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De Souza TPP, Cantão LXS, Rodrigues MQRB, Gonçalves DB, Nagem RAP, Rocha REO, Godoi RR, Lima WJN, Galdino AS, Minardi RCDM, Lima LHFD. Glycosylation and charge distribution orchestrates the conformational ensembles of a biotechnologically promissory phytase in different pHs - a computational study. J Biomol Struct Dyn 2024; 42:5030-5041. [PMID: 37325852 DOI: 10.1080/07391102.2023.2223685] [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: 03/27/2023] [Accepted: 06/06/2023] [Indexed: 06/17/2023]
Abstract
Phytases [myo-inositol(1,2,3,4,5,6) hexakisphosphate phosphohydrolases] are phytate-specific phosphatases not present in monogastric animals. Nevertheless, they are an essential supplement to feeding such animals and for human special diets. It is crucial, hence, the biotechnological use of phytases with intrinsic stability and activity at the acid pHs from gastric environments. Here we use Metadynamics (METADY) simulations to probe the conformational space of the Aspergillus nidulans phytase and the differential effects of pH and glycosylation in this same space. The results suggest that strategic combinations of pH and glycosylation affect the stability of native-like conformations and alternate these structures from a metastable to a stable profile. Furthermore, the protein segments previously reported as more thermosensitive in phytases from this family present a pivotal role in the conformational changes at different conditions, especially H2, H5-7, L8, L10, L12, and L17. Also, the glycosylations and the pH-dependent charge balance modulate the mobility and interactions at these same regions, with consequences for the surface solvation and active site exposition. Finally, although the glycosylations have stabilized the native structure and improved the substrate docking at all the studied pHs, the data suggest a higher phytate receptivity at catalytic poses for the unglycosylated structure at pH 6.5 and the glycosylated one at pH 4.5. This behavior agrees with the exact change in optimum pH reported for this enzyme, expressed on low or high glycosylating systems. We hope the results and insights presented here will be helpful in future approaches for rational engineering of technologically promising phytases and intelligent planning of their heterologous expression systems and conditions for use.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Thaís P P De Souza
- Microbial Biotechnology Laboratory, Universidade Federal de São João Del-Rei, Divinópolis, Minas Gerais, Brazil
| | - Letícia Xavier Silva Cantão
- Laboratory of Bioinformatics and Systems (LBS), Department Of Computer Science, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | | | - Daniel Bonoto Gonçalves
- Department of Biosystems Engineering, Universidade Federal de São João Del-Rei, São João Del-Rei, Minas Gerais, Brazil
| | - Ronaldo Alves Pinto Nagem
- Institute of Biological Sciences Department of Biochemistry and Immunology, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Rafael Eduardo Oliveira Rocha
- Laboratory of Bioinformatics and Systems (LBS), Department Of Computer Science, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
- Laboratory Of Molecular Modeling and Bioinformatics, Department of Exacts and Biological Sciences (DECEB), Universidade Federal de São João Del-Rei, Sete Lagoas, Minas Gerais, Brazil
| | - Renato Ramos Godoi
- Institute of Biological Sciences Department of Biochemistry and Immunology, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - William James Nogueira Lima
- Institute of Agricultural Sciences, Universidade Federal de Minas Gerais, Campus Regional de Montes Claros, Montes Claros, Minas Gerais, Brazil
| | - Alexsandro Sobreira Galdino
- Microbial Biotechnology Laboratory, Universidade Federal de São João Del-Rei, Divinópolis, Minas Gerais, Brazil
| | - Raquel Cardoso de Melo Minardi
- Laboratory of Bioinformatics and Systems (LBS), Department Of Computer Science, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Leonardo Henrique França de Lima
- Laboratory Of Molecular Modeling and Bioinformatics, Department of Exacts and Biological Sciences (DECEB), Universidade Federal de São João Del-Rei, Sete Lagoas, Minas Gerais, Brazil
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Rahban M, Zolghadri S, Salehi N, Ahmad F, Haertlé T, Rezaei-Ghaleh N, Sawyer L, Saboury AA. Thermal stability enhancement: Fundamental concepts of protein engineering strategies to manipulate the flexible structure. Int J Biol Macromol 2022; 214:642-654. [DOI: 10.1016/j.ijbiomac.2022.06.154] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 06/22/2022] [Accepted: 06/23/2022] [Indexed: 01/28/2023]
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Corrêa TLR, de Araújo EF. Fungal phytases: from genes to applications. Braz J Microbiol 2020; 51:1009-1020. [PMID: 32410091 PMCID: PMC7455620 DOI: 10.1007/s42770-020-00289-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 04/30/2020] [Indexed: 12/18/2022] Open
Abstract
Phytic acid stores 60-90% of the inorganic phosphorus in legumes, oil seeds, and cereals, making it inaccessible for metabolic processes in living systems. In addition, given its negative charge, phytic acid complexes with divalent cations, starch, and proteins. Inorganic phosphorous can be released from phytic acid upon the action of phytases. Phytases are phosphatases produced by animals, plants, and microorganisms, notably Aspergillus niger, and are employed as animal feed additive, in chemical industry and for ethanol production. Given the industrial relevance of phytases produced by filamentous fungi, this work discusses the functional characterization of fungal phytase-coding genes/proteins, highlighting the physicochemical parameters that govern the enzymatic activity, the development of phytase super-producing strains, and key features for industrial applications.
