Human muscle pathology is associated with altered phosphoprotein profile of mitochondrial proteins in the skeletal muscle

Murburn posttranslational modifications of proteins: Cellular redox processes and murzyme-mediated metabolo-proteomics

Murburn concept constitutes the thesis that diffusible reactive species or DRS are obligatorily involved in routine metabolic and physiological activities. Murzymes are defined as biomolecules/proteins that generate/modulate/sustain/utilize DRS. Murburn posttranslational modifications (PTMs) result because murburn/murzyme functionalism is integral to cellular existence. Cells must incorporate the inherently stochastic nature of operations mediated by DRS. Due to the earlier/inertial stigmatic perception that DRS are mere agents of chaos, several such outcomes were either understood as deterministic modulations sponsored by house-keeping enzymes or deemed as unregulated nonenzymatic events resulting out of "oxidative stress". In the current review, I dispel the myths around DRS-functions, and undertake systematic parsing and analyses of murburn modifications of proteins. Although it is impossible to demarcate all PTMs into the classical or murburn modalities, telltale signs of the latter are evident from the relative inaccessibility of the locus, non-specificities and mechanistic details. It is pointed out that while many murburn PTMs may be harmless, some others could have deleterious or beneficial physiological implications. Some details of reversible/irreversible modifications of amino acid residues and cofactors that may be subjected to phosphorylation, halogenation, glycosylation, alkylation/acetylation, hydroxylation/oxidation, etc. are listed, along with citations of select proteins where such modifications have been reported. The contexts of these modifications and their significance in (patho)physiology/aging and therapy are also presented. With more balanced explorations and statistically verified data, a definitive understanding of normal versus pathological contexts of murburn modifications would be obtainable in the future.

Neuroanatomical zones of human traumatic brain injury reveal significant differences in protein profile and protein oxidation: Implications for secondary injury events

Traumatic brain injury (TBI) causes significant neurological deficits and long-term degenerative changes. Primary injury in TBI entails distinct neuroanatomical zones, i.e., contusion (Ct) and pericontusion (PC). Their dynamic expansion could contribute to unpredictable neurological deterioration in patients. Molecular characterization of these zones compared with away from contusion (AC) zone is invaluable for TBI management. Using proteomics-based approach, we were able to distinguish Ct, PC and AC zones in human TBI brains. Ct was associated with structural changes (blood-brain barrier (BBB) disruption, neuroinflammation, axonal injury, demyelination and ferroptosis), while PC was associated with initial events of secondary injury (glutamate excitotoxicity, glial activation, accumulation of cytoskeleton proteins, oxidative stress, endocytosis) and AC displayed mitochondrial dysfunction that could contribute to secondary injury events and trigger long-term degenerative changes. Phosphoproteome analysis in these zones revealed that certain differentially phosphorylated proteins synergistically contribute to the injury events along with the differentially expressed proteins. Non-synaptic mitochondria (ns-mito) was associated with relatively more differentially expressed proteins (DEPs) compared to synaptosomes (Syn), while the latter displayed increased protein oxidation including tryptophan (Trp) oxidation. Proteomic analysis of immunocaptured complex I (CI) from Syn revealed increased Trp oxidation in Ct > PC > AC (vs. control). Oxidized W272 in the ND1 subunit of CI, revealed local conformational changes in ND1 and the neighboring subunits, as indicated by molecular dynamics simulation (MDS). Taken together, neuroanatomical zones in TBI show distinct protein profile and protein oxidation representing different primary and secondary injury events with potential implications for TBI pathology and neurological status of the patients.

Mitochondrial Complex I Inhibition in Dopaminergic Neurons Causes Altered Protein Profile and Protein Oxidation: Implications for Parkinson's disease

Mitochondrial dysfunction and oxidative stress are critical to neurodegeneration in Parkinson's disease (PD). Mitochondrial dysfunction in PD entails inhibition of the mitochondrial complex I (CI) in the dopaminergic neurons of substantia nigra. The events contributing to CI inhibition and downstream pathways are not completely elucidated. We conducted proteomic analysis in a dopaminergic neuronal cell line exposed individually to neurotoxic CI inhibitors: rotenone (Rot), paraquat (Pq) and 1-methyl-4-phenylpyridinium (MPP⁺). Mass spectrometry (MS) revealed the involvement of biological processes including cell death pathways, structural changes and metabolic processes among others, most of which were common across all models. The proteomic changes induced by Pq were significantly higher than those induced by Rot and MPP⁺. Altered metabolic processes included downregulated mitochondrial proteins such as CI subunits. MS of CI isolated from the models revealed oxidative post-translational modifications with Tryptophan (Trp) oxidation as the predominant modification. Further, 62 peptides in 22 subunits of CI revealed Trp oxidation with 16 subunits common across toxins. NDUFV1 subunit had the greatest number of oxidized Trp and Rot model displayed the highest number of Trp oxidation events compared to the other models. Molecular dynamics simulation (MDS) of NDUFV1 revealed that oxidized Trp 433 altered the local conformation thereby changing the distance between the Fe-S clusters, Fe-S 301(N1a) to Fe-S 502 (N3) and Fe-S 802 (N4) to Fe-S 801 (N5), potentially affecting the efficiency of electron transfer. The events triggered by the neurotoxins represent CI damage, mitochondrial dysfunction and neurodegeneration in PD.

Identification of mitochondria-related hub genes in sarcopenia and functional regulation of MFG-E8 on ROS-mediated mitochondrial dysfunction and cell cycle arrest

Sarcopenia has high prevalence in the elderly population, but the genes and pathways related to aging in elderly patients with sarcopenia are poorly understood. Milk fat globule epidermal growth factor 8 (MFG-E8) is a peripheral membrane glycoprotein isolated from the milk fat globule membrane (MFGM). It has been found to exhibit various nutritional effects, including antibacterial, anti-cancer, anti-oxidant, anti-sarcopenia, and improving brain development and cognitive effects. This study aimed to investigate key differentially expressed genes (DEGs) and pathways associated with the progression of sarcopenia using bioinformatics analysis and in vitro myoblast experiment. The gene expression profiles of GSE8479 and GSE9676, which includes 40 young normal samples and 55 elderly samples, were downloaded from the Gene Expression Omnibus Database (GEO). Over 3253 DEGs were identified in the young and elderly samples (adjusted p value <0.05). A total of 213 co-expressed significantly DEGs were identified with Venn diagrams, including 82 up-regulated DEGs and 131 down-regulated DEGs. Based on the analysis of Gene Ontology (GO), protein-protein interaction (PPI) networks and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway, 10 hub genes screened by our study have been proved to play a role in regulating the occurrence and development of aging-related sarcopenia mainly via metabolic pathways, Huntington's disease, Parkinson's disease, oxidative phosphorylation and non-alcoholic fatty liver disease pathways. To further verify the protective effect of MFG-E8 on oxidative stress injured myoblasts, the cell cycle distribution, cell viability and reactive oxygen species (ROS) production were measured. The protein and mRNA levels of Akt, extracellular regulated protein kinases (ERK), p21Cip1, p27Kip1, cyclin D1, cyclin E1, cyclin-dependent kinase (CDK) 2 and 4 were quantified using qRT-PCR and western blot analysis. The results indicated that MFG-E8 has potential anti-sarcopenia effects by promoting ERK