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Yang X, Zhang Z, Wu L, Yang M, Li S, Gao J. Conserved Residues Lys64 and Glu78 at the Subunit Surface of Tau Glutathione Transferase in Rice Affect Structure and Enzymatic Properties. Int J Mol Sci 2023; 25:398. [PMID: 38203568 PMCID: PMC10778600 DOI: 10.3390/ijms25010398] [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: 11/27/2023] [Revised: 12/24/2023] [Accepted: 12/25/2023] [Indexed: 01/12/2024] Open
Abstract
Glutathione transferases (GSTs) are a superfamily of dimeric proteins associated with the detoxification of various reactive electrophiles and responsive to a multitude of stressors. We individually substituted Lys64 and Glu78 with Ala using site-directed mutagenesis to understand the role of subunit interactions in the structure and enzymatic properties of a rice GST (OsGSTU17). The wild-type OsGSTU17 lost the conserved hydrogen bond between subunits in tau class GSTs due to conserved Tyr92 replaced with Phe92, but still exhibited high substrate activities, and thermal stability remained in its dimeric structure. The significant decrease in thermal stability and obvious changes in the structure of mutant K64A implied that conserved Lys64 might play an essential role in the structural stability of tau class GSTs. The mutant E78A, supposed to be deprived of hydrogen and salt bonds between subunits, appeared in the soluble form of dimers, even though its tertiary structure altered and stability declined dramatically. These results suggest that the hydrogen and ionic bonds provided by conserved residues are not as important for OsGSTU17 dimerization and enzymatic properties. These results further supplement our understanding of the relationship between the structure and function of GSTs and provide a theoretical basis for improving crop resistance through targeted modification of GSTs.
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Affiliation(s)
- Xue Yang
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, China; (X.Y.); (Z.Z.); (L.W.)
| | - Zhe Zhang
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, China; (X.Y.); (Z.Z.); (L.W.)
| | - Lei Wu
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, China; (X.Y.); (Z.Z.); (L.W.)
| | - Meiying Yang
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, China; (X.Y.); (Z.Z.); (L.W.)
| | - Siyuan Li
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, China; (X.Y.); (Z.Z.); (L.W.)
| | - Jie Gao
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun 666303, China
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Sankar S, Chandra N. SiteMotif: A graph-based algorithm for deriving structural motifs in Protein Ligand binding sites. PLoS Comput Biol 2022; 18:e1009901. [PMID: 35202398 PMCID: PMC8903255 DOI: 10.1371/journal.pcbi.1009901] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 03/08/2022] [Accepted: 02/07/2022] [Indexed: 12/03/2022] Open
Abstract
Studying similarities in protein molecules has become a fundamental activity in much of biology and biomedical research, for which methods such as multiple sequence alignments are widely used. Most methods available for such comparisons cater to studying proteins which have clearly recognizable evolutionary relationships but not to proteins that recognize the same or similar ligands but do not share similarities in their sequence or structural folds. In many cases, proteins in the latter class share structural similarities only in their binding sites. While several algorithms are available for comparing binding sites, there are none for deriving structural motifs of the binding sites, independent of the whole proteins. We report the development of SiteMotif, a new algorithm that compares binding sites from multiple proteins and derives sequence-order independent structural site motifs. We have tested the algorithm at multiple levels of complexity and demonstrate its performance in different scenarios. We have benchmarked against 3 current methods available for binding site comparison and demonstrate superior performance of our algorithm. We show that SiteMotif identifies new structural motifs of spatially conserved residues in proteins, even when there is no sequence or fold-level similarity. We expect SiteMotif to be useful for deriving key mechanistic insights into the mode of ligand interaction, predict the ligand type that a protein can bind and improve the sensitivity of functional annotation. A large number of biological functions are orchestrated by proteins. The function of proteins is governed by its structure and its interacting ligand. However, it is known that not all residues are involved in ligand recognition. More specifically, residues that are located within 4.5 Å of ligand atoms are considered to be ’binding sites’. Here, we have developed an algorithm called SiteMotif that efficiently aligns multiple binding sites into a common frame. This process enables us to derive conservation among the binding site residues in a sequence order independent manner. The algorithm was validated extensively across five different levels and measured binding site similarities in each of them. Previous research has found multiple instances where different proteins have comparable binding sites and hence perform the same function. We present the ability of our method to detect such scenarios. Finally, As a use case, we applied SiteMotif to a set of glutathione binding proteins and derived a site based sequence motif characteristic of all glutathione binding proteins.
