DETAILED METHODS for negative mutation in oxalate transporter SLC26A6 associated with enteric hyperoxaluria and nephrolithiasis”

Biochemical and hormone measurements were performed using standard techniques on an Alinity C auto-analyzer (Abbott Diagnostics, Rungis, France). Urinary oxalate excretion was measured by an enzymatic method using oxalate oxidase. Normal values for oxalate excretion were determined on healthy volunteers in our service and define as the lower and upper limits of the 95% confidence interval. Creatinine was measured using an isotope dilution-mass spectrometry (IDMS)-traceable enzymatic creatinine assay. Estimated GFR (eGFR) was determined using plasma creatinine value by the CKD Epidemiology Collaboration formula. 1 The relationship between parathormone (PTH) secretion and calcemia was tested using the calcium-loading test as described by Pak and Broadus. 2 ,3 This test also allowed assessing apparent digestive calcium absorption and net bone resorption. Specificity epitope-tagged μl KCl buffer; 130 mM KCl, 5 mM glucose, 20 mM HEPES, pH 7.4) of an outwardly directed chloride gradient. Cell uptake of 14 C-oxalate was terminated by a series (3X) of 2-minute washes with ice cold K-gluconate (as above) stop buffer. The stop buffer was removed and cells were lysed by sequential 5-minute incubations of each well with 200 μl 0.1 N NaOH followed by 200 μl 0.1 N HCl. The lysate was added to 5 ml of Opti-Fluor (PerkinElmer) scintillation cocktail and counted in a Tri-Carb 2910 TR (PerkinElmer) liquid scintillation analyzer.

[1]  Marta Sawicka,et al.  Cryo-EM structures and functional characterization of murine Slc26a9 reveal mechanism of uncoupled chloride transport , 2019, eLife.

[2]  The UniProt Consortium,et al.  UniProt: a worldwide hub of protein knowledge , 2018, Nucleic Acids Res..

[3]  Torsten Schwede,et al.  SWISS-MODEL: homology modelling of protein structures and complexes , 2018, Nucleic Acids Res..

[4]  Michael Feig,et al.  PREFMD: a web server for protein structure refinement via molecular dynamics simulations , 2018, Bioinform..

[5]  P. Aronson,et al.  N-glycosylation critically regulates function of oxalate transporter SLC26A6. , 2016, American journal of physiology. Cell physiology.

[6]  Silvio C. E. Tosatto,et al.  The RING 2.0 web server for high quality residue interaction networks , 2016, Nucleic Acids Res..

[7]  Itay Mayrose,et al.  ConSurf 2016: an improved methodology to estimate and visualize evolutionary conservation in macromolecules , 2016, Nucleic Acids Res..

[8]  E. Alexov,et al.  SAAFEC: Predicting the Effect of Single Point Mutations on Protein Folding Free Energy Using a Knowledge-Modified MM/PBSA Approach , 2016, International journal of molecular sciences.

[9]  F. Cunningham,et al.  The Ensembl Variant Effect Predictor , 2016, bioRxiv.

[10]  Tugba G. Kucukkal,et al.  Structural and physico-chemical effects of disease and non-disease nsSNPs on proteins. , 2015, Current opinion in structural biology.

[11]  Andrew Cowley,et al.  Using EMBL‐EBI Services via Web Interface and Programmatically via Web Services , 2014, Current protocols in bioinformatics.

[12]  Douglas E. V. Pires,et al.  DUET: a server for predicting effects of mutations on protein stability using an integrated computational approach , 2014, Nucleic Acids Res..

[13]  Harold I Feldman,et al.  Estimating glomerular filtration rate from serum creatinine and cystatin C. , 2012, The New England journal of medicine.

[14]  Pierrick Craveur,et al.  PredyFlexy: flexibility and local structure prediction from sequence , 2012, Nucleic Acids Res..

[15]  D. Higgins,et al.  Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega , 2011, Molecular systems biology.

[16]  Hyeon Joo,et al.  OPM database and PPM web server: resources for positioning of proteins in membranes , 2011, Nucleic Acids Res..

[17]  Silvio C. E. Tosatto,et al.  RING: networking interacting residues, evolutionary information and energetics in protein structures , 2011, Bioinform..

[18]  M. DePristo,et al.  The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. , 2010, Genome research.

[19]  Richard Durbin,et al.  Sequence analysis Fast and accurate short read alignment with Burrows – Wheeler transform , 2009 .

[20]  M. Vihinen,et al.  Pathogenic or not? And if so, then how? Studying the effects of missense mutations using bioinformatics methods , 2009, Human mutation.

[21]  Pierre Tufféry,et al.  PCE: web tools to compute protein continuum electrostatics , 2005, Nucleic Acids Res..

[22]  Conrad C. Huang,et al.  UCSF Chimera—A visualization system for exploratory research and analysis , 2004, J. Comput. Chem..

[23]  P. Shannon,et al.  Cytoscape: a software environment for integrated models of biomolecular interaction networks. , 2003, Genome research.

[24]  Bruno O Villoutreix,et al.  Structural bioinformatics: methods, concepts and applications to blood coagulation proteins. , 2002, Current protein & peptide science.

[25]  J. Moult,et al.  SNPs, protein structure, and disease , 2001, Human mutation.

[26]  A. Broadus,et al.  Pathophysiological studies in idiopathic hypercalciuria: use of an oral calcium tolerance test to characterize distinctive hypercalciuric subgroups. , 1978, The Journal of clinical endocrinology and metabolism.

[27]  C. Pak,et al.  A simple test for the diagnosis of absorptive, resorptive and renal hypercalciurias. , 1975, The New England journal of medicine.

[28]  Nick V Grishin,et al.  PROMALS3D: multiple protein sequence alignment enhanced with evolutionary and three-dimensional structural information. , 2014, Methods in molecular biology.