Novel Endogenous, Insulin-Stimulated Akt2 Protein Interaction Partners in L6 Myoblasts.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:26465754", "kind": "science-record", "revision": 7, "content_hash": "sha256:237cfe26d077d51ff2cd7dd59b02d07bd1d47f322cc95a8e384af71a03371eda", "created_at": "2026-11-01T15:40:11Z", "updated_at": "2026-11-01T21:58:38Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Novel Endogenous, Insulin-Stimulated Akt2 Protein Interaction Partners in L6 Myoblasts.", "doi": "10.1371/journal.pone.0140255", "pmid": "26465754", "authors": ["Michael Caruso", "Xiangmin Zhang", "Danjun Ma", "Zhao Yang", "Yue Qi", "Zhengping Yi"], "journal": "PloS one", "year": 2015, "abstract": "Insulin resistance and Type 2 diabetes are marked by an aberrant response in the insulin signaling network. The phosphoinositide-dependent serine/threonine kinase, Akt2, plays a key role in insulin signaling and glucose uptake, most notably within skeletal muscle. Protein-protein interaction regulates the functional consequence of Akt2 and in turn, Akt2's role in glucose uptake. However, only few insulin-responsive Akt2 interaction partners have been identified in skeletal muscle cells. In the present work, rat L6 myoblasts, a widely used insulin sensitive skeletal muscle cell line, were used to examine endogenous, insulin-stimulated Akt2 protein interaction partners. Akt2 co-immunoprecipitation was coupled with 1D-SDS-PAGE and fractions were analyzed by HPLC-ESI-MS/MS to reveal Akt2 protein-protein interactions. The pull-down assay displayed specificity for the Akt2 isoform; Akt1 and Akt3 unique peptides were not detected. A total of 49 were detected with a significantly increased (47) or decreased (2) association with Akt2 following insulin administration (n = 4; p<0.05). Multiple pathways were identified for the novel Akt2 interaction partners, such as the EIF2 and ubiquitination pathways. These data suggest that multiple new endogenous proteins may associate with Akt2 under basal as well as insulin-stimulated conditions, providing further insight into the insulin signaling network. Data are available via ProteomeXchange with identifier PXD002557.", "claims": [{"id": "claim-method", "statement": "For comparisons to assess the effects of insulin stimulation, statistical significance was assessed using 2-tailed independent t tests, and differences were considered statistically significant at p<0.05.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26465754", "locator": "sections[7] \"Statistical analysis\" paragraph 2", "quote": "For comparisons to assess the effects of insulin stimulation, statistical significance was assessed using 2-tailed independent t tests, and differences were considered statistically significant at p<0.05."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE repository with the dataset identifier PXD002557.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26465754", "locator": "sections[6] \"In-gel trypsin digestion, mass spectrometry, data analysis and bioinformatics\" paragraph 8", "quote": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE repository with the dataset identifier PXD002557."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Using two-tailed independent t tests (p<0.05), the study identified 49 insulin-responsive Akt2 interaction partners, with the mass-spectrometry data deposited in ProteomeXchange via PRIDE under identifier PXD002557.", "kind": "quantitative", "target": {"value": 0.05, "unit": "p-value", "tolerance": null, "source": "A total of 49 were detected with a significantly increased (47) or decreased (2) association with Akt2 following insulin administration (n = 4; p<0.05)."}, "evidence": [{"asset": "source:pmid:26465754", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "A total of 49 were detected with a significantly increased (47) or decreased (2) association with Akt2 following insulin administration (n = 4; p<0.05)."}, {"asset": "source:pmid:26465754", "locator": "sections[7] \"Statistical analysis\" paragraph 2", "quote": "For comparisons to assess the effects of insulin stimulation, statistical significance was assessed using 2-tailed independent t tests, and differences were considered statistically significant at p<0.05."}, {"asset": "source:pmid:26465754", "locator": "sections[6] \"In-gel trypsin digestion, mass spectrometry, data analysis and bioinformatics\" paragraph 8", "quote": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE repository with the dataset identifier PXD002557."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Using two-tailed independent t tests (p<0.05), the study identified 49 insulin-responsive Akt2 interaction partners, with the mass-spectrometry data deposited in ProteomeXchange via PRIDE under identifier PXD002557.", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:26465754"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:PXD002557"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:PXD002557"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:26465754", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1371/journal.pone.0140255", "sha256": "sha256:f450f84e515a50c90918739219a999bcaf8df6a549157b608e19c6dbea27710a", "bytes": 34903, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1371/journal.pone.0140255", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC4605787", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:PXD002557", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=PXD002557", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD002557", "version": null, "note": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE repository with the dataset identifier PXD002557.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE repository with the dataset identifier PXD002557.