Molecular dynamic simulation and functional analysis of pathogenic PTEN mutations in glioblastoma

Abstract

PTEN, a dual-phosphatase and scaffold protein, is one of the most commonly mutated tumour suppressor gene across various cancer types in human. The aim of this study therefore was to investigate the stability, structural and functional effects, and pathogenicity of 12 missense PTEN mutations (R15S, E18G, G36R, N49I, Y68H, I101T, C105F, D109N, V133I, C136Y, R173C and N276S) found by next generation sequencing of the PTEN gene in tissue samples obtained from glioblastoma patients. Computational tools and molecular dynamic simulation programs were used to identify the deleterious effects of these mutations. Furthermore, PTEN mRNA and protein expression levels were evaluated by qRT-PCR, Western Blot, and immunohistochemistry staining methods. Various computational tools predicted strong deleterious effects for the G36R, C105F, C136Y and N276S mutations. Molecular dynamic simulation revealed a significant decrease in protein stability for the Y68H and N276S mutations when compared with the wild type protein; whereas, C105F, D109N, V133I and R173C showed partial stability reduction. Significant residual fluctuations were observed in the R15S, N49I and C136Y mutations and radius of gyration graphs revealed the most compact structure for D109N and least for C136Y. In summary, our study is the first one to show the presence of PTEN E18G, N49I, D109N and N276S mutations in glioblastoma patients; where, D109N is neutral and N276S is a damaging and disease-associated mutation.

Communicated by Ramaswamy H. Sarma

Keywords:

• PTEN
• pathogenic mutation
• glioblastoma
• molecular dynamic simulation
• computational biology

Disclosure statement

The authors declare that they have no competing interests.

Web resources

http://www.bioinformatics.babraham.ac.uk

http://www.usadellab.org/cms/?page=trimmomatic

http://bio-bwa.sourceforge.net

http://samtools.sourceforge.net

https://software.broadinstitute.org/gatk/

https://www.ensembl.org/info/docs/tools/vep/index.html

Additional information

Funding

This work was supported by the Ege University Scientific Research Projects Coordination (TGA-2020-22041). The numerical calculations reported in this paper were partially performed at TUBITAK ULAKBIM, High Performance and Grid Computing Centre.