lac by modulating their interactions and water environment. This study offers molecular level of understanding on the function of surfactants in biosystem.
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Affiliation(s)
- Yujie Liu
- College of Environmental Science and Engineering, Hunan University, Changsha, 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control, Hunan University, Ministry of Education, Changsha, 410082, PR China
| | - Zhifeng Liu
- College of Environmental Science and Engineering, Hunan University, Changsha, 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control, Hunan University, Ministry of Education, Changsha, 410082, PR China.
| | - Guangming Zeng
- College of Environmental Science and Engineering, Hunan University, Changsha, 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control, Hunan University, Ministry of Education, Changsha, 410082, PR China.
| | - Ming Chen
- College of Environmental Science and Engineering, Hunan University, Changsha, 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control, Hunan University, Ministry of Education, Changsha, 410082, PR China
| | - Yilin Jiang
- College of Environmental Science and Engineering, Hunan University, Changsha, 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control, Hunan University, Ministry of Education, Changsha, 410082, PR China
| | - Binbin Shao
- College of Environmental Science and Engineering, Hunan University, Changsha, 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control, Hunan University, Ministry of Education, Changsha, 410082, PR China
| | - Zhigang Li
- College of Environmental Science and Engineering, Hunan University, Changsha, 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control, Hunan University, Ministry of Education, Changsha, 410082, PR China
| | - Yang Liu
- College of Environmental Science and Engineering, Hunan University, Changsha, 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control, Hunan University, Ministry of Education, Changsha, 410082, PR China
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Wang C, Greene D, Xiao L, Qi R, Luo R. Recent Developments and Applications of the MMPBSA Method. Front Mol Biosci 2018; 4:87. [PMID: 29367919 PMCID: PMC5768160 DOI: 10.3389/fmolb.2017.00087] [Citation(s) in RCA: 399] [Impact Index Per Article: 57.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 11/30/2017] [Indexed: 12/23/2022] Open
Abstract
The Molecular Mechanics Poisson-Boltzmann Surface Area (MMPBSA) approach has been widely applied as an efficient and reliable free energy simulation method to model molecular recognition, such as for protein-ligand binding interactions. In this review, we focus on recent developments and applications of the MMPBSA method. The methodology review covers solvation terms, the entropy term, extensions to membrane proteins and high-speed screening, and new automation toolkits. Recent applications in various important biomedical and chemical fields are also reviewed. We conclude with a few future directions aimed at making MMPBSA a more robust and efficient method.
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Affiliation(s)
- Changhao Wang
- Chemical and Materials Physics Graduate Program, University of California, Irvine, Irvine, CA, United States
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States
- Department of Physics and Astronomy, University of California, Irvine, Irvine, CA, United States
| | - D'Artagnan Greene
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States
| | - Li Xiao
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA, United States
| | - Ruxi Qi
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States
| | - Ray Luo
- Chemical and Materials Physics Graduate Program, University of California, Irvine, Irvine, CA, United States
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA, United States
- Department of Chemical Engineering and Materials Science, University of California, Irvine, Irvine, CA, United States
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