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Ullah A, Ul Haq M, Iqbal M, Irfan M, Khan S, Muhammad R, Ullah A, Khurram M, Alharbi M, Alasmari AF, Ahmad S. A computational quest for identifying potential vaccine candidates against Moraxella lacunata: a multi-pronged approach. J Biomol Struct Dyn 2024; 42:2976-2989. [PMID: 37177816 DOI: 10.1080/07391102.2023.2212793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 04/27/2023] [Indexed: 05/15/2023]
Abstract
Moraxella lacunata is an emerging gram-negative bacterium that is responsible for multiple nosocomial infections. The bacterium is evolving resistance to several antibiotics, and currently, no effective licensed vaccines are available, which warrants the search for new therapeutics. A multi-epitope-based vaccine has been designed for M. lacunata. The complete proteome of M. lacunata contains 10,110 core proteins. Subcellular localization analysis revealed the presence of five proteins in the extracellular matrix, while 19 proteins were predicted to be located in the outer membrane, and 21 proteins were predicted to be located in the periplasmic region. Only two proteins, the type VI secretion system tube protein (Hcp) and the transporter substrate-binding domain-containing protein, were selected for epitope prediction as they fulfilled all the criteria for being potential vaccine candidates. Shortlisted epitopes from the selected proteins were fused together using "GPGPG" linkers to overcome the limitations of single-epitope vaccines. Next, the cholera toxin-B adjuvant was attached to the peptide epitope using an EAAAK linker. Docking analysis was performed to examine the interaction between the vaccine and immune cell receptors, revealing robust intermolecular interactions and a stable binding conformation. Molecular dynamics simulation findings revealed no drastic changes in the binding conformation of complexes during the simulation period. The net binding free energy of vaccine-receptor complexes was estimated using the molecular mechanics energies combined with the Poisson-Boltzmann and surface area continuum solvation (MM-PBSA) method. The reported values were -586.38 kcal/mol, -283.74 kcal/mol, and -296.88 kcal/mol for the TLR-4-vaccine complex, MHC-I-vaccine complex, and MHC-II-vaccine complex, respectively. Furthermore, the molecular mechanics energies combined with the generalized Born and surface area continuum solvation (MM-GBSA) analysis predicted binding free energies of -596.69 kcal/mol, -287.39 kcal/mol, and -298.28 kcal/mol for the TLR-4-vaccine complex, MHC-I-vaccine complex, and MHC-II-vaccine complex, respectively. The theoretical vaccine design proposed in the study could potentially serve as a powerful therapeutic against targeted pathogens, subject to validation through experimental studies.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Asad Ullah
- Department of Health and Biological Sciences, Abasyn University, Peshawar, Pakistan
| | - Mahboob Ul Haq
- Department of Pharmacy, Abasyn University, Peshawar, Pakistan
| | - Madiha Iqbal
- Department of Health and Biological Sciences, Abasyn University, Peshawar, Pakistan
| | - Muhammad Irfan
- College of Dentistry, Department of Oral Biology, University of Florida, Gainesville, FL, USA
| | - Saifullah Khan
- Institute of Biotechnology and Microbiology, Bacha Khan University, Charsadda, Pakistan
| | - Riaz Muhammad
- Department of Health and Biological Sciences, Abasyn University, Peshawar, Pakistan
| | - Amin Ullah
- Department of Health and Biological Sciences, Abasyn University, Peshawar, Pakistan
| | | | - Metab Alharbi
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Abdullah F Alasmari
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Sajjad Ahmad
- Department of Health and Biological Sciences, Abasyn University, Peshawar, Pakistan
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de Oliveira EG, Filho CADC, Rodrigues RAL. An overview of viral chitinases: General properties and biotechnological potential. Exp Biol Med (Maywood) 2023; 248:2053-2061. [PMID: 38057942 PMCID: PMC10800131 DOI: 10.1177/15353702231208408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2023] Open
Abstract
Chitin is a biopolymer profusely present in nature and of pivotal importance as a structural component in cells. It is degraded by chitinases, enzymes naturally produced by different organisms. Chitinases are proteins enrolled in many cellular mechanisms, including the remodeling process of the fungal cell wall, the cell growth process, the autolysis of filamentous fungi, and cell separation of yeasts, among others. These enzymes also have properties with different biotechnological applications. They are used to produce polymers, for biological control, biofilm formation, and as antitumor and anti-inflammatory target molecules. Chitinases are classified into different glycoside hydrolase (GH) families and are widespread in microorganisms, including viruses. Among them, the GH18 family is highly predominant in the viral genomes, being present and active enzymes in baculoviruses and nucleocytoplasmic large DNA viruses (NCLDV), especially chloroviruses from the Phycodnaviridae family. These viral enzymes contain one or more GH domains and seem to be involved during the viral replication cycle. Curiously, only a few DNA viruses have these enzymes, and studying their properties could be a key feature for biological and biotechnological novelties. Here, we provide an overview of viral chitinases and their probable function in viral infection, showing evidence of at least two distinct origins for these enzymes. Finally, we discuss how these enzymes can be applied as biotechnological tools and what one can expect for the coming years on these GHs.
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Affiliation(s)
- Ellen Gonçalves de Oliveira
- Laboratório de Vírus, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
| | - Clécio Alonso da Costa Filho
- Laboratório de Vírus, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
| | - Rodrigo Araújo Lima Rodrigues
- Laboratório de Vírus, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
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Wang S, Khan FI. Investigation of Molecular Interactions Mechanism of Pembrolizumab and PD-1. Int J Mol Sci 2023; 24:10684. [PMID: 37445859 DOI: 10.3390/ijms241310684] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 06/07/2023] [Accepted: 06/09/2023] [Indexed: 07/15/2023] Open
Abstract
Human programmed cell death protein 1 (PD-1) is a checkpoint protein involved in the regulation of immune response. Antibodies are widely used as inhibitors that block the immune checkpoint, preventing strong immune responses. Pembrolizumab is an FDA-approved IgG4 antibody with PD-1 inhibitory ability for the treatment of melanoma. In this study, we investigated the effect of Pembrolizumab on the conformational changes in PD-1 using extensive molecular modeling and simulation approaches. Our study revealed that during the 200 ns simulation, the average values of the solvent accessible surface area, the radius of gyration, and internal hydrogen bonds of PD-1 were 64.46 nm2, 1.38 nm and 78, respectively, while these values of PD-1 in the PD-1/Pembrolizumab complex were 67.29 nm2, 1.39 nm and 76, respectively. The RMSD value of PD-1 gradually increased until 80 ns and maintained its stable conformation at 0.32 nm after 80 ns, while this value of PD-1 in the PD-1/Pembrolizumab complex maintained an increasing trend during 200 ns. The interaction between PD-1 and Pembrolizumab led to a flexible but stable structure of PD-1. PD-1 rotated around the rotation axis of the C'D loop and gradually approached Pembrolizumab. The number of hydrogen bonds involved in the interactions on the C and C' strands increased from 4 at 100 ns to 7 at 200 ns. The strong affinity of Pembrolizumab for the C'D and FG loops of PD-1 disrupted the interactions between PD-1 and PD-L1. Inhibition of the interaction between PD-1 and PD-L1 increased the T cell activity, and is effective in controlling and curing cancer. Further experimental work can be performed to support this finding.
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Affiliation(s)
- Simiao Wang
- Department of Biological Sciences, School of Science, Xi'an Jiaotong-Liverpool University, Suzhou 215123, China
| | - Faez Iqbal Khan
- Department of Biological Sciences, School of Science, Xi'an Jiaotong-Liverpool University, Suzhou 215123, China
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Akram F, Jabbar Z, Aqeel A, Haq IU, Tariq S, Malik K. A Contemporary Appraisal on Impending Industrial and Agricultural Applications of Thermophilic-Recombinant Chitinolytic Enzymes from Microbial Sources. Mol Biotechnol 2022; 64:1055-1075. [PMID: 35397055 DOI: 10.1007/s12033-022-00486-0] [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: 12/18/2021] [Accepted: 03/25/2022] [Indexed: 01/09/2023]
Abstract
The ability of chitinases to degrade the second most abundant polymer, chitin, into potentially useful chitooligomers and chitin derivatives has not only rendered them fit for chitinous waste management but has also made them important from industrial point of view. At the same time, they have also been recognized to have an imperative role as promising biocontrol agents for controlling plant diseases. As thermostability is an important property for an industrially important enzyme, various bacterial and fungal sources are being exploited to obtain such stable enzymes. These stable enzymes can also play a role in agriculture by maintaining their stability under adverse environmental conditions for longer time duration when used as biocontrol agent. Biotechnology has also played its role in the development of recombinant chitinases with enhanced activity, thermostability, fungicidal and insecticidal activity via recombinant DNA techniques. Furthermore, a relatively new approach of generating pathogen-resistant transgenic plants has opened new ways for sustainable agriculture by minimizing the yield loss of valuable crops and plants. This review focuses on the potential applications of thermostable and recombinant microbial chitinases in industry and agriculture.
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Affiliation(s)
- Fatima Akram
- Institute of Industrial Biotechnology, Government College University, Lahore, 54000, Pakistan.
| | - Zuriat Jabbar
- Institute of Industrial Biotechnology, Government College University, Lahore, 54000, Pakistan
| | - Amna Aqeel
- Institute of Industrial Biotechnology, Government College University, Lahore, 54000, Pakistan
| | - Ikram Ul Haq
- Institute of Industrial Biotechnology, Government College University, Lahore, 54000, Pakistan.,Pakistan Academy of Sciences, Islamabad, Pakistan
| | - Shahbaz Tariq
- Institute of Industrial Biotechnology, Government College University, Lahore, 54000, Pakistan
| | - Kausar Malik
- Centre for Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
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Khan FI, Rehman MT, Sameena F, Hussain T, AlAjmi MF, Lai D, Khan MKA. Investigating the binding mechanism of topiramate with bovine serum albumin using spectroscopic and computational methods. J Mol Recognit 2022; 35:e2958. [PMID: 35347772 DOI: 10.1002/jmr.2958] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 03/20/2022] [Accepted: 03/28/2022] [Indexed: 11/10/2022]
Abstract
Various spectroscopic techniques involving fluorescence spectroscopy, circular dichroism (CD), and computational approaches were used to elucidate the molecular aspects of interaction between the antiepileptic drug topiramate and the multifunctional transport protein bovine serum albumin (BSA) under physiological conditions. Topiramate quenched BSA fluorescence in a static quenching mode, according to the Stern-Volmer quenching constant (Ksv ) data derived from fluorescence spectroscopy for the topiramate-BSA complex. The binding constant was also used to calculate the binding affinity for the topiramate-BSA interaction. Fluorescence and circular dichroism experiments demonstrate that the protein's tertiary structure is affected by the microenvironmental alterations generated by topiramate binding to BSA. To establish the exact binding site, interacting residues, and interaction forces involved in the binding of topiramate to BSA, molecular modeling and simulation approaches were used. According to the MMPBSA calculations, the average binding energy between topiramate and BSA is -421.05 kJ/mol. Topiramate was discovered to have substantial interactions with BSA, changing the structural dynamic and Gibbs free energy landscape patterns.
