Working with Proteins in silico: A Review of Online Available Tools for Basic Identification of Proteins

Yavuz, Caner; Öztürk, Zahide Neslihan

doi:10.24925/turjaf.v5i1.65-70.926

Cited by 2 publications

(2 citation statements)

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“…We have determined structures of 72 allelic Pi54 proteins and studied their interaction with the AvrPi54 protein by molecular docking using in silico tools, aimed to find more suitable alleles which can be used in breeding programs to develop blast resistance in rice. The online available bioinformatics tools for protein modelling and interaction have been used in this study [21]. Thus it saves the time and cost of the experimental structure determinations by X-Ray Crystallography and nuclear magnetic resonance.…”

Section: Introductionmentioning

confidence: 99%

Variation in the LRR region of Pi54 protein alters its interaction with the AvrPi54 protein revealed by in silico analysis

et al. 2019

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Rice blast, caused by the ascomycete fungus Magnaporthe oryzae is a destructive disease of rice and responsible for causing extensive damage to the crop. Pi54, a dominant blast resistance gene cloned from rice line Tetep, imparts a broad spectrum resistance against various M. oryzae isolates. Many of its alleles have been explored from wild Oryza species and landraces whose sequences are available in the public domain. Its cognate effector gene AvrPi54 has also been cloned from M. oryzae. Complying with the Flor’s gene-for-gene system, Pi54 protein interacts with AvrPi54 protein following fungal invasion leading to the resistance responses in rice cell that prevents the disease development. In the present study Pi54 alleles from 72 rice lines were used to understand the interaction of Pi54 (R) proteins with AvrPi54 (Avr) protein. The physiochemical properties of these proteins varied due to the nucleotide level polymorphism. The ab initio tertiary structures of these R- and Avr- proteins were generated and subjected to the in silico interaction. In this interaction, the residues in the LRR region of R- proteins were shown to interact with the Avr protein. These R proteins were found to have variable strengths of binding due to the differential spatial arrangements of their amino acid residues. Additionally, molecular dynamic simulations were performed for the protein pairs that showed stronger interaction than Pi54tetep (original Pi54 from Tetep) protein. We found these proteins were forming h-bond during simulation which indicated an effective binding. The root mean square deviation values and potential energy values were stable during simulation which validated the docking results. From the interaction studies and the molecular dynamics simulations, we concluded that the AvrPi54 protein interacts directly with the resistant Pi54 proteins through the LRR region of Pi54 proteins. Some of the Pi54 proteins from the landraces namely Casebatta, Tadukan, Varun dhan, Govind, Acharmita, HPR-2083, Budda, Jatto, MTU-4870, Dobeja-1, CN-1789, Indira sona, Kulanji pille and Motebangarkaddi cultivars show stronger binding with the AvrPi54 protein, thus these alleles can be effectively used for the rice blast resistance breeding program in future.

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Section: Introductionmentioning

confidence: 99%

Variation in the LRR region of Pi54 protein alters its interaction with the AvrPi54 protein revealed by in silico analysis

et al. 2019

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“…However, AQP homologues have been found in a wide range of insect genomic databases of which three have been characterized in Hemiptera [10,39]. Nowadays, bioinformatic analysis is a powerful tool to predict protein function by identifying conserved motifs and/or specific domains in protein families [40].…”

Section: Discussionmentioning

confidence: 99%

Silencing of Aquaporin Homologue Accumulates Uric Acid and Decreases the Lifespan of the Asian Citrus Psyllid, Diaphorina citri (Hemiptera: Liviidae)

Santos‐Ortega

Killiny

2021

Insects

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The Asian citrus psyllid, Diaphorina citri Kuwayama is devastating the citrus industry worldwide. It transmits ‘Candidatus Liberibacter asiaticus’, the pathogen of Huanglongbing in citrus. RNA interference is an excellent tool for functional genomics and for screening target genes for pest control. Herein, we silenced the aquaporin (AQP) gene (DcAQP) homologue in D. citri to study its functionality and whether it could be a good target for a control strategy. AQP is an integral membrane channel protein that aids in the rapid flux of water and other small solutes that move across the lipid membrane. In Hemiptera, it is well established that AQP plays important roles in adjusting to physiological challenges including (1) regulating osmotic stress between the gut lumen and hemolymph after imbibing large quantities of a low nitrogen, sugar-rich liquid diet; (2) avoiding or preventing dehydration and desiccation; and (3) surviving at elevated temperatures. The dsRNA-DcAQP was applied twice to nymphs of the 4th and 5th instars through a soaking technique. Silencing AQP caused a significant increase in nymph mortality. Emerged adults showed malformations and a shorter lifespan. Silencing DcAQP provoked alterations in some metabolites and increased the uric acid content in emerged adults. DcAQP could be a useful target to control D. citri.

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Working with Proteins in silico: A Review of Online Available Tools for Basic Identification of Proteins

Cited by 2 publications

References 57 publications

Variation in the LRR region of Pi54 protein alters its interaction with the AvrPi54 protein revealed by in silico analysis

Variation in the LRR region of Pi54 protein alters its interaction with the AvrPi54 protein revealed by in silico analysis

Silencing of Aquaporin Homologue Accumulates Uric Acid and Decreases the Lifespan of the Asian Citrus Psyllid, Diaphorina citri (Hemiptera: Liviidae)

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