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Li X, Xie Y, Zhang Q, Hua X, Peng L, Li K, Yu Q, Chen Y, Yao H, He J, Huang Y, Wang R, Wang T, Wang J, Li X, Yang Y. Monomerization of abscisic acid receptors through CARKs-mediated phosphorylation. THE NEW PHYTOLOGIST 2022; 235:533-549. [PMID: 35388459 DOI: 10.1111/nph.18149] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 03/25/2022] [Indexed: 06/14/2023]
Abstract
Cytosolic ABA Receptor Kinases (CARKs) play a pivotal role in abscisic acid (ABA)-dependent pathway in response to dehydration, but their regulatory mechanism in ABA signaling remains unexplored. In this study, we showed that CARK4/5 of CARK family physically interacted with ABA receptors (RCARs/PYR1/PYLs), including RCAR3, RCAR11-RCAR14, while CARK2/7/11 only interacted with RCAR11-RCAR14, but not RCAR3. It indicates that the members in CARK family function redundantly and differentially in ABA signaling. RCAR12 can form heterodimer with RCAR3 in vitro and in vivo. Moreover, the members of CARK family can form homodimer or heterodimer in a kinase activity dependent manner. ITC (isothermal titration calorimetry) analysis demonstrated that the phosphorylation of RCAR12 by CARK1 enhanced the ABA binding affinity. The phosphor-mimic RCAR12T105D significantly displayed ABA-induced inhibition of the phosphatase ABI1 (ABA insensitive 1) activity, leading to upregulation of ABA-responsive genes RD29A and RD29B in cark157:RCAR12T105D transgenic plants, which exhibited ABA hypersensitive phenotype. The transcription factor ABI5 (ABA insensitive 5) activates the transcriptions of CARK1 and CARK3 by binding to ABA-response elements (ABREs) of their promoters. Collectively, our data imply that the dimeric CARKs phosphorylate homodimer or heterodimer ABA receptors, leading to monomerization for triggering ABA responses in Arabidopsis.
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Affiliation(s)
- Xiaoyi Li
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, 610065, China
| | - Yiting Xie
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, 610065, China
| | - Qian Zhang
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, 610065, China
| | - Xinyue Hua
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, 610065, China
| | - Lu Peng
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, 610065, China
| | - Kexuan Li
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, 610065, China
| | - Qin Yu
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, 610065, China
| | - Yihong Chen
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, 610065, China
| | - Huan Yao
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, 610065, China
| | - Juan He
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, 610065, China
| | - Yaling Huang
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, 610065, China
| | - Ruolin Wang
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, 610065, China
| | - Tao Wang
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, 610065, China
| | - Jianmei Wang
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, 610065, China
| | - Xufeng Li
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, 610065, China
| | - Yi Yang
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, 610065, China
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Wu M, Dorosh L, Schmitt-Ulms G, Wille H, Stepanova M. Aggregation of Aβ40/42 chains in the presence of cyclic neuropeptides investigated by molecular dynamics simulations. PLoS Comput Biol 2021; 17:e1008771. [PMID: 33711010 PMCID: PMC7990313 DOI: 10.1371/journal.pcbi.1008771] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Revised: 03/24/2021] [Accepted: 02/04/2021] [Indexed: 11/18/2022] Open
Abstract
Alzheimer’s disease is associated with the formation of toxic aggregates of amyloid beta (Aβ) peptides. Despite tremendous efforts, our understanding of the molecular mechanisms of aggregation, as well as cofactors that might influence it, remains incomplete. The small cyclic neuropeptide somatostatin-14 (SST14) was recently found to be the most selectively enriched protein in human frontal lobe extracts that binds Aβ42 aggregates. Furthermore, SST14’s presence was also found to promote the formation of toxic Aβ42 oligomers in vitro. In order to elucidate how SST14 influences the onset of Aβ oligomerization, we performed all-atom molecular dynamics simulations of model mixtures of Aβ42 or Aβ40 peptides with SST14 molecules and analyzed the structure and dynamics of early-stage aggregates. For comparison we also analyzed the aggregation of Aβ42 in the presence of arginine vasopressin (AVP), a different cyclic neuropeptide. We observed the formation of self-assembled aggregates containing the Aβ chains and small cyclic peptides in all mixtures of Aβ42–SST14, Aβ42–AVP, and Aβ40–SST14. The Aβ42–SST14 mixtures were found to develop compact, dynamically stable, but small aggregates with the highest exposure of hydrophobic residues to the solvent. Differences in the morphology and dynamics of aggregates that comprise SST14 or AVP appear to reflect distinct (1) regions of the Aβ chains they interact with; (2) propensities to engage in hydrogen bonds with Aβ peptides; and (3) solvent exposures of hydrophilic and hydrophobic groups. The presence of SST14 was found to impede aggregation in the Aβ42–SST14 system despite a high hydrophobicity, producing a stronger “sticky surface” effect in the aggregates at the onset of Aβ42–SST14 oligomerization. Improper folding of proteins causes disorders known as protein misfolding diseases. Under normal conditions most proteins adopt particular folds, which allow them functioning properly. However, for reasons that are not yet fully understood, proteins may misfold and aggregate, forming deposits known as amyloid fibrils, which accumulate in the brain or other tissues. This process affects functioning of the nervous system, gradually causing loss of cognitive abilities. Alzheimer’s disease is one of the most common diseases from this group. A better understanding of the aggregation of peptides implicated in Alzheimer’s disease, known as amyloid beta (Aβ) peptides, may facilitate the development of treatments that ameliorate or prevent the disease. We use detailed molecular dynamics simulations to investigate the influence of somatostatin-14 (SST14), a cyclic neuropeptide that might be involved in the amyloidogenic aggregation of Aβ, on molecular processes occurring at the onset of Aβ aggregation. Results of these simulations explain how the presence of SST14 might alter pathways of aggregation of Aβ, shedding light upon the possible role of extrinsic factors in the aggregation at a molecular level.
