Thermodynamic Stability of Human γD-Crystallin Mutants Using Alchemical Free-Energy Calculations

Aguayo‐Ortiz, Rodrigo; González-Navejas, Augusto; Palomino-Vizcaino, Giovanni; Rodríguez-Meza, Oscar; Costas, Miguel; Quintanar, Liliana; Domı́nguez, Laura

doi:10.1021/acs.jpcb.9b01818

Cited by 9 publications

(11 citation statements)

References 62 publications

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“…29−32 A recent computational and experimental study performed by our research group demonstrated that W42R is the most destabilizing mutation of HγDC. 33 In agreement with previous results, we found that the W42R mutant is highly prone to aggregate due to its low stability and solubility. 24,34 However, the instability caused by the W42R mutation has not been fully understood.…”

Section: Introductionsupporting

confidence: 93%

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Effects of Mutating Trp42 Residue on γD-Crystallin Stability

Aguayo‐Ortiz

Domı́nguez

2019

J. Chem. Inf. Model.

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Oligomerization and aggregation of γD-crystallins (HγDC) in the eye lens is one of the main causes of cataract development. To date, several congenital mutations related to this protein are known to promote the formation of aggregates. Previous studies have demonstrated that mutations in W42 residue of HγDC lead to the generation of partially unfolded intermediates that are more prone to aggregate. To understand the role of W42 in the stability of HγDC, we performed alchemical free-energy calculations and all-atom molecular dynamics simulations of different W42 mutant models. Our results suggest that substitution of W42 by small size and/or polar residues promotes HγDC denaturation due to the entry of water molecules into the hydrophobic core of the N-terminal domain. Similar behavior was observed in the C-terminal domain of HγDC when mutating the W130 residue located in a homologous position. Moreover, the exposure of the hydrophobic core residues could lead to the formation of aggregation-prone partially unfolded species. Overall, this study takes a step toward understanding the role of HγDC in cataract development.

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Section: Introductionsupporting

confidence: 93%

“…For the alchemical free-energy calculations and MD simulations, we employed the same methodology described in our previous work. 33 2.1. Model Preparation.…”

Section: Models and Methodsmentioning

confidence: 99%

Effects of Mutating Trp42 Residue on γD-Crystallin Stability

Aguayo‐Ortiz

Domı́nguez

2019

J. Chem. Inf. Model.

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“…One of the most accepted involves the formation of a partially unfolded intermediate state where the N-terminal domain is completely unfolded while the C-terminal remains folded. This partially unfolded intermediate has been proposed as the starting point for intermolecular interactions between protomers that induce aggregate development (Aguayo-Ortiz et al, 2019;Flaugh, Kosinski-Collins & King, 2005;Whitley et al, 2017). Other models include domain swapping events (Mahler et al, 2011;Moreau & King, 2012), intramolecular disulfide bridge formation (Serebryany & King, 2015), dimerisation (Serebryany et al, 2016;Ray, Hall & Carver, 2016) or a simple condensation mechanism, in which subtle modifications in the protein surface induce association and aggregation (Forsythe et al, 2019;Thorn et al, 2019;Pande et al, 2010;Pande, Mokhor & Pande, 2015;Wong et al, 2019).…”

Section: Introductionmentioning

confidence: 99%

Aggregation pathways of human γ D crystallin induced by metal ions revealed by time dependent methods

