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López‐Pérez E, de Gómez‐Puyou MT, Nuñez CJ, Zapién DM, Guardado SA, Beltrán HI, Pérez‐Hernández G. Ordered-domain unfolding of thermophilic isolated β subunit ATP synthase. Protein Sci 2023; 32:e4689. [PMID: 37252686 PMCID: PMC10273367 DOI: 10.1002/pro.4689] [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] [Received: 10/13/2022] [Revised: 05/23/2023] [Accepted: 05/25/2023] [Indexed: 05/31/2023]
Abstract
The flexibility of the ATP synthase's β subunit promotes its role in the ATP synthase rotational mechanism, but its domains stability remains unknown. A reversible thermal unfolding of the isolated β subunit (Tβ) of the ATP synthase from Bacillus thermophilus PS3, tracked through circular dichroism and molecular dynamics, indicated that Tβ shape transits from an ellipsoid to a molten globule through an ordered unfolding of its domains, preserving the β-sheet residual structure at high temperature. We determined that part of the stability origin of Tβ is due to a transversal hydrophobic array that crosses the β-barrel formed at the N-terminal domain and the Rossman fold of the nucleotide-binding domain (NBD), while the helix bundle of the C-terminal domain is the less stable due to the lack of hydrophobic residues, and thus the more flexible to trigger the rotational mechanism of the ATP synthase.
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Affiliation(s)
- Edgar López‐Pérez
- Unidad Cuajimalpa, Departamento de Ciencias NaturalesUniversidad Autónoma MetropolitanaCiudad de MéxicoMexico
| | - Marietta Tuena de Gómez‐Puyou
- Departamento de Bioquímica y Biología EstructuralInstituto de Fisiología Celular, Universidad Nacional Autónoma de MéxicoCiudad de MéxicoMexico
| | - Concepción José Nuñez
- Departamento de Bioquímica y Biología EstructuralInstituto de Fisiología Celular, Universidad Nacional Autónoma de MéxicoCiudad de MéxicoMexico
| | - Denise Martínez Zapién
- Unidad Cuajimalpa, Departamento de Ciencias NaturalesUniversidad Autónoma MetropolitanaCiudad de MéxicoMexico
| | - Salomón Alas Guardado
- Unidad Cuajimalpa, Departamento de Ciencias NaturalesUniversidad Autónoma MetropolitanaCiudad de MéxicoMexico
| | - Hiram Isaac Beltrán
- División de Ciencias Básicas e Ingeniería, Departamento de Ciencias BásicasUniversidad Autónoma Metropolitana, Unidad AzcapotzalcoCiudad de MéxicoMexico
| | - Gerardo Pérez‐Hernández
- Unidad Cuajimalpa, Departamento de Ciencias NaturalesUniversidad Autónoma MetropolitanaCiudad de MéxicoMexico
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2
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Liang Q, Yuan M, Xu L, Lio E, Zhang F, Mou H, Secundo F. Application of enzymes as a feed additive in aquaculture. MARINE LIFE SCIENCE & TECHNOLOGY 2022; 4:208-221. [PMID: 37073222 PMCID: PMC10077164 DOI: 10.1007/s42995-022-00128-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 02/28/2022] [Indexed: 05/03/2023]
Abstract
Modern aquaculture must be sustainable in terms of energy consumption, raw materials used, and environmental impact, so alternatives are needed to replace fish feed with other raw materials. Enzyme use in the agri-food industry is based on their efficiency, safety, and protection of the environment, which aligns with the requirements of a resource-saving production system. Enzyme supplementation in fish feed can improve digestibility and absorption of both plant- and animal-derived ingredients, increasing the growth parameters of aquacultural animals. Herein we summarized the recent literature that reported the use of digestive enzymes (amylases, lipases, proteases, cellulases, and hemicellulases) and non-digestive enzymes (phytases, glucose oxidase, and lysozyme) in fish feed. In addition, we analyzed how critical steps of the pelleting process, including microencapsulation and immobilization, can interfere with enzyme activity in the final fish feed product. Supplementary Information The online version contains supplementary material available at 10.1007/s42995-022-00128-z.
