{
"@id": "./",
"filename": "isa.investigation.xlsx",
"identifier": "2025_CoBiSe",
"title": "A novel biosensor for ferrous iron developed via CoBiSe: A computational method for rapid biosensor design ",
"description": "Genetically encoded biosensors enable monitoring of metabolite dynamics in living organisms. We present CoBiSe, a computational approach using Constraint Network Analysis to identify optimal insertion sites for reporter modules in molecular recognition elements (MREs). Applied to the iron-binding protein DtxR from Corynebacterium glutamicum, CoBiSe identified a flexible connective loop (residues 138-150) for inserting the reporter module, resulting in IronSenseR, a novel ratiometric biosensor for ferrous iron (Fe\u00b2\u207a). IronSenseR demonstrates high specificity for Fe\u00b2\u207a with dissociation constants of 1.78 \u00b1 0.03 \u00b5M (FeSO\u2084) and 2.90 \u00b1 0.12 \u00b5M (FeCl\u2082), while showing no binding to Fe\u00b3\u207a and other divalent cations. In vivo assessment in Escherichia coli, Pseudomonas putida and Corynebacterium glutamicum confirmed IronSenseR's capability to detect changes in the intracellular iron pool. The creation of IronSenseR underlines that, by reducing search space and eliminating labor-intensive screening, CoBiSe streamlines biosensor development and enables precise creation of next-generation biosensors for diverse metabolites.",
"people": [
{
"@id": "0009-0007-2900-9550",
"firstName": "Athanasios",
"lastName": "Papadopoulos",
"email": "Papadopoulos@hhu.de",
"affiliation": "Center for Structural Studies",
"comments": [
{
"name": "ORCID",
"value": "0009-0007-2900-9550"
}
]
},
{
"@id": "0009-0001-8509-9163",
"firstName": "Manuel ",
"lastName": "Anlauf",
"midInitials": "T.",
"email": "manuel.anlauf@hhu.de",
"affiliation": "Center for Advanced Imaging",
"comments": [
{
"name": "ORCID",
"value": "0009-0001-8509-9163"
}
]
},
{
"@id": "0000-0001-5969-4471",
"firstName": "Jens",
"lastName": "Reiners",
"email": "jens.reiners@hhu.de",
"affiliation": "Center for Structural Studies",
"comments": [
{
"name": "ORCID",
"value": "0000-0001-5969-4471"
}
]
},
{
"@id": "0009-0007-1343-0068",
"firstName": "Sueng-Hyun",
"lastName": "Paik",
"email": "s.paik@fz-juelich.de",
"affiliation": "Institute of Molecular Enzyme Technology",
"comments": [
{
"name": "ORCID",
"value": "0009-0007-1343-0068"
}
]
},
{
"@id": "0000-0001-7060-4879",
"firstName": "Aileen",
"lastName": "Krueger",
"email": "ai.krueger@fz-juelich.de",
"affiliation": "Institute of Bio- and Geosciences",
"comments": [
{
"name": "ORCID",
"value": "0000-0001-7060-4879"
}
]
},
{
"@id": "0000-0003-1164-1914",
"firstName": "Benita",
"lastName": "Lueckel",
"email": "lueckel@fz-juelich.de",
"affiliation": "Institute of Bio- and Geosciences",
"comments": [
{
"name": "ORCID",
"value": "0000-0003-1164-1914"
}
]
},
{
"@id": "0000-0002-4701-8254",
"firstName": "Michael",
"lastName": "Bott",
"email": "m.bott@fz-juelich.de",
"affiliation": "Institute of Bio- and Geosciences",
"comments": [
{
"name": "ORCID",
"value": "0000-0002-4701-8254"
}
]
},
{
"@id": "0000-0002-0096-8084",
"firstName": "Thomas",
"lastName": "Drepper",
"email": "t.drepper@fz-juelich.de",
"affiliation": "Institute of Molecular Enzyme Technology",
"comments": [
{
"name": "ORCID",
"value": "0000-0002-0096-8084"
}
]
},
{
"@id": "0000-0001-6209-7950",
"firstName": "Julia",
"lastName": "Frunzke",
"email": "j.frunzke@fz-juelich.de",
"affiliation": "Institute of Bio- and Geosciences",
"comments": [
{
"name": "ORCID",
"value": "0000-0001-6209-7950"
}
]
},
{
"@id": "0000-0001-8613-1447",
"firstName": "Holger",
"lastName": "Gohlke",
"email": "h.gohlke@fz-juelich.de",
"affiliation": "Institute for Pharmaceutical and Medicinal Chemistry",
"comments": [
{
"name": "ORCID",
"value": "0000-0001-8613-1447"
}
]
},
{
"@id": "0000-0001-7734-3771",
"firstName": "Stefanie",
"lastName": "Weidtkamp-Peters",
"email": "Stefanie.Weidtkamp-Peters@hhu.de",
"affiliation": "Center for Advanced Imaging",
"comments": [
{
"name": "ORCID",
"value": "0000-0001-7734-3771"
}
]
},
{
"@id": "0000-0003-0780-9251",
"firstName": "Sander",
"lastName": "Smits",
"midInitials": " H.J.",
"email": "Sander.Smits@hhu.de",
"affiliation": "Center for Structural Studies & Institute for Biochemistry",
"comments": [
{
"name": "ORCID",
"value": "0000-0003-0780-9251"
}
]
},
{
"@id": "0000-0002-9562-7708",
"firstName": "Christoph ",
"lastName": "Gertzen",
"midInitials": "G.W.",
"email": "christoph.gertzen@hhu.de",
"affiliation": "Center for Structural Studies & Institute for Pharmaceutical and Medicinal Chemistry",
"comments": [
{
"name": "ORCID",
"value": "0000-0002-9562-7708"
}
]
}
],
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{
"@id": "studies/CoBiSe/",
"filename": "studies/CoBiSe/isa.study.xlsx",
"identifier": "CoBiSe",
"title": "Computational prediction for rapid biosensor design",
"description": "FASTA sequences for MDtxR and prot files for sFB biosensors"
},
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"title": "Characterization of IronSenseR",
"description": "The novel ratiometric Matryoshka based IronSenseR was investigated upon functional and structural analysis. ",
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"type": "Raw Data File"
}
],
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"name": "studies/Functional_characterization_IronSenseR/resources/Plasmids/pAZ240_pRSET_10xHis_lin.dna",
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}
],
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"@id": "studies/Functional_characterization_IronSenseR/resources/Plasmids/pAZ183_pRSET_10xHis_EK_MDtxRGA_D141.dna",
"name": "studies/Functional_characterization_IronSenseR/resources/Plasmids/pAZ183_pRSET_10xHis_EK_MDtxRGA_D141.dna",
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],
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"name": "studies/Functional_characterization_IronSenseR/resources/Plasmids/pAZ240_pRSET_10xHis_lin.dna",
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],
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],
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{
"@id": "#Process_plasmid_generation_11",
"name": "plasmid generation_11",
"executesProtocol": {
"@id": "#Protocol_./studies/Functional_characterization_IronSenseR/protocols/Molecular_cloning.md",
"name": "./studies/Functional_characterization_IronSenseR/protocols/Molecular cloning.md",
"parameters": [
{
"@id": "#ProtocolParameter/#UserTerm_insertion_Site",
"parameterName": {
"@id": "#UserTerm_insertion_Site",
"annotationValue": "insertion Site"
}
}
]
},
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_insertion_Site",
"parameterName": {