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Affiliation(s)
- Faez Iqbal Khan
- School of Electronic Science and Engineering, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
| | - Md Tabish Rehman
- Department of Pharmacognosy, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh, Saudi Arabia
| | - Fathima Sameena
- School of Life Sciences, B.S. Abdur Rahman Crescent Institute of Science and technology, GST Road, Vandalur, Chennai
| | - Tabish Hussain
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Mohamed F AlAjmi
- Department of Pharmacognosy, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh, Saudi Arabia
| | - Dakun Lai
- School of Electronic Science and Engineering, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
| | - Md Khurshid Alam Khan
- School of Life Sciences, B.S. Abdur Rahman Crescent Institute of Science and technology, GST Road, Vandalur, Chennai
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Khan FI, Lobb KA, Lai D. The Molecular Basis of the Effect of Temperature on the Structure and Function of SARS-CoV-2 Spike Protein. Front Mol Biosci 2022; 9:794960. [PMID: 35463957 PMCID: PMC9019816 DOI: 10.3389/fmolb.2022.794960] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 01/27/2022] [Indexed: 12/14/2022] Open
Abstract
The remarkable rise of the current COVID-19 pandemic to every part of the globe has raised key concerns for the current public healthcare system. The spike (S) protein of SARS-CoV-2 shows an important part in the cell membrane fusion and receptor recognition. It is a key target for vaccine production. Several researchers studied the nature of this protein under various environmental conditions. In this work, we applied molecular modeling and extensive molecular dynamics simulation approaches at 0°C (273.15 K), 20°C (293.15 K), 40°C (313.15 K), and 60°C (333.15 K) to study the detailed conformational alterations in the SARS-CoV-2 S protein. Our aim is to understand the influence of temperatures on the structure, function, and dynamics of the S protein of SARS-CoV-2. The structural deviations, and atomic and residual fluctuations were least at low (0°C) and high (60°C) temperature. Even the internal residues of the SARS-CoV-2 S protein are not accessible to solvent at high temperature. Furthermore, there was no unfolding of SARS-CoV-2 spike S reported at higher temperature. The most stable conformations of the SARS-CoV-2 S protein were reported at 20°C, but the free energy minimum region of the SARS-CoV-2 S protein was sharper at 40°C than other temperatures. Our findings revealed that higher temperatures have little or no influence on the stability and folding of the SARS-CoV-2 S protein.
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Affiliation(s)
- Faez Iqbal Khan
- Department of Biological Sciences, School of Science, Xi’an Jiaotong-Liverpool University, Suzhou, Jiangsu, China
- School of Electronic Science and Engineering, University of Electronic Science and Technology of China, Chengdu, China
| | - Kevin A. Lobb
- Department of Chemistry, Rhodes University, Grahamstown, South Africa
- *Correspondence: Dakun Lai, ; Kevin A. Lobb,
| | - Dakun Lai
- School of Electronic Science and Engineering, University of Electronic Science and Technology of China, Chengdu, China
- *Correspondence: Dakun Lai, ; Kevin A. Lobb,
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Khan FI, Hassan F, Lai D. In Silico Studies on Psilocybin Drug Derivatives Against SARS-CoV-2 and Cytokine Storm of Human Interleukin-6 Receptor. Front Immunol 2022; 12:794780. [PMID: 35095870 PMCID: PMC8796858 DOI: 10.3389/fimmu.2021.794780] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 12/27/2021] [Indexed: 12/15/2022] Open
Abstract
Various metabolites identified with therapeutic mushrooms have been found from different sources and are known to have antibacterial, antiviral, and anticancer properties. Over thousands soil growth-based mushroom metabolites have been discovered, and utilized worldwide to combat malignancy. In this study, psilocybin-mushroom that contains the psychedelic compounds such as psilacetin, psilocin, and psilocybine were screened and found to be inhibitors of SARS-CoV-2 Mprotease. It has been found that psilacetin, psilocin, and psilocybine bind to Mprotease with −6.0, −5.4, and −5.8 kcal/mol, respectively. Additionally, the psilacetin was found to inhibit human interleukin-6 receptors to reduce cytokine storm. The binding of psilacetin to Mprotease of SARS-CoV-2 and human interleukin-6 receptors changes the structural dynamics and Gibbs free energy patterns of proteins. These results suggested that psilocybin-mushroom could be utilized as viable potential chemotherapeutic agents for SARS-CoV-2.
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Affiliation(s)
- Faez Iqbal Khan
- School of Electronic Science and Engineering, University of Electronic Science and Technology of China, Chengdu, China
| | - Fakhrul Hassan
- Faculty of Rehabilitation and Allied Health Sciences, Riphah International University, Islamabad, Pakistan
| | - Dakun Lai
- School of Electronic Science and Engineering, University of Electronic Science and Technology of China, Chengdu, China
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Recombinant production and characterisation of two chitinases from Rasamsonia emersonii, and assessment of their potential industrial applicability. Appl Microbiol Biotechnol 2021; 105:7769-7783. [PMID: 34581845 DOI: 10.1007/s00253-021-11578-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 09/03/2021] [Accepted: 09/08/2021] [Indexed: 12/22/2022]
Abstract
Rasamsonia emersonii (previously Talaromyces emersonii) is a thermophilic filamentous fungus displaying optimum growth at 45 °C. It has a history of use in commercial food enzyme production. Its unfractionated chitinolytic secretome was partially characterised in the early 1990s; however, no individual chitinase from this source has been described in literature previously. This study describes two GH18 chitinases originating from the R. emersonii genome, expressed in the methylotrophic yeast P. pastoris. Chit1 comprises of a GH18 catalytic domain and Chit2 comprises of a GH18 catalytic domain and a chitin-binding motif at the C-terminal. The chitinases were expressed as glycoproteins. The apparent molecular weight of Chit1 was 35.8-42.1 kDa with a smearing tail associated with glyco-sidechains visible up to 72.2 kDa. This became two bands of 30.8 and 29.0 kDa upon de-glycosylation. The apparent molecular weight of Chit2 was 50.4 kDa, reducing to 48.2 kDa upon de-glycosylation. Both chitinases displayed endo-chitinase and chitobiosidase activity, temperature optima of 50-55 °C and low pH optima (pH 4.5 or lower); Chit1 displayed a pH optimum of 3.5, retaining > 60% maximum activity at pH 2.2, a pH range lower than most enzymes of fungal origin. Chit2 displayed the highest chitin-degrading ability at 3456 µmol/mg on 4-NP-triacetylchitotriose, but lost activity faster than Chit1, which displayed 403 µmol/mg on the same substrate. The predicted D values (time required to reduce the enzyme activity to 10% of its original value at 50 °C) were 19.2 and 2.3 days for Chit1 and Chit2, respectively. Thus, Chit1 can be considered one of few hyperthermostable chitinase enzymes described in literature to date. Their physicochemical properties render these chitinases likely suitable for shrimp chitin processing including one-step chitin hydrolysis and alternative sustainable protein processing and the attractive emerging application of mushroom food waste valorisation.Key points• Two GH18 chitinases originating from the industrially relevant thermophilic fungus R. emersonii were cloned and expressed in P. pastoris.• The purified recombinant chitinases showed low pH and high temperature optima and appreciable thermostability at industrially relevant temperatures.• The chitinases displayed characteristics that indicate their likely suitability to several industrial applications including sustainable alternative protein processing, food waste valorisation of commercial mushroom production and one-step shrimp chitin processing.
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Numan M, Bukhari SA, Rehman MU, Mustafa G, Sadia B. Phylogenetic analyses, protein modeling and active site prediction of two pathogenesis related (PR2 and PR3) genes from bread wheat. PLoS One 2021; 16:e0257392. [PMID: 34506613 PMCID: PMC8432781 DOI: 10.1371/journal.pone.0257392] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 08/31/2021] [Indexed: 11/18/2022] Open
Abstract
Wheat is a major staple food and has been extensively grown around the globe. Sessile nature of plants has exposed them to a lot of biotic and abiotic stresses including fungal pathogen attack. Puccinia graminis f.sp. tritici causes stem rust in the wheat crop and leads to 70% decrease in its production. Pathogenesis-related (PR) proteins provide plants with defense against different fungal pathogens as these proteins have antifungal activities. This study was designed to screen Pakistani wheat varieties for PR2 and PR3 proteins and their in silico characterization. PR2 and PR3 genes were screened and isolated by PCR amplification from wheat variety Chenab-70 and Frontana, respectively. The nucleotide sequences of PR2 and PR3 genes were deposited in GenBank with accession numbers MT303867 and MZ766118, respectively. Physicochemical properties, secondary and tertiary structure predictions, and molecular docking of protein sequences of PR2 and PR3 were performed using different bioinformatics tools and software. PR2 and PR3 genes were identified to encode β-1,3-glucanase and chitinase proteins, respectively. Molecular docking of both PR2 and PR3 proteins with beta-glucan and chitin (i.e. their respective ligands) showed crucial amino acid residues involved in molecular interactions. Conclusively, molecular docking analysis of β-1,3-glucanase and chitinase proteins revealed crucial amino acid residues which are involved in ligand binding and important interactions which might have important role in plant defense against fungal pathogens. Moreover, the active residues in the active sties of these proteins can be identified through mutational studies and resulting information might help understanding how these proteins are involved in plant defense mechanisms.
