β-Methylamino-L-alanine substitution of serine in SOD1 suggests a direct role in ALS etiology

Exposure to the environmental toxin β-methylamino-L-alanine (BMAA) is linked to amyotrophic lateral sclerosis (ALS), but its disease-promoting mechanism remains unknown. We propose that incorporation of BMAA into the ALS-linked protein Cu,Zn superoxide dismutase (SOD1) upon translation promotes protein misfolding and aggregation, which has been linked to ALS onset and progression. Using molecular simulation and predictive energetic computation, we demonstrate that substituting any serine with BMAA in SOD1 results in structural destabilization and aberrant dynamics, promoting neurotoxic SOD1 aggregation. We propose that translational incorporation of BMAA into SOD1 is directly responsible for its toxicity in neurodegeneration, and BMAA modification of SOD1 may serve as a biomarker of ALS.

[1]  N. Dokholyan,et al.  Glutathionylation at Cys-111 induces dissociation of wild type and FALS mutant SOD1 dimers. , 2011, Biochemistry.

[2]  P. Cox,et al.  The Non-Protein Amino Acid BMAA Is Misincorporated into Human Proteins in Place of l-Serine Causing Protein Misfolding and Aggregation , 2013, PloS one.

[3]  Yuko Okamoto,et al.  Generalized-ensemble algorithms: enhanced sampling techniques for Monte Carlo and molecular dynamics simulations. , 2003, Journal of molecular graphics & modelling.

[4]  Deborah C. Mash,et al.  Dietary exposure to an environmental toxin triggers neurofibrillary tangles and amyloid deposits in the brain , 2016, Proceedings of the Royal Society B: Biological Sciences.

[5]  Stanley B. Prusiner,et al.  Nobel Lecture: Prions , 1998 .

[6]  A. Fersht,et al.  Principles of protein stability derived from protein engineering experiments , 1993 .

[7]  Nikolay V Dokholyan,et al.  The rate and equilibrium constants for a multistep reaction sequence for the aggregation of superoxide dismutase in amyotrophic lateral sclerosis. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[8]  Jennifer Stine Elam,et al.  Amyloid-like filaments and water-filled nanotubes formed by SOD1 mutant proteins linked to familial ALS , 2003, Nature Structural Biology.

[9]  N. Dokholyan,et al.  The Complex Molecular Biology of Amyotrophic Lateral Sclerosis (als) , 2022 .

[10]  Lucjan Piela,et al.  Theoretical model of prion propagation: A misfolded protein induces misfolding , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[11]  M. Karplus,et al.  Folding thermodynamics of a model three-helix-bundle protein. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[12]  K. E. Fladmark,et al.  Quantitative proteomics analysis of zebrafish exposed to sub-lethal dosages of β-methyl-amino-L-alanine (BMAA) , 2016, Scientific Reports.

[13]  Eun Jung Choi,et al.  Incorporation of Noncanonical Amino Acids into Rosetta and Use in Computational Protein-Peptide Interface Design , 2012, PloS one.

[14]  Y. Lyubchenko,et al.  Nonnative SOD1 trimer is toxic to motor neurons in a model of amyotrophic lateral sclerosis , 2015, Proceedings of the National Academy of Sciences.

[15]  H. Stanley,et al.  Discrete molecular dynamics studies of the folding of a protein-like model. , 1998, Folding & design.

[16]  H. Ke,et al.  A Phosphomimetic Mutation Stabilizes SOD1 and Rescues Cell Viability in the Context of an ALS-Associated Mutation. , 2016, Structure.

[17]  Shuangye Yin,et al.  Eris: an automated estimator of protein stability , 2007, Nature Methods.

[18]  P. Nunn,et al.  Guam amyotrophic lateral sclerosis-parkinsonism-dementia linked to a plant excitant neurotoxin. , 1987, Science.

[19]  Bing Zhang,et al.  ALS-linked SOD1 in glial cells enhances ß-N-Methylamino L-Alanine (BMAA)-induced toxicity in Drosophila , 2012, F1000Research.