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Affiliation(s)
- Min Wu
- Department of Electrical and Computer Engineering, University of Alberta, Edmonton, Canada
| | - Lyudmyla Dorosh
- Department of Electrical and Computer Engineering, University of Alberta, Edmonton, Canada
| | - Gerold Schmitt-Ulms
- Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - Holger Wille
- Department of Biochemistry, University of Alberta, Edmonton, Canada
- Centre for Prions and Protein Folding Diseases, Edmonton, Canada
- Neuroscience and Mental Health Institute, University of Alberta, Edmonton, Canada
| | - Maria Stepanova
- Department of Electrical and Computer Engineering, University of Alberta, Edmonton, Canada
- * E-mail:
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Bhatnagar N, Kim R, Han S, Song J, Lee GS, Lee S, Min MK, Kim BG. Ectopic Expression of OsPYL/RCAR7, an ABA Receptor Having Low Signaling Activity, Improves Drought Tolerance without Growth Defects in Rice. Int J Mol Sci 2020; 21:ijms21114163. [PMID: 32545174 PMCID: PMC7312952 DOI: 10.3390/ijms21114163] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 06/08/2020] [Accepted: 06/08/2020] [Indexed: 01/04/2023] Open
Abstract
Overexpression of abscisic acid (ABA) receptors has been reported to enhance drought tolerance, but also to cause stunted growth and decreased crop yield. Here, we constructed transgenic rice for all monomeric ABA receptors and observed that only transgenic rice over-expressing OsPYL/RCAR7 showed similar phenotype with wild type, without total yield loss when grown under normal growth condition in a paddy field. Even though transgenic rice over-expressing OsPYL/RCAR7 showed neither an ABA-sensitivity nor an osmotic stress tolerance in plate assay, it showed drought tolerance. We investigated the ABA-dependent interaction with OsPP2CAs and ABA signaling induction by OsPYL/RCAR7. In yeast two hybrid assay, OsPYL/RCAR7 required critically higher ABA concentrations to interact with OsPP2CAs than other ABA receptors, and co-immunoprecipitation assay showed strong interaction under ABA treatment. When ABA-responsive signaling activity was monitored using a transient expression system in rice protoplasts, OsPYL/RCAR7 had the lowest ABA-responsive signaling activity as compared with other ABA receptors. OsPYL/RCAR7 also showed weak suppression of phosphatase activity as compared with other ABA receptors in vitro. Transcriptome analysis of transgenic rice over-expressing OsPYL/RCAR7 suggested that only a few genes were induced similar to control under without exogenous ABA, but a large number of genes was induced under ABA treatment compared with control. We conclude that OsPYL/RCAR7 is a novel functional ABA receptor that has low ABA signaling activity and exhibits high ABA dependence. These results lay the foundation for a new strategy to improve drought stress tolerance without compromising crop growth.
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Affiliation(s)
- Nikita Bhatnagar
- Metabolic Engineering Division, National Institute of Agricultural Sciences, RDA, Jeonju, Jeollabuk-do 54874, Korea; (N.B.); (R.K.); (J.S.)
| | - Rigyeong Kim
- Metabolic Engineering Division, National Institute of Agricultural Sciences, RDA, Jeonju, Jeollabuk-do 54874, Korea; (N.B.); (R.K.); (J.S.)
| | - Seungsu Han
- Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Korea; (S.H.); (S.L.)
| | - Jaeeun Song
- Metabolic Engineering Division, National Institute of Agricultural Sciences, RDA, Jeonju, Jeollabuk-do 54874, Korea; (N.B.); (R.K.); (J.S.)
| | - Gang Seob Lee
- Biosafety Division, National Institute of Agricultural Sciences, RDA, Jeonju, Jeollabuk-do 54874, Korea;
| | - Sangho Lee
- Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Korea; (S.H.); (S.L.)
| | - Myung Ki Min
- Metabolic Engineering Division, National Institute of Agricultural Sciences, RDA, Jeonju, Jeollabuk-do 54874, Korea; (N.B.); (R.K.); (J.S.)
