Additional file 1 of NEB mutations disrupt the super-relaxed state of myosin and remodel the muscle metabolic proteome in nemaline myopathy
Creators: name: Ranu, Natasha
name: Laitila, Jenni
name: Dugdale, Hannah F.
name: Mariano, Jennifer
name: Kolb, Justin S.
name: Wallgren-Pettersson, Carina
name: Witting, Nanna
name: Vissing, John
name: Vilchez, Juan Jesus
name: Fiorillo, Chiara
name: Zanoteli, Edmar
name: Auranen, Mari
name: Jokela, Manu
name: Tasca, Giorgio
name: Claeys, Kristl G.
name: Voermans, Nicol C.
name: Palmio, Johanna
name: Huovinen, Sanna
name: Moggio, Maurizio
name: Beck, Thomas Nyegaard
name: Kontrogianni-Konstantopoulos, Aikaterini
name: Granzier, Henk
name: Ochala, Julien
Publisher: name: figshare
Year: 2024
Subjects: subject: Biophysics
subject: Biochemistry
subject: Physical Sciences not elsewhere classified
subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Physiology
subject: Pharmacology
subject: Biotechnology
subject: Chemical Sciences not elsewhere classified
subject: Cancer
subject: Hematology
subject: Virology
subject: Computational Biology

description: Additional file 1: Fig. S1. Myosin-binding protein C (MyBP-C) content and phosphorylation level. A–C display typical western blots and data normalized to GAPDH with total slow MyBP-C (A), S59 (B) and T84 (C) phosphorylation levels. Fig. S2. Pearson Correlations. Each individual sample was compared to each other, revealing samples in the same experimental groups are more similar to each other than any other fibres in the opposing experimental group. This includes WT_2 fibre, which was calculated to be a pure type 2x fibre, similar to all other cNEB KO myofibres. Table S1. Patient and control muscle biopsy samples used. Table S2. All proteins detected in manually dissected fibres originating from WT and cNEB KO mice. All proteins detected during LC-MS/MS tandem mass spectrometry, following filtration of missing values. #protein abundance values. Significant upregulation in each experimental group determined based on p &lt; 0.05. Table S3. Proteins assigned to functional clusters detected in manually dissected fibres originating from WT and cNEB KO mice. Metascape determined both enrichment and p values for protein clusters and associated proteins. Visual representation of pathway clusters found in Fig. 4. Table S4. Fibre type classification. Overall fibre type per sample was calculated utilizing protein abundances from mass spectrometry and previously outlined myosin heavy chain percentages for each fibre type. Table S5. All proteins detected in WT enzymatically disassociated fibres with and without piperine administration. All proteins detected during LC-MS/MS tandem mass spectrometry, following filtration of missing values. #Protein abundance values. Significant upregulation in each experimental group determined based on p &lt; 0.05. Table S6. Uniprot ligand binding for significant proteins detected in WT enzymatically disassociated fibres with and without piperine administration. Likely ligand binding for all significant proteins (p &lt; 0.05) obtained with and without piperine administration determined via the DAVID bioinformatic database.