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Affiliation(s)
- Thamy Lívia Ribeiro Corrêa
- Department of Microbiology/BIOAGRO, Federal University of Viçosa, Av. Peter Henry Rolfs s/n, Vicosa, MG, 36570-000, Brazil.
| | - Elza Fernandes de Araújo
- Department of Microbiology/BIOAGRO, Federal University of Viçosa, Av. Peter Henry Rolfs s/n, Vicosa, MG, 36570-000, Brazil
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Integrative Structural and Computational Biology of Phytases for the Animal Feed Industry. Catalysts 2020. [DOI: 10.3390/catal10080844] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Resistance to high temperature, acidic pH and proteolytic degradation during the pelleting process and in the digestive tract are important features of phytases as animal feed. The integration of insights from structural and in silico analyses into factors affecting thermostability, acid stability, proteolytic stability, catalytic efficiency and specific activity, as well as N-glycosylation, could improve the limitations of marginal stable biocatalysts with trade-offs between stability and activity. Synergistic mutations give additional benefits to single substitutions. Rigidifying the flexible loops or inter-molecular interactions by reinforcing non-bonded interactions or disulfide bonds, based on structural and roof mean square fluctuation (RMSF) analyses, are contributing factors to thermostability. Acid stability is normally achieved by targeting the vicinity residue at the active site or at the neighboring active site loop or the pocket edge adjacent to the active site. Extending the positively charged surface, altering protease cleavage sites and reducing the affinity of protease towards phytase are among the reported contributing factors to improving proteolytic stability. Remodeling the active site and removing steric hindrance could enhance phytase activity. N-glycosylation conferred improved thermostability, proteases degradation and pH activity. Hence, the integration of structural and computational biology paves the way to phytase tailoring to overcome the limitations of marginally stable phytases to be used in animal feeds.
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Sutthibutpong T, Rattanarojpong T, Khunrae P. Effects of helix and fingertip mutations on the thermostability of xyn11A investigated by molecular dynamics simulations and enzyme activity assays. J Biomol Struct Dyn 2017; 36:3978-3992. [DOI: 10.1080/07391102.2017.1404934] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Thana Sutthibutpong
- Theoretical and Computational Physics Group, Department of Physics, Faculty of Science, King Mongkut’s University of Technology Thonburi (KMUTT), 126 Pracha-Uthit Road, Bang Mod, Thrung Khru, Bangkok 10140, Thailand
- Theoretical and Computational Science Center (TaCS), Science Laboratory Building, Faculty of Science, King Mongkut’s University of Technology Thonburi (KMUTT), 126 Pracha-Uthit Road, Bang Mod, Thrung Khru, Bangkok 10140, Thailand
| | - Triwit Rattanarojpong
- Department of Microbiology, Science Laboratory Building, Faculty of Science, King Mongkut’s University of Technology Thonburi, 126 Pracha-Uthit Road, Bang Mod, Thrung Khru, Bangkok 10140, Thailand
| | - Pongsak Khunrae
- Department of Microbiology, Science Laboratory Building, Faculty of Science, King Mongkut’s University of Technology Thonburi, 126 Pracha-Uthit Road, Bang Mod, Thrung Khru, Bangkok 10140, Thailand
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Abstract
Using structure and sequence based analysis we can engineer proteins to increase their thermal stability.
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Affiliation(s)
- H. Pezeshgi Modarres
- Molecular Cell Biomechanics Laboratory
- Departments of Bioengineering and Mechanical Engineering
- University of California Berkeley
- Berkeley
- USA
| | - M. R. Mofrad
- Molecular Cell Biomechanics Laboratory
- Departments of Bioengineering and Mechanical Engineering
- University of California Berkeley
- Berkeley
- USA
| | - A. Sanati-Nezhad
- BioMEMS and Bioinspired Microfluidic Laboratory
- Department of Mechanical and Manufacturing Engineering
- University of Calgary
- Calgary
- Canada
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Jiang X, Chen G, Wang L. Structural and dynamic evolution of the amphipathic N-terminus diversifies enzyme thermostability in the glycoside hydrolase family 12. Phys Chem Chem Phys 2016; 18:21340-50. [DOI: 10.1039/c6cp02998a] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The N-terminus diversifies enzyme thermostability in the GH12 family, which was investigated by MD simulations, and provides potential applications in protein engineering.
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Affiliation(s)
- Xukai Jiang
- State Key Laboratory of Microbial Technology
- Shandong University
- Jinan 250100
- China
| | - Guanjun Chen
- State Key Laboratory of Microbial Technology
- Shandong University
- Jinan 250100
- China
| | - Lushan Wang
- State Key Laboratory of Microbial Technology
- Shandong University
- Jinan 250100
- China
- State Key Laboratory of Biochemical Engineering
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