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "Akt2 partners L6 myoblasts -  Novel Endogenous, Insulin-Stimulated Akt2 Protein Interaction Partners in L6 Myoblasts", "resolution_checked_at": "2026-10-31T18:35:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:26465754:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:07a1dfdf6dd1b121c4424f6c078d60fc32131de2365293e683740b158766e067", "bytes": 299, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[6]/table-wrap[1]#pone.0140255.t001", "version": null, "note": "The effect of insulin on Akt2 interaction partner ROCK2.Peak area (PA) for each protein is normalized against Akt2 PA in the same sample.", "structure": {"pmcid": "PMC4605787", "section_index": 6, "section_title": "In-gel trypsin digestion, mass spectrometry, data analysis and bioinformatics", "row_count": 0, "column_count": 0}, "table": {"label": "Table 1", "caption": "The effect of insulin on Akt2 interaction partner ROCK2.Peak area (PA) for each protein is normalized against Akt2 PA in the same sample.", "rows": [], "row_count": 0, "column_count": 0, "numeric_cells": 0, "header_rows": 0, "locator": "section[6]/table-wrap[1]#pone.0140255.t001"}}, {"id": "asset:table:pmid:26465754:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:8f031a8e08a0c65c417072bc55e3930c9b60ac2aab0cb5df8188a90201545a9b", "bytes": 374, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[9]/table-wrap[1]#pone.0140255.t002", "version": null, "note": "Significantly changed Akt2 protein interaction partners in L6 myoblasts upon insulin stimulation (n = 4, P<0.05).Each protein was detected in > 4 of the samples as well as not detected in any of the NIgG samples.", "structure": {"pmcid": "PMC4605787", "section_index": 9, "section_title": "Results", "row_count": 0, "column_count": 0}, "table": {"label": "Table 2", "caption": "Significantly changed Akt2 protein interaction partners in L6 myoblasts upon insulin stimulation (n = 4, P<0.05).Each protein was detected in > 4 of the samples as well as not detected in any of the NIgG samples.", "rows": [], "row_count": 0, "column_count": 0, "numeric_cells": 0, "header_rows": 0, "locator": "section[9]/table-wrap[1]#pone.0140255.t002"}}], "gaps": ["asset:data:geo:PXD002557 not downloaded", "asset:data:geo:PXD002557 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "network_analysis", "specific": "ppi_network", "label": "Network / pathway analysis", "dsl_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.7, "band": "medium", "quote": "Protein-protein interaction"}}, {"id": "method-2", "family": null, "specific": null, "label": "two-tailed independent t-test", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "For comparisons to assess the effects of insulin stimulation, statistical significance was assessed using 2-tailed independent t tests, and differences were considered statistically significant at p<0.05."}}], "targets": [{"id": "target-published-estimate", "claim_id": "claim-target-result", "operation": "build_graph", "expected_value": 0.05, "unit": "p-value", "tolerance": null, "state": "complete", "note": "The threshold the paper applied to its own result, as the paper states it. A run that reproduces the effect is judged against this threshold."}], "gaps": ["method.reader_named_unmapped"]}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: ppi_network."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["PXD002557"], "resolved_accessions": ["PXD002557"], "statements": ["The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE repository with the dataset identifier PXD002557."], "basis": "The paper names PXD002557 in ProteomeXchange Consortium via the PRIDE repository and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "assets": ["source:pmid:26465754", "data:geo:PXD002557", "asset:table:pmid:26465754:1", "asset:table:pmid:26465754:2"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:PXD002557"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:25:12Z", "independence": "same_provider"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 8, "usage": {"prompt_tokens": 65175, "completion_tokens": 2691, "cached_tokens": 2104}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:26465754", "type": "paper", "label": "pmid:26465754"}, {"id": "source:pmid:26465754", "type": "manuscript", "label": "PMID 26465754 full text"}, {"id": "data:geo:PXD002557", "type": "dataset", "label": "GEO PXD002557"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:26465754", "type": "paper", "label": "pmid:26465754"}, {"id": "source:pmid:26465754", "type": "manuscript", "label": "PMID 26465754 full text"}, {"id": "data:geo:PXD002557", "type": "dataset", "label": "GEO PXD002557"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-26465754", "type": "extraction", "used": ["source:pmid:26465754"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-PXD002557", "type": "accession_resolution", "used": ["data:geo:PXD002557"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}, {"id": "agent:minimax-reader", "type": "software", "label": "MiniMax literature reader"}], "source_run_id": "reading-sci-2026-11-01", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:26465754", "parent_hash": "sha256:6b8c727f1d648d4604a07f118d9c7f06e01f8fa849d285107cea065a3b835b89", "fork_of": null, "generation": 6}, "gaps": ["asset:data:geo:PXD002557 licence not read", "asset:data:geo:PXD002557 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "animal_model", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.642, "evidence": ["skeletal muscle cells. In the present work, rat L6 myoblasts, a widely used insulin sensitiv"], "order_basis": "paper_text_order:557", "id": "assay:1"}, {"role": "data_generation", "definition_id": "mass_spectrometry", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["SDS-PAGE and fractions were analyzed by HPLC-ESI-MS/MS to reveal Akt2 protein-protein interactio", "n to generate peptide fragments used in HPLC-ESI-MS/MS analysis for identification of co-immunop", "s and literature search were used to analyze proteomic data and to identify significantly enriched", "involved. Experimental workflow design, and proteomics data acquisition and analysis.(A). Experimen"], "order_basis": "paper_text_order:813", "id": "assay:2"}, {"role": "analysis", "definition_id": "network_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.7, "evidence": ["Protein-protein interaction"], "order_basis": "consumes_earlier_output", "id": "assay:3"}]}