- Correspondence: (M.K.M.); (B.-G.K.)
| | - Beom-Gi Kim
- Metabolic Engineering Division, National Institute of Agricultural Sciences, RDA, Jeonju, Jeollabuk-do 54874, Korea; (N.B.); (R.K.); (J.S.)
- Correspondence: (M.K.M.); (B.-G.K.)
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Abstract
AbstractThe dynamics of proteins in solution includes a variety of processes, such as backbone and side-chain fluctuations, interdomain motions, as well as global rotational and translational (i.e. center of mass) diffusion. Since protein dynamics is related to protein function and essential transport processes, a detailed mechanistic understanding and monitoring of protein dynamics in solution is highly desirable. The hierarchical character of protein dynamics requires experimental tools addressing a broad range of time- and length scales. We discuss how different techniques contribute to a comprehensive picture of protein dynamics, and focus in particular on results from neutron spectroscopy. We outline the underlying principles and review available instrumentation as well as related analysis frameworks.
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Wiseglass G, Pri-Tal O, Mosquna A. ABA signaling components in Phelipanche aegyptiaca. Sci Rep 2019; 9:6476. [PMID: 31019234 PMCID: PMC6482195 DOI: 10.1038/s41598-019-42976-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 04/12/2019] [Indexed: 11/09/2022] Open
Abstract
Obligate root holoparasite Phelipanche aegyptiaca is an agricultural pest, which infests its hosts and feeds on the sap, subsequently damaging crop yield and quality. Its notoriously viable seed bank may serve as an ideal pest control target. The phytohormone abscisic acid (ABA) was shown to regulate P. aegyptiaca seed dormancy following strigolactones germination stimulus. Transcription analysis of signaling components revealed five ABA receptors and two co-receptors (PP2C). Transcription of lower ABA-affinity subfamily III receptors was absent in all tested stages of P. aegyptiaca development and parasitism stages. P. aegyptiaca ABA receptors interacted with the PP2Cs, and inhibited their activity in an ABA-dependent manner. Moreover, sequence analysis revealed multiple alleles in two P. aegyptiaca ABA receptors, with many non-synonymous mutations. Functional analysis of selected receptor alleles identified a variant with substantially decreased inhibitory effect of PP2Cs activity in-vitro. These results provide evidence that P. aegyptiaca is capable of biochemically perceiving ABA. In light of the possible involvement of ABA in parasitic activities, the discovery of active ABA receptors and PP2Cs could provide a new biochemical target for the agricultural management of P. aegyptiaca. Furthermore, the potential genetic loss of subfamily III receptors in this species, could position P. aegyptiaca as a valuable model in the ABA perception research field.
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Affiliation(s)
- Gil Wiseglass
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, the Hebrew University of Jerusalem, Rehovot, 7610001, Israel
| | - Oded Pri-Tal
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, the Hebrew University of Jerusalem, Rehovot, 7610001, Israel
| | - Assaf Mosquna
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, the Hebrew University of Jerusalem, Rehovot, 7610001, Israel.
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Tao F, Liu H. Molecular Dynamics Simulations Reveal Differentiated Context-Dependent Conformational Dynamics of Two Proteins of the Same Family. J Phys Chem B 2018; 122:10686-10699. [PMID: 30407824 DOI: 10.1021/acs.jpcb.8b08468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The Arabidopsis pyrabactin resistant 1 (PYR1)-like family of proteins (PYLs) are receptors of abscisic acid (ABA), an essential small signaling molecule in plants. Here, we report a comparative molecular dynamics (MD) study on two PYL members, PYR1 and PYL10, which, despite their highly similar sequences and structures, have been suggested to belong to two different subclasses of PYLs, one being dimeric and relying on binding to ABA to inhibit downstream type 2C protein phosphatases (PP2Cs) and the other being monomeric and able to constitutively inhibit downstream PP2Cs without ABA. MD simulations have been carried out on these proteins in various monomeric or complexation states. Analyses of the simulations unambiguously confirm that ABA has large effects on the conformational dynamics of PYR1 but not PYL10, whereas a downstream PP2C has much larger effects on PYL10 than on PYR1. The differentiated effects are consistent with the functional differences between the two proteins. Potential of mean forces (PMFs) calculated by umbrella sampling showed that binding to ABA strengthens the PYR1-PP2C complex, increasing the PMF change for dissociation from 7.5 to 12.0 kcal mol-1. On the other hand, the same PMF change for an apo-PYL10-PP2C complex was computed to be 9.5 kcal mol-1, suggesting stronger binding in apo-PYL10-PP2C than in apo-PYR1-PP2C. Several specific sequence features that may contribute to the functional differentiation between PYR1 and PYL10 are suggested based on the intersubunit residue-residue contacts occurred in the simulations.