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Affiliation(s)
- Qingping Liang
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266003 China
| | - Mingxue Yuan
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266003 China
| | - Liping Xu
- College of Biology and Geography, Yili Normal University, Yining, 835000 China
| | - Elia Lio
- Istituto di Scienze e Tecnologie Chimiche “Giulio Natta”, CNR, Via Mario Bianco n. 9, 20131 Milan, Italy
| | - Fang Zhang
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266003 China
| | - Haijin Mou
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266003 China
| | - Francesco Secundo
- Istituto di Scienze e Tecnologie Chimiche “Giulio Natta”, CNR, Via Mario Bianco n. 9, 20131 Milan, Italy
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3
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Mulliri S, Laaksonen A, Spanu P, Farris R, Farci M, Mingoia F, Roviello GN, Mocci F. Spectroscopic and In Silico Studies on the Interaction of Substituted Pyrazolo[1,2-a]benzo[1,2,3,4]tetrazine-3-one Derivatives with c-Myc G4-DNA. Int J Mol Sci 2021; 22:6028. [PMID: 34199659 PMCID: PMC8199725 DOI: 10.3390/ijms22116028] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 05/29/2021] [Accepted: 05/30/2021] [Indexed: 12/14/2022] Open
Abstract
Herein we describe a combined experimental and in silico study of the interaction of a series of pyrazolo[1,2-a]benzo[1,2,3,4]tetrazin-3-one derivatives (PBTs) with parallel G-quadruplex (GQ) DNA aimed at correlating their previously reported anticancer activities and the stabilizing effects observed by us on c-myc oncogene promoter GQ structure. Circular dichroism (CD) melting experiments were performed to characterize the effect of the studied PBTs on the GQ thermal stability. CD measurements indicate that two out of the eight compounds under investigation induced a slight stabilizing effect (2-4 °C) on GQ depending on the nature and position of the substituents. Molecular docking results allowed us to verify the modes of interaction of the ligands with the GQ and estimate the binding affinities. The highest binding affinity was observed for ligands with the experimental melting temperatures (Tms). However, both stabilizing and destabilizing ligands showed similar scores, whilst Molecular Dynamics (MD) simulations, performed across a wide range of temperatures on the GQ in water solution, either unliganded or complexed with two model PBT ligands with the opposite effect on the Tms, consistently confirmed their stabilizing or destabilizing ability ascertained by CD. Clues about a relation between the reported anticancer activity of some PBTs and their ability to stabilize the GQ structure of c-myc emerged from our study. Furthermore, Molecular Dynamics simulations at high temperatures are herein proposed for the first time as a means to verify the stabilizing or destabilizing effect of ligands on the GQ, also disclosing predictive potential in GQ-targeting drug discovery.
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Affiliation(s)
- Simone Mulliri
- Department of Chemical and Geological Sciences, University of Cagliari, I-09042 Monserrato, Italy; (S.M.); (R.F.); (M.F.)
| | - Aatto Laaksonen
- State Key Laboratory of Materials-Oriented and Chemical Engineering, Nanjing Tech University, Nanjing 210009, China
- Division of Physical Chemistry, Department of Materials and Environmental Chemistry, Arrhenius Laboratory, Stockholm University, 10691 Stockholm, Sweden
- Centre of Advanced Research in Bionanoconjugates and Biopolymers, Petru Poni Institute of Macromolecular Chemistry, 700487 Iasi, Romania
- Department of Engineering Sciences and Mathematics, Division of Energy Science, Luleå University of Technology, SE-97187 Luleå, Sweden
| | - Pietro Spanu
- Istituto di Chimica Biomolecolare, ICB-CNR-Trav. La Crucca 3, 07100 Sassari, Italy;
| | - Riccardo Farris
- Department of Chemical and Geological Sciences, University of Cagliari, I-09042 Monserrato, Italy; (S.M.); (R.F.); (M.F.)
| | - Matteo Farci
- Department of Chemical and Geological Sciences, University of Cagliari, I-09042 Monserrato, Italy; (S.M.); (R.F.); (M.F.)
| | - Francesco Mingoia
- Istituto per lo Studio dei Materiali Nanostrutturati ISMN-CNR, Via U. La Malfa 153, I-90146 Palermo, Italy;
| | - Giovanni N. Roviello
- Istituto di Biostrutture e Bioimmagini, IBB-CNR, Via Mezzocannone 16, I-80134 Naples, Italy
| | - Francesca Mocci
- Department of Chemical and Geological Sciences, University of Cagliari, I-09042 Monserrato, Italy; (S.M.); (R.F.); (M.F.)
