Effect of naturally-occurring mutations on the stability and function of cancer-associated NQO1: Comparison of experiments and computation
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Effect of naturally-occurring mutations on the stability and function of cancer-associated NQO1 : Comparison of experiments and computation. / Pacheco-Garcia, Juan Luis; Cagiada, Matteo; Tienne-Matos, Kelly; Salido, Eduardo; Lindorff-Larsen, Kresten; L. Pey, Angel.
In: Frontiers in Molecular Biosciences, Vol. 9, 1063620, 2022.Research output: Contribution to journal › Journal article › Research › peer-review
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TY - JOUR
T1 - Effect of naturally-occurring mutations on the stability and function of cancer-associated NQO1
T2 - Comparison of experiments and computation
AU - Pacheco-Garcia, Juan Luis
AU - Cagiada, Matteo
AU - Tienne-Matos, Kelly
AU - Salido, Eduardo
AU - Lindorff-Larsen, Kresten
AU - L. Pey, Angel
PY - 2022
Y1 - 2022
N2 - Recent advances in DNA sequencing technologies are revealing a large individual variability of 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 many 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 (> 5,000 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 this multifunctional protein associated with disease.
AB - Recent advances in DNA sequencing technologies are revealing a large individual variability of 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 many 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 (> 5,000 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 this multifunctional protein associated with disease.
KW - protein function
KW - protein stability
KW - genotype-phenotype correlations
KW - computational prediction
KW - sequence conservation
KW - MICE LEADS
KW - BINDING
KW - OXIDOREDUCTASE-1
KW - SUSCEPTIBILITY
KW - RECOGNITION
KW - DEGRADATION
KW - DISRUPTION
KW - VARIANTS
KW - NAD(P)H
KW - GENE
U2 - 10.3389/fmolb.2022.1063620
DO - 10.3389/fmolb.2022.1063620
M3 - Journal article
C2 - 36504709
VL - 9
JO - Frontiers in Molecular Biosciences
JF - Frontiers in Molecular Biosciences
SN - 2296-889X
M1 - 1063620
ER -
ID: 329877403