Computational analysis of deleterious missense mutations in aspartoacylase that cause Canavan’s disease

Sreevishnupriya, K.; Chandrasekaran, Prabha; Senthilkumar, A.; Sethumadhavan, Rao; Shanthi, V.; Daisy, P.; Nisha, J.; Ramanathan, K.; Rajasekaran, R.

doi:10.1007/s11427-012-4406-8

Cited by 4 publications

(4 citation statements)

References 57 publications

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“…Previous computational studies of ASPA C152W have shown that this variant is likely to be destabilized [16] and consistently it exhibits a lower expression level in vivo [15]. Somewhat perplexingly, thermal unfolding experiments find the C152W variant to be stable, albeit with very low activity [21].…”

Section: Exposure Of a Degron As A Possible Mechanism For Increased Turnover Of Aspa C152wmentioning

confidence: 96%

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Mapping the degradation pathway of a disease-linked aspartoacylase variant

et al. 2021

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Canavan disease is a severe progressive neurodegenerative disorder that is characterized by swelling and spongy degeneration of brain white matter. The disease is genetically linked to polymorphisms in the aspartoacylase (ASPA) gene, including the substitution C152W. ASPA C152W is associated with greatly reduced protein levels in cells, yet biophysical experiments suggest a wild-type like thermal stability. Here, we use ASPA C152W as a model to investigate the degradation pathway of a disease-causing protein variant. When we expressed ASPA C152W in Saccharomyces cerevisiae, we found a decreased steady state compared to wild-type ASPA as a result of increased proteasomal degradation. However, molecular dynamics simulations of ASPA C152W did not substantially deviate from wild-type ASPA, indicating that the native state is structurally preserved. Instead, we suggest that the C152W substitution interferes with the de novo folding pathway resulting in increased proteasomal degradation before reaching its stable conformation. Systematic mapping of the protein quality control components acting on misfolded and aggregation-prone species of C152W, revealed that the degradation is highly dependent on the molecular chaperone Hsp70, its co-chaperone Hsp110 as well as several quality control E3 ubiquitin-protein ligases, including Ubr1. In addition, the disaggregase Hsp104 facilitated refolding of aggregated ASPA C152W, while Cdc48 mediated degradation of insoluble ASPA protein. In human cells, ASPA C152W displayed increased proteasomal turnover that was similarly dependent on Hsp70 and Hsp110. Our findings underscore the use of yeast to determine the protein quality control components involved in the degradation of human pathogenic variants in order to identify potential therapeutic targets.

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Section: Exposure Of a Degron As A Possible Mechanism For Increased Turnover Of Aspa C152wmentioning

confidence: 96%

“…On the molecular level, some disease-linked ASPA variants have been found to trigger the loss-of-function phenotype by perturbing the active site or protein stability [15,16]. However, the majority of disease-linked ASPA variants remain to be examined.…”

Section: Introductionmentioning

confidence: 99%

Mapping the degradation pathway of a disease-linked aspartoacylase variant

et al. 2021

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“…Previous computational studies of ASPA C152W have shown that this variant is likely to be destabilized (Sreevishnupriya et al, 2012) and consistently it exhibits a lower expression level in vivo (Hershfield et al, 2007). Somewhat perplexingly, thermal unfolding experiments find the C152W variant to be stable, albeit with very low activity (Zano et al, 2013).…”

Section: Exposure Of a Degron As A Possible Mechanism For Increased Tmentioning

confidence: 96%

“…On the molecular level, some disease-linked ASPA variants have been found to trigger the loss-offunction phenotype by perturbing the active site or protein stability (Hershfield et al, 2007;Sreevishnupriya et al, 2012). However, the majority of disease-linked ASPA variants remain to be examined.…”

Section: Introductionmentioning

confidence: 99%

Evolutionarily conserved chaperone-mediated proteasomal degradation of a disease-linked aspartoacylase variant

Gersing

Wang

Grønbæk-Thygesen

et al. 2020

Preprint

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Canavan disease is a severe progressive neurodegenerative disorder that is characterized by swelling and spongy degeneration of brain white matter. The disease is genetically linked to polymorphisms in the aspartoacylase (ASPA) gene, including the substitution C152W. ASPA C152W is associated with greatly reduced protein levels in cells, yet biophysical experiments suggest a wild-type like thermal stability. Here, we examine the stability and degradation pathway of ASPA C152W. When we expressed ASPA C152W in Saccharomyces cerevisiae, we found a decreased steady state compared to wild-type ASPA as a result of increased proteasomal degradation. However, molecular dynamics simulations of ASPA C152W did not substantially deviate from wild-type ASPA, indicating that the native state is structurally preserved. Instead, we suggest that the C152W substitution prevents ASPA from reaching its stable native conformation, presumably by impacting on de novo folding. Systematic mapping of the protein quality control components acting on misfolded and aggregation-prone species of C152W, revealed that the degradation is highly dependent on the molecular chaperone Hsp70, its co-chaperone Hsp110 as well as several quality control E3 ubiquitin-protein ligases, including Ubr1. In human cells, ASPA C152W displayed increased proteasomal turnover that was similarly dependent on Hsp70 and Hsp110. We propose that Hsp110 is a potential therapeutic target for misfolding ASPA variants that trigger Canavan disease due to excessive degradation.

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Computational Identification of Significant Missense Mutations in AKT1 Gene

Shanthi

Rajasekaran

Ramanathan

2014

Cell Biochem Biophys

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The AKT1 gene is of supreme importance in cell signaling and human cancer. In the present study, we aim to understand the phenotype variations that were believed to have the highest impact in AKT1 gene by different computational approaches. The analysis was initiated with SIFT tool followed by PolyPhen 2.0, I-Mutant 2.0, and SNPs&GO tools with the aid of 22 nonsynonymous (nsSNPs) retrieved from dbSNP. A total of five AKT1 variants such as E17K, E17S, E319G, L357P, and P388T are found to exert deleterious effects on the protein structure and function. Furthermore, the molecular docking study indicates the lesser binding affinity of inhibitor with the mutant structure than the native type. In addition, root mean square deviation and hydrogen bond details were also analyzed in the 10 ns molecular dynamics simulation study. These computational evidences suggested that E17K, E17S, E319G, L357P, and P388T variants of AKT1 could destabilize the protein networks, thus causing functional deviations of protein to some extent. Moreover, the findings strongly indicate that screening for AKT1, E17K, E17S, E319G, L357P, and P388T variants may be useful for disease molecular diagnosis and also to design the potential AKT inhibitors.

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Computational analysis of deleterious missense mutations in aspartoacylase that cause Canavan’s disease

Cited by 4 publications

References 57 publications

Mapping the degradation pathway of a disease-linked aspartoacylase variant

Mapping the degradation pathway of a disease-linked aspartoacylase variant

Evolutionarily conserved chaperone-mediated proteasomal degradation of a disease-linked aspartoacylase variant

Computational Identification of Significant Missense Mutations in AKT1 Gene

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