Counterintuitive structural and functional effects due to
naturally occurring mutations targeting the active site of the
disease-associated NQO1 enzyme

J 2023

Counterintuitive structural and functional effects due to naturally occurring mutations targeting the active site of the disease-associated NQO1 enzyme

PACHECO-GARCIA, Juan Luis; Ernesto ANOZ-CARBONELL; Dmitry S LOGINOV; Daniel KAVAN; Eduardo SALIDO et al.

Základní údaje

Originální název

Counterintuitive structural and functional effects due to naturally occurring mutations targeting the active site of the disease-associated NQO1 enzyme

Autoři

PACHECO-GARCIA, Juan Luis; Ernesto ANOZ-CARBONELL; Dmitry S LOGINOV; Daniel KAVAN; Eduardo SALIDO; Petr MAN; Milagros MEDINA a Angel L PEY

Vydání

FEBS Journal, MALDEN, Blackwell, 2023, 1742-464X

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10608 Biochemistry and molecular biology

Stát vydavatele

Spojené státy

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 5.500

Označené pro přenos do RIV

Ano

Kód RIV

RIV/00216224:90127/23:00139194

Organizační jednotka

CIISB II

Klíčová slova anglicky

catalytic mechanism; genotype-phenotype correlations; protein structure-function; structural stability

Štítky

ne MU, rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 28. 3. 2025 11:26, Mgr. Eva Dubská

Anotace

V originále

Our knowledge on the genetic diversity of the human genome is exponentially growing. However, our capacity to establish genotype-phenotype correlations on a large scale requires a combination of detailed experimental and computational work. This is a remarkable task in human proteins which are typically multifunctional and structurally complex. In addition, mutations often prevent the determination of mutant high-resolution structures by X-ray crystallography. We have characterized here the effects of five mutations in the active site of the disease-associated NQO1 protein, which are found either in cancer cell lines or in massive exome sequencing analysis in human population. Using a combination of H/D exchange, rapid-flow enzyme kinetics, binding energetics and conformational stability, we show that mutations in both sets may cause counterintuitive functional effects that are explained well by their effects on local stability regarding different functional features. Importantly, mutations predicted to be highly deleterious (even those affecting the same protein residue) may cause mild to catastrophic effects on protein function. These functional effects are not well explained by current predictive bioinformatic tools and evolutionary models that account for site conservation and physicochemical changes upon mutation. Our study also reinforces the notion that naturally occurring mutations not identified as disease-associated can be highly deleterious. Our approach, combining protein biophysics and structural biology tools, is readily accessible to broadly increase our understanding of genotype-phenotype correlations and to improve predictive computational tools aimed at distinguishing disease-prone against neutral missense variants in the human genome.

Návaznosti

90127, velká výzkumná infrastruktura

Název: CIISB II

Citovat

PACHECO-GARCIA, Juan Luis; Ernesto ANOZ-CARBONELL; Dmitry S LOGINOV; Daniel KAVAN; Eduardo SALIDO; Petr MAN; Milagros MEDINA a Angel L PEY. Counterintuitive structural and functional effects due to naturally occurring mutations targeting the active site of the disease-associated NQO1 enzyme. FEBS Journal. MALDEN: Blackwell, 2023, roč. 290, č. 7, s. 1855-1873. ISSN 1742-464X. Dostupné z: https://doi.org/10.1111/febs.16677.

@article{2487224,
   author = {PachecoandGarcia, Juan Luis and AnozandCarbonell, Ernesto and Loginov, Dmitry S and Kavan, Daniel and Salido, Eduardo and Man, Petr and Medina, Milagros and Pey, Angel L},
   article_location = {MALDEN},
   article_number = {7},
   doi = {https://doi.org/10.1111/febs.16677},
   keywords = {catalytic mechanism; genotype-phenotype correlations; protein structure-function; structural stability},
   language = {eng},
   issn = {1742-464X},
   journal = {FEBS Journal},
   title = {Counterintuitive structural and functional effects due to naturally occurring mutations targeting the active site of the disease-associated NQO1 enzyme},
   url = {https://febs.onlinelibrary.wiley.com/doi/10.1111/febs.16677},
   volume = {290},
   year = {2023}
}

TY  - JOUR
ID  - 2487224
AU  - Pacheco-Garcia, Juan Luis - Anoz-Carbonell, Ernesto - Loginov, Dmitry S - Kavan, Daniel - Salido, Eduardo - Man, Petr - Medina, Milagros - Pey, Angel L
PY  - 2023
TI  - Counterintuitive structural and functional effects due to naturally occurring mutations targeting the active site of the disease-associated NQO1 enzyme
JF  - FEBS Journal
VL  - 290
IS  - 7
SP  - 1855-1873
EP  - 1855-1873
PB  - Blackwell
SN  - 1742464X
KW  - catalytic mechanism
KW  - genotype-phenotype correlations
KW  - protein structure-function
KW  - structural stability
UR  - https://febs.onlinelibrary.wiley.com/doi/10.1111/febs.16677
N2  - Our knowledge on the genetic diversity of the human genome is exponentially growing. However, our capacity to establish genotype-phenotype correlations on a large scale requires a combination of detailed experimental and computational work. This is a remarkable task in human proteins which are typically multifunctional and structurally complex. In addition, mutations often prevent the determination of mutant high-resolution structures by X-ray crystallography. We have characterized here the effects of five mutations in the active site of the disease-associated NQO1 protein, which are found either in cancer cell lines or in massive exome sequencing analysis in human population. Using a combination of H/D exchange, rapid-flow enzyme kinetics, binding energetics and conformational stability, we show that mutations in both sets may cause counterintuitive functional effects that are explained well by their effects on local stability regarding different functional features. Importantly, mutations predicted to be highly deleterious (even those affecting the same protein residue) may cause mild to catastrophic effects on protein function. These functional effects are not well explained by current predictive bioinformatic tools and evolutionary models that account for site conservation and physicochemical changes upon mutation. Our study also reinforces the notion that naturally occurring mutations not identified as disease-associated can be highly deleterious. Our approach, combining protein biophysics and structural biology tools, is readily accessible to broadly increase our understanding of genotype-phenotype correlations and to improve predictive computational tools aimed at distinguishing disease-prone against neutral missense variants in the human genome.
ER  -

PACHECO-GARCIA, Juan Luis; Ernesto ANOZ-CARBONELL; Dmitry S LOGINOV; Daniel KAVAN; Eduardo SALIDO; Petr MAN; Milagros MEDINA a Angel L PEY. Counterintuitive structural and functional effects due to naturally occurring mutations targeting the active site of the disease-associated NQO1 enzyme. \textit{FEBS Journal}. MALDEN: Blackwell, 2023, roč.~290, č.~7, s.~1855-1873. ISSN~1742-464X. Dostupné z: https://doi.org/10.1111/febs.16677.

Přehled o publikaci