Journal Article

Molecular Dynamics Simulation of Kir6.2 Variants Reveals Potential Association with Diabetes Mellitus

Ahmed, Elsadig Mohamed, Alzahrani, Salem M., Alharbi, Zeyad M., Barnawi, Jameel, Mir, Mohammad Muzaffar, Eleragi, Ali M. S., Bedaiwi, Ruqaiah I., Ajmal, Mohammad Rehan, Elfaki, Imadeldin, Tayeb, Faris Jamal, Mir, Rashid, Elangeeb, Mohamed E.

2024

Overview

Diabetes mellitus (DM) represents a problem for the healthcare system worldwide. DM has very serious complications such as blindness, kidney failure, and cardiovascular disease. In addition to the very bad socioeconomic impacts, it influences patients and their families and communities. The global costs of DM and its complications are huge and expected to rise by the year 2030. DM is caused by genetic and environmental risk factors. Genetic testing will aid in early diagnosis and identification of susceptible individuals or populations using ATP-sensitive potassium (KATP) channels present in different tissues such as the pancreas, myocardium, myocytes, and nervous tissues. The channels respond to different concentrations of blood sugar, stimulation by hormones, or ischemic conditions. In pancreatic cells, they regulate the secretion of insulin and glucagon. Mutations in the KCNJ11 gene that encodes the Kir6.2 protein (a major constituent of KATP channels) were reported to be associated with Type 2 DM, neonatal diabetes mellitus (NDM), and maturity-onset diabetes of the young (MODY). Kir6.2 harbors binding sites for ATP and phosphatidylinositol 4,5-diphosphate (PIP2). The ATP inhibits the KATP channel, while the (PIP2) activates it. A Kir6.2 mutation at tyrosine330 (Y330) was demonstrated to reduce ATP inhibition and predisposes to NDM. In this study, we examined the effect of mutations on the Kir6.2 structure using bioinformatics tools and molecular dynamic simulations (SIFT, PolyPhen, SNAP2, PANTHER, PhD&SNP, SNP&Go, I-Mutant, MuPro, MutPred, ConSurf, HOPE, and GROMACS). Our results indicated that M199R, R201H, R206H, and Y330H mutations influence Kir6.2 structure and function and therefore may cause DM. We conclude that MD simulations are useful techniques to predict the effects of mutations on protein structure. In addition, the M199R, R201H, R206H, and Y330H variant in the Kir6.2 protein may be associated with DM. These results require further verification in protein–protein interactions, Kir6.2 function, and case-control studies.

• Publisher: MDPI AG
• Subject: Amino acids / ATP-sensitive potassium channels (KATP channels) / Binding Sites / bioinformatics / Diabetes / diabetes mellitus / Diabetes Mellitus - genetics / Diabetes Mellitus - metabolism / Disease / Genes / Genetic Predisposition to Disease / genetic testing / Glucose / Humans / Insulin / KCNJ11 gene / Metabolism / Molecular dynamics / Molecular Dynamics Simulation / Mutation / nsSNPs / Potassium / Potassium Channels, Inwardly Rectifying - chemistry / Potassium Channels, Inwardly Rectifying - genetics / Potassium Channels, Inwardly Rectifying - metabolism / Protein Binding / Proteins / Simulation