Antioxidant activity and antioxidant proteins dynamic simulation of Malaysia upland rice genotypes

Upland rice is known as a type of rice specifically grown in hilly area that thrive under minimum irrigation. Upland rice is high in antioxidants compared to wetland rice. Due to that, the consumption of upland rice as an alternative carbohydrate has been associated with a reduced incidence of chron...

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Main Author:	Kamdi, Nurul Hafifi
Format:	Thesis
Language:	English
Published:	2018
Subjects:	Q Science (General)
Online Access:	http://eprints.utm.my/id/eprint/81459/1/NurulHafifiKamdiMFS2018.pdf
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spelling	my-utm-ep.814592019-08-23T05:18:52Z Antioxidant activity and antioxidant proteins dynamic simulation of Malaysia upland rice genotypes 2018 Kamdi, Nurul Hafifi Q Science (General) Upland rice is known as a type of rice specifically grown in hilly area that thrive under minimum irrigation. Upland rice is high in antioxidants compared to wetland rice. Due to that, the consumption of upland rice as an alternative carbohydrate has been associated with a reduced incidence of chronic diseases such as diabetes in Asia. However, the study of antioxidant activity for Malaysia upland rice via in vitro, in vivo or in silico is still lacking. In the present study, the antioxidant activity assessments were performed on pigmented upland rice (Hitam, Bario and Udang), non-pigmented (Wai and Putih) and control wetland varieties (MR220, MR219 and several commercially available white and pigmented rice). Three antioxidant assays namely ferric reducing antioxidant power (FRAP) assay, DPPH (2,2-diphenyl-1-picrylhydrazyl) radical scavenging and superoxide dismutase (SOD) enzyme assay were implemented on raw and cooked rice extracts. Results showed that all three pigmented upland rice exhibited higher antioxidant activity than other wetland rice cultivars. Hitam rice had the highest activities of FRAP, DPPH and SOD assays with the value of 9.63 ± 0.52 Fe2+mmol/100g, 78.34% radical scavenging activity (RSA) and 35.72 U/g, respectively. Udang and Bario rice exhibited lower antioxidant activity than Hitam. Meanwhile, white rice had the lowest total content of antioxidants. Data elucidated that an average of 75% of the total antioxidant and enzymatic activities were decomposed or inactivated after all the rice were cooked. To study the stability effect of antioxidant proteins towards high temperature in order to mimic the cooking process, in silico protein modelling were conducted on three unique upland rice antioxidant proteins chosen from an earlier upland rice seed profiling data. The molecular dynamic (MD) simulation of manganese superoxide dismutase (SOD [Mn]), dehydroascorbate reductase (DHAR), and glyoxalase (GLX) were executed at different temperatures (310 K, 318 K and 373 K) using GROMACS. Trajectory results on the 50 ns simulation at those temperatures were presented in the RMSD (structural stability) and RMSF (structural flexibility) plots, gyration graphs (Rg) for structural compaction, secondary structure analysis as well as bonds analysis. Results showed that all three antioxidant protein structures were stable at 310 K and 318 K but, least stable at 373 K. These findings corresponded to the analysis of secondary structure, structure flexibility and types of bonds from the proteins three-dimensional (3D) model. This study also revealed that SOD [Mn] protein from Triticum aestivum was more stable at 310K and 373K than upland rice (Oryza sativa) and Zea mays when all simulated proteins were compared. This information could provide insights into a better understanding the roles of SOD [Mn] catalytic action and protein-protein interactions which might also be applied to other antioxidant proteins yet to be discovered. Taken together, the findings present valuable knowledge on antioxidant activity and thermostability of antioxidant proteins in upland rice. These findings suggest that upland rice might be a good source of natural antioxidant and a potential source of nutraceuticals in the future. 2018 Thesis http://eprints.utm.my/id/eprint/81459/ http://eprints.utm.my/id/eprint/81459/1/NurulHafifiKamdiMFS2018.pdf application/pdf en public http://dms.library.utm.my:8080/vital/access/manager/Repository/vital:124921 masters Universiti Teknologi Malaysia Biosciences and Medical Engineering
institution	Universiti Teknologi Malaysia
collection	UTM Institutional Repository
language	English
topic	Q Science (General)