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Affiliation(s)
- Santhosh Sankar
- Department of Biochemistry, Indian Institute of Science, Bangalore, Karnataka, India
| | - Nagasuma Chandra
- Department of Biochemistry, Indian Institute of Science, Bangalore, Karnataka, India
- BioSystems Science and Engineering, Indian Institute of Science, Bangalore, Karnataka, India
- * E-mail:
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Giantulli S, Tortorella E, Brasili F, Scarpa S, Cerroni B, Paradossi G, Bedini A, Morrone S, Silvestri I, Domenici F. Effect of 1-MHz ultrasound on the proinflammatory interleukin-6 secretion in human keratinocytes. Sci Rep 2021; 11:19033. [PMID: 34561481 PMCID: PMC8463532 DOI: 10.1038/s41598-021-98141-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 08/02/2021] [Indexed: 02/08/2023] Open
Abstract
Keratinocytes, the main cell type of the skin, are one of the most exposed cells to environmental factors, providing a first defence barrier for the host and actively participating in immune response. In fact, keratinocytes express pattern recognition receptors that interact with pathogen associated molecular patterns and damage associated molecular patterns, leading to the production of cytokines and chemokines, including interleukin (IL)-6. Herein, we investigated whether mechanical energy transported by low intensity ultrasound (US) could generate a mechanical stress able to induce the release of inflammatory cytokine such IL-6 in the human keratinocyte cell line, HaCaT. The extensive clinical application of US in both diagnosis and therapy suggests the need to better understand the related biological effects. Our results point out that US promotes the overexpression and secretion of IL-6, associated with the activation of nuclear factor-κB (NF-κB). Furthermore, we observed a reduced cell viability dependent on exposure parameters together with alterations in membrane permeability, paving the way for further investigating the molecular mechanisms related to US exposure.
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Affiliation(s)
- Sabrina Giantulli
- grid.7841.aDepartment of Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | - Elisabetta Tortorella
- grid.7841.aDepartment of Molecular Medicine, Sapienza University of Rome, Rome, Italy ,grid.6530.00000 0001 2300 0941Department of Chemical Sciences and Technologies, University of Rome Tor Vergata, Rome, Italy
| | - Francesco Brasili
- grid.6530.00000 0001 2300 0941Department of Chemical Sciences and Technologies, University of Rome Tor Vergata, Rome, Italy ,grid.7841.aDepartment of Physics, Sapienza University of Rome, Rome, Italy ,grid.5326.20000 0001 1940 4177CNR-NANOTEC, Institute of Nanotechnology, Soft and Living Matter Laboratory, Rome, Italy
| | - Susanna Scarpa
- grid.7841.aDepartment of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Barbara Cerroni
- grid.6530.00000 0001 2300 0941Department of Chemical Sciences and Technologies, University of Rome Tor Vergata, Rome, Italy
| | - Gaio Paradossi
- grid.6530.00000 0001 2300 0941Department of Chemical Sciences and Technologies, University of Rome Tor Vergata, Rome, Italy
| | - Angelico Bedini
- grid.425425.00000 0001 2218 2472INAIL, Italian Worker’s Compensation Authority, Rome, Italy
| | - Stefania Morrone
- grid.7841.aDepartment of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Ida Silvestri
- grid.7841.aDepartment of Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | - Fabio Domenici
- grid.6530.00000 0001 2300 0941Department of Chemical Sciences and Technologies, University of Rome Tor Vergata, Rome, Italy
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Yang X, Wu Z, Gao J. Effects of conserved Arg20, Glu74 and Asp77 on the structure and function of a tau class glutathione S-transferase in rice. PLANT MOLECULAR BIOLOGY 2021; 105:451-462. [PMID: 33387174 DOI: 10.1007/s11103-020-01099-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 11/24/2020] [Indexed: 06/12/2023]
Abstract
The relative position of domains is critical for enzymatic properties of tau class glutathione S-transferases, and altering the position of linker far away from the active center affects catalytic property. Glutathione S-transferases (GSTs) are a family of phase II detoxification enzymes whose main function is to improve plant resistance to stresses. To understand the structural effects of tau class GSTs on their function, using OsGSTU17 as an example, we predicted the residues involved in the interactions between its domains and linker region. We further detected the structural changes in mutants and the corresponding changes in terms of substrate activity and kinetic parameters. Four pairs of residues, including Ala14 and Trp165, Arg20 and Tyr154, Glu74 and Arg98, Asp77 and Met87, forming hydrogen bonds and salt bridges were found to play important roles in maintaining the relative position between the domains and linker region inside the protein. The hydrogen bond between Trp165 and Ala14 affected the structural stability has been demonstrated in our previous study. The mutant R20A lost almost all catalytic activity. Interestingly, the mutant E74A exhibited a significant decrease in activity towards 7-chloro-4-nitrobenzo-2-oxa-1, 3-diazole, 1-chloro-2, 4-dinitrobenzene and 4-nitrobenzyl chloride, while its activity towards substrate cumene hydroperoxide remained unchanged. Compared with other mutants, the mutant D77A exhibited decreased affinity to its substrates and increased activity towards 1-chloro-2, 4-dinitrobenzene and cumene hydroperoxide, but its thermodynamic stability did not change significantly. The relative position of individual domain was critical for enzymatic properties, and the linker which is far away from the active site could change the enzymatic properties of GSTs via altering the relative position of the individual domain. Our results provide insights into the relationship between structure and function of tau class GSTs.