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Affiliation(s)
- Muhammad Numan
- Department of Biochemistry, Government College University, Faisalabad, Pakistan
| | - Shazia Anwer Bukhari
- Department of Biochemistry, Government College University, Faisalabad, Pakistan
- * E-mail:
| | - Mahmood-ur- Rehman
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | - Ghulam Mustafa
- Department of Biochemistry, Government College University, Faisalabad, Pakistan
| | - Bushra Sadia
- Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad, Pakistan
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Khan FI, Kang T, Ali H, Lai D. Remdesivir Strongly Binds to RNA-Dependent RNA Polymerase, Membrane Protein, and Main Protease of SARS-CoV-2: Indication From Molecular Modeling and Simulations. Front Pharmacol 2021; 12:710778. [PMID: 34305617 PMCID: PMC8293383 DOI: 10.3389/fphar.2021.710778] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 06/15/2021] [Indexed: 12/28/2022] Open
Abstract
Development of new drugs is a time-taking and expensive process. Comprehensive efforts are being made globally toward the search of therapeutics against SARS-CoV-2. Several drugs such as remdesivir, favipiravir, ritonavir, and lopinavir have been included in the treatment regimen and shown effective results in several cases. Among the existing broad-spectrum antiviral drugs, remdesivir is found to be more effective against SARS-CoV-2. Remdesivir has broad-spectrum antiviral action against many single-stranded RNA viruses including pathogenic SARS-CoV and Middle East respiratory syndrome coronavirus (MERS-CoV). In this study, we proposed that remdesivir strongly binds to membrane protein (Mprotein), RNA-dependent RNA polymerase (RDRP), and main protease (Mprotease) of SARS-CoV-2. It might show antiviral activity by inhibiting more than one target. It has been found that remdesivir binds to Mprotease, Mprotein, and RDRP with -7.8, -7.4, and -7.1 kcal/mol, respectively. The structure dynamics study suggested that binding of remdesivir leads to unfolding of RDRP. It has been found that strong binding of remdesivir to Mprotein leads to decrease in structural deviations and gyrations. Additionally, the average solvent-accessible surface area of Mprotein decreases from 127.17 to 112.12 nm2, respectively. Furthermore, the eigenvalues and the trace of the covariance matrix were found to be low in case of Mprotease-remdesivir, Mprotein-remdesivir, and RDRP-remdesivir. Binding of remdesivir to Mprotease, Mprotein, and RDRP reduces the average motions in protein due to its strong binding. The MMPBSA calculations also suggested that remdesivir has strong binding affinity with Mprotein, Mprotease, and RDRP. The detailed analysis suggested that remdesivir has more than one target of SARS-CoV-2.
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Affiliation(s)
- Faez Iqbal Khan
- School of Electronic Science and Engineering, University of Electronic Science and Technology of China, Chengdu, China
| | - Tongzhou Kang
- School of Electronic Science and Engineering, University of Electronic Science and Technology of China, Chengdu, China
| | - Haider Ali
- Faculty of Medicine, International Ala-Too University, Bishkek, Kyrgyzstan
| | - Dakun Lai
- School of Electronic Science and Engineering, University of Electronic Science and Technology of China, Chengdu, China
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Khan FI, Song H, Hassan F, Tian J, Tang L, Lai D, Juan F. Impact of amino acid substitutions on the behavior of a photoactivatable near infrared fluorescent protein PAiRFP1. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 253:119572. [PMID: 33631627 DOI: 10.1016/j.saa.2021.119572] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Revised: 01/16/2021] [Accepted: 01/29/2021] [Indexed: 06/12/2023]
Abstract
A photoactivatable near-infrared fluorescent protein (NIR-FP) PAiRFP1 has been developed by 15 amino acid substitutions in its nonfluorescent template Agp2. In our previous communication, we investigated the role of three amino acids in PHY domain distal from BV molecule. The impact of the twelve amino acids in GAF domain, especially five residues near BV-binding pocket is unclear. In this paper, PCR based reverse mutagenesis, spectroscopic methods, molecular modelling and simulations have been employed to explore the roles of these substitutions during the molecular evolution of PAiRFP1. It was found that the residue L163 is important for protein folding in PAiRFP1. The residues F244 and C280 exerted remarkable effects on molar extinction coefficient, NIR fluorescence quantum yield, molecular brightness, fluorescence fold, and dark recovery rate. The residues F244 and V276 modulate the maximum absorption and emission peak position. The reverse mutant L168M exhibited a higher fluorescence fold than PAiRFP1. Additionally, the reverse mutants V203A, V294E, S218G and D127G possessed better spectral properties than PAiRFP1. This study is important for the rational design of a better BphP-based photoactivatable NIR-FPs.
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Affiliation(s)
- Faez Iqbal Khan
- School of Electronic Science and Engineering, University of Electronic Science and Technology of China, Chengdu, China
| | - Honghong Song
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
| | - Fakhrul Hassan
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
| | - Jing Tian
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
| | - Lixia Tang
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
| | - Dakun Lai
- School of Electronic Science and Engineering, University of Electronic Science and Technology of China, Chengdu, China.
| | - Feng Juan
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China.
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Akram F, Akram R, Ikram Ul Haq, Nawaz A, Jabbar Z, Ahmed Z. Biotechnological Eminence of Chitinases: A Focus on Thermophilic Enzyme Sources, Production Strategies and Prominent Applications. Protein Pept Lett 2021; 28:1009-1022. [PMID: 33602064 DOI: 10.2174/0929866528666210218215359] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 12/24/2020] [Accepted: 01/20/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND Chitin, the second most abundant polysaccharide in nature, is a constantly valuable and renewable raw material after cellulose. Due to advancement in technology, industrial interest has grown to take advantage of the chitin. OBJECTIVE Now, biomass is being treated with diverse microbial enzymes or cells for the production of desired products under best industrial conditions. Glycosidic bonds in chitin structure are degraded by chitinase enzymes, which are characterized into number of glycoside hydrolase (GHs) families. METHODS Thermophilic microorganisms are remarkable sources of industrially important thermostable enzymes, having ability to survive harsh industrial processing conditions. Thermostable chitinases have an edge over mesophilic chitinases as they can hydrolyse the substrate at relatively high temperatures and exhibit decreased viscosity, significantly reduced contamination risk, thermal and chemical stability and increased solubility. Various methods are employed to purify the enzyme and increase its yield by optimizing various parameters such as temperature, pH, agitation, and by investigating the effect of different chemicals and metal ions etc. Results: Thermostable chitinase enzymes show high specific activity at elevated temperature which distinguish them from mesophiles. Genetic engineering can be used for further improvement of natural chitinases, and unlimited potential for the production of thermophilic chitinases has been highlighted due to advancement in synthetic biological techniques. Thermostable chitinases are then used in different fields such as bioremediation, medicine, agriculture and pharmaceuticals. CONCLUSION This review will provide information about chitinases, biotechnological potential of thermostable enzyme and the methods by which they are being produced and optimized for several industrial applications. Some of the applications of thermostable chitinases have also been briefly described.
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Affiliation(s)
- Fatima Akram
- Institute of Industrial Biotechnology, GC University, Lahore-54000, . Pakistan
| | - Rabia Akram
- Institute of Industrial Biotechnology, GC University, Lahore-54000, . Pakistan
| | - Ikram Ul Haq
- Institute of Industrial Biotechnology, GC University, Lahore-54000, . Pakistan
| | - Ali Nawaz
- Institute of Industrial Biotechnology, GC University, Lahore-54000, . Pakistan
| | - Zuriat Jabbar
- Institute of Industrial Biotechnology, GC University, Lahore-54000, . Pakistan
| | - Zeeshan Ahmed
- Institute of Industrial Biotechnology, GC University, Lahore-54000, . Pakistan
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Bhagwat P, Amobonye A, Singh S, Pillai S. A comparative analysis of GH18 chitinases and their isoforms from Beauveria bassiana: An in-silico approach. Process Biochem 2021. [DOI: 10.1016/j.procbio.2020.10.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Khan FI, Hassan F, Anwer R, Juan F, Lai D. Comparative Analysis of Bacteriophytochrome Agp2 and Its Engineered Photoactivatable NIR Fluorescent Proteins PAiRFP1 and PAiRFP2. Biomolecules 2020; 10:biom10091286. [PMID: 32906690 PMCID: PMC7564321 DOI: 10.3390/biom10091286] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 08/27/2020] [Accepted: 09/04/2020] [Indexed: 12/11/2022] Open
Abstract
Two photoactivatable near infrared fluorescent proteins (NIR FPs) named “PAiRFP1” and “PAiRFP2” are formed by directed molecular evolution from Agp2, a bathy bacteriophytochrome of Agrobacterium tumefaciens C58. There are 15 and 24 amino acid substitutions in the structure of PAiRFP1 and PAiRFP2, respectively. A comprehensive molecular exploration of these bacteriophytochrome photoreceptors (BphPs) are required to understand the structure dynamics. In this study, the NIR fluorescence emission spectra for PAiRFP1 were recorded upon repeated excitation and the fluorescence intensity of PAiRFP1 tends to increase as the irradiation time was prolonged. We also predicted that mutations Q168L, V244F, and A480V in Agp2 will enhance the molecular stability and flexibility. During molecular dynamics (MD) simulations, the average root mean square deviations of Agp2, PAiRFP1, and PAiRFP2 were found to be 0.40, 0.49, and 0.48 nm, respectively. The structure of PAiRFP1 and PAiRFP2 were more deviated than Agp2 from its native conformation and the hydrophobic regions that were buried in PAiRFP1 and PAiRFP2 core exposed to solvent molecules. The eigenvalues and the trace of covariance matrix were found to be high for PAiRFP1 (597.90 nm2) and PAiRFP2 (726.74 nm2) when compared with Agp2 (535.79 nm2). It was also found that PAiRFP1 has more sharp Gibbs free energy global minima than Agp2 and PAiRFP2. This comparative analysis will help to gain deeper understanding on the structural changes during the evolution of photoactivatable NIR FPs. Further work can be carried out by combining PCR-based directed mutagenesis and spectroscopic methods to provide strategies for the rational designing of these PAiRFPs.