- Centre of Advanced Research in Bionanoconjugates and Biopolymers, Petru Poni Institute of Macromolecular Chemistry, 700487 Iasi, Romania
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5
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Janati-Fard F, Housaindokht MR, Monhemi H, Esmaeili AA, Nakhaei Pour A. The influence of two imidazolium-based ionic liquids on the structure and activity of glucose oxidase: Experimental and theoretical studies. Int J Biol Macromol 2018; 114:656-665. [DOI: 10.1016/j.ijbiomac.2018.03.083] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Revised: 02/27/2018] [Accepted: 03/17/2018] [Indexed: 01/27/2023]
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Petrović D, Frank D, Kamerlin SCL, Hoffmann K, Strodel B. Shuffling Active Site Substate Populations Affects Catalytic Activity: The Case of Glucose Oxidase. ACS Catal 2017; 7:6188-6197. [PMID: 29291138 PMCID: PMC5745072 DOI: 10.1021/acscatal.7b01575] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2017] [Revised: 07/25/2017] [Indexed: 12/17/2022]
Abstract
![]()
Glucose oxidase has
wide applications in the pharmaceutical, chemical,
and food industries. Many recent studies have enhanced key properties
of this enzyme using directed evolution, yet without being able to
reveal why these mutations are actually beneficial. This work presents
a synergistic combination of experimental and computational methods,
indicating how mutations, even when distant from the active site,
positively affect glucose oxidase catalysis. We have determined the
crystal structures of glucose oxidase mutants containing molecular
oxygen in the active site. The catalytically important His516 residue
has been previously shown to be flexible in the wild-type enzyme.
The molecular dynamics simulations performed in this work allow us
to quantify this floppiness, revealing that His516 exists in two states:
catalytic and noncatalytic. The relative populations of these two
substates are almost identical in the wild-type enzyme, with His516
readily shuffling between them. In the glucose oxidase mutants, on
the other hand, the mutations enrich the catalytic His516 conformation
and reduce the flexibility of this residue, leading to an enhancement
in their catalytic efficiency. This study stresses the benefit of
active site preorganization with respect to enzyme conversion rates
by reducing molecular reorientation needs. We further suggest that
the computational approach based on Hamiltonian replica exchange molecular
dynamics, used in this study, may be a general approach to screening
in silico for improved enzyme variants involving flexible catalytic
residues.
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Affiliation(s)
- Dušan Petrović
- Institute
of Complex Systems: Structural Biochemistry, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - David Frank
- Institute
of Molecular Biotechnology, RWTH Aachen University, Worringerweg
1, 52074 Aachen, Germany
| | | | - Kurt Hoffmann
- Institute
of Molecular Biotechnology, RWTH Aachen University, Worringerweg
1, 52074 Aachen, Germany
| | - Birgit Strodel
- Institute
of Complex Systems: Structural Biochemistry, Forschungszentrum Jülich, 52425 Jülich, Germany
- Institute
of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
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7
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Janati-Fard F, Housaindokht MR, Monhemi H, Nakhaeipour A. How a multimeric macromolecule is affected by divalent salts? Experimental and simulation study. Int J Biol Macromol 2017; 106:284-292. [PMID: 28782614 DOI: 10.1016/j.ijbiomac.2017.08.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Revised: 07/29/2017] [Accepted: 08/02/2017] [Indexed: 10/19/2022]
Abstract
Salts exist in any cell and living organism in contact with biological macromolecules. How these salts affect biomolecules such as enzyme is important from both basic sciences and practical technologies. It was observed that divalent salts can change structure and function of protein at higher concentrations. Here, we investigated the effect of divalent salt on the behavior of a multimeric enzyme. We treated glucose oxidase as dimer-active enzyme in different CaCl2 concentration and seen that the enzyme become inactive at high concentration of salt. These experimental results are in agreement with recently published researches. To find a possible mechanism, a series of molecular dynamics simulation of the enzyme were performed at different salt concentration. According to the MD simulation, the conformational changes at the active site and FAD-binding site support the hypothesis of enzyme inactivation at high CaCl2 concentration. MD simulations also showed that enzyme has an unstable conformation at higher salt concentration which is in agreement with our experimental data. Detailed structural properties of the enzyme have been analyzed under different conditions. To the best of our knowledge, this is the first study that bears detailed structural mechanism about the salt effects on multimeric macromolecules.