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Affiliation(s)
- Feng Tao
- School of Life Sciences , University of Science and Technology of China , 230027 Hefei , Anhui , China
| | - Haiyan Liu
- School of Life Sciences , University of Science and Technology of China , 230027 Hefei , Anhui , China.,Hefei National Laboratory for Physical Sciences at the Microscales , 230027 Hefei , Anhui , China
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Ge H, Li X, Chen S, Zhang M, Liu Z, Wang J, Li X, Yang Y. The Expression of CARK1 or RCAR11 Driven by Synthetic Promoters Increases Drought Tolerance in Arabidopsis thaliana. Int J Mol Sci 2018; 19:ijms19071945. [PMID: 29970817 PMCID: PMC6073707 DOI: 10.3390/ijms19071945] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 06/26/2018] [Accepted: 06/27/2018] [Indexed: 12/14/2022] Open
Abstract
Drought stress hinders plant growth and development, and abscisic acid (ABA) stimulates plants to respond to drought. Here, to increase plant tolerance to drought, we designed three synthetic promoters (Ap, Dp, ANDp) to determine transcription activity and drought stress resistance in plants resulting from combinations of (1) synthetic promoters and (2) the functional genes CARK1 (cytosolic ABA receptor kinase 1) and RCAR11 (regulatory components of ABA receptor 11). Transient expression of eGFP and the dual-luciferase assay demonstrated that the basal transcriptional activities of Ap and ANDp were present at low levels under normal conditions, while the synthetic promoters were apparently induced upon either treatment of exogenous ABA or co-transformation with effector DREB2A (dehydration-responsive element binding protein 2A). Analysis of the transgenic plants (Ap:CARK1, Dp:CARK1, ANDp:CARK1, and Dp:RCAR11-Ap:CARK1) showed that the synthetic promoters Ap, Dp, and ANDp increased the expression of exogenous genes in transgenic plants upon treatment of ABA or d-mannitol. ANDp:CARK1 and Dp:RCAR11-Ap:CARK1 transgenic plants were sensitive to ABA and d-mannitol during cotyledon greening and root growth. A drought tolerance assay revealed that ANDp:CARK1 and Dp:RCAR11-Ap:CARK1 exhibited a higher survival rate than others upon drought stress. These results indicate that the combinations ANDp:CARK1 and Dp:RCAR11-Ap:CARK1 can be used to generate drought stress resistance in plants.
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Affiliation(s)
- Hu Ge
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China.
| | - Xiaoyi Li
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China.
| | - Shisi Chen
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China.
| | - Mengru Zhang
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China.
| | - Zhibin Liu
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China.
| | - Jianmei Wang
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China.
| | - Xufeng Li
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China.
| | - Yi Yang
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China.
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Mercer RCC, Daude N, Dorosh L, Fu ZL, Mays CE, Gapeshina H, Wohlgemuth SL, Acevedo-Morantes CY, Yang J, Cashman NR, Coulthart MB, Pearson DM, Joseph JT, Wille H, Safar JG, Jansen GH, Stepanova M, Sykes BD, Westaway D. A novel Gerstmann-Sträussler-Scheinker disease mutation defines a precursor for amyloidogenic 8 kDa PrP fragments and reveals N-terminal structural changes shared by other GSS alleles. PLoS Pathog 2018; 14:e1006826. [PMID: 29338055 PMCID: PMC5786331 DOI: 10.1371/journal.ppat.1006826] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 01/26/2018] [Accepted: 12/18/2017] [Indexed: 11/29/2022] Open
Abstract
To explore pathogenesis in a young Gerstmann-Sträussler-Scheinker Disease (GSS) patient, the corresponding mutation, an eight-residue duplication in the hydrophobic region (HR), was inserted into the wild type mouse PrP gene. Transgenic (Tg) mouse lines expressing this mutation (Tg.HRdup) developed spontaneous neurologic syndromes and brain extracts hastened disease in low-expressor Tg.HRdup mice, suggesting de novo formation of prions. While Tg.HRdup mice exhibited spongiform change, PrP aggregates and the anticipated GSS hallmark of a proteinase K (PK)-resistant 8 kDa fragment deriving from the center of PrP, the LGGLGGYV insertion also imparted alterations in PrP's unstructured N-terminus, resulting in a 16 kDa species following thermolysin exposure. This species comprises a plausible precursor to the 8 kDa PK-resistant fragment and its detection in adolescent Tg.HRdup mice suggests that an early start to accumulation could account for early disease of the index case. A 