Single-Nucleotide Polymorphism of PPARγ, a Protein at the Crossroads of Physiological and Pathological Processes

Abstract

Genome polymorphisms are responsible for phenotypic differences between humans and for individual susceptibility to genetic diseases and therapeutic responses. Non-synonymous single-nucleotide polymorphisms (nsSNPs) lead to protein variants with a change in the amino acid sequence that may affect the structure and/or function of the protein and may be utilized as efficient structural and functional markers of association to complex diseases. This study is focused on nsSNP variants of the ligand binding domain of PPARγ a nuclear receptor in the superfamily of ligand inducible transcription factors that play an important role in regulating lipid metabolism and in several processes ranging from cellular differentiation and development to carcinogenesis. Here we selected nine nsSNPs variants of the PPARγ ligand binding domain, V290M, R357A, R397C, F360L, P467L, Q286P, R288H, E324K, and E460K, expressed in cancer tissues and/or associated with partial lipodystrophy and insulin resistance. The effects of a single amino acid change on the thermodynamic stability of PPARγ, its spectral properties, and molecular dynamics have been investigated. The nsSNPs PPARγ variants show alteration of dynamics and tertiary contacts that impair the correct reciprocal positioning of helices 3 and 12, crucially important for PPARγ functioning.

Characterization of human frataxin missense variants in cancer tissues

“…The AMBER03 force field (Duan et al, ) was used to simulate wild‐type FXN and all its variants. The equilibration strategy adopted for the eight systems is quite standard and is explained in detail in (Di Carlo et al, ; Petrosino et al, ). The temperature, for the production simulations, was held fixed at 300 and 355 K using the v‐rescale thermostat (Bussi, Donadio, & Parrinello, ) with a coupling time of 0.1 ps.…”

“…The effects exerted by somatic mutations on the proteins range from changes in the protein stability, to alterations in the protein functions and in protein-protein interactions (Lori et al, 2013;Lori et al, 2016;Pasquo et al, 2012;Petrosino et al, 2017;Stefl, Nishi, Petukh, Panchenko, & Alexov, 2013). Computational studies based on protein structural information may provide a rationale for the changes induced by mutation (Casadio, Vassura, Tiwari, Fariselli, & Martelli, 2011;Peng, Alexov, & Basu, 2019;Petukh, Kucukkal, & Alexov, 2015); however, direct physicochemical studies of the protein variants may reveal all the local minor structural changes responsible of modifications in protein functions without dramatic alterations of the global protein folding (Lori et al, 2016).…”

“…The AMBER03 force field (Duan et al, 2003) was used to simulate wild-type FXN and all its variants. The equilibration strategy adopted for the eight systems is quite standard and is explained in detail in (Di Carlo et al, 2015;Petrosino et al, 2017).…”

The phosphoglycerate kinase 1 variants found in carcinoma cells display different catalytic activity and conformational stability compared to the native enzyme

“…PGK1 wild type and variants (110–160 μg/mL) were heated from 20°C to 80°C in 20 mM Tris-HCl, pH 8.0, 200 mM NaCl, 0.2 mM DTT, in a 0.1 cm quartz cuvette with a heating rate of 1 degree x min -1 controlled by a Jasco programmable Peltier element as described in [ 27 , 29 ]. The dichroic activity at 222 nm and the photomultiplier were continuously monitored in parallel every 0.5°C [ 35 ].…”

“…The effect of nsSNVs on protein stability, protein-protein interactions and protein functions has been investigated for several other protein families [ 26 – 29 ]. Indeed, large-scale computational studies utilizing structural information indicate that a single amino acid substitution will affect either protein-protein interactions and protein stability [ 30 , 31 ].…”