Fernández-Silva

French-Pacheco

Rivillas‐Acevedo

et al. 2020

PeerJ

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Cataract formation is a slow accumulative process due to protein aggregates promoted by different factors over time. Zinc and copper ions have been reported to induce the formation of aggregates opaque to light in the human gamma D crystallin (HγD) in a concentration and temperature dependent manner. In order to gain insight into the mechanism of metal-induced aggregation of HγD under conditions that mimic more closely the slow, accumulative process of the disease, we have studied the non-equilibrium process with the minimal metal dose that triggers HγD aggregation. Using a wide variety of biophysics techniques such as turbidimetry, dynamic light scattering, fluorescence, nuclear magnetic resonance and computational methods, we obtained information on the molecular mechanisms for the formation of aggregates. Zn(II) ions bind to different regions at the protein, probably with similar affinities. This binding induces a small conformational rearrangement within and between domains and aggregates via the formation of metal bridges without any detectable unfolded intermediates. In contrast, Cu(II)-induced aggregation includes a lag time, in which the N-terminal domain partially unfolds while the C-terminal domain and parts of the N-terminal domain remain in a native-like conformation. This partially unfolded intermediate is prone to form the high-molecular weight aggregates. Our results clearly show that different external factors can promote protein aggregation following different pathways.

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“…Human γD crystallin (HγDC) is one of the most abundant crystallins in the central lens nucleus, and its thermodynamic stability and aggregation are associated with the development of age-related cataracts [10]. Aguayo-Ortiz R et al, [41] have used alchemical free energy calculations to predict changes in the thermodynamic stability (ΔΔG) of 10 alanine-scanning variants and 12 HγDC mutations associated with the development of congenital cataracts. These results showed that changes in ΔΔG are associated with the significant position of the motif, thus affecting thermodynamic stability.…”

Section: G171s Xtalbgmentioning

confidence: 99%

In silico analysis and high-risk pathogenic phenotype predictions of non-synonymous single nucleotide polymorphisms in human Crystallin beta A4 gene associated with congenital cataract

Wang

Huang

et al. 2020

PLoS ONE

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In order to provide a cost-effective method to narrow down the number of pathogenic Crystallin beta A4 (CRYBA4) non-synonymous single nucleotide polymorphisms (nsSNPs), we collected nsSNP information of the CRYBA4 gene from SNP databases and literature, predicting the pathogenicity and possible changes of protein properties and structures using multiple bioinformatics tools. The nsSNP data of the CRYBA4 gene were collected from 4 databases and published literature. According to 12 criteria, six bioinformatics tools were chosen to predict the pathogenicity. I-Mutant 2.0, Mupro and INPS online tools were used to analyze the effects of amino acid substitution on protein stability by calculating the value of ΔΔG. ConSurf, SOPMA, GETAREA and HOPE online tools were used to predict the evolutionary conservation of amino acids, solvent accessible surface areas, and the physical and chemical properties and changes of protein structure. All 157 CRYBA4 nsSNPs were analyzed. Forty-four CRYBA4 high-risk pathogenic nsSNPs (predicted to be pathogenic by all six software tools) were detected out of the 157 CRYBA4 nsSNPs, four of which (c.283C>T, p.R95W; c.449T>A, p.V150D; c.475G>A, p.G159R; c.575G>C, p.R192P) should be focused on because of their high potential pathogenicity and possibility of changing protein properties. Thirty high-risk nsSNPs were predicted to cause a decrease of protein stability. Twenty-nine high-risk nsSNPs occurred in evolutionary conserved positions. Twenty-two high-risk nsSNPs occurred in the core of the protein. It is predicted that these high-risk pathogenic nsSNPs can cause changes in the physical and chemical properties of amino acids, resulting in structural changes of proteins and changes in the interactions between domains and other molecules, thus affecting the function of proteins. This study provides important reference value when narrowing down the number of pathogenic CRYBA4 nsSNPs and studying the pathogenesis of congenital cataracts. By using this method, we can easily find 44 high-risk pathogenic nsSNPs out of 157 CRYBA4 nsSNPs.

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Thermodynamic Stability of Human γD-Crystallin Mutants Using Alchemical Free-Energy Calculations

Cited by 9 publications

References 62 publications

Effects of Mutating Trp42 Residue on γD-Crystallin Stability

Effects of Mutating Trp42 Residue on γD-Crystallin Stability

Aggregation pathways of human γ D crystallin induced by metal ions revealed by time dependent methods

In silico analysis and high-risk pathogenic phenotype predictions of non-synonymous single nucleotide polymorphisms in human Crystallin beta A4 gene associated with congenital cataract

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