16 kDa thermolysin-resistant signature was also found in GSS patients with P102L, A117V, H187R and F198S alleles and has coordinates similar to GSS stop codon mutations. Our data suggest a novel shared pathway of GSS pathogenesis that is fundamentally distinct from that producing structural alterations in the C-terminus of PrP, as observed in other prion diseases such as Creutzfeldt-Jakob Disease and scrapie. Prion diseases can be sporadic, infectious or genetic. The central event of all prion diseases is the structural conversion of the cellular prion protein (PrPC) to its disease associated conformer, PrPSc. Gerstmann-Sträussler-Scheinker Disease (GSS) is a genetic prion disease presenting as a multi-systemic neurological syndrome. A novel mutation, an eight amino acid insertion, was discovered in a young GSS patient. We created transgenic mice expressing this mutation and found that they recapitulate key features of the disease; namely PrP deposition in the brain and a low molecular weight proteinase K (PK) resistant internal PrP fragment. While structural investigations did not reveal a gross alteration in the conformation of this mutant PrP, the insertion lying at the boundary of the globular domain causes alterations in the unstructured amino terminal portion of the protein such that it becomes resistant to digestion by the enzyme thermolysin. We demonstrate by kinetic analysis and sequential digestion that this novel thermolysin resistant species is a precursor to the pathognomonic PK resistant fragment. Analysis of samples from other GSS patients revealed this same signature, suggesting a common molecular pathway.
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Affiliation(s)
- Robert C. C. Mercer
- Centre for Prions and Protein Folding Diseases, University of Alberta, Edmonton, Alberta, Canada
- Department of Medicine (Neurology), University of Alberta, Edmonton, Alberta, Canada
| | - Nathalie Daude
- Centre for Prions and Protein Folding Diseases, University of Alberta, Edmonton, Alberta, Canada
| | - Lyudmyla Dorosh
- National Research Council of Canada, Edmonton, Alberta, Canada
- Department of Electrical and Computer Engineering, University of Alberta, Edmonton, Alberta, Canada
| | - Ze-Lin Fu
- Centre for Prions and Protein Folding Diseases, University of Alberta, Edmonton, Alberta, Canada
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Charles E. Mays
- Centre for Prions and Protein Folding Diseases, University of Alberta, Edmonton, Alberta, Canada
| | - Hristina Gapeshina
- Centre for Prions and Protein Folding Diseases, University of Alberta, Edmonton, Alberta, Canada
| | - Serene L. Wohlgemuth
- Centre for Prions and Protein Folding Diseases, University of Alberta, Edmonton, Alberta, Canada
| | | | - Jing Yang
- Centre for Prions and Protein Folding Diseases, University of Alberta, Edmonton, Alberta, Canada
| | - Neil R. Cashman
- Brain Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Michael B. Coulthart
- Canadian Creutzfeldt-Jakob Disease Surveillance System, Centre for Foodborne, Environmental and Zoonotic Infectious Diseases, Public Health Agency of Canada, Ottawa, Ontario, Canada
| | - Dawn M. Pearson
- Department of Clinical Neurosciences, University of Calgary, Calgary, Alberta, Canada
| | - Jeffrey T. Joseph
- Hotchkiss Brain Institute and Calgary Laboratory Services, University of Calgary, Calgary, Alberta, Canada
| | - Holger Wille
- Centre for Prions and Protein Folding Diseases, University of Alberta, Edmonton, Alberta, Canada
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Jiri G. Safar
- Departments of Pathology and Neurology, School of Medicine Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Gerard H. Jansen
- Canadian Creutzfeldt-Jakob Disease Surveillance System, Centre for Foodborne, Environmental and Zoonotic Infectious Diseases, Public Health Agency of Canada, Ottawa, Ontario, Canada
- Division of Anatomical Pathology, University of Ottawa, Ottawa, Ontario, Canada
| | - Maria Stepanova
- National Research Council of Canada, Edmonton, Alberta, Canada
- Department of Electrical and Computer Engineering, University of Alberta, Edmonton, Alberta, Canada
| | - Brian D. Sykes
- Centre for Prions and Protein Folding Diseases, University of Alberta, Edmonton, Alberta, Canada
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada
| | - David Westaway
- Centre for Prions and Protein Folding Diseases, University of Alberta, Edmonton, Alberta, Canada
- Department of Medicine (Neurology), University of Alberta, Edmonton, Alberta, Canada
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada
- * E-mail:
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Pri-Tal O, Shaar-Moshe L, Wiseglass G, Peleg Z, Mosquna A. Non-redundant functions of the dimeric ABA receptor BdPYL1 in the grass Brachypodium. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 92:774-786. [PMID: 28891214 DOI: 10.1111/tpj.13714] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 08/31/2017] [Accepted: 09/04/2017] [Indexed: 05/05/2023]
Abstract
Abiotic stresses have severe detrimental effects on agricultural productivity worldwide. Abscisic acid (ABA) levels rise in response to abiotic stresses, and play a role in coordinating physiological responses. ABA elicits its effects by binding a family of soluble receptors, increasing affinity of the receptors to type 2C phosphatases (PP2Cs) leading to phosphatase inhibition. In the current study, we conducted a comprehensive analysis of the ABA signaling pathway in the cereal model grass Brachypodium distachyon. The Brachypodium genome encodes a family of 10 functionally conserved ABA receptors. The 10th in the series, BdPYL10, encodes a defective receptor and is likely a pseudogene. Combinatorial protein interaction assay further validated computational analysis, which grouped Brachypodium ABA receptors into three subfamilies, similarly to Arabidopsis classification. Brachypodium subfamily III receptors inhibited PP2C activity in vitro and complemented Arabidopsis quadruple (pyr1/pyl1/pyl2/pyl4) mutant. BdPYL1 T-DNA mutant exhibited clear ABA hyposensitivity phenotypes during seedling establishment and in mature plants. Single receptor predominance is in agreement with high transcriptional abundance of only a small Brachypodium ABA receptors subset, harboring the higher marginal significance of BdPYL1. Our findings suggest that unlike the highly redundant ABA core signaling components of Arabidopsis, Brachypodium encompasses a more compact and specialized ABA receptor apparatus. This organization may contribute to plant adaptations to ecological niches. These results lay the groundwork for targeting the prominent ABA receptors for stress perception in grasses, and reveal functional differences and commonalities between monocots and eudicots.
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Affiliation(s)
- Oded Pri-Tal
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, 7610001, Israel
| | - Lidor Shaar-Moshe
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, 7610001, Israel
| | - Gil Wiseglass
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, 7610001, Israel
| | - Zvi Peleg
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, 7610001, Israel
| | - Assaf Mosquna
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, 7610001, Israel
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10
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Dorosh L, Stepanova M. Probing oligomerization of amyloid beta peptide in silico. MOLECULAR BIOSYSTEMS 2017; 13:165-182. [PMID: 27844078 DOI: 10.1039/c6mb00441e] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Aggregation of amyloid β (Aβ) peptide is implicated in fatal Alzheimer's disease, for which no cure is available. Understanding the mechanisms responsible for this aggregation is required in order for therapies to be developed. In an effort to better understand the molecular mechanisms involved in spontaneous aggregation of Aβ peptide, extensive molecular dynamics simulations are reported, and the results are analyzed through a combination of structural biology tools and a novel essential collective dynamics method. Several model systems composed of ten or twelve Aβ17-42 chains in water are investigated, and the influence of metal ions is probed. The results suggest that Aβ monomers tend to aggregate into stable globular-like oligomers with 13-23% of β-sheet content. Two stages of oligomer formation have been identified: quick collapse within the first 40 ns of the simulation, characterized by a decrease in inter-chain separation and build-up of β-sheets, and the subsequent slow relaxation of the oligomer structure. The resulting oligomers comprise a stable, coherently moving sub-aggregate of 6-9 strongly inter-correlated chains. Cu2+ and Fe2+ ions have been found to develop coordination bonds with carboxylate groups of E22, D23 and A42, which remain stable during 200 ns simulations. The presence of Fe2+, and particularly Cu2+ ions, in negatively charged cavities has been found to cause significant changes in the structure and dynamics of the oligomers. The results indicate, in particular, that formation of non-fibrillar oligomers might be involved in early template-free aggregation of Aβ17-42 monomers, with charged species such as Cu2+ or Fe2+ ions playing an important role.