"@id": "#UserTerm_insertion_Site",
"annotationValue": "insertion Site"
}
},
"value": {
"@id": "#UserTerm_S148",
"annotationValue": "S148"
}
}
],
"inputs": [
{
"@id": "studies/Functional_characterization_IronSenseR/resources/Plasmids/pAZ240_pRSET_10xHis_lin.dna",
"name": "studies/Functional_characterization_IronSenseR/resources/Plasmids/pAZ240_pRSET_10xHis_lin.dna",
"type": "Raw Data File"
}
],
"outputs": [
{
"@id": "studies/Functional_characterization_IronSenseR/resources/Plasmids/pAZ190_pRSET_10xHis_EK_MDtxRGA_S148.dna",
"name": "studies/Functional_characterization_IronSenseR/resources/Plasmids/pAZ190_pRSET_10xHis_EK_MDtxRGA_S148.dna",
"type": "Raw Data File"
}
]
},
{
"@id": "#Process_plasmid_generation_12",
"name": "plasmid generation_12",
"executesProtocol": {
"@id": "#Protocol_./studies/Functional_characterization_IronSenseR/protocols/Molecular_cloning.md",
"name": "./studies/Functional_characterization_IronSenseR/protocols/Molecular cloning.md",
"parameters": [
{
"@id": "#ProtocolParameter/#UserTerm_insertion_Site",
"parameterName": {
"@id": "#UserTerm_insertion_Site",
"annotationValue": "insertion Site"
}
}
]
},
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_insertion_Site",
"parameterName": {
"@id": "#UserTerm_insertion_Site",
"annotationValue": "insertion Site"
}
},
"value": {
"@id": "#UserTerm_G149",
"annotationValue": "G149"
}
}
],
"inputs": [
{
"@id": "studies/Functional_characterization_IronSenseR/resources/Plasmids/pAZ240_pRSET_10xHis_lin.dna",
"name": "studies/Functional_characterization_IronSenseR/resources/Plasmids/pAZ240_pRSET_10xHis_lin.dna",
"type": "Raw Data File"
}
],
"outputs": [
{
"@id": "studies/Functional_characterization_IronSenseR/resources/Plasmids/pAZ191_pRSET_10xHis_EK_MDtxRGA_G149.dna",
"name": "studies/Functional_characterization_IronSenseR/resources/Plasmids/pAZ191_pRSET_10xHis_EK_MDtxRGA_G149.dna",
"type": "Raw Data File"
}
]
},
{
"@id": "#Process_plasmid_generation_13",
"name": "plasmid generation_13",
"executesProtocol": {
"@id": "#Protocol_./studies/Functional_characterization_IronSenseR/protocols/Molecular_cloning.md",
"name": "./studies/Functional_characterization_IronSenseR/protocols/Molecular cloning.md",
"parameters": [
{
"@id": "#ProtocolParameter/#UserTerm_insertion_Site",
"parameterName": {
"@id": "#UserTerm_insertion_Site",
"annotationValue": "insertion Site"
}
}
]
},
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_insertion_Site",
"parameterName": {
"@id": "#UserTerm_insertion_Site",
"annotationValue": "insertion Site"
}
},
"value": {
"@id": "#UserTerm_V150",
"annotationValue": "V150"
}
}
],
"inputs": [
{
"@id": "studies/Functional_characterization_IronSenseR/resources/Plasmids/pAZ240_pRSET_10xHis_lin.dna",
"name": "studies/Functional_characterization_IronSenseR/resources/Plasmids/pAZ240_pRSET_10xHis_lin.dna",
"type": "Raw Data File"
}
],
"outputs": [
{
"@id": "studies/Functional_characterization_IronSenseR/resources/Plasmids/pAZ192_pRSET_10xHis_EK_MDtxRGA_V150.dna",
"name": "studies/Functional_characterization_IronSenseR/resources/Plasmids/pAZ192_pRSET_10xHis_EK_MDtxRGA_V150.dna",
"type": "Raw Data File"
}
]
}
],
"assays": [
{
"filename": "assays/Expression_and_Purification/isa.assay.xlsx",
"@id": "assays/Expression_and_Purification/",
"dataFiles": [
{
"@id": "studies/Functional_characterization_IronSenseR/resources/Plasmids/pAZ180_pRSET_10xHis_EK_MDtxRGA_I138.dna",
"name": "studies/Functional_characterization_IronSenseR/resources/Plasmids/pAZ180_pRSET_10xHis_EK_MDtxRGA_I138.dna",
"type": "Raw Data File"
},
{
"@id": "studies/Functional_characterization_IronSenseR/resources/Plasmids/pAZ181_pRSET_10xHis_EK_MDtxRGA_G139.dna",
"name": "studies/Functional_characterization_IronSenseR/resources/Plasmids/pAZ181_pRSET_10xHis_EK_MDtxRGA_G139.dna",
"type": "Raw Data File"
},
{
"@id": "studies/Functional_characterization_IronSenseR/resources/Plasmids/pAZ182_pRSET_10xHis_EK_MDtxRGA_L140.dna",
"name": "studies/Functional_characterization_IronSenseR/resources/Plasmids/pAZ182_pRSET_10xHis_EK_MDtxRGA_L140.dna",
"type": "Raw Data File"
},
{
"@id": "studies/Functional_characterization_IronSenseR/resources/Plasmids/pAZ183_pRSET_10xHis_EK_MDtxRGA_D141.dna",
"name": "studies/Functional_characterization_IronSenseR/resources/Plasmids/pAZ183_pRSET_10xHis_EK_MDtxRGA_D141.dna",
"type": "Raw Data File"
},
{
"@id": "studies/Functional_characterization_IronSenseR/resources/Plasmids/pAZ184_pRSET_10xHis_EK_MDtxRGA_Q142.dna",
"name": "studies/Functional_characterization_IronSenseR/resources/Plasmids/pAZ184_pRSET_10xHis_EK_MDtxRGA_Q142.dna",
"type": "Raw Data File"
},
{
"@id": "studies/Functional_characterization_IronSenseR/resources/Plasmids/pAZ185_pRSET_10xHis_EK_MDtxRGA_A143.dna",
"name": "studies/Functional_characterization_IronSenseR/resources/Plasmids/pAZ185_pRSET_10xHis_EK_MDtxRGA_A143.dna",
"type": "Raw Data File"
},
{
"@id": "studies/Functional_characterization_IronSenseR/resources/Plasmids/pAZ186_pRSET_10xHis_EK_MDtxRGA_D144.dna",
"name": "studies/Functional_characterization_IronSenseR/resources/Plasmids/pAZ186_pRSET_10xHis_EK_MDtxRGA_D144.dna",
"type": "Raw Data File"
},
{
"@id": "studies/Functional_characterization_IronSenseR/resources/Plasmids/pAZ187_pRSET_10xHis_EK_MDtxRGA_E145.dna",
"name": "studies/Functional_characterization_IronSenseR/resources/Plasmids/pAZ187_pRSET_10xHis_EK_MDtxRGA_E145.dna",
"type": "Raw Data File"
},
{
"@id": "studies/Functional_characterization_IronSenseR/resources/Plasmids/pAZ188_pRSET_10xHis_EK_MDtxRGA_P146.dna",
"name": "studies/Functional_characterization_IronSenseR/resources/Plasmids/pAZ188_pRSET_10xHis_EK_MDtxRGA_P146.dna",
"type": "Raw Data File"
},
{
"@id": "studies/Functional_characterization_IronSenseR/resources/Plasmids/pAZ189_pRSET_10xHis_EK_MDtxRGA_D147.dna",
"name": "studies/Functional_characterization_IronSenseR/resources/Plasmids/pAZ189_pRSET_10xHis_EK_MDtxRGA_D147.dna",
"type": "Raw Data File"
},
{
"@id": "studies/Functional_characterization_IronSenseR/resources/Plasmids/pAZ190_pRSET_10xHis_EK_MDtxRGA_S148.dna",
"name": "studies/Functional_characterization_IronSenseR/resources/Plasmids/pAZ190_pRSET_10xHis_EK_MDtxRGA_S148.dna",
"type": "Raw Data File"
},
{
"@id": "studies/Functional_characterization_IronSenseR/resources/Plasmids/pAZ191_pRSET_10xHis_EK_MDtxRGA_G149.dna",
"name": "studies/Functional_characterization_IronSenseR/resources/Plasmids/pAZ191_pRSET_10xHis_EK_MDtxRGA_G149.dna",
"type": "Raw Data File"
},
{
"@id": "studies/Functional_characterization_IronSenseR/resources/Plasmids/pAZ192_pRSET_10xHis_EK_MDtxRGA_V150.dna",
"name": "studies/Functional_characterization_IronSenseR/resources/Plasmids/pAZ192_pRSET_10xHis_EK_MDtxRGA_V150.dna",
"type": "Raw Data File"
},
{