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Affiliation(s)
- Faez Iqbal Khan
- School of Electronic Science and Engineering, University of Electronic Science and Technology of China, Chengdu 610054, China;
| | - Fakhrul Hassan
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China; (F.H.); (F.J.)
| | - Razique Anwer
- Department of Pathology, College of Medicine, Imam Mohammad ibn Saud Islamic University (IMSIU), Riyadh 13317, Saudi Arabia;
| | - Feng Juan
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China; (F.H.); (F.J.)
| | - Dakun Lai
- School of Electronic Science and Engineering, University of Electronic Science and Technology of China, Chengdu 610054, China;
- Correspondence: ; Tel.: +86-182-0052-9516
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Anand K, Khan FI, Singh T, Elumalai P, Balakumar C, Premnath D, Lai D, Chuturgoon AA, Saravanan M. Green Synthesis, Experimental and Theoretical Studies to Discover Novel Binders of Exosomal Tetraspanin CD81 Protein. ACS OMEGA 2020; 5:17973-17982. [PMID: 32743170 PMCID: PMC7391369 DOI: 10.1021/acsomega.0c01166] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 06/17/2020] [Indexed: 06/11/2023]
Abstract
A new class of benzothiazole-appended quinoline derivatives (6-8) was synthesized via one-pot TPGS micellar-mediated acid-catalyzed nucleophilic addition, followed by aerobic oxidative cyclization of 3-formylquinoline-2-one (2), 3-formylquinoline-2-thione (3), and 2-azidoquinoline-3-carbaldehyde (4) individually with 2-amino thiophenol (5). The structures of the prepared compounds were confirmed using suitable spectroscopic methods complemented with single-crystal X-ray diffraction analysis. Time-dependent density functional theory-based optimization of molecular structures, bond lengths, bond angles, HOMO-LUMO energy gaps, and molecular electrostatic potential maps was theoretically computed at the B3LYP/6-311++g(d) level. The molecular docking studies recommended that 6-8 bound to the active site cavity of CD81 effectively with the binding energies of -6.9, -6.3, and -6.5 kcal mol-1, respectively. Further, MD simulation studies of compound 6 suggested that the binding resulted in the stabilization of the CD81 molecule. Thus, all theoretical predictions associated with the experimental verifications motivated to discover novel approaches for cancer therapy.
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Affiliation(s)
- Krishnan Anand
- Department
of Chemical Pathology, School of Pathology, Faculty of Health Sciences
and National Health Laboratory Service, University of the Free State, Bloemfontein 9300, South Africa
| | - Faez I. Khan
- School
of Electronic Science and Engineering, University
of Electronic Science and Technology of China, Chengdu 610054, PR China
| | - Thishana Singh
- Faculty
of Agriculture, Engineering and Science, School of Chemistry and Physics, University of Kwazulu-Natal, Westville Campus, Durban 4013, South Africa
| | - Palani Elumalai
- Science
Department, Texas A&M University at
Qatar, Texas A&M
Engineering Building, Education City, P.O. Box 23874, Doha 0000, Qatar
| | | | - Dhanaraj Premnath
- Department
of Biotechnology, School of Agriculture and Biosciences, Karunya Institute of Technology and Science, Karunya Nagar, Coimbatore 641114, India
| | - Dakun Lai
- School
of Electronic Science and Engineering, University
of Electronic Science and Technology of China, Chengdu 610054, PR China
| | - Anil A. Chuturgoon
- Discipline
of Medical Biochemistry, School of Laboratory Medicine and Medical
Science, University of KwaZulu-Natal, Durban 4000, South Africa
| | - Muthupandian Saravanan
- Department
of Microbiology and Immunology, Division of Biomedical Sciences, School
of Medicine, College of Health Sciences, Mekelle University, Mekelle 1871, Ethiopia
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Transcriptome Analysis of Dimorphic Fungus Sporothrix schenckii Exposed to Temperature Stress. Int Microbiol 2020; 24:25-35. [PMID: 32691258 PMCID: PMC7873001 DOI: 10.1007/s10123-020-00136-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Revised: 06/12/2020] [Accepted: 07/14/2020] [Indexed: 11/03/2022]
Abstract
PURPOSE Sporothrix schenckii is a thermally dimorphic fungus. In a saprotrophic environment or culturing at 25 °C, it grows as mycelia, whereas in host tissues or culturing at 37 °C, it undergoes dimorphic transition and division into pathogenic yeast cells. S. schenckii can cause serious disseminated sporotrichosis in immunocompromised hosts and presents an emerging global health problem. The mycelium-to-yeast transition was a consequence of the adaptive process to different environment. Some studies showed that the transition was significantly related to the virulence and pathogenesis of dimorphic fungi. However the genetic mechanisms of this complicated biological process are poorly understood. METHOD Our study presented a comparative transcriptomic analysis perspective on temperature stress in a visceral isolates of S. schenckii, obtaining more genetic information related to dimorphic transition. RESULTS The 9.38 Gbp dataset was generated and assembled into 14,423 unigenes. Compared with gene and protein databases, 9561 unigenes were annotated. Comparative analysis identified 1259 genes expressed differentially in mycelium and yeast phase, and were categorized into a number of important biological processes, such as synthesis and metabolism, transmembrane transport, biocatalysis, oxidation reduction, and cellular signal transduction. CONCLUSIONS The findings suggested that temperature-dependent transition was tightly associated with stress adaptation, growth and development, signal regulation, adhesion, and colonization, which was predicted to be related with virulence and pathogenesis. Collection of these data should offer fine-scale insights into the mechanisms of dimorphism and pathogenesis of S. schenckii, and meanwhile facilitate the evolutionary and function studies of other dimorphic fungi.
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Qausain S, Khan FI, Lai D, Hassan MI, Basheeruddin M, Ahmed N, Khan MKA. Mechanistic insights into the urea-induced denaturation of a non-seleno thiol specific antioxidant human peroxiredoxin 6. Int J Biol Macromol 2020; 161:1171-1180. [PMID: 32485253 DOI: 10.1016/j.ijbiomac.2020.05.168] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Revised: 05/18/2020] [Accepted: 05/19/2020] [Indexed: 12/24/2022]
Abstract
Peroxiredoxin 6 (Prdx6) is a unique enzyme among mammalian peroxiredoxins as it lacks resolving cysteine. It is found to be involved in number of different diseases including tumours and its expression level is highest in lungs as compared to other organs. It has been found that Prdx6 plays a significant role different metabolic diseases, ocular damage, neurodegeneration and male infertility. It is a bifunctional protein having phospholipase A2 and peroxidase (also has the ability to reduce phospholipid hydroperoxides) activities. In order to complete the peroxidise reaction cycle it requires glutathione catalyzed by glutathione S-transferase. Equilibrium unfolding and conformational stability of Prdx6 was studied by using urea as a chemical denaturant to understand the changes it goes under cellular stress conditions. Three different spectroscopic methods were employed to monitor urea-induced denaturation. From the results obtained, it was found that the urea denaturation of Prdx6 follows a variable two state process due to non-coincidence of the normalized transition curves obtained from different optical probes. The different denaturation curves were normalized and thermodynamic parameters, ΔGDo, Gibbs free energy change related to the urea-induced denaturation, midpoint of denaturation (Cm), and m = (δΔGD / [urea]) were obtained. The structural information of Prdx6 were further analysed by several parameters obtained by 100 ns MD simulation. The results of MD simulation clearly favour the outcome of spectroscopic studies.
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Affiliation(s)
- Sana Qausain
- School of Life Sciences, B.S. Abdur Rahman Crescent Institute of Science and Technology, GST Road, Vandalur, Chennai 600048, India
| | - Faez Iqbal Khan
- School of Electronic Science and Engineering, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
| | - Dakun Lai
- School of Electronic Science and Engineering, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
| | - Md Imtaiyaz Hassan
- Center for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Mohd Basheeruddin
- School of Life Sciences, B.S. Abdur Rahman Crescent Institute of Science and Technology, GST Road, Vandalur, Chennai 600048, India
| | - Neesar Ahmed
- School of Life Sciences, B.S. Abdur Rahman Crescent Institute of Science and Technology, GST Road, Vandalur, Chennai 600048, India
| | - Md Khurshid Alam Khan
- School of Life Sciences, B.S. Abdur Rahman Crescent Institute of Science and Technology, GST Road, Vandalur, Chennai 600048, India.
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Khan FI, Hassan F, Ali H, Lai D. Mechanism of pH-induced conformational changes in MurE ligase obtained from Salmonella enterica serovar Typhi. J Biomol Struct Dyn 2020; 39:1898-1905. [PMID: 32141393 DOI: 10.1080/07391102.2020.1739560] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Faez Iqbal Khan
- School of Electronic Science and Engineering, University of Electronic Science and Technology of China, Chengdu, China
| | - Fakhrul Hassan
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
| | - Haider Ali
- Faculty of medicine, International Ala-too University, Bishkek, Kyrgyzstan
| | - Dakun Lai
- School of Electronic Science and Engineering, University of Electronic Science and Technology of China, Chengdu, China
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Hassan F, Khan FI, Song H, Lai D, Juan F. Effects of reverse genetic mutations on the spectral and photochemical behavior of a photoactivatable fluorescent protein PAiRFP1. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 228:117807. [PMID: 31806482 DOI: 10.1016/j.saa.2019.117807] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 10/29/2019] [Accepted: 11/15/2019] [Indexed: 06/10/2023]
Abstract
Bacteriophytochrome photoreceptors (BphPs) containing biliverdin (BV) have great potential for the development of genetically engineered near-infrared fluorescent proteins (NIR FPs). We investigated a photoactivatable fluorescent protein PAiRFP1, was engineered through directed molecular evolution. The coexistence of both red light absorbing (Pr) and far-red light absorbing (Pfr) states in dark is essential for the photoactivation of PAiRFP1. The PCR based site-directed reverse mutagenesis, spectroscopic measurements and molecular dynamics (MD) simulations were performed on three targeted sites V386A, V480A and Y498H in PHY domain to explore their potential effects during molecular evolution of PAiRFP1. We found that these substitutions did not affect the coexistence of Pr and Pfr states but led to slight changes in the photophysical parameters. The covalent docking of biliverdin (cis and trans form) with PAiRFP1 was followed by several 100 ns MD simulations to provide some theoretical explanations for the coexistence of Pr and pfr states. The results suggested that experimentally observed coexistence of Pr and Pfr states in both PAiRFP1 and mutants were resulted from the improved stability of Pr state. The use of experimental and computational work provided useful understanding of Pr and Pfr states and the effects of these mutations on the photophysical properties of PAiRFP1.
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Affiliation(s)
- Fakhrul Hassan
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
| | - Faez Iqbal Khan
- School of Electronic Science and Engineering, University of Electronic Science and Technology of China, Chengdu, China.
| | - Honghong Song
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
| | - Dakun Lai
- School of Electronic Science and Engineering, University of Electronic Science and Technology of China, Chengdu, China.
| | - Feng Juan
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China.