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Affiliation(s)
- L Dorosh
- Department of Electrical and Computer Engineering, University of Alberta, Edmonton, Alberta, Canada. and National Research Council of Canada, Edmonton, Alberta, Canada
| | - M Stepanova
- Department of Electrical and Computer Engineering, University of Alberta, Edmonton, Alberta, Canada. and National Research Council of Canada, Edmonton, Alberta, Canada and Department of Physics, Astronomy, and Materials Science, Missouri State University, Springfield, MO, USA
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11
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Gordon CS, Rajagopalan N, Risseeuw EP, Surpin M, Ball FJ, Barber CJ, Buhrow LM, Clark SM, Page JE, Todd CD, Abrams SR, Loewen MC. Characterization of Triticum aestivum Abscisic Acid Receptors and a Possible Role for These in Mediating Fusairum Head Blight Susceptibility in Wheat. PLoS One 2016; 11:e0164996. [PMID: 27755583 PMCID: PMC5068739 DOI: 10.1371/journal.pone.0164996] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 10/04/2016] [Indexed: 01/31/2023] Open
Abstract
Abscisic acid (ABA) is a well-characterized plant hormone, known to mediate developmental aspects as well as both abiotic and biotic stress responses. Notably, the exogenous application of ABA has recently been shown to increase susceptibility to the fungal pathogen Fusarium graminearum, the causative agent of Fusarium head blight (FHB) in wheat and other cereals. However roles and mechanisms associated with ABA's modulation of pathogen responses remain enigmatic. Here the identification of putative ABA receptors from available genomic databases for Triticum aestivum (bread wheat) and Brachypodium distachyon (a model cereal) are reported. A number of these were cloned for recombinant expression and their functionality as ABA receptors confirmed by in vitro assays against protein phosphatases Type 2Cs. Ligand selectivity profiling of one of the wheat receptors (Ta_PYL2DS_FL) highlighted unique activities compared to Arabidopsis AtPYL5. Mutagenic analysis showed Ta_PYL2DS_FL amino acid D180 as being a critical contributor to this selectivity. Subsequently, a virus induced gene silencing (VIGS) approach was used to knockdown wheat Ta_PYL4AS_A (and similar) in planta, yielding plants with increased early stage resistance to FHB progression and decreased mycotoxin accumulation. Together these results confirm the existence of a family of ABA receptors in wheat and Brachypodium and present insight into factors modulating receptor function at the molecular level. That knockdown of Ta_PYL4AS_A (and similar) leads to early stage FHB resistance highlights novel targets for investigation in the future development of disease resistant crops.
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Affiliation(s)
- Cameron S. Gordon
- Department of Biochemistry, University of Saskatchewan, 107 Wiggins Rd., Saskatoon, SK, S7N 5E5, Canada
- National Research Council of Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada
| | | | - Eddy P. Risseeuw
- National Research Council of Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada
| | - Marci Surpin
- Valent BioSciences Corporation, 870 Technology Way, Libertyville, Illinois, 60048, United States of America
| | - Fraser J. Ball
- National Research Council of Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada
| | - Carla J. Barber
- National Research Council of Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada
| | - Leann M. Buhrow
- National Research Council of Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada
| | - Shawn M. Clark
- National Research Council of Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada
| | - Jonathan E. Page
- National Research Council of Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada
| | - Chris D. Todd
- Department of Biology, University of Saskatchewan, 112 Science Place, Saskatoon, SK, S7N 5E2, Canada
| | - Suzanne R. Abrams
- National Research Council of Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada
- Department of Chemistry, University of Saskatchewan, 110 Science Place, Saskatoon, SK, S7N 5C9, Canada
| | - Michele C. Loewen
- Department of Biochemistry, University of Saskatchewan, 107 Wiggins Rd., Saskatoon, SK, S7N 5E5, Canada
- National Research Council of Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada
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12
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Mane JY, Stepanova M. Understanding the dynamics of monomeric, dimeric, and tetrameric α-synuclein structures in water. FEBS Open Bio 2016; 6:666-86. [PMID: 27398307 PMCID: PMC4932447 DOI: 10.1002/2211-5463.12069] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 04/05/2016] [Accepted: 04/06/2016] [Indexed: 01/20/2023] Open
Abstract
Human α‐synuclein (αS) is an intrinsically disordered protein associated with Parkinson's disease. Molecular mechanisms of corruptive misfolding and aggregation of αS resulting in the disease, as well as the structure and other properties of the corresponding oligomers are not entirely understood yet, preventing the development of efficient therapies. In this study, we investigate the folding dynamics of initially unfolded hypothetical αS constructs in water using all‐atom molecular dynamics simulations. We also employ the novel essential collective dynamics method to analyze the results obtained from the simulations. Our comparative analysis of monomeric, dimeric, and tetrameric αS models reveals pronounced differences in their structure and stability, emphasizing the importance of small oligomers, particularly dimers, in the process of misfolding.
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Affiliation(s)
- Jonathan Y Mane
- Department of Electrical and Computer Engineering University of Alberta Edmonton Canada; National Institute for Nanotechnology National Research Council Canada Edmonton Canada
| | - Maria Stepanova
- Department of Electrical and Computer Engineering University of Alberta Edmonton Canada; National Institute for Nanotechnology National Research Council Canada Edmonton Canada; Department of Physics, Astronomy, and Materials Science Missouri State University Springfield MO USA
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13
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Abstract
Lipids are important signaling compounds in plants. They can range from small lipophilic molecules like the dicarboxylic acid Azelaic acid to complex phosphoglycerolipids and regulate plant development as well as the response to biotic and abiotic stress. While their intracellular function is well described, several lipophilic signals are known to be found in the plant phloem and can, thus, also play a role in long-distance signaling. Mostly, they play a role in the pathogen response and systemic acquired resistance. This is particularly true for oxylipins, dehydroabietinal, and azelaic acid. However, several phospholipids have now been described in phloem exudates. Their intracellular function as well as implications and a model for long-distance signaling are discussed in this chapter.