[20]  A. Desideri,et al.  Role of the tertiary and quaternary structures in the stability of dimeric copper, zinc superoxide dismutases. , 2000, Archives of biochemistry and biophysics.

[21]  M. Karplus,et al.  Effective energy function for proteins in solution , 1999, Proteins.

[22]  R. Swendsen,et al.  THE weighted histogram analysis method for free‐energy calculations on biomolecules. I. The method , 1992 .

[23]  Nikolay V Dokholyan,et al.  Modifications of Superoxide Dismutase (SOD1) in Human Erythrocytes , 2009, Journal of Biological Chemistry.

[24]  Pradeep Kota,et al.  Rational coupled dynamics network manipulation rescues disease-relevant mutant cystic fibrosis transmembrane conductance regulator , 2014, Chemical science.

[25]  Feng Ding,et al.  Direct Observation of Protein Folding, Aggregation, and a Prion-like Conformational Conversion* , 2005, Journal of Biological Chemistry.

[26]  J. Borreguero,et al.  Mechanism for the α‐helix to β‐hairpin transition , 2003, Proteins.

[27]  P. Andersen,et al.  Soluble misfolded subfractions of mutant superoxide dismutase-1s are enriched in spinal cords throughout life in murine ALS models , 2007, Proceedings of the National Academy of Sciences.

[28]  Nikolay V Dokholyan,et al.  FALS mutations in Cu, Zn superoxide dismutase destabilize the dimer and increase dimer dissociation propensity: A large-scale thermodynamic analysis , 2006, Amyloid : the international journal of experimental and clinical investigation : the official journal of the International Society of Amyloidosis.

[29]  F. Ding,et al.  Ab initio folding of proteins with all-atom discrete molecular dynamics. , 2008, Structure.

[30]  Helix versus sheet formation in a small peptide. , 2003, Physical review. E, Statistical, nonlinear, and soft matter physics.

[31]  Feng Ding,et al.  Modeling backbone flexibility improves protein stability estimation. , 2007, Structure.

[32]  Feng Ding,et al.  Dynamical roles of metal ions and the disulfide bond in Cu, Zn superoxide dismutase folding and aggregation , 2008, Proceedings of the National Academy of Sciences.

[33]  Nikolay V Dokholyan,et al.  Common dynamical signatures of familial amyotrophic lateral sclerosis-associated structurally diverse Cu, Zn superoxide dismutase mutants. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[34]  S. Ackerman,et al.  Editing-defective tRNA synthetase causes protein misfolding and neurodegeneration , 2006, Nature.

[35]  N. Dokholyan,et al.  Non-native Soluble Oligomers of Cu/Zn Superoxide Dismutase (SOD1) Contain a Conformational Epitope Linked to Cytotoxicity in Amyotrophic Lateral Sclerosis (ALS) , 2014, Biochemistry.

[36]  Avijit Chakrabartty,et al.  Structure, folding, and misfolding of Cu,Zn superoxide dismutase in amyotrophic lateral sclerosis. , 2006, Biochimica et biophysica acta.

[37]  Sebastian Doniach,et al.  Protein misfolding and amyloid formation for the peptide GNNQQNY from yeast prion protein Sup35: simulation by reaction path annealing. , 2005, Journal of molecular biology.

[38]  K. Takano ON SOLUTION OF , 1983 .

[39]  Feng Ding,et al.  Correction: Emergence of Protein Fold Families through Rational Design , 2006, PLoS Comput. Biol..

[40]  Nikolay V. Dokholyan,et al.  Engineering extrinsic disorder to control protein activity in living cells , 2016, Science.

[41]  Michael Feig,et al.  MMTSB Tool Set: enhanced sampling and multiscale modeling methods for applications in structural biology. , 2004, Journal of molecular graphics & modelling.

[42]  F. Ding,et al.  Structural and thermodynamic effects of post-translational modifications in mutant and wild type Cu, Zn superoxide dismutase. , 2011, Journal of molecular biology.