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bioRxiv · 10.1101/2022.09.30.510258

Effect of naturally-occurring mutations on the stability and function of cancer-associated NQO1: comparison of experiments and computation.

Pacheco-Garcia, J. L.·Cagiada, M.·Tienne-Matos, K.·Salido, E.·Lindorff-Larsen, K.·Pey, A. L.
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Abstract

Recent advances in DNA sequencing technologies are revealing a large variability in the human genome. Our capacity to establish genotype-phenotype correlations in such large-scale is, however, limited. This task is particularly challenging due to the multifunctional nature of proteins. Here we describe an extensive analysis of the stability and function of naturally-occurring variants (found in the COSMIC and gnomAD databases) of the cancer-associated human NAD(P)H: quinone oxidoreductase 1 (NQO1). First, we performed in silico saturation mutagenesis studies (>5000 substitutions) aimed to identify regions in NQO1 important for stability and function. We then experimentally characterized twenty-two naturally-occurring variants in terms of protein levels during bacterial expression, solubility, thermal stability and coenzyme binding. These studies showed a good overall correlation between experimental analysis and computational predictions; also the magnitude of the effects of the substitutions are similarly distributed in variants from the COSMIC and gnomAD databases. Outliers in these experimental-computational genotype-phenotype correlations remain, and we discuss these on the grounds and limitations of our approaches. Our work represents a further step to characterize the mutational landscape of NQO1 in the human genome and may help to improve high-throughput in silico tools for genotype-phenotype correlations in multifunctional proteins associated with disease.

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Pacheco-Garcia, J. L., Cagiada, M., Tienne-Matos, K., Salido, E., Lindorff-Larsen, K., Pey, A. L.. 2022-10-03. Effect of naturally-occurring mutations on the stability and function of cancer-associated NQO1: comparison of experiments and computation.. https://doi.org/10.1101/2022.09.30.510258

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