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Affiliation(s)
- Fatemeh Janati-Fard
- Biophysical Chemistry Laboratory, Department of Chemistry, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Mohammad R Housaindokht
- Biophysical Chemistry Laboratory, Department of Chemistry, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran; Research and Technology Center of Biomolecules, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran.
| | - Hassan Monhemi
- Research and Technology Center of Biomolecules, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Ali Nakhaeipour
- Biophysical Chemistry Laboratory, Department of Chemistry, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran
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Dubey MK, Zehra A, Aamir M, Meena M, Ahirwal L, Singh S, Shukla S, Upadhyay RS, Bueno-Mari R, Bajpai VK. Improvement Strategies, Cost Effective Production, and Potential Applications of Fungal Glucose Oxidase (GOD): Current Updates. Front Microbiol 2017; 8:1032. [PMID: 28659876 PMCID: PMC5468390 DOI: 10.3389/fmicb.2017.01032] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 05/23/2017] [Indexed: 01/15/2023] Open
Abstract
Fungal glucose oxidase (GOD) is widely employed in the different sectors of food industries for use in baking products, dry egg powder, beverages, and gluconic acid production. GOD also has several other novel applications in chemical, pharmaceutical, textile, and other biotechnological industries. The electrochemical suitability of GOD catalyzed reactions has enabled its successful use in bioelectronic devices, particularly biofuel cells, and biosensors. Other crucial aspects of GOD such as improved feeding efficiency in response to GOD supplemental diet, roles in antimicrobial activities, and enhancing pathogen defense response, thereby providing induced resistance in plants have also been reported. Moreover, the medical science, another emerging branch where GOD was recently reported to induce several apoptosis characteristics as well as cellular senescence by downregulating Klotho gene expression. These widespread applications of GOD have led to increased demand for more extensive research to improve its production, characterization, and enhanced stability to enable long term usages. Currently, GOD is mainly produced and purified from Aspergillus niger and Penicillium species, but the yield is relatively low and the purification process is troublesome. It is practical to build an excellent GOD-producing strain. Therefore, the present review describes innovative methods of enhancing fungal GOD production by using genetic and non-genetic approaches in-depth along with purification techniques. The review also highlights current research progress in the cost effective production of GOD, including key advances, potential applications and limitations. Therefore, there is an extensive need to commercialize these processes by developing and optimizing novel strategies for cost effective GOD production.
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Affiliation(s)
- Manish K. Dubey
- Laboratory of Mycopathology and Microbial Technology, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu UniversityVaranasi, India
| | - Andleeb Zehra
- Laboratory of Mycopathology and Microbial Technology, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu UniversityVaranasi, India
| | - Mohd Aamir
- Laboratory of Mycopathology and Microbial Technology, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu UniversityVaranasi, India
| | - Mukesh Meena
- Laboratory of Mycopathology and Microbial Technology, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu UniversityVaranasi, India
| | - Laxmi Ahirwal
- Laboratory of Molecular Biology, Department of Botany, Dr. Hari Singh Gour UniversitySagar, India
| | - Siddhartha Singh
- Laboratory of Molecular Biology, Department of Botany, Dr. Hari Singh Gour UniversitySagar, India
| | - Shruti Shukla
- Department of Energy and Materials Engineering, Dongguk UniversitySeoul, South Korea
| | - Ram S. Upadhyay
- Laboratory of Mycopathology and Microbial Technology, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu UniversityVaranasi, India
| | - Ruben Bueno-Mari
- Research and Development (R+D) Department, Laboratorios LokímicaValencia, Spain
| | - Vivek K. Bajpai
- Department of Applied Microbiology and Biotechnology, Yeungnam UniversityGyeongsan, South Korea
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9
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Janati-Fard F, Housaindokht MR, Monhemi H. Investigation of structural stability and enzymatic activity of glucose oxidase and its subunits. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/j.molcatb.2016.09.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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10