"@id": "studies/Functional_characterization_IronSenseR/resources/Plasmids/pAZ199_pRSET_10xHis_EK_MDtxRGA_G149_H98A.dna",
"name": "studies/Functional_characterization_IronSenseR/resources/Plasmids/pAZ199_pRSET_10xHis_EK_MDtxRGA_G149_H98A.dna",
"type": "Raw Data File"
},
{
"@id": "studies/Functional_characterization_IronSenseR/resources/Plasmids/pAZ200_pRSET_10xHis_EK_MDtxRGA_G149_C102A.dna",
"name": "studies/Functional_characterization_IronSenseR/resources/Plasmids/pAZ200_pRSET_10xHis_EK_MDtxRGA_G149_C102A.dna",
"type": "Raw Data File"
},
{
"@id": "studies/Functional_characterization_IronSenseR/resources/Plasmids/pAZ198_pRSET_10xHis_EK_MDtxRGA_G149_H79A.dna",
"name": "studies/Functional_characterization_IronSenseR/resources/Plasmids/pAZ198_pRSET_10xHis_EK_MDtxRGA_G149_H79A.dna",
"type": "Raw Data File"
}
],
"materials": {
"samples": [
{
"@id": "#Sample_MDtxR_I138",
"name": "MDtxR I138"
},
{
"@id": "#Sample_MDtxR_G139",
"name": "MDtxR G139"
},
{
"@id": "#Sample_MDtxR_L140",
"name": "MDtxR L140"
},
{
"@id": "#Sample_MDtxR_D141",
"name": "MDtxR D141"
},
{
"@id": "#Sample_MDtxR_Q142",
"name": "MDtxR Q142"
},
{
"@id": "#Sample_MDtxR_A143",
"name": "MDtxR A143"
},
{
"@id": "#Sample_MDtxR_D144",
"name": "MDtxR D144"
},
{
"@id": "#Sample_MDtxR_E145",
"name": "MDtxR E145"
},
{
"@id": "#Sample_MDtxR_P146",
"name": "MDtxR P146"
},
{
"@id": "#Sample_MDtxR_D147",
"name": "MDtxR D147"
},
{
"@id": "#Sample_MDtxR_S148",
"name": "MDtxR S148"
},
{
"@id": "#Sample_MDtxR_G149",
"name": "MDtxR G149"
},
{
"@id": "#Sample_MDtxR_V150",
"name": "MDtxR V150"
},
{
"@id": "#Sample_MDtxRGA_G149_H98A",
"name": "MDtxRGA_G149_H98A"
},
{
"@id": "#Sample_MDtxRGA_G149_C102A",
"name": "MDtxRGA_G149_C102A"
},
{
"@id": "#Sample_MDtxRGA_G149_H79A",
"name": "MDtxRGA_G149_H79A"
}
]
},
"processSequence": [
{
"@id": "#Process_Expression_and_Purification_fro_0",
"name": "Expression and Purification fro_0",
"executesProtocol": {
"@id": "#Protocol_./assays/Expression_and_Purification/dataset/2024-10-24-241018-25-Expression-Purification-and-Characterization-of-pAZ180-192-MDtxRGA-with-various-insertion-sites.pdf",
"name": "./assays/Expression_and_Purification/dataset/2024-10-24-241018-25-Expression-Purification-and-Characterization-of-pAZ180-192-MDtxRGA-with-various-insertion-sites.pdf"
},
"inputs": [
{
"@id": "studies/Functional_characterization_IronSenseR/resources/Plasmids/pAZ180_pRSET_10xHis_EK_MDtxRGA_I138.dna",
"name": "studies/Functional_characterization_IronSenseR/resources/Plasmids/pAZ180_pRSET_10xHis_EK_MDtxRGA_I138.dna",
"type": "Raw Data File"
},
{
"@id": "studies/Functional_characterization_IronSenseR/resources/Plasmids/pAZ181_pRSET_10xHis_EK_MDtxRGA_G139.dna",
"name": "studies/Functional_characterization_IronSenseR/resources/Plasmids/pAZ181_pRSET_10xHis_EK_MDtxRGA_G139.dna",
"type": "Raw Data File"
},
{
"@id": "studies/Functional_characterization_IronSenseR/resources/Plasmids/pAZ182_pRSET_10xHis_EK_MDtxRGA_L140.dna",
"name": "studies/Functional_characterization_IronSenseR/resources/Plasmids/pAZ182_pRSET_10xHis_EK_MDtxRGA_L140.dna",
"type": "Raw Data File"
},
{
"@id": "studies/Functional_characterization_IronSenseR/resources/Plasmids/pAZ183_pRSET_10xHis_EK_MDtxRGA_D141.dna",
"name": "studies/Functional_characterization_IronSenseR/resources/Plasmids/pAZ183_pRSET_10xHis_EK_MDtxRGA_D141.dna",
"type": "Raw Data File"
},
{
"@id": "studies/Functional_characterization_IronSenseR/resources/Plasmids/pAZ184_pRSET_10xHis_EK_MDtxRGA_Q142.dna",
"name": "studies/Functional_characterization_IronSenseR/resources/Plasmids/pAZ184_pRSET_10xHis_EK_MDtxRGA_Q142.dna",
"type": "Raw Data File"
},
{
"@id": "studies/Functional_characterization_IronSenseR/resources/Plasmids/pAZ185_pRSET_10xHis_EK_MDtxRGA_A143.dna",
"name": "studies/Functional_characterization_IronSenseR/resources/Plasmids/pAZ185_pRSET_10xHis_EK_MDtxRGA_A143.dna",
"type": "Raw Data File"
},
{
"@id": "studies/Functional_characterization_IronSenseR/resources/Plasmids/pAZ186_pRSET_10xHis_EK_MDtxRGA_D144.dna",
"name": "studies/Functional_characterization_IronSenseR/resources/Plasmids/pAZ186_pRSET_10xHis_EK_MDtxRGA_D144.dna",
"type": "Raw Data File"
},
{
"@id": "studies/Functional_characterization_IronSenseR/resources/Plasmids/pAZ187_pRSET_10xHis_EK_MDtxRGA_E145.dna",
"name": "studies/Functional_characterization_IronSenseR/resources/Plasmids/pAZ187_pRSET_10xHis_EK_MDtxRGA_E145.dna",
"type": "Raw Data File"
},
{
"@id": "studies/Functional_characterization_IronSenseR/resources/Plasmids/pAZ188_pRSET_10xHis_EK_MDtxRGA_P146.dna",
"name": "studies/Functional_characterization_IronSenseR/resources/Plasmids/pAZ188_pRSET_10xHis_EK_MDtxRGA_P146.dna",
"type": "Raw Data File"
},
{
"@id": "studies/Functional_characterization_IronSenseR/resources/Plasmids/pAZ189_pRSET_10xHis_EK_MDtxRGA_D147.dna",
"name": "studies/Functional_characterization_IronSenseR/resources/Plasmids/pAZ189_pRSET_10xHis_EK_MDtxRGA_D147.dna",
"type": "Raw Data File"
},
{
"@id": "studies/Functional_characterization_IronSenseR/resources/Plasmids/pAZ190_pRSET_10xHis_EK_MDtxRGA_S148.dna",
"name": "studies/Functional_characterization_IronSenseR/resources/Plasmids/pAZ190_pRSET_10xHis_EK_MDtxRGA_S148.dna",
"type": "Raw Data File"
},
{
"@id": "studies/Functional_characterization_IronSenseR/resources/Plasmids/pAZ191_pRSET_10xHis_EK_MDtxRGA_G149.dna",
"name": "studies/Functional_characterization_IronSenseR/resources/Plasmids/pAZ191_pRSET_10xHis_EK_MDtxRGA_G149.dna",
"type": "Raw Data File"
},
{
"@id": "studies/Functional_characterization_IronSenseR/resources/Plasmids/pAZ192_pRSET_10xHis_EK_MDtxRGA_V150.dna",
"name": "studies/Functional_characterization_IronSenseR/resources/Plasmids/pAZ192_pRSET_10xHis_EK_MDtxRGA_V150.dna",
"type": "Raw Data File"
},
{
"@id": "studies/Functional_characterization_IronSenseR/resources/Plasmids/pAZ199_pRSET_10xHis_EK_MDtxRGA_G149_H98A.dna",
"name": "studies/Functional_characterization_IronSenseR/resources/Plasmids/pAZ199_pRSET_10xHis_EK_MDtxRGA_G149_H98A.dna",
"type": "Raw Data File"
},
{
"@id": "studies/Functional_characterization_IronSenseR/resources/Plasmids/pAZ200_pRSET_10xHis_EK_MDtxRGA_G149_C102A.dna",
"name": "studies/Functional_characterization_IronSenseR/resources/Plasmids/pAZ200_pRSET_10xHis_EK_MDtxRGA_G149_C102A.dna",
"type": "Raw Data File"
}
],
"outputs": [
{
"@id": "#Sample_MDtxR_I138",
"name": "MDtxR I138"
},
{
"@id": "#Sample_MDtxR_G139",
"name": "MDtxR G139"
},
{
"@id": "#Sample_MDtxR_L140",
"name": "MDtxR L140"
},
{
"@id": "#Sample_MDtxR_D141",
"name": "MDtxR D141"
},
{
"@id": "#Sample_MDtxR_Q142",
"name": "MDtxR Q142"
},
{
"@id": "#Sample_MDtxR_A143",
"name": "MDtxR A143"
},
{
"@id": "#Sample_MDtxR_D144",
"name": "MDtxR D144"
},
{
"@id": "#Sample_MDtxR_E145",
"name": "MDtxR E145"
},
{
"@id": "#Sample_MDtxR_P146",
"name": "MDtxR P146"