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14
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Stueker O, Ortega VA, Goss GG, Stepanova M. Understanding interactions of functionalized nanoparticles with proteins: a case study on lactate dehydrogenase. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2014; 10:2006-2021. [PMID: 24591162 DOI: 10.1002/smll.201303639] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2013] [Revised: 01/10/2014] [Indexed: 06/03/2023]
Abstract
Nanomaterials in biological solutions are known to interact with proteins and have been documented to affect protein function, such as enzyme activity. Understanding the interactions of nanoparticles with biological components at the molecular level will allow for rational designs of nanomaterials for use in medical technologies. Here we present the first detailed molecular mechanics model of functionalized gold nanoparticle (NP) interacting with an enzyme (L-lactate dehydrogenase (LDH) enzyme). Molecular dynamics (MD) simulations of the response of LDH to the NP binding demonstrate that although atomic motions (dynamics) of the main chain exhibit only a minor response to the binding, the dynamics of side chains are significantly constrained in all four active sites that predict alteration in kinetic properties of the enzyme. It is also demonstrated that the 5 nm gold NPs cause a decrease in the maximal velocity of the enzyme reaction (V(max)) and a trend towards a reduced affinity (increased K(m)) for the β-NAD binding site, while pyruvate enzyme kinetics (K(m) and V(max)) are not significantly altered in the presence of the gold NPs. These results demonstrate that modeling of NP:protein interactions can be used to understand alterations in protein function.
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Affiliation(s)
- Oliver Stueker
- National Institute for Nanotechnology, National Research Council of Canada, 11421 Saskatchewan Drive, EdmontonAlberta, T6G 2M9, Canada; Department of Electrical and Computer Engineering, University of Alberta, 9107-116 Street, Edmonton, Alberta, T6G 2V4, Canada
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15
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Dorosh L, Rajagopalan N, Loewen MC, Stepanova M. Molecular mechanisms in the selective basal activation of pyrabactin receptor 1: Comparative analysis of mutants. FEBS Open Bio 2014; 4:496-509. [PMID: 24944884 PMCID: PMC4060014 DOI: 10.1016/j.fob.2014.05.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Revised: 05/10/2014] [Accepted: 05/13/2014] [Indexed: 01/29/2023] Open
Abstract
Pyrabactin receptors (PYR) play a central role in abscisic acid (ABA) signal transduction; they are ABA receptors that inhibit type 2C protein phosphatases (PP2C). Molecular aspects contributing to increased basal activity of PYR against PP2C are studied by molecular dynamics (MD) simulations. An extensive series of MD simulations of the apo-form of mutagenized PYR1 as a homodimer and in complex with homology to ABA-insensitive 1 (HAB1) phosphatase are reported. In order to investigate the detailed molecular mechanisms mediating PYR1 activity, the MD data was analyzed by essential collective dynamics (ECD), a novel approach that allows the identification, with atomic resolution, of persistent dynamic correlations based on relatively short MD trajectories. Employing the ECD method, the effects of select mutations on the structure and dynamics of the PYR1 complexes were investigated and considered in the context of experimentally determined constitutive activities against HAB1. Approaches to rationally design constitutively active PYR1 constructs to increase PP2C inhibition are discussed.
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Key Words
- ABA, A8S abscisic acid
- Abscisic acid signaling
- CA, constitutively active
- Constitutively active mutations
- ECD, essential collective dynamics
- Essential collective dynamics analysis
- HAB1, homology to ABA insensitive 1
- MD, molecular dynamics
- Molecular dynamics simulations
- P2M, N-(pyridin-2-ylmethyl) naphthalene-1-sulfonamide or C16H14N2O2S
- PCA, principal component analysis
- PDB, Protein Data Bank
- PP2C, phosphatase type 2C
- PYL, PYR1-like
- PYR1, pyrabactin resistance 1
- PYV, pyrabactin or C16H13BrN2O2S
- Pyrabactin resistance
- RCAR, regulatory component of ABA response
- WT, wild type
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Affiliation(s)
- Lyudmyla Dorosh
- National Research Council of Canada, Edmonton, Alberta, Canada ; Department of Electrical and Computer Engineering, University of Alberta, Edmonton, Alberta, Canada
| | | | - Michele C Loewen
- National Research Council of Canada, Saskatoon, Saskatchewan, Canada ; Department of Biochemistry, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Maria Stepanova
- National Research Council of Canada, Edmonton, Alberta, Canada ; Department of Electrical and Computer Engineering, University of Alberta, Edmonton, Alberta, Canada
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