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Affiliation(s)
- Xue Yang
- College of Life Sciences, Jilin Agricultural University, Changchun, 130118, China
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China
| | - Zhihai Wu
- College of Life Sciences, Jilin Agricultural University, Changchun, 130118, China.
| | - Jie Gao
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, 666303, Yunnan, China.
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Mengla, 666303, China.
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A Computational Method to Predict Effects of Residue Mutations on the Catalytic Efficiency of Hydrolases. Catalysts 2021. [DOI: 10.3390/catal11020286] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
With scientific and technological advances, growing research has focused on engineering enzymes that acquire enhanced efficiency and activity. Thereinto, computer-based enzyme modification makes up for the time-consuming and labor-intensive experimental methods and plays a significant role. In this study, for the first time, we collected and manually curated a data set for hydrolases mutation, including structural information of enzyme-substrate complexes, mutated sites and Kcat/Km obtained from vitro assay. We further constructed a classification model using the random forest algorithm to predict the effects of residue mutations on catalytic efficiency (increase or decrease) of hydrolases. This method has achieved impressive performance on a blind test set with the area under the receiver operating characteristic curve of 0.86 and the Matthews Correlation Coefficient of 0.659. Our results demonstrate that computational mutagenesis has an instructive effect on enzyme modification, which may expedite the design of engineering hydrolases.
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Hasan MS, Singh V, Islam S, Islam MS, Ahsan R, Kaundal A, Islam T, Ghosh A. Genome-wide identification and expression profiling of glutathione S-transferase family under multiple abiotic and biotic stresses in Medicago truncatula L. PLoS One 2021; 16:e0247170. [PMID: 33606812 PMCID: PMC7894904 DOI: 10.1371/journal.pone.0247170] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 02/02/2021] [Indexed: 12/21/2022] Open
Abstract
Glutathione transferases (GSTs) constitute an ancient, ubiquitous, multi-functional antioxidant enzyme superfamily that has great importance on cellular detoxification against abiotic and biotic stresses as well as plant development and growth. The present study aimed to a comprehensive genome-wide identification and functional characterization of GST family in one of the economically important legume plants-Medicago truncatula. Here, we have identified a total of ninety-two putative MtGST genes that code for 120 proteins. All these members were classified into twelve classes based on their phylogenetic relationship and the presence of structural conserved domain/motif. Among them, 7 MtGST gene pairs were identified to have segmental duplication. Expression profiling of MtGST transcripts revealed their high level of organ/tissue-specific expression in most of the developmental stages and anatomical tissues. The transcripts of MtGSTU5, MtGSTU8, MtGSTU17, MtGSTU46, and MtGSTU47 showed significant up-regulation in response to various abiotic and biotic stresses. Moreover, transcripts of MtGSTU8, MtGSTU14, MtGSTU28, MtGSTU30, MtGSTU34, MtGSTU46 and MtGSTF8 were found to be highly upregulated in response to drought treatment for 24h and 48h. Among the highly stress-responsive MtGST members, MtGSTU17 showed strong affinity towards its conventional substrates reduced glutathione (GSH) and 1-chloro-2,4-dinitrobenzene (CDNB) with the lowest binding energy of-5.7 kcal/mol and -6.5 kcal/mol, respectively. Furthermore, the substrate-binding site residues of MtGSTU17 were found to be highly conserved. These findings will facilitate the further functional and evolutionary characterization of GST genes in Medicago.
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Affiliation(s)
- Md. Soyib Hasan
- Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet, Bangladesh
| | - Vishal Singh
- Department of Plants, Soils, and Climate, College of Agriculture and Applied Sciences, Utah State University, Logan, Utah, United States of America
| | - Shiful Islam
- Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet, Bangladesh
| | - Md. Sifatul Islam
- Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet, Bangladesh
| | - Raju Ahsan
- Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet, Bangladesh
| | - Amita Kaundal
- Department of Plants, Soils, and Climate, College of Agriculture and Applied Sciences, Utah State University, Logan, Utah, United States of America
| | - Tahmina Islam
- Department of Botany, University of Dhaka, Dhaka, Bangladesh
| | - Ajit Ghosh
- Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet, Bangladesh
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Genetic Improvement of Cereals and Grain Legumes. Genes (Basel) 2020; 11:genes11111255. [PMID: 33113769 PMCID: PMC7692374 DOI: 10.3390/genes11111255] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 10/22/2020] [Indexed: 12/24/2022] Open
Abstract
The anticipated population growth by 2050 will be coupled with increased food demand. To achieve higher and sustainable food supplies in order to feed the global population by 2050, a 2.4% rise in the yield of major crops is required. The key to yield improvement is a better understanding of the genetic variation and identification of molecular markers, quantitative trait loci, genes, and pathways related to higher yields and increased tolerance to biotic and abiotic stresses. Advances in genetic technologies are enabling plant breeders and geneticists to breed crop plants with improved agronomic traits. This Special Issue is an effort to report the genetic improvements by adapting genomic techniques and genomic selection.
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