},
{
"@id": "#Sample_MDtxR_D147",
"name": "MDtxR D147"
},
{
"@id": "#Sample_MDtxR_S148",
"name": "MDtxR S148"
},
{
"@id": "#Sample_MDtxR_G149",
"name": "MDtxR G149"
},
{
"@id": "#Sample_MDtxR_V150",
"name": "MDtxR V150"
},
{
"@id": "#Sample_MDtxRGA_G149_H98A",
"name": "MDtxRGA_G149_H98A"
},
{
"@id": "#Sample_MDtxRGA_G149_C102A",
"name": "MDtxRGA_G149_C102A"
}
]
},
{
"@id": "#Process_Expression_and_Purification_fro_1",
"name": "Expression and Purification fro_1",
"executesProtocol": {
"@id": "#Protocol_./assays/Expression_and_Purification/dataset/2025-01-28-250128-IMAC-of-pAZ198-pAZ199-pAZ200-MDtxRGA-G149-putative-mutants-deficient-of-ion-binding.pdf",
"name": "./assays/Expression_and_Purification/dataset/2025-01-28-250128-IMAC-of-pAZ198-pAZ199-pAZ200-MDtxRGA-G149-putative-mutants-deficient-of-ion-binding.pdf"
},
"inputs": [
{
"@id": "studies/Functional_characterization_IronSenseR/resources/Plasmids/pAZ198_pRSET_10xHis_EK_MDtxRGA_G149_H79A.dna",
"name": "studies/Functional_characterization_IronSenseR/resources/Plasmids/pAZ198_pRSET_10xHis_EK_MDtxRGA_G149_H79A.dna",
"type": "Raw Data File"
}
],
"outputs": [
{
"@id": "#Sample_MDtxRGA_G149_H79A",
"name": "MDtxRGA_G149_H79A"
}
]
}
],
"comments": [
{
"@id": "#Comment_title_IronSenseR_protein_prification",
"name": "title",
"value": "IronSenseR protein prification"
},
{
"@id": "#Comment_description_Affinity_based_protein_purification_of_ronSenseR._",
"name": "description",
"value": "Affinity based protein purification of ronSenseR. "
}
]
},
{
"filename": "assays/In_vivo_E_coli/isa.assay.xlsx",
"@id": "assays/In_vivo_E_coli/",
"dataFiles": [
{
"@id": "studies/Functional_characterization_IronSenseR/resources/Plasmids/pAZ191_pRSET_10xHis_EK_MDtxRGA_G149.dna",
"name": "studies/Functional_characterization_IronSenseR/resources/Plasmids/pAZ191_pRSET_10xHis_EK_MDtxRGA_G149.dna",
"type": "Raw Data File"
},
{
"@id": "assays/In_vivo_E_coli/dataset/241218_MDtxR_GA/Figure_description_iron_paper_MAN.docx",
"name": "assays/In_vivo_E_coli/dataset/241218_MDtxR_GA/Figure_description_iron_paper_MAN.docx",
"type": "Raw Data File"
},
{
"@id": "assays/In_vivo_E_coli/dataset/241218_MDtxR_GA/GA_20_BPD_C1.tiff",
"name": "assays/In_vivo_E_coli/dataset/241218_MDtxR_GA/GA 20 BPD C1.tiff",
"type": "Raw Data File"
},
{
"@id": "assays/In_vivo_E_coli/dataset/241218_MDtxR_GA/GA_20_BPD_C2.tiff",
"name": "assays/In_vivo_E_coli/dataset/241218_MDtxR_GA/GA 20 BPD C2.tiff",
"type": "Raw Data File"
},
{
"@id": "assays/In_vivo_E_coli/dataset/241218_MDtxR_GA/GA_20_BPD_merge.tiff",
"name": "assays/In_vivo_E_coli/dataset/241218_MDtxR_GA/GA 20 BPD merge.tiff",
"type": "Raw Data File"
},
{
"@id": "assays/In_vivo_E_coli/dataset/241218_MDtxR_GA/GA_20_BPD_ratio_ROIs.tiff",
"name": "assays/In_vivo_E_coli/dataset/241218_MDtxR_GA/GA 20 BPD ratio ROIs.tiff",
"type": "Raw Data File"
},
{
"@id": "assays/In_vivo_E_coli/dataset/241218_MDtxR_GA/GA_20_BPD_ratio.tiff",
"name": "assays/In_vivo_E_coli/dataset/241218_MDtxR_GA/GA 20 BPD ratio.tiff",
"type": "Raw Data File"
},
{
"@id": "assays/In_vivo_E_coli/dataset/241218_MDtxR_GA/GA_20_BPD_TD.tiff",
"name": "assays/In_vivo_E_coli/dataset/241218_MDtxR_GA/GA 20 BPD TD.tiff",
"type": "Raw Data File"
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"name": "assays/In_vivo_P_putida/dataset/250527/Layout 1.tif",
"type": "Raw Data File"
},
{
"@id": "assays/In_vivo_P_putida/dataset/250527/Layout_2.tif",
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"type": "Raw Data File"
},
{
"@id": "assays/In_vivo_P_putida/dataset/250527/Project1.prism",
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"type": "Raw Data File"
}
]
}
],
"comments": [
{
"@id": "#Comment_title_In_vivo_function_of_IronSenseR_tested_in_P_putida",
"name": "title",
"value": "In vivo function of IronSenseR tested in P putida"
}
]
}
]
},
{
"@id": "studies/PLACEHOLDER_STUDY_CNA/",
"filename": "studies/PLACEHOLDER_STUDY_CNA/isa.study.xlsx",
"identifier": "PLACEHOLDER_STUDY_CNA",
"assays": [
{
"filename": "assays/CNA/isa.assay.xlsx",
"@id": "assays/CNA/",
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"name": "assays/Structural_modeling_of_sFP_Biosensors/dataset/Structural data sFP biosensors /AF3/fold_250114_af3_atpque2m/pIDDT_fold_250114_af3_atpque2m_model_all.pse",
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{
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"name": "assays/Structural_modeling_of_sFP_Biosensors/dataset/Structural data sFP biosensors /AF3/fold_240524_af3_tre_co4/pIDDT_fold_240524_af3_tre_co4_model_all.pse",
"type": "Raw Data File"
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{
"@id": "assays/Structural_modeling_of_sFP_Biosensors/dataset/Structural_data_sFP_biosensors_/AF3/fold_250114_af3_hyper3/pIDDT_fold_250114_af3_hyper3_model_all.pse",
"name": "assays/Structural_modeling_of_sFP_Biosensors/dataset/Structural data sFP biosensors /AF3/fold_250114_af3_hyper3/pIDDT_fold_250114_af3_hyper3_model_all.pse",
"type": "Raw Data File"
},
{
"@id": "assays/Structural_modeling_of_sFP_Biosensors/dataset/resources/Structural_data_sFP_biosensors_/AF3/fold_250114_af3_percevalhr/pIDDT_fold_250114_af3_percevalhr_full_data.pse",
"name": "assays/Structural_modeling_of_sFP_Biosensors/dataset/resources/Structural data sFP biosensors /AF3/fold_250114_af3_percevalhr/pIDDT_fold_250114_af3_percevalhr_full_data.pse",
"type": "Raw Data File"
},
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},
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"@id": "assays/CNA/dataset/CNAs/CNA_results/251106_30RexYFP_dimer_CNA.pse",
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"type": "Raw Data File"
},
{
"@id": "assays/CNA/dataset/CNAs/CNA_results/251107_MalE_CNA.pse",
"name": "assays/CNA/dataset/CNAs/CNA_results/251107_MalE_CNA.pse",
"type": "Raw Data File"
},
{
"@id": "assays/CNA/dataset/CNAs/CNA_results/251107_TreCO4_CNA.pse",
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"type": "Raw Data File"
},
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"@id": "assays/CNA/dataset/CNAs/CNA_results/251107_HyPer3_OxyRrd.pse",
"name": "assays/CNA/dataset/CNAs/CNA_results/251107_HyPer3_OxyRrd.pse",
"type": "Raw Data File"
},
{
"@id": "assays/CNA/dataset/CNAs/CNA_results/251107_Perceval_GlnK_trimer.pse",
"name": "assays/CNA/dataset/CNAs/CNA_results/251107_Perceval_GlnK_trimer.pse",
"type": "Raw Data File"
},
{
"@id": "studies/CoBiSe/resources/DtxR/DtxR_C_glutamicum.pdb",
"name": "studies/CoBiSe/resources/DtxR/DtxR_C_glutamicum.pdb",
"type": "Raw Data File"
}
],
"materials": {
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{
"@id": "#Sample_./assays/CNA/dataset/CNAs/CNA_results/251107_DtxR_CNA.pse",
"name": "./assays/CNA/dataset/CNAs/CNA_results/251107_DtxR_CNA.pse"