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Molecular Dynamic Studies of the Complex Polyethylenimine and Glucose Oxidase. Int J Mol Sci 2016; 17:ijms17111796. [PMID: 27801788 PMCID: PMC5133797 DOI: 10.3390/ijms17111796] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Revised: 10/18/2016] [Accepted: 10/20/2016] [Indexed: 12/28/2022] Open
Abstract
Glucose oxidase (GOx) is an enzyme produced by Aspergillus, Penicillium and other fungi species. It catalyzes the oxidation of β-d-glucose (by the molecular oxygen or other molecules, like quinones, in a higher oxidation state) to form d-glucono-1,5-lactone, which hydrolyses spontaneously to produce gluconic acid. A coproduct of this enzymatic reaction is hydrogen peroxide (H2O2). GOx has found several commercial applications in chemical and pharmaceutical industries including novel biosensors that use the immobilized enzyme on different nanomaterials and/or polymers such as polyethylenimine (PEI). The problem of GOx immobilization on PEI is retaining the enzyme native activity despite its immobilization onto the polymer surface. Therefore, the molecular dynamic (MD) study of the PEI ligand (C14N8_07_B22) and the GOx enzyme (3QVR) was performed to examine the final complex PEI-GOx stabilization and the affinity of the PEI ligand to the docking sites of the GOx enzyme. The docking procedure showed two places/regions of major interaction of the protein with the polymer PEI: (LIG1) of −5.8 kcal/mol and (LIG2) of −4.5 kcal/mol located inside the enzyme and on its surface, respectively. The values of enthalpy for the PEI-enzyme complex, located inside of the protein (LIG1) and on its surface (LIG2) were computed. Docking also discovered domains of the GOx protein that exhibit no interactions with the ligand or have even repulsive characteristics. The structural data clearly indicate some differences in the ligand PEI behavior bound at the two places/regions of glucose oxidase.
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Kumar K, Patel K, Agrawal DC, Khire JM. Insights into the unfolding pathway and identification of thermally sensitive regions of phytase from Aspergillus niger by molecular dynamics simulations. J Mol Model 2015; 21:163. [PMID: 26037148 DOI: 10.1007/s00894-015-2696-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Accepted: 05/04/2015] [Indexed: 11/29/2022]
Abstract
Thermal stability is of great importance in the application of commercial phytases. Phytase A (PhyA) is a monomeric protein comprising twelve α-helices and ten β-sheets. Comparative molecular dynamics (MD) simulations (at 310, 350, 400, and 500 K) revealed that the thermal stability of PhyA from Aspergillus niger (A. niger) is associated with its conformational rigidity. The most thermally sensitive regions were identified as loops 8 (residues 83-106), 10 (161-174), 14 (224-230), 17 (306-331), and 24 (442-444), which are present on the surface of the protein. It was observed that solvent-exposed loops denature before or show higher flexibility than buried residues. We observed that PhyA begins to unfold at loops 8 and 14, which further extends to loop 24 at the C-terminus. The intense movement of loop 8 causes the helix H2 and beta-sheet B3 to fluctuate at high temperature. The high flexibility of the H2, H10, and H12 helices at high temperature resulted in complete denaturation. The high mobility of loop 14 easily transfers to the adjacent helices H7, H8, and H9, which fluctuate and partially unfold at high temperature (500 K). It was also observed that the salt bridges Asp110-Lys149, Asp205-Lys277, Asp335-Arg136, Asp416-Arg420, and Glu387-Arg400 are important influences on the structural stability but not the thermostability, as the lengths of these salt bridges did not increase with rising temperature. The salt bridges Glu125-Arg163, Asp299-Arg136, Asp266-Arg219, Asp339-Lys278, Asp335-Arg136, and Asp424-Arg428 are all important for thermostability, as the lengths of these bridges increased dramatically with increasing temperature. Here, for the first time, we have computationally identified the thermolabile regions of PhyA, and this information could be used to engineer novel thermostable phytases. Numerous homologous phytases of fungal as well as bacterial origin are known, and these homologs show high sequence similarity. Our findings could prove useful in attempts to increase the thermostability of homologous phytases via protein engineering.
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Affiliation(s)
- Kapil Kumar
- NCIM, Biochemical Sciences Division, Dr. Homi Bhabha Road, Pune, 411 008, India
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