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20
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Gupta P, Khan FI, Roy S, Anwar S, Dahiya R, Alajmi MF, Hussain A, Rehman MT, Lai D, Hassan MI. Functional implications of pH-induced conformational changes in the Sphingosine kinase 1. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 225:117453. [PMID: 31446356 DOI: 10.1016/j.saa.2019.117453] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 06/21/2019] [Accepted: 08/05/2019] [Indexed: 06/10/2023]
Abstract
Sphingosine kinase 1 (SphK1) catalyzes the conversion of sphingosine to sphingosine-1-phosphate that acts as a bioactive signalling molecule, and regulates various cellular processes including lymphocyte trafficking, angiogenesis and response to apoptotic stimuli. Abnormal expression of SphK1 has been observed in a wide range of cancers highlighting their role in tumour growth and metastasis. This enzyme also plays a critical role in metabolic and inflammatory diseases, including pulmonary fibrosis, diabetic neuropathy and Alzheimer's disease. In the present study, we have investigated the structural and conformational changes in SphK1 at varying pH using various spectroscopic techniques. Consistent results were observed with the function of SphK1 at corresponding pH values. SphK1 maintains its secondary and tertiary structure in the pH range of 7.5-10.0. However, protein aggregation was observed in the acidic pH range (4.0-6.5). At pH 2.0, the SphK1 exists in the molten-globule state. Kinase assay also shows that SphK1 activity was optimal in the pH range of 7.5-8.5. To complement in vitro results, we have performed 100 ns molecular dynamics simulation to examine the effect of pH on the structural stability of SphK1 at molecular level. SphK1 maintains its native conformation in the alkaline pH range with some residual fluctuations detected at acidic pH. A considerable correlation was noticed between spectroscopic, enzymatic activity and MD simulation studies. pH dependent structural changes can be further implicated to understand its association with disease condition, and cellular homeostasis with respect to protein function under variable pH conditions.
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Affiliation(s)
- Preeti Gupta
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India
| | - Faez Iqbal Khan
- School of Electronic Science and Engineering, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
| | - Sonam Roy
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India
| | - Saleha Anwar
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India
| | - Rashmi Dahiya
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India
| | - Mohammed F Alajmi
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Afzal Hussain
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Md Tabish Rehman
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Dakun Lai
- School of Electronic Science and Engineering, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
| | - Md Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India.
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Khan FI, Lai D, Anwer R, Azim I, Khan MKA. Identifying novel sphingosine kinase 1 inhibitors as therapeutics against breast cancer. J Enzyme Inhib Med Chem 2020; 35:172-186. [PMID: 31752564 PMCID: PMC6882459 DOI: 10.1080/14756366.2019.1692828] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Sphingosine kinase 1 (SphK1) is a promising therapeutic target against several diseases including mammary cancer. The aim of present work is to identify a potent lead compound against breast cancer using ligand-based virtual screening, molecular docking, MD simulations, and the MMPBSA calculations. The LBVS in molecular and virtual libraries yielded 20,800 hits, which were reduced to 621 by several parameters of drug-likeness, lead-likeness, and PAINS. Furthermore, 55 compounds were selected by ADMET descriptors carried forward for molecular interaction studies with SphK1. The binding energy (ΔG) of three screened compounds namely ZINC06823429 (–11.36 kcal/mol), ZINC95421501 (–11.29 kcal/mol), and ZINC95421070 (–11.26 kcal/mol) exhibited stronger than standard drug PF-543 (–9.9 kcal/mol). Finally, it was observed that the ZINC06823429 binds tightly to catalytic site of SphK1 and remain stable during MD simulations. This study provides a significant understanding of SphK1 inhibitors that can be used in the development of potential therapeutics against breast cancer.
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Affiliation(s)
- Faez Iqbal Khan
- School of Electronic Science and Engineering, University of Electronic Science and Technology of China, Chengdu, China
| | - Dakun Lai
- School of Electronic Science and Engineering, University of Electronic Science and Technology of China, Chengdu, China
| | - Razique Anwer
- Department of Pathology, College of Medicine, Imam Mohammad ibn Saud Islamic University, Riyadh, Saudi Arabia
| | - Iffat Azim
- Department of Bioengineering, Faculty of Engineering, Integral University, Lucknow, India
| | - Mohd Kalim Ahmad Khan
- Department of Bioengineering, Faculty of Engineering, Integral University, Lucknow, India
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Structure solution and analyses of the first true lipase obtained from metagenomics indicate potential for increased thermostability. N Biotechnol 2019; 53:65-72. [DOI: 10.1016/j.nbt.2019.07.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 06/24/2019] [Accepted: 07/07/2019] [Indexed: 01/05/2023]
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Furkan M, Siddiqi MK, Zakariya SM, Khan FI, Hassan MI, Khan RH. An In Vitro elucidation of the antiaggregatory potential of Diosminover thermally induced unfolding of hen egg white lysozyme; A preventive quest for lysozyme amyloidosis. Int J Biol Macromol 2019; 129:1015-1023. [DOI: 10.1016/j.ijbiomac.2019.02.107] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 02/18/2019] [Accepted: 02/18/2019] [Indexed: 01/24/2023]
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Husain FM, Ahmad I, Khan FI, Al-Shabib NA, Baig MH, Hussain A, Rehman MT, Alajmi MF, Lobb KA. Seed Extract of Psoralea corylifolia and Its Constituent Bakuchiol Impairs AHL-Based Quorum Sensing and Biofilm Formation in Food- and Human-Related Pathogens. Front Cell Infect Microbiol 2018; 8:351. [PMID: 30410871 PMCID: PMC6211212 DOI: 10.3389/fcimb.2018.00351] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2018] [Accepted: 09/14/2018] [Indexed: 01/18/2023] Open
Abstract
The emergence of multi-drug resistance in pathogenic bacteria in clinical settings as well as food-borne infections has become a serious health concern. The problem of drug resistance necessitates the need for alternative novel therapeutic strategies to combat this menace. One such approach is targeting the quorum-sensing (QS) controlled virulence and biofilm formation. In this study, we first screened different fractions of Psoralea corylifolia (seed) for their anti-QS property in the Chromobacterium violaceum 12472 strain. The methanol fraction was found to be the most active fraction and was selected for further bioassays. At sub-inhibitory concentrations, the P. corylifolia methanol fraction (PCMF) reduced QS-regulated virulence functions in C. violaceum CVO26 (violacein); Pseudomonas aeruginosa (elastase, protease, pyocyanin, chitinase, exopolysaccharides (EPS), and swarming motility), A. hydrophila (protease, EPS), and Serratia marcescens (prodigiosin). Biofilm formation in all the test pathogens was reduced significantly (p ≤ 0.005) in a concentration-dependent manner. The β-galactosidase assay showed that the PCMF at 1,000 μg/ml downregulated las-controlled transcription in PAO1. In vivo studies with C. elegans demonstrated increased survival of the nematodes after treatment with the PCMF. Bakuchiol, a phytoconstituent of the extract, demonstrated significant inhibition of QS-regulated violacein production in C. violaceum and impaired biofilm formation in the test pathogens. The molecular docking results suggested that bakuchiol efficiently binds to the active pockets of LasR and RhlR, and the complexes were stabilized by several hydrophobic interactions. Additionally, the molecular dynamics simulation of LasR, LasR-bakuchiol, RhlR, and RhlR-bakuchiol complexes for 50 ns revealed that the binding of bakuchiol to LasR and RhlR was fairly stable. The study highlights the anti-infective potential of the PCMF and bakuchiol instead of bactericidal or bacteriostatic action, as the extract targets QS-controlled virulence and the biofilm.
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Affiliation(s)
- Fohad Mabood Husain
- Department of Food Science and Nutrition, College of Food and Agriculture Sciences, King Saud University, Riyadh, Saudi Arabia.,Department of Agricultural Microbiology, Aligarh Muslim University, Aligarh, India
| | - Iqbal Ahmad
- Department of Food Science and Nutrition, College of Food and Agriculture Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Faez Iqbal Khan
- Department of Chemistry, Rhodes University, Grahamstown, South Africa
| | - Nasser A Al-Shabib
- Department of Food Science and Nutrition, College of Food and Agriculture Sciences, King Saud University, Riyadh, Saudi Arabia
| | | | - Afzal Hussain
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Md Tabish Rehman
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Mohamed F Alajmi
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Kevin A Lobb
- Department of Chemistry, Rhodes University, Grahamstown, South Africa
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Integrated Functional-Omics Analysis of Thermomyces lanuginosus Reveals its Potential for Simultaneous Production of Xylanase and Substituted Xylooligosaccharides. Appl Biochem Biotechnol 2018; 187:1515-1538. [PMID: 30267287 DOI: 10.1007/s12010-018-2873-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 08/24/2018] [Indexed: 11/27/2022]
Abstract
Thermophiles have several beneficial properties for the conversion of biomass at high temperatures. Thermomyces lanuginosus is a thermophilic filamentous fungus that was shown to secrete 40 glycoside hydrolases and 25 proteases when grown on different carbon sources. Among the 13 identified glycoside hydrolases with high expression levels, 9 were reduced sugar glycosidases (RSGs) belonging to seven GH families, and 7 of the 10 identified proteases were exopeptidases belonging to six different protease families. High expression of RSGs and exopeptidases may allow the fungus to efficiently degrade oligosaccharides and oligopeptides in saprophytic habitats. There were no xylan side chain-degrading enzymes predicted in the genome of T. lanuginosus, and only one thermophilic GH11 xylanase (g4601.t1) and one GH43 xylosidase (g3706.t1) were detected by liquid chromatography-mass spectrometry/mass spectrometry when T. lanuginosus grown on xylan, which led to the accumulation of substituted xylooligosaccharides (SXOS) during corncob xylan degradation where SXOS output made up more than 8% of the total xylan. The SXOS are beneficial prebiotics and important inducers for enzymes secretion of microorganisms. Thus, T. lanuginosus exhibits distinct advantages in utilizing cheap raw materials producing one thermostable xylanase and the high value-added SXOS as well as microbial inoculants to compost by batch fermentation.