}
]
},
"processSequence": [
{
"@id": "#Process_CNA_retrospective",
"name": "CNA retrospective",
"executesProtocol": {
"@id": "#Protocol_./assays/CNA/protocols/Computational_insertion_site_identification.md",
"name": "./assays/CNA/protocols/Computational insertion site identification.md"
},
"inputs": [
{
"@id": "assays/Structural_modeling_of_sFP_Biosensors/dataset/Structural_data_sFP_biosensors_/AF3/fold_250114_af3_atpque2m/pIDDT_fold_250114_af3_atpque2m_model_all.pse",
"name": "assays/Structural_modeling_of_sFP_Biosensors/dataset/Structural data sFP biosensors /AF3/fold_250114_af3_atpque2m/pIDDT_fold_250114_af3_atpque2m_model_all.pse",
"type": "Raw Data File"
},
{
"@id": "assays/Structural_modeling_of_sFP_Biosensors/dataset/Structural_data_sFP_biosensors_/AF3/fold_250114_af3_rexyfp/pIDDT_fold_250114_af3_rexyfp_model_all.pse",
"name": "assays/Structural_modeling_of_sFP_Biosensors/dataset/Structural data sFP biosensors /AF3/fold_250114_af3_rexyfp/pIDDT_fold_250114_af3_rexyfp_model_all.pse",
"type": "Raw Data File"
},
{
"@id": "assays/Structural_modeling_of_sFP_Biosensors/dataset/Structural_data_sFP_biosensors_/AF3/fold_240524_af3_malb2/pIDDT_fold_240524_af3_malb2_model_all.pse",
"name": "assays/Structural_modeling_of_sFP_Biosensors/dataset/Structural data sFP biosensors /AF3/fold_240524_af3_malb2/pIDDT_fold_240524_af3_malb2_model_all.pse",
"type": "Raw Data File"
},
{
"@id": "assays/Structural_modeling_of_sFP_Biosensors/dataset/Structural_data_sFP_biosensors_/AF3/fold_240524_af3_tre_co4/pIDDT_fold_240524_af3_tre_co4_model_all.pse",
"name": "assays/Structural_modeling_of_sFP_Biosensors/dataset/Structural data sFP biosensors /AF3/fold_240524_af3_tre_co4/pIDDT_fold_240524_af3_tre_co4_model_all.pse",
"type": "Raw Data File"
},
{
"@id": "assays/Structural_modeling_of_sFP_Biosensors/dataset/Structural_data_sFP_biosensors_/AF3/fold_250114_af3_hyper3/pIDDT_fold_250114_af3_hyper3_model_all.pse",
"name": "assays/Structural_modeling_of_sFP_Biosensors/dataset/Structural data sFP biosensors /AF3/fold_250114_af3_hyper3/pIDDT_fold_250114_af3_hyper3_model_all.pse",
"type": "Raw Data File"
},
{
"@id": "assays/Structural_modeling_of_sFP_Biosensors/dataset/resources/Structural_data_sFP_biosensors_/AF3/fold_250114_af3_percevalhr/pIDDT_fold_250114_af3_percevalhr_full_data.pse",
"name": "assays/Structural_modeling_of_sFP_Biosensors/dataset/resources/Structural data sFP biosensors /AF3/fold_250114_af3_percevalhr/pIDDT_fold_250114_af3_percevalhr_full_data.pse",
"type": "Raw Data File"
}
],
"outputs": [
{
"@id": "assays/CNA/dataset/CNAs/CNA_results/251106_QUE2m_CNA.pse",
"name": "assays/CNA/dataset/CNAs/CNA_results/251106_QUE2m_CNA.pse",
"type": "Raw Data File"
},
{
"@id": "assays/CNA/dataset/CNAs/CNA_results/251106_30RexYFP_dimer_CNA.pse",
"name": "assays/CNA/dataset/CNAs/CNA_results/251106_30RexYFP_dimer_CNA.pse",
"type": "Raw Data File"
},
{
"@id": "assays/CNA/dataset/CNAs/CNA_results/251107_MalE_CNA.pse",
"name": "assays/CNA/dataset/CNAs/CNA_results/251107_MalE_CNA.pse",
"type": "Raw Data File"
},
{
"@id": "assays/CNA/dataset/CNAs/CNA_results/251107_TreCO4_CNA.pse",
"name": "assays/CNA/dataset/CNAs/CNA_results/251107_TreCO4_CNA.pse",
"type": "Raw Data File"
},
{
"@id": "assays/CNA/dataset/CNAs/CNA_results/251107_HyPer3_OxyRrd.pse",
"name": "assays/CNA/dataset/CNAs/CNA_results/251107_HyPer3_OxyRrd.pse",
"type": "Raw Data File"
},
{
"@id": "assays/CNA/dataset/CNAs/CNA_results/251107_Perceval_GlnK_trimer.pse",
"name": "assays/CNA/dataset/CNAs/CNA_results/251107_Perceval_GlnK_trimer.pse",
"type": "Raw Data File"
}
]
},
{
"@id": "#Process_CNA_prospective_of_DtxR",
"name": "CNA prospective of DtxR",
"executesProtocol": {
"@id": "#Protocol_./assays/CNACoBiSe/protocols/Computational_insertion_site_identification.md",
"name": "./assays/CNACoBiSe/protocols/Computational insertion site identification.md"
},
"inputs": [
{
"@id": "studies/CoBiSe/resources/DtxR/DtxR_C_glutamicum.pdb",
"name": "studies/CoBiSe/resources/DtxR/DtxR_C_glutamicum.pdb",
"type": "Raw Data File"
}
],
"outputs": [
{
"@id": "#Sample_./assays/CNA/dataset/CNAs/CNA_results/251107_DtxR_CNA.pse",
"name": "./assays/CNA/dataset/CNAs/CNA_results/251107_DtxR_CNA.pse"
}
]
}
],
"comments": [
{
"@id": "#Comment_title_Central_network_Analysis",
"name": "title",
"value": "Central network Analysis"
},
{
"@id": "#Comment_description_The_rigid_and_flexible_regions_within_a_binding_protein_were_computationally_identified._The_binding_proteins_are_used_as_molecular_recognition_element_(MRE)_for_biosensor_creation,_and_the_flexible_elements_are_putative_insertion_regions_for_biosensor_cassette._",
"name": "description",
"value": "The rigid and flexible regions within a binding protein were computationally identified. The binding proteins are used as molecular recognition element (MRE) for biosensor creation, and the flexible elements are putative insertion regions for biosensor cassette. "
}
]
}
]
},
{
"@id": "studies/PLACEHOLDER_STUDY_In_vitro_characterization_IronSenseR/",
"filename": "studies/PLACEHOLDER_STUDY_In_vitro_characterization_IronSenseR/isa.study.xlsx",
"identifier": "PLACEHOLDER_STUDY_In_vitro_characterization_IronSenseR",
"assays": [
{
"filename": "assays/In_vitro_characterization_IronSenseR/isa.assay.xlsx",
"@id": "assays/In_vitro_characterization_IronSenseR/",
"dataFiles": [
{
"@id": "assays/In_vitro_characterization_IronSenseR/dataset/In_vitro/Eva_241025_MDtxRGA_180-192_20mM_MOPS_pH7.0_0-25uM_FeIISO4.xlsx",
"name": "assays/In_vitro_characterization_IronSenseR/dataset/In vitro/Eva_241025_MDtxRGA_180-192_20mM_MOPS_pH7.0_0-25uM_FeIISO4.xlsx",
"type": "Raw Data File"
},
{
"@id": "assays/In_vitro_characterization_IronSenseR/dataset/In_vitro/Eva_241119_pAZ191_MDtxRGA_G149_20mMMOPSpH7.0_0-25\u00b5M_Fe2SO4_biological_triplicates.xlsx",
"name": "assays/In_vitro_characterization_IronSenseR/dataset/In vitro/Eva_241119_pAZ191_MDtxRGA_G149_20mMMOPSpH7.0_0-25\u00b5M_Fe2SO4_biological_triplicates.xlsx",
"type": "Raw Data File"
},
{
"@id": "assays/In_vitro_characterization_IronSenseR/dataset/In_vitro/Eva_250129_MDtxRGA_G149_pAZ198_199_200_biol.RepI-III_0-25_FeSO4.xlsx",
"name": "assays/In_vitro_characterization_IronSenseR/dataset/In vitro/Eva_250129_MDtxRGA_G149_pAZ198_199_200_biol.RepI-III_0-25_FeSO4.xlsx",
"type": "Raw Data File"
},
{
"@id": "assays/In_vitro_characterization_IronSenseR/dataset/In_vitro/Eva_241119_pAZ191_MDtxRGA_G149_20mMMOPSpH7.0_0-25\u00b5M_Ions_biological_triplicates.xlsx",
"name": "assays/In_vitro_characterization_IronSenseR/dataset/In vitro/Eva_241119_pAZ191_MDtxRGA_G149_20mMMOPSpH7.0_0-25\u00b5M_Ions_biological_triplicates.xlsx",
"type": "Raw Data File"
},
{
"@id": "assays/In_vitro_characterization_IronSenseR/dataset/In_vitro/Eva_251023_pAZ191_MDtxR_G149_Tit_CaSo4_CuSO4_ZnSO4_20mM_MOPS_pH7.0.xlsx",