spellingShingle	Q Science (General) Kamdi, Nurul Hafifi Antioxidant activity and antioxidant proteins dynamic simulation of Malaysia upland rice genotypes
description	Upland rice is known as a type of rice specifically grown in hilly area that thrive under minimum irrigation. Upland rice is high in antioxidants compared to wetland rice. Due to that, the consumption of upland rice as an alternative carbohydrate has been associated with a reduced incidence of chronic diseases such as diabetes in Asia. However, the study of antioxidant activity for Malaysia upland rice via in vitro, in vivo or in silico is still lacking. In the present study, the antioxidant activity assessments were performed on pigmented upland rice (Hitam, Bario and Udang), non-pigmented (Wai and Putih) and control wetland varieties (MR220, MR219 and several commercially available white and pigmented rice). Three antioxidant assays namely ferric reducing antioxidant power (FRAP) assay, DPPH (2,2-diphenyl-1-picrylhydrazyl) radical scavenging and superoxide dismutase (SOD) enzyme assay were implemented on raw and cooked rice extracts. Results showed that all three pigmented upland rice exhibited higher antioxidant activity than other wetland rice cultivars. Hitam rice had the highest activities of FRAP, DPPH and SOD assays with the value of 9.63 ± 0.52 Fe2+mmol/100g, 78.34% radical scavenging activity (RSA) and 35.72 U/g, respectively. Udang and Bario rice exhibited lower antioxidant activity than Hitam. Meanwhile, white rice had the lowest total content of antioxidants. Data elucidated that an average of 75% of the total antioxidant and enzymatic activities were decomposed or inactivated after all the rice were cooked. To study the stability effect of antioxidant proteins towards high temperature in order to mimic the cooking process, in silico protein modelling were conducted on three unique upland rice antioxidant proteins chosen from an earlier upland rice seed profiling data. The molecular dynamic (MD) simulation of manganese superoxide dismutase (SOD [Mn]), dehydroascorbate reductase (DHAR), and glyoxalase (GLX) were executed at different temperatures (310 K, 318 K and 373 K) using GROMACS. Trajectory results on the 50 ns simulation at those temperatures were presented in the RMSD (structural stability) and RMSF (structural flexibility) plots, gyration graphs (Rg) for structural compaction, secondary structure analysis as well as bonds analysis. Results showed that all three antioxidant protein structures were stable at 310 K and 318 K but, least stable at 373 K. These findings corresponded to the analysis of secondary structure, structure flexibility and types of bonds from the proteins three-dimensional (3D) model. This study also revealed that SOD [Mn] protein from Triticum aestivum was more stable at 310K and 373K than upland rice (Oryza sativa) and Zea mays when all simulated proteins were compared. This information could provide insights into a better understanding the roles of SOD [Mn] catalytic action and protein-protein interactions which might also be applied to other antioxidant proteins yet to be discovered. Taken together, the findings present valuable knowledge on antioxidant activity and thermostability of antioxidant proteins in upland rice. These findings suggest that upland rice might be a good source of natural antioxidant and a potential source of nutraceuticals in the future.
format	Thesis
qualification_level	Master's degree
author	Kamdi, Nurul Hafifi
author_facet	Kamdi, Nurul Hafifi
author_sort	Kamdi, Nurul Hafifi
title	Antioxidant activity and antioxidant proteins dynamic simulation of Malaysia upland rice genotypes
title_short	Antioxidant activity and antioxidant proteins dynamic simulation of Malaysia upland rice genotypes
title_full	Antioxidant activity and antioxidant proteins dynamic simulation of Malaysia upland rice genotypes
title_fullStr	Antioxidant activity and antioxidant proteins dynamic simulation of Malaysia upland rice genotypes
title_full_unstemmed	Antioxidant activity and antioxidant proteins dynamic simulation of Malaysia upland rice genotypes
title_sort	antioxidant activity and antioxidant proteins dynamic simulation of malaysia upland rice genotypes
granting_institution	Universiti Teknologi Malaysia
granting_department	Biosciences and Medical Engineering
publishDate	2018
url	http://eprints.utm.my/id/eprint/81459/1/NurulHafifiKamdiMFS2018.pdf
_version_	1747818337005469696

Antioxidant activity and antioxidant proteins dynamic simulation of Malaysia upland rice genotypes

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