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Ali S, Khan FI, Chen W, Rahaman A, Wang Y. Open and closed states of Mrlip1 DAG lipase revealed by molecular dynamics simulation. MOLECULAR SIMULATION 2018. [DOI: 10.1080/08927022.2018.1513647] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Shahid Ali
- School of Food Science and Engineering, South China University of Technology, Guangzhou, People’s Republic of China
| | - Faez Iqbal Khan
- Department of Chemistry, Rhodes University, Grahamstown, South Africa
| | - Wenwen Chen
- School of Biological Sciences, Nanyang Technological University, Singapore
| | - Abdul Rahaman
- School of Food Science and Engineering, South China University of Technology, Guangzhou, People’s Republic of China
| | - Yonghua Wang
- School of Food Science and Engineering, South China University of Technology, Guangzhou, People’s Republic of China
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Jiang CH, Huang CX, Chen YJ, Chuang YC, Huang BY, Yang CN. Molecular Modeling for Structural Insights Concerning the Activation Mechanisms of F1174L and R1275Q Mutations on Anaplastic Lymphoma Kinase. Molecules 2018; 23:molecules23071610. [PMID: 30004444 PMCID: PMC6100628 DOI: 10.3390/molecules23071610] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 06/28/2018] [Accepted: 06/29/2018] [Indexed: 11/29/2022] Open
Abstract
Anaplastic lymphoma kinase (ALK) is a receptor tyrosine kinase involved in various cancers. In its basal state, the structure of ALK is in an autoinhibitory form stabilized by its A-loop, which runs from the N-lobe to the C-lobe of the kinase. Specifically, the A-loop adopts an inhibitory pose with its proximal A-loop helix (αAL-helix) to anchor the αC-helix orientation in an inactive form in the N-lobe; the distal portion of the A-loop is packed against the C-lobe to block the peptide substrate from binding. Upon phosphorylation of the first A-loop tyrosine (Y1278), the αAL-helix unfolds; the distal A-loop detaches from the C-lobe and reveals the P+1 pocket that accommodates the residues immediately after their phosphorylation, and ALK is activated accordingly. Recently, two neuroblastoma mutants, F1174L and R1275Q, have been determined to cause ALK activation without phosphorylation on Y1278. Notably, F1174 is located on the C-terminus of the αC-helix and away from the A-loop, whereas R1275 sits on the αAL-helix. In this molecular modeling study, we investigated the structural impacts of F1174L and R1275Q that lead to the gain-of-function event. Wild-type ALK and ALK with phosphorylated Y1278 were also modeled for comparison. Our modeling suggests that the replacement of F1174 with a smaller residue, namely leucine, moves the αC-helix and αAL-helix into closer contact and further distorts the distal portion of the A-loop. In wild-type ALK, R1275 assumes the dual role of maintaining the αAL-helix–αC-helix interaction in an inactive form and securing αAL-helix conformation through the D1276–R1275 interaction. Accordingly, mutating R1275 to a glutamine reorients the αC-helix to an active form and deforms the entire A-loop. In both F1174L and R1275Q mutants, the A-loop rearranges itself to expose the P+1 pocket, and kinase activity resumes.
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Affiliation(s)
- Cheng-Han Jiang
- Department of Life Sciences, National University of Kaohsiung, Kaohsiung 811, Taiwan.
| | - Chong-Xian Huang
- Department of Life Sciences, National University of Kaohsiung, Kaohsiung 811, Taiwan.
| | - Ya-Jyun Chen
- Department of Life Sciences, National University of Kaohsiung, Kaohsiung 811, Taiwan.
| | - Yu-Chung Chuang
- Department of Life Sciences, National University of Kaohsiung, Kaohsiung 811, Taiwan.
| | - Bo-Yen Huang
- Department of Life Sciences, National University of Kaohsiung, Kaohsiung 811, Taiwan.
| | - Chia-Ning Yang
- Department of Life Sciences, National University of Kaohsiung, Kaohsiung 811, Taiwan.
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Syed SB, Khan FI, Khan SH, Srivastava S, Hasan GM, Lobb KA, Islam A, Hassan MI, Ahmad F. Unravelling the unfolding mechanism of human integrin linked kinase by GdmCl-induced denaturation. Int J Biol Macromol 2018; 117:1252-1263. [PMID: 29885398 DOI: 10.1016/j.ijbiomac.2018.06.025] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 05/26/2018] [Accepted: 06/06/2018] [Indexed: 12/14/2022]
Abstract
Integrin-linked kinase (ILK) is a ubiquitously expressed Ser/Thr kinase which plays significant role in the cell-matrix interactions and growth factor signalling. In this study, guanidinium chloride (GdmCl)-induced unfolding of kinase domain of ILK (ILK193-446) was carried out at pH 7.5 and 25 °C. Eventually, denaturation curves of mean residue ellipticity at 222 nm ([θ]222) and fluorescence emission spectrum were analysed to estimate stability parameters. The optical properties maximum emission (λmax) and difference absorption coefficient at 292 nm (Δε292) were analysed. The denaturation curve was measured only in the GdmCl molar concentration ranging 3.0-4.2 M because protein was aggregating below 3.0 M of GdmCl concentrations. The denaturation process of ILK193-446 was found as reversible at [GdmCl] ≥ 3.0 M. Moreover, a coincidence of normalized denaturation curves of optical properties ([θ]222, Δε292 and λmax) suggesting that GdmCl-induced denaturation of ILK193-446 is a two-state process. In addition, 100 ns molecular dynamics simulations were performed to see the effects of GdmCl on the structure and stability of ILK193-446. Both the spectroscopic and molecular dynamics approaches provided clear insights into the stability and conformational properties of ILK193-446.
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Affiliation(s)
- Sunayana Begum Syed
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India
| | - Faez Iqbal Khan
- Computational Mechanistic Chemistry and Drug Discovery, Rhodes University, South Africa
| | - Sabab Hasan Khan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India
| | - Saurabha Srivastava
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India
| | - Gulam Mustafa Hasan
- Department of Biochemistry, College of Medicine, Prince Sattam Bin Abdulaziz University, P.O. Box 173, Al-Kharj 11942, Saudi Arabia
| | - Kevin A Lobb
- Computational Mechanistic Chemistry and Drug Discovery, Rhodes University, South Africa
| | - Asimul Islam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India
| | - Md Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India.
| | - Faizan Ahmad
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India
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Sosnowska ME, Jankiewicz U, Kutwin M, Chwalibog A, Gałązka A. Influence of salts and metal nanoparticles on the activity and thermal stability of a recombinant chitinase from Stenotrophomonas maltophilia N4. Enzyme Microb Technol 2018; 116:6-15. [PMID: 29887018 DOI: 10.1016/j.enzmictec.2018.05.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2017] [Revised: 03/08/2018] [Accepted: 05/04/2018] [Indexed: 11/28/2022]
Abstract
Cells of Escherichia coli Rosetta, containing plasmid pET-28a with sequences of DNA of chitinase from Stenotrophomonas maltophilia N4, were used for the efficient synthesis of recombinant chitinolytic enzyme. The objective of this study was to improve thermal stability of the recombinant chitinase by salts and metal nanoparticles (NP). The studied chitinase was thermolabile and largely lost its activity in the first minutes of storage at 50 and 60 °C. The optimum temperature for colloidal chitin hydrolysis by the enzyme was 50 °C. Application of sodium aurothiomalate hydrate and manganese chloride enhanced the activity of the recombinant enzyme. In general, chitinase activity was higher when silver nanoparticles (Ag-NP) were used, but lower for other NP. The thermal stability of chitinase immobilized on Ag-NP and manganese chloride was significantly higher than that of free chitinase. Chitinase thermal stability after gold and manganese oxide nanoparticle application was higher than that of the control at 50 °C. Platinum nanoparticles had no significant effect on thermostability. The Ag-NP had a smaller diameter (from 2 to 20 nm) than Au-NP (from 5 to 70 nm) and Pt-NP (from 4 to 80 nm). The TEM analysis showed that the used NP had a higher affinity for chitinase than for the synthetic substrate. The type, size, and location of the NP on the enzyme played a major role in the thermal stability of chitinase.
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Affiliation(s)
- Malwina Ewa Sosnowska
- Department of Animal Nutrition and Biotechnology, Warsaw University of Life Sciences, Ciszewskiego 8, Warsaw, 02-786 Poland; Department of Biochemistry, Warsaw University of Life Sciences, Nowoursynowska 159, Warsaw, 02-776 Poland
| | - Urszula Jankiewicz
- Department of Biochemistry, Warsaw University of Life Sciences, Nowoursynowska 159, Warsaw, 02-776 Poland
| | - Marta Kutwin
- Department of Animal Nutrition and Biotechnology, Warsaw University of Life Sciences, Ciszewskiego 8, Warsaw, 02-786 Poland
| | - André Chwalibog
- Department of Veterinary and Animal Sciences, University of Copenhagen, Groennegaardsvej 3, 1870 Frederiksberg, Denmark.
| | - Agnieszka Gałązka
- Department of Biochemistry, Warsaw University of Life Sciences, Nowoursynowska 159, Warsaw, 02-776 Poland
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Khan S, Khan FI, Mohammad T, Khan P, Hasan GM, Lobb KA, Islam A, Ahmad F, Imtaiyaz Hassan M. Exploring molecular insights into the interaction mechanism of cholesterol derivatives with the Mce4A: A combined spectroscopic and molecular dynamic simulation studies. Int J Biol Macromol 2018; 111:548-560. [DOI: 10.1016/j.ijbiomac.2017.12.160] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Revised: 11/16/2017] [Accepted: 12/30/2017] [Indexed: 01/08/2023]
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Implications of molecular diversity of chitin and its derivatives. Appl Microbiol Biotechnol 2017; 101:3513-3536. [DOI: 10.1007/s00253-017-8229-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 02/26/2017] [Accepted: 03/04/2017] [Indexed: 02/03/2023]
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Khan FI, Lan D, Durrani R, Huan W, Zhao Z, Wang Y. The Lid Domain in Lipases: Structural and Functional Determinant of Enzymatic Properties. Front Bioeng Biotechnol 2017; 5:16. [PMID: 28337436 PMCID: PMC5343024 DOI: 10.3389/fbioe.2017.00016] [Citation(s) in RCA: 217] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 02/22/2017] [Indexed: 01/08/2023] Open
Abstract
Lipases are important industrial enzymes. Most of the lipases operate at lipid–water interfaces enabled by a mobile lid domain located over the active site. Lid protects the active site and hence responsible for catalytic activity. In pure aqueous media, the lid is predominantly closed, whereas in the presence of a hydrophobic layer, it is partially opened. Hence, the lid controls the enzyme activity. In the present review, we have classified lipases into different groups based on the structure of lid domains. It has been observed that thermostable lipases contain larger lid domains with two or more helices, whereas mesophilic lipases tend to have smaller lids in the form of a loop or a helix. Recent developments in lipase engineering addressing the lid regions are critically reviewed here. After on, the dramatic changes in substrate selectivity, activity, and thermostability have been reported. Furthermore, improved computational models can now rationalize these observations by relating it to the mobility of the lid domain. In this contribution, we summarized and critically evaluated the most recent developments in experimental and computational research on lipase lids.
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Affiliation(s)
- Faez Iqbal Khan
- School of Food Science and Engineering, South China University of Technology, Guangzhou, China; School of Chemistry and Chemical Engineering, Henan University of Technology, Zhengzhou, China
| | - Dongming Lan
- School of Food Science and Engineering, South China University of Technology , Guangzhou , China
| | - Rabia Durrani
- School of Bioscience and Bioengineering, South China University of Technology , Guangzhou , China
| | - Weiqian Huan
- School of Bioscience and Bioengineering, South China University of Technology , Guangzhou , China
| | - Zexin Zhao
- School of Bioscience and Bioengineering, South China University of Technology , Guangzhou , China
| | - Yonghua Wang
- School of Food Science and Engineering, South China University of Technology , Guangzhou , China
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An Q, Wang F, Lan D, Khan FI, Durrani R, Yang B, Wang Y. Improving phospholipase activity of PLA
1
by protein engineering and its effects on oil degumming. EUR J LIPID SCI TECH 2017. [DOI: 10.1002/ejlt.201600110] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Qun An
- School of Bioscience and BioengineeringSouth China University of TechnologyGuangzhouP. R. China
| | - Fanghua Wang
- School of Food Science and EngineeringState Key Laboratory of Pulp and Paper EngineeringSouth China University of TechnologyGuangzhouP. R. China
| | - Dongming Lan
- School of Food Science and EngineeringState Key Laboratory of Pulp and Paper EngineeringSouth China University of TechnologyGuangzhouP. R. China
| | - Faez Iqbal Khan
- School of Chemistry and Chemical EngineeringHenan University of TechnologyZhengzhouP. R. China
| | - Rabia Durrani
- School of Bioscience and BioengineeringSouth China University of TechnologyGuangzhouP. R. China
| | - Bo Yang
- School of Bioscience and BioengineeringSouth China University of TechnologyGuangzhouP. R. China
| | - Yonghua Wang
- School of Food Science and EngineeringState Key Laboratory of Pulp and Paper EngineeringSouth China University of TechnologyGuangzhouP. R. China
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Shamsi TN, Parveen R, Ahamad S, Fatima S. Structural and Biophysical Characterization of Cajanus cajan Protease Inhibitor. J Nat Sci Biol Med 2017; 8:186-192. [PMID: 28781485 PMCID: PMC5523526 DOI: 10.4103/0976-9668.210018] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
CONTEXT A large number of studies have proven that Protease inhibitors (PIs), specifically serine protease inhibitors, show immense divergence in regulation of proteolysis by targeting their specific proteases and hence, they play a key role in healthcare. OBJECTIVE We aimed to access in-vitro anticancer potential of PI from Cajanus cajan (CCPI). Also, crystallization of CCPI was targetted alongwith structure determination and its structure-function relationship. MATERIALS AND METHODS CCPI was purified from Cajanus cajan seeds by chromatographic techniques. The purity and molecular mass was determined by SDS-PAGE. Anticancer potential of CCPI was determined by MTT assay in normal HEK and cancerous A549 cells. The crystallization screening of CCPI was performed by commercially available screens. CCPI sequence was subject to BLASTp with homologous PIs. Progressive multiple alignment was performed using clustalw2 and was modelled using ab initio protocol of I-TASSER. RESULTS The results showed ~14kDa CCPI was purified in homogeneity. Also, CCPI showed low cytotoxic effects of in HEK i.e., 27% as compared with 51% cytotoxicity in A549 cells. CCPI crystallized at 16°C using 15% PEG 6000 in 0.1M potassium phosphate buffer (pH 6.0) in 2-3weeks as rod or needles visualized as clusters under the microscope. The molecular modelling revealed that it contains 3 beta sheets, 3 beta hairpins, 2 β-bulges, 6 strands, 3 helices, 1helix-helix interaction, 41 β-turns and 27 γ-turns. DISCUSSION AND CONCLUSION The results indicate that CCPI may help to treat cancer in vivo aswell. Also, this is the first report on preliminary crystallization and structural studies of CCPI.
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Affiliation(s)
- Tooba Naz Shamsi
- Department of Biotechnology, Jamia Millia Islamia, New Delhi, India
| | - Romana Parveen
- Department of Biotechnology, Jamia Millia Islamia, New Delhi, India
| | - Shahzaib Ahamad
- Department of Biotechnology, College of Engineering and Technology, IFTM, Moradabad, Uttar Pradesh, India
| | - Sadaf Fatima
- Department of Biotechnology, Jamia Millia Islamia, New Delhi, India
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Khan FI, Bisetty K, Gu KR, Singh S, Permaul K, Hassan MI, Wei DQ. Molecular dynamics simulation of chitinase I from Thermomyces lanuginosus SSBP to ensure optimal activity. MOLECULAR SIMULATION 2016. [DOI: 10.1080/08927022.2016.1237024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Faez Iqbal Khan
- School of Chemistry and Chemical Engineering, Henan University of Technology, Henan, China
| | - Krishna Bisetty
- Department of Chemistry, Durban University of Technology, Durban, South Africa
| | - Ke-Ren Gu
- School of Chemistry and Chemical Engineering, Henan University of Technology, Henan, China
| | - Suren Singh
- Department of Biotechnology and Food Technology, Durban University of Technology, Durban, South Africa
| | - Kugen Permaul
- Department of Biotechnology and Food Technology, Durban University of Technology, Durban, South Africa
| | - Md. Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Science, Jamia Millia Islamia, New Delhi, India
| | - Dong-Qing Wei
- School of Chemistry and Chemical Engineering, Henan University of Technology, Henan, China
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A functional natural deep eutectic solvent based on trehalose: Structural and physicochemical properties. Food Chem 2016; 217:560-567. [PMID: 27664672 DOI: 10.1016/j.foodchem.2016.09.012] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 08/16/2016] [Accepted: 09/03/2016] [Indexed: 11/21/2022]
Abstract
In this study, the natural deep eutectic solvents (NADESs) based on trehalose and choline chloride have been prepared to enhance the protein thermostability. The results of fourier transform infrared spectroscopy and (1)H nuclear magnetic resonance spectroscopy suggested that there were intensive hydrogen-bonding interactions between trehalose and choline chloride in TCCL3-DES and TCCL3-DES75. The physicochemical properties of TCCL3-DES and TCCL3-DES75 were investigated in the temperature range of 293.15-363.15K. Our results revealed that the thermostability of lysozyme, a model protein used in this study was dramatically increased in TCCL3-DES75, as evidenced by the disappearance of the denaturing peak from their Differential Scanning Calorimetry (DSC) traces. The results of circular dichroism (CD) experiments further demonstrated that the lysozyme in TCCL3-DES75 unfolded partially at 90°C and recovered to the initial structure at 20°C. The study suggests that TCCL3-DES75 might be a potential solvent for stabilizing proteins.
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Khan FI, Bisetty K, Singh S, Permaul K, Hassan MI. Chitinase from Thermomyces lanuginosus SSBP and its biotechnological applications. Extremophiles 2016; 19:1055-66. [PMID: 26462798 DOI: 10.1007/s00792-015-0792-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Accepted: 10/03/2015] [Indexed: 12/30/2022]
Abstract
Chitinases are ubiquitous class of extracellular enzymes, which have gained attention in the past few years due to their wide biotechnological applications. The effectiveness of conventional insecticides is increasingly compromised by the occurrence of resistance; thus, chitinase offers a potential alternative to the use of chemical fungicides. The thermostable enzymes from thermophilic microorganisms have numerous industrial, medical, environmental and biotechnological applications due to their high stability for temperature and pH. Thermomyces lanuginosus produced a large number of chitinases, of which chitinase I and II are successfully cloned and purified recently. Molecular dynamic simulations revealed that the stability of these enzymes are maintained even at higher temperature. In this review article we have focused on chitinases from different sources, mainly fungal chitinase of T. lanuginosus and its industrial application.
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Khan FI, Nizami B, Anwer R, Gu KR, Bisetty K, Hassan MI, Wei DQ. Structure prediction and functional analyses of a thermostable lipase obtained from Shewanella putrefaciens. J Biomol Struct Dyn 2016; 35:2123-2135. [PMID: 27366981 DOI: 10.1080/07391102.2016.1206837] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Previous experimental studies on thermostable lipase from Shewanella putrefaciens suggested the maximum activity at higher temperatures, but with little information on its conformational profile. In this study, the three-dimensional structure of lipase was predicted and a 60 ns molecular dynamics (MD) simulation was carried out at temperatures ranging from 300 to 400 K to better understand its thermostable nature at the molecular level. MD simulations were performed in order to predict the optimal activity of thermostable lipase. The results suggested strong conformational temperature dependence. The thermostable lipase maintained its bio-active conformation at 350 K during the 60 ns MD simulations.
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Affiliation(s)
- Faez Iqbal Khan
- a School of Chemistry and Chemical Engineering , Henan University of Technology , Zhengzhou 450001 , Henan , China
| | - Bilal Nizami
- b School of Pharmacy and Pharmacology , University of KwaZulu-Natal , Durban 4000 , South Africa
| | - Razique Anwer
- c Department of Anatomy (Microbiology) , Al-Imam Muhammad Ibn Saud Islamic University , Riyadh , Saudi Arabia
| | - Ke-Ren Gu
- a School of Chemistry and Chemical Engineering , Henan University of Technology , Zhengzhou 450001 , Henan , China
| | - Krishna Bisetty
- d Department of Chemistry , Durban University of Technology , Durban 4000 , South Africa
| | - Md Imtaiyaz Hassan
- e Centre for Interdisciplinary Research in Basic Science, Jamia Millia Islamia , New Delhi 110025 , India
| | - Dong-Qing Wei
- a School of Chemistry and Chemical Engineering , Henan University of Technology , Zhengzhou 450001 , Henan , China
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Khan FI, Aamir M, Wei DQ, Ahmad F, Hassan MI. Molecular mechanism of Ras-related protein Rab-5A and effect of mutations in the catalytically active phosphate-binding loop. J Biomol Struct Dyn 2016; 35:105-118. [PMID: 26727234 DOI: 10.1080/07391102.2015.1134346] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Ras-related protein (Rab-5a) is primarily involved in the regulation of early endosome fusion during endocytosis and takes part in the budding process. During GTP hydrolysis, Rab5a was spotted in the cytoplasmic side of early endosomes in association with the GTP. Previous study suggested that the substitution of alanine with proline at position 30 of Rab5a reduces the GTPase activity around 12-fold, while, with arginine substitution stimulates the intrinsic GTP hydrolysis by 5-fold. Most of the other substitutions at this position show a little or no effect on the GTPase activity. In this paper, structure analysis and molecular dynamics (MD) simulation studies of human Rab5a and its mutants have been extensively carried out. The effect of binding of a non-hydrolyzable GTP analog guanosine-5'-(β, γ)-imidotriphosphate (GppNHp) with Rab5a and its mutants are described. The objective of the current study is to perform a detailed examination of structural flexibility of Rab5a and its mutants p.Ala30Pro and p.Ala30Arg using MD simulations. Our observations suggest that mutant p.Ala30Arg stabilize the protein molecule when bound to GppNHp which offers additional contacts. Despite an in silico approach, this study provides a deep insight into the impact of mutation on the structure, function, stability, and mechanism of binding of GppNHp to the Rab5a at molecular level.
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Affiliation(s)
- Faez Iqbal Khan
- a School of Chemistry and Chemical Engineering , Henan University of Technology , Henan 450001 , China
| | - Mohd Aamir
- b Centre for Interdisciplinary Research in Basic Science , Jamia Millia Islamia , New Delhi 110025 , India
| | - Dong-Qing Wei
- a School of Chemistry and Chemical Engineering , Henan University of Technology , Henan 450001 , China
| | - Faizan Ahmad
- b Centre for Interdisciplinary Research in Basic Science , Jamia Millia Islamia , New Delhi 110025 , India
| | - Md Imtaiyaz Hassan
- b Centre for Interdisciplinary Research in Basic Science , Jamia Millia Islamia , New Delhi 110025 , India
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Khan FI, Wei DQ, Gu KR, Hassan MI, Tabrez S. Current updates on computer aided protein modeling and designing. Int J Biol Macromol 2016; 85:48-62. [DOI: 10.1016/j.ijbiomac.2015.12.072] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Revised: 12/17/2015] [Accepted: 12/21/2015] [Indexed: 12/15/2022]
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Kovacic F, Mandrysch A, Poojari C, Strodel B, Jaeger KE. Structural features determining thermal adaptation of esterases. Protein Eng Des Sel 2016; 29:65-76. [PMID: 26647400 PMCID: PMC5943684 DOI: 10.1093/protein/gzv061] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Revised: 10/26/2015] [Accepted: 10/28/2015] [Indexed: 11/14/2022] Open
Abstract
The adaptation of microorganisms to extreme living temperatures requires the evolution of enzymes with a high catalytic efficiency under these conditions. Such extremophilic enzymes represent valuable tools to study the relationship between protein stability, dynamics and function. Nevertheless, the multiple effects of temperature on the structure and function of enzymes are still poorly understood at the molecular level. Our analysis of four homologous esterases isolated from bacteria living at temperatures ranging from 10°C to 70°C suggested an adaptation route for the modulation of protein thermal properties through the optimization of local flexibility at the protein surface. While the biochemical properties of the recombinant esterases are conserved, their thermal properties have evolved to resemble those of the respective bacterial habitats. Molecular dynamics simulations at temperatures around the optimal temperatures for enzyme catalysis revealed temperature-dependent flexibility of four surface-exposed loops. While the flexibility of some loops increased with raising the temperature and decreased with lowering the temperature, as expected for those loops contributing to the protein stability, other loops showed an increment of flexibility upon lowering and raising the temperature. Preserved flexibility in these regions seems to be important for proper enzyme function. The structural differences of these four loops, distant from the active site, are substantially larger than for the overall protein structure, indicating that amino acid exchanges within these loops occurred more frequently thereby allowing the bacteria to tune atomic interactions for different temperature requirements without interfering with the overall enzyme function.
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Affiliation(s)
- Filip Kovacic
- Institute of Molecular Enzyme Technology, Heinrich-Heine-University Duesseldorf, Forschungszentrum Juelich, D-52426 Juelich, Germany
| | - Agathe Mandrysch
- Institute of Molecular Enzyme Technology, Heinrich-Heine-University Duesseldorf, Forschungszentrum Juelich, D-52426 Juelich, Germany
| | - Chetan Poojari
- Institute of Complex Systems, ICS-6: Structural Biochemistry, Forschungszentrum Juelich GmbH, D-52426 Juelich, Germany Department of Physics, Tampere University of Technology, FI-33101 Tampere, Finland
| | - Birgit Strodel
- Institute of Complex Systems, ICS-6: Structural Biochemistry, Forschungszentrum Juelich GmbH, D-52426 Juelich, Germany Institute of Theoretical and Computational Chemistry, Heinrich-Heine-University Duesseldorf, D-40225 Düsseldorf, Germany
| | - Karl-Erich Jaeger
- Institute of Molecular Enzyme Technology, Heinrich-Heine-University Duesseldorf, Forschungszentrum Juelich, D-52426 Juelich, Germany Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Juelich GmbH, D-52426 Juelich, Germany
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43
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Yang S, Fu X, Yan Q, Jiang Z, Wang J. Biochemical Characterization of a Novel Acidic Exochitinase from Rhizomucor miehei with Antifungal Activity. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2016; 64:461-469. [PMID: 26709620 DOI: 10.1021/acs.jafc.5b05127] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
A novel chitinase gene (RmChi44) from Rhizomucor miehei was cloned and expressed in Escherichia coli as an intracellular soluble and active protein. The recombinant chitinase (RmChi44) was purified to homogeneity and biochemically characterized. The molecular mass of RmChi44 was estimated to be 44.6 kDa on SDS-PAGE. RmChi44 displayed an acidic pH optimum of 4.5 and was stable within pH 4.5-9.0. The optimal temperature of RmChi44 was found to be 50 °C. The Km values of RmChi44 for colloidal chitin and glycol chitin were 4.02 and 1.55 mg/mL, respectively. RmChi44 hydrolyzed colloidal chitin to yield mainly N-acetyl chitobiose, exhibiting an exotype cleavage pattern. Moreover, the enzyme displayed β-N-acetylglucosaminidase activity, splitting N-acetyl COSs with degree of polymerization (DP) 2-5 into their monomer. In addition, RmChi44 showed antifungal activity against some phytopathogenic fungi. This is the first report on an exochitinase showing β-N-acetylglucosaminidase activity and antifungal activity from Rhizomucor species.
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Affiliation(s)
- Shaoqing Yang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University , Beijing 100083, China
| | - Xin Fu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University , Beijing 100083, China
| | - Qiaojuan Yan
- Bioresource Utilization Laboratory, College of Engineering, China Agricultural University , Beijing 100083, China
| | - Zhengqiang Jiang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University , Beijing 100083, China
| | - Jing Wang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University , Beijing 100083, China
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44
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Gramany V, Khan FI, Govender A, Bisetty K, Singh S, Permaul K. Cloning, expression, and molecular dynamics simulations of a xylosidase obtained from Thermomyces lanuginosus. J Biomol Struct Dyn 2015; 34:1681-92. [DOI: 10.1080/07391102.2015.1089186] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Vashni Gramany
- Department of Biotechnology and Food Technology, Durban University of Technology, P.O. Box 1334, Durban 4001, South Africa
| | - Faez Iqbal Khan
- Department of Biotechnology and Food Technology, Durban University of Technology, P.O. Box 1334, Durban 4001, South Africa
- Department of Chemistry, Durban University of Technology, P.O. Box 1334, Durban 4001, South Africa
| | - Algasan Govender
- Department of Biotechnology and Food Technology, Durban University of Technology, P.O. Box 1334, Durban 4001, South Africa
| | - Krishna Bisetty
- Department of Chemistry, Durban University of Technology, P.O. Box 1334, Durban 4001, South Africa
| | - Suren Singh
- Department of Biotechnology and Food Technology, Durban University of Technology, P.O. Box 1334, Durban 4001, South Africa
| | - Kugenthiren Permaul
- Department of Biotechnology and Food Technology, Durban University of Technology, P.O. Box 1334, Durban 4001, South Africa
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45
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Anwer R, Qumaizi KIA, Shaqha WMA, Khan FI. From Pancreatic to Non-Pancreatic Insulin: A Miraculous Journey. ACTA ACUST UNITED AC 2015. [DOI: 10.3923/ijbc.2015.302.317] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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46
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Large scale analysis of the mutational landscape in β-glucuronidase: A major player of mucopolysaccharidosis type VII. Gene 2015; 576:36-44. [PMID: 26415878 DOI: 10.1016/j.gene.2015.09.062] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Revised: 08/17/2015] [Accepted: 09/23/2015] [Indexed: 11/22/2022]
Abstract
The lysosomal storage disorders are a group of 50 unique inherited diseases characterized by unseemly lipid storage in lysosomes. These malfunctions arise due to genetic mutations that result in deficiency or reduced activities of the lysosomal enzymes, which are responsible for catabolism of biological macromolecules. Sly syndrome or mucopolysaccharidosis type VII is a lysosomal storage disorder associated with the deficiency of β-glucuronidase (EC 3.2.1.31) that catalyzes the hydrolysis of β-D-glucuronic acid residues from the non-reducing terminal of glycosaminoglycan. The effects of the disease causing mutations on the framework of the sequences and structure of β-glucuronidase (GUSBp) were analyzed utilizing a variety of bioinformatic tools. These analyses showed that 211 mutations may result in alteration of the biological activity of GUSBp, including previously experimentally validated mutations. Finally, we refined 90 disease causing mutations, which presumably cause a significant impact on the structure, function, and stability of GUSBp. Stability analyses showed that mutations p.Phe208Pro, p.Phe539Gly, p.Leu622Gly, p.Ile499Gly and p.Ile586Gly caused the highest impact on GUSBp stability and function because of destabilization of the protein structure. Furthermore, structures of wild type and mutant GUSBp were subjected to molecular dynamics simulation to examine the relative structural behaviors in the explicit conditions of water. In a broader view, the use of in silico approaches provided a useful understanding of the effect of single point mutations on the structure-function relationship of GUSBp.
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