"name": "assays/In_vitro_characterization_IronSenseR/dataset/In vitro/Eva_251023_pAZ191_MDtxR_G149_Tit_CaSo4_CuSO4_ZnSO4_20mM_MOPS_pH7.0.xlsx",
"type": "Raw Data File"
}
],
"materials": {
"samples": [
{
"@id": "#Sample_MDtxR_I138",
"name": "MDtxR I138"
},
{
"@id": "#Sample_MDtxR_G139",
"name": "MDtxR G139"
},
{
"@id": "#Sample_MDtxR_L140",
"name": "MDtxR L140"
},
{
"@id": "#Sample_MDtxR_D141",
"name": "MDtxR D141"
},
{
"@id": "#Sample_MDtxR_Q142",
"name": "MDtxR Q142"
},
{
"@id": "#Sample_MDtxR_A143",
"name": "MDtxR A143"
},
{
"@id": "#Sample_MDtxR_D144",
"name": "MDtxR D144"
},
{
"@id": "#Sample_MDtxR_E145",
"name": "MDtxR E145"
},
{
"@id": "#Sample_MDtxR_P146",
"name": "MDtxR P146"
},
{
"@id": "#Sample_MDtxR_D147",
"name": "MDtxR D147"
},
{
"@id": "#Sample_MDtxR_S148",
"name": "MDtxR S148"
},
{
"@id": "#Sample_MDtxR_G149",
"name": "MDtxR G149"
},
{
"@id": "#Sample_MDtxR_V150",
"name": "MDtxR V150"
},
{
"@id": "#Sample_MDtxR_G149_Binding_deficient_variants",
"name": "MDtxR G149 Binding deficient variants"
}
]
},
"processSequence": [
{
"@id": "#Process_Screening_of_putative_IronSense",
"name": "Screening of putative IronSense",
"executesProtocol": {
"@id": "#Protocol_./assays/In_vitro_characterization_IronSenseR/protocols/Functional_characterization.md",
"name": "./assays/In_vitro_characterization_IronSenseR/protocols/Functional characterization.md"
},
"inputs": [
{
"@id": "#Sample_MDtxR_I138",
"name": "MDtxR I138"
},
{
"@id": "#Sample_MDtxR_G139",
"name": "MDtxR G139"
},
{
"@id": "#Sample_MDtxR_L140",
"name": "MDtxR L140"
},
{
"@id": "#Sample_MDtxR_D141",
"name": "MDtxR D141"
},
{
"@id": "#Sample_MDtxR_Q142",
"name": "MDtxR Q142"
},
{
"@id": "#Sample_MDtxR_A143",
"name": "MDtxR A143"
},
{
"@id": "#Sample_MDtxR_D144",
"name": "MDtxR D144"
},
{
"@id": "#Sample_MDtxR_E145",
"name": "MDtxR E145"
},
{
"@id": "#Sample_MDtxR_P146",
"name": "MDtxR P146"
},
{
"@id": "#Sample_MDtxR_D147",
"name": "MDtxR D147"
},
{
"@id": "#Sample_MDtxR_S148",
"name": "MDtxR S148"
},
{
"@id": "#Sample_MDtxR_G149",
"name": "MDtxR G149"
},
{
"@id": "#Sample_MDtxR_V150",
"name": "MDtxR V150"
}
],
"outputs": [
{
"@id": "assays/In_vitro_characterization_IronSenseR/dataset/In_vitro/Eva_241025_MDtxRGA_180-192_20mM_MOPS_pH7.0_0-25uM_FeIISO4.xlsx",
"name": "assays/In_vitro_characterization_IronSenseR/dataset/In vitro/Eva_241025_MDtxRGA_180-192_20mM_MOPS_pH7.0_0-25uM_FeIISO4.xlsx",
"type": "Raw Data File"
},
{
"@id": "assays/In_vitro_characterization_IronSenseR/dataset/In_vitro/Eva_241025_MDtxRGA_180-192_20mM_MOPS_pH7.0_0-25uM_FeIISO4.xlsx",
"name": "assays/In_vitro_characterization_IronSenseR/dataset/In vitro/Eva_241025_MDtxRGA_180-192_20mM_MOPS_pH7.0_0-25uM_FeIISO4.xlsx",
"type": "Raw Data File"
},
{
"@id": "assays/In_vitro_characterization_IronSenseR/dataset/In_vitro/Eva_241025_MDtxRGA_180-192_20mM_MOPS_pH7.0_0-25uM_FeIISO4.xlsx",
"name": "assays/In_vitro_characterization_IronSenseR/dataset/In vitro/Eva_241025_MDtxRGA_180-192_20mM_MOPS_pH7.0_0-25uM_FeIISO4.xlsx",
"type": "Raw Data File"
},
{
"@id": "assays/In_vitro_characterization_IronSenseR/dataset/In_vitro/Eva_241025_MDtxRGA_180-192_20mM_MOPS_pH7.0_0-25uM_FeIISO4.xlsx",
"name": "assays/In_vitro_characterization_IronSenseR/dataset/In vitro/Eva_241025_MDtxRGA_180-192_20mM_MOPS_pH7.0_0-25uM_FeIISO4.xlsx",
"type": "Raw Data File"
},
{
"@id": "assays/In_vitro_characterization_IronSenseR/dataset/In_vitro/Eva_241025_MDtxRGA_180-192_20mM_MOPS_pH7.0_0-25uM_FeIISO4.xlsx",
"name": "assays/In_vitro_characterization_IronSenseR/dataset/In vitro/Eva_241025_MDtxRGA_180-192_20mM_MOPS_pH7.0_0-25uM_FeIISO4.xlsx",
"type": "Raw Data File"
},
{
"@id": "assays/In_vitro_characterization_IronSenseR/dataset/In_vitro/Eva_241025_MDtxRGA_180-192_20mM_MOPS_pH7.0_0-25uM_FeIISO4.xlsx",
"name": "assays/In_vitro_characterization_IronSenseR/dataset/In vitro/Eva_241025_MDtxRGA_180-192_20mM_MOPS_pH7.0_0-25uM_FeIISO4.xlsx",
"type": "Raw Data File"
},
{
"@id": "assays/In_vitro_characterization_IronSenseR/dataset/In_vitro/Eva_241025_MDtxRGA_180-192_20mM_MOPS_pH7.0_0-25uM_FeIISO4.xlsx",
"name": "assays/In_vitro_characterization_IronSenseR/dataset/In vitro/Eva_241025_MDtxRGA_180-192_20mM_MOPS_pH7.0_0-25uM_FeIISO4.xlsx",
"type": "Raw Data File"
},
{
"@id": "assays/In_vitro_characterization_IronSenseR/dataset/In_vitro/Eva_241025_MDtxRGA_180-192_20mM_MOPS_pH7.0_0-25uM_FeIISO4.xlsx",
"name": "assays/In_vitro_characterization_IronSenseR/dataset/In vitro/Eva_241025_MDtxRGA_180-192_20mM_MOPS_pH7.0_0-25uM_FeIISO4.xlsx",
"type": "Raw Data File"
},
{
"@id": "assays/In_vitro_characterization_IronSenseR/dataset/In_vitro/Eva_241025_MDtxRGA_180-192_20mM_MOPS_pH7.0_0-25uM_FeIISO4.xlsx",
"name": "assays/In_vitro_characterization_IronSenseR/dataset/In vitro/Eva_241025_MDtxRGA_180-192_20mM_MOPS_pH7.0_0-25uM_FeIISO4.xlsx",
"type": "Raw Data File"
},
{
"@id": "assays/In_vitro_characterization_IronSenseR/dataset/In_vitro/Eva_241025_MDtxRGA_180-192_20mM_MOPS_pH7.0_0-25uM_FeIISO4.xlsx",
"name": "assays/In_vitro_characterization_IronSenseR/dataset/In vitro/Eva_241025_MDtxRGA_180-192_20mM_MOPS_pH7.0_0-25uM_FeIISO4.xlsx",
"type": "Raw Data File"
},
{
"@id": "assays/In_vitro_characterization_IronSenseR/dataset/In_vitro/Eva_241025_MDtxRGA_180-192_20mM_MOPS_pH7.0_0-25uM_FeIISO4.xlsx",
"name": "assays/In_vitro_characterization_IronSenseR/dataset/In vitro/Eva_241025_MDtxRGA_180-192_20mM_MOPS_pH7.0_0-25uM_FeIISO4.xlsx",
"type": "Raw Data File"
},
{
"@id": "assays/In_vitro_characterization_IronSenseR/dataset/In_vitro/Eva_241025_MDtxRGA_180-192_20mM_MOPS_pH7.0_0-25uM_FeIISO4.xlsx",
"name": "assays/In_vitro_characterization_IronSenseR/dataset/In vitro/Eva_241025_MDtxRGA_180-192_20mM_MOPS_pH7.0_0-25uM_FeIISO4.xlsx",
"type": "Raw Data File"
},
{
"@id": "assays/In_vitro_characterization_IronSenseR/dataset/In_vitro/Eva_241025_MDtxRGA_180-192_20mM_MOPS_pH7.0_0-25uM_FeIISO4.xlsx",
"name": "assays/In_vitro_characterization_IronSenseR/dataset/In vitro/Eva_241025_MDtxRGA_180-192_20mM_MOPS_pH7.0_0-25uM_FeIISO4.xlsx",
"type": "Raw Data File"
}
]
},
{
"@id": "#Process_Characterization_of_MDtxR_G149__0",
"name": "Characterization of MDtxR G149 _0",
"executesProtocol": {
"@id": "#Protocol_./assays/In_vitro_characterization_IronSenseR/protocols/Functional_characterization.md",
"name": "./assays/In_vitro_characterization_IronSenseR/protocols/Functional characterization.md",
"parameters": [
{
"@id": "#ProtocolParameter/#UserTerm_Ions",
"parameterName": {
"@id": "#UserTerm_Ions",
"annotationValue": "Ions"
}
}
]
},
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_Ions",
"parameterName": {
"@id": "#UserTerm_Ions",
"annotationValue": "Ions"
}
},
"value": {
"@id": "#UserTerm_FeSO4",
"annotationValue": "FeSO4"
}
}
],
"inputs": [
{
"@id": "#Sample_MDtxR_G149",
"name": "MDtxR G149"
},
{
"@id": "#Sample_MDtxR_G149_Binding_deficient_variants",
"name": "MDtxR G149 Binding deficient variants"
}
],
"outputs": [
{
"@id": "assays/In_vitro_characterization_IronSenseR/dataset/In_vitro/Eva_241119_pAZ191_MDtxRGA_G149_20mMMOPSpH7.0_0-25\u00b5M_Fe2SO4_biological_triplicates.xlsx",
"name": "assays/In_vitro_characterization_IronSenseR/dataset/In vitro/Eva_241119_pAZ191_MDtxRGA_G149_20mMMOPSpH7.0_0-25\u00b5M_Fe2SO4_biological_triplicates.xlsx",
"type": "Raw Data File"
},
{
"@id": "assays/In_vitro_characterization_IronSenseR/dataset/In_vitro/Eva_250129_MDtxRGA_G149_pAZ198_199_200_biol.RepI-III_0-25_FeSO4.xlsx",
"name": "assays/In_vitro_characterization_IronSenseR/dataset/In vitro/Eva_250129_MDtxRGA_G149_pAZ198_199_200_biol.RepI-III_0-25_FeSO4.xlsx",
"type": "Raw Data File"
}
]
},
{
"@id": "#Process_Characterization_of_MDtxR_G149__1",
"name": "Characterization of MDtxR G149 _1",
"executesProtocol": {
"@id": "#Protocol_./assays/In_vitro_characterization_IronSenseR/protocols/Functional_characterization.md",
"name": "./assays/In_vitro_characterization_IronSenseR/protocols/Functional characterization.md",
"parameters": [
{
"@id": "#ProtocolParameter/#UserTerm_Ions",
"parameterName": {
"@id": "#UserTerm_Ions",
"annotationValue": "Ions"
}
}
]
},
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_Ions",
"parameterName": {
"@id": "#UserTerm_Ions",
"annotationValue": "Ions"
}
},
"value": {
"@id": "#UserTerm_Various_Ions",
"annotationValue": "Various Ions"
}
}
],
"inputs": [
{
"@id": "#Sample_MDtxR_G149",
"name": "MDtxR G149"
},
{
"@id": "#Sample_MDtxR_G149",
"name": "MDtxR G149"
}
],
"outputs": [
{
"@id": "assays/In_vitro_characterization_IronSenseR/dataset/In_vitro/Eva_241119_pAZ191_MDtxRGA_G149_20mMMOPSpH7.0_0-25\u00b5M_Ions_biological_triplicates.xlsx",
"name": "assays/In_vitro_characterization_IronSenseR/dataset/In vitro/Eva_241119_pAZ191_MDtxRGA_G149_20mMMOPSpH7.0_0-25\u00b5M_Ions_biological_triplicates.xlsx",
"type": "Raw Data File"
},
{
"@id": "assays/In_vitro_characterization_IronSenseR/dataset/In_vitro/Eva_251023_pAZ191_MDtxR_G149_Tit_CaSo4_CuSO4_ZnSO4_20mM_MOPS_pH7.0.xlsx",
"name": "assays/In_vitro_characterization_IronSenseR/dataset/In vitro/Eva_251023_pAZ191_MDtxR_G149_Tit_CaSo4_CuSO4_ZnSO4_20mM_MOPS_pH7.0.xlsx",
"type": "Raw Data File"
}
]
}
],
"comments": [
{
"@id": "#Comment_title_Activity_of_IrnSenseR",
"name": "title",
"value": "Activity of IrnSenseR"
},
{
"@id": "#Comment_description_IronSenseR_activity_was_estimated_upon_binding_of_metal_ions_by_in_vitro_titration__assays.",
"name": "description",
"value": "IronSenseR activity was estimated upon binding of metal ions by in vitro titration assays."
}
]
}
]
},
{
"@id": "studies/PLACEHOLDER_STUDY_In_vivo_C_glutamicum/",
"filename": "studies/PLACEHOLDER_STUDY_In_vivo_C_glutamicum/isa.study.xlsx",
"identifier": "PLACEHOLDER_STUDY_In_vivo_C_glutamicum",
"assays": [
{
"filename": "assays/In_vivo_C_glutamicum/isa.assay.xlsx",
"@id": "assays/In_vivo_C_glutamicum/",
"dataFiles": [
{
"@id": "studies/Functional_characterization_IronSenseR/resources/Strains/C_glutamicum.md",
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"type": "Raw Data File"
},
{
"@id": "assays/In_vivo_C_glutamicum/dataset/20250525_IronBiosensor.xlsx",
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"type": "Raw Data File"
},
{
"@id": "assays/In_vivo_C_glutamicum/dataset/20250526_IronBiosensor_afterfridge_raw.xlsx",
"name": "assays/In_vivo_C_glutamicum/dataset/20250526_IronBiosensor_afterfridge_raw.xlsx",
"type": "Raw Data File"
},
{
"@id": "assays/In_vivo_C_glutamicum/dataset/20250526_IronBiosensor_afterfridge.xlsx",
"name": "assays/In_vivo_C_glutamicum/dataset/20250526_IronBiosensor_afterfridge.xlsx",
"type": "Raw Data File"
},
{
"@id": "assays/In_vivo_C_glutamicum/dataset/20250526_IronBiosensor_normiert_after_fridge.pzfx",
"name": "assays/In_vivo_C_glutamicum/dataset/20250526_IronBiosensor_normiert_after fridge.pzfx",
"type": "Raw Data File"
}
],
"materials": {},
"processSequence": [
{
"@id": "#Process_C_glutamicum_in_vivo",
"name": "C glutamicum in vivo",
"executesProtocol": {
"@id": "#Protocol_./assays/In_vivo_C_glutamicum/protocols/Functional_Characterization_in_vivo_C_glutamicum.md",
"name": "./assays/In_vivo_C_glutamicum/protocols/Functional Characterization in vivo C glutamicum.md"
},
"inputs": [
{
"@id": "studies/Functional_characterization_IronSenseR/resources/Strains/C_glutamicum.md",
"name": "studies/Functional_characterization_IronSenseR/resources/Strains/C glutamicum.md",
"type": "Raw Data File"
},
{
"@id": "studies/Functional_characterization_IronSenseR/resources/Strains/C_glutamicum.md",
"name": "studies/Functional_characterization_IronSenseR/resources/Strains/C glutamicum.md",
"type": "Raw Data File"
},
{
"@id": "studies/Functional_characterization_IronSenseR/resources/Strains/C_glutamicum.md",
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},
{
"@id": "studies/Functional_characterization_IronSenseR/resources/Strains/C_glutamicum.md",
"name": "studies/Functional_characterization_IronSenseR/resources/Strains/C glutamicum.md",
"type": "Raw Data File"
}
],
"outputs": [
{
"@id": "assays/In_vivo_C_glutamicum/dataset/20250525_IronBiosensor.xlsx",
"name": "assays/In_vivo_C_glutamicum/dataset/20250525_IronBiosensor.xlsx",
"type": "Raw Data File"
},
{
"@id": "assays/In_vivo_C_glutamicum/dataset/20250526_IronBiosensor_afterfridge_raw.xlsx",
"name": "assays/In_vivo_C_glutamicum/dataset/20250526_IronBiosensor_afterfridge_raw.xlsx",
"type": "Raw Data File"
},
{
"@id": "assays/In_vivo_C_glutamicum/dataset/20250526_IronBiosensor_afterfridge.xlsx",
"name": "assays/In_vivo_C_glutamicum/dataset/20250526_IronBiosensor_afterfridge.xlsx",
"type": "Raw Data File"
},
{
"@id": "assays/In_vivo_C_glutamicum/dataset/20250526_IronBiosensor_normiert_after_fridge.pzfx",
"name": "assays/In_vivo_C_glutamicum/dataset/20250526_IronBiosensor_normiert_after fridge.pzfx",
"type": "Raw Data File"
}
]
}
],
"comments": [
{
"@id": "#Comment_title_In_vivo_function_of_IronSenseR_tested_in_C_glutamicum",
"name": "title",
"value": "In vivo function of IronSenseR tested in C glutamicum"
}
]
}
]
},
{
"@id": "studies/PLACEHOLDER_STUDY_Small_angle_Xray_scattering/",
"filename": "studies/PLACEHOLDER_STUDY_Small_angle_Xray_scattering/isa.study.xlsx",
"identifier": "PLACEHOLDER_STUDY_Small_angle_Xray_scattering",
"assays": [
{
"filename": "assays/Small_angle_Xray_scattering/isa.assay.xlsx",
"@id": "assays/Small_angle_Xray_scattering/",
"dataFiles": [
{
"@id": "assays/Small_angle_Xray_scattering/dataset/241115_SEC_SAXS_pAZ191_MDtxRGA_G149/211115_SEC_SAXS_pAZ191_MDtxRGA_G149.docx",
"name": "assays/Small_angle_Xray_scattering/dataset/241115_SEC SAXS pAZ191 MDtxRGA G149/211115 SEC SAXS pAZ191 MDtxRGA G149.docx",
"type": "Raw Data File"
},
{
"@id": "assays/Small_angle_Xray_scattering/dataset/241115_SEC_SAXS_pAZ191_MDtxRGA_G149/Bildschirmfoto_2024-11-22_um_16.55.05.png",
"name": "assays/Small_angle_Xray_scattering/dataset/241115_SEC SAXS pAZ191 MDtxRGA G149/Bildschirmfoto 2024-11-22 um 16.55.05.png",
"type": "Raw Data File"
}
],
"materials": {
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{
"@id": "#Sample_MDtxR_G149",
"name": "MDtxR G149"
}
]
},
"processSequence": [
{
"@id": "#Process_SAXS_",
"name": "SAXS ",
"executesProtocol": {
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"name": "./assays/Small_angle_Xray_scattering/protocols/Structural analysis by small angle X-ray scattering.md"
},
"inputs": [
{
"@id": "#Sample_MDtxR_G149",
"name": "MDtxR G149"
},
{
"@id": "#Sample_MDtxR_G149",
"name": "MDtxR G149"
},
{
"@id": "#Sample_MDtxR_G149",
"name": "MDtxR G149"
},
{
"@id": "#Sample_MDtxR_G149",
"name": "MDtxR G149"
},
{
"@id": "#Sample_MDtxR_G149",
"name": "MDtxR G149"
},
{
"@id": "#Sample_MDtxR_G149",
"name": "MDtxR G149"
},
{
"@id": "#Sample_MDtxR_G149",
"name": "MDtxR G149"
},
{
"@id": "#Sample_MDtxR_G149",
"name": "MDtxR G149"
}
],
"outputs": [
{
"@id": "assays/Small_angle_Xray_scattering/dataset/241115_SEC_SAXS_pAZ191_MDtxRGA_G149/211115_SEC_SAXS_pAZ191_MDtxRGA_G149.docx",
"name": "assays/Small_angle_Xray_scattering/dataset/241115_SEC SAXS pAZ191 MDtxRGA G149/211115 SEC SAXS pAZ191 MDtxRGA G149.docx",
"type": "Raw Data File"
},
{
"@id": "assays/Small_angle_Xray_scattering/dataset/241115_SEC_SAXS_pAZ191_MDtxRGA_G149/211115_SEC_SAXS_pAZ191_MDtxRGA_G149.docx",
"name": "assays/Small_angle_Xray_scattering/dataset/241115_SEC SAXS pAZ191 MDtxRGA G149/211115 SEC SAXS pAZ191 MDtxRGA G149.docx",
"type": "Raw Data File"
},
{
"@id": "assays/Small_angle_Xray_scattering/dataset/241115_SEC_SAXS_pAZ191_MDtxRGA_G149/211115_SEC_SAXS_pAZ191_MDtxRGA_G149.docx",
"name": "assays/Small_angle_Xray_scattering/dataset/241115_SEC SAXS pAZ191 MDtxRGA G149/211115 SEC SAXS pAZ191 MDtxRGA G149.docx",
"type": "Raw Data File"
},
{
"@id": "assays/Small_angle_Xray_scattering/dataset/241115_SEC_SAXS_pAZ191_MDtxRGA_G149/211115_SEC_SAXS_pAZ191_MDtxRGA_G149.docx",
"name": "assays/Small_angle_Xray_scattering/dataset/241115_SEC SAXS pAZ191 MDtxRGA G149/211115 SEC SAXS pAZ191 MDtxRGA G149.docx",
"type": "Raw Data File"
},
{
"@id": "assays/Small_angle_Xray_scattering/dataset/241115_SEC_SAXS_pAZ191_MDtxRGA_G149/211115_SEC_SAXS_pAZ191_MDtxRGA_G149.docx",
"name": "assays/Small_angle_Xray_scattering/dataset/241115_SEC SAXS pAZ191 MDtxRGA G149/211115 SEC SAXS pAZ191 MDtxRGA G149.docx",
"type": "Raw Data File"
},
{
"@id": "assays/Small_angle_Xray_scattering/dataset/241115_SEC_SAXS_pAZ191_MDtxRGA_G149/211115_SEC_SAXS_pAZ191_MDtxRGA_G149.docx",
"name": "assays/Small_angle_Xray_scattering/dataset/241115_SEC SAXS pAZ191 MDtxRGA G149/211115 SEC SAXS pAZ191 MDtxRGA G149.docx",
"type": "Raw Data File"
},
{
"@id": "assays/Small_angle_Xray_scattering/dataset/241115_SEC_SAXS_pAZ191_MDtxRGA_G149/211115_SEC_SAXS_pAZ191_MDtxRGA_G149.docx",
"name": "assays/Small_angle_Xray_scattering/dataset/241115_SEC SAXS pAZ191 MDtxRGA G149/211115 SEC SAXS pAZ191 MDtxRGA G149.docx",
"type": "Raw Data File"
},
{
"@id": "assays/Small_angle_Xray_scattering/dataset/241115_SEC_SAXS_pAZ191_MDtxRGA_G149/Bildschirmfoto_2024-11-22_um_16.55.05.png",
"name": "assays/Small_angle_Xray_scattering/dataset/241115_SEC SAXS pAZ191 MDtxRGA G149/Bildschirmfoto 2024-11-22 um 16.55.05.png",
"type": "Raw Data File"
}
]
}
],
"comments": [
{
"@id": "#Comment_title_SAXS_of_IronSenseR",
"name": "title",
"value": "SAXS of IronSenseR"
},
{
"@id": "#Comment_description_The_in_solution_strucutre_of_IonenseR_was_determined,_revealing_monomeric_biosensors._",
"name": "description",
"value": "The in solution strucutre of IonenseR was determined, revealing monomeric biosensors. "
}
]
}
]
},
{
"@id": "studies/PLACEHOLDER_STUDY_Structural_modeling_for_CoBiSe/",
"filename": "studies/PLACEHOLDER_STUDY_Structural_modeling_for_CoBiSe/isa.study.xlsx",
"identifier": "PLACEHOLDER_STUDY_Structural_modeling_for_CoBiSe",
"assays": [
{
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"@id": "assays/Structural_modeling_for_CoBiSe/",
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{
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"name": "assays/Structural_modeling_for_CoBiSe/dataset/MDtxRGA/0_241017_af3_mdtxrga_i138/fold_241017_af3_mdtxrga_i138_full_data.pse",
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"name": "assays/Structural_modeling_for_CoBiSe/dataset/MDtxRGA/3_241017_af3_mdtxrga_d141/fold_241017_af3_mdtxrga_d141_full_data.pse",
"type": "Raw Data File"
},
{
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"type": "Raw Data File"
},
{
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"name": "assays/Structural_modeling_for_CoBiSe/dataset/MDtxRGA/7_241017_af3_mdtxrga_e145/fold_241017_af3_mdtxrga_e145_full_data.pse",
"type": "Raw Data File"
},
{
"@id": "assays/Structural_modeling_for_CoBiSe/dataset/MDtxRGA/8_241017_af3_mdtxrga_p146/fold_241017_af3_mdtxrga_p146_full_data.pse",
"name": "assays/Structural_modeling_for_CoBiSe/dataset/MDtxRGA/8_241017_af3_mdtxrga_p146/fold_241017_af3_mdtxrga_p146_full_data.pse",
"type": "Raw Data File"
},
{
"@id": "assays/Structural_modeling_for_CoBiSe/dataset/MDtxRGA/9_241017_af3_mdtxrga_d147/fold_241017_af3_mdtxrga_d147_full_data.pse",
"name": "assays/Structural_modeling_for_CoBiSe/dataset/MDtxRGA/9_241017_af3_mdtxrga_d147/fold_241017_af3_mdtxrga_d147_full_data.pse",
"type": "Raw Data File"
},
{
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"name": "assays/Structural_modeling_for_CoBiSe/dataset/MDtxRGA/10_241017_af3_mdtxrga_s148/fold_241017_af3_mdtxrga_s148_full_data.pse",
"type": "Raw Data File"
},
{
"@id": "assays/Structural_modeling_for_CoBiSe/dataset/MDtxRGA/11_241017_af3_mdtxrga_g149/fold_241017_af3_mdtxrga_g149_full_data.pse",
"name": "assays/Structural_modeling_for_CoBiSe/dataset/MDtxRGA/11_241017_af3_mdtxrga_g149/fold_241017_af3_mdtxrga_g149_full_data.pse",
"type": "Raw Data File"
},
{
"@id": "assays/Structural_modeling_for_CoBiSe/dataset/MDtxRGA/12_241017_af3_mdtxrga_v150/fold_241017_af3_mdtxrga_v150_full_data.pse",
"name": "assays/Structural_modeling_for_CoBiSe/dataset/MDtxRGA/12_241017_af3_mdtxrga_v150/fold_241017_af3_mdtxrga_v150_full_data.pse",
"type": "Raw Data File"
}
],
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},
{
"@id": "#Comment_description_Pre-existing_biosensors_were_modeled_and_ind_use_in_retrospective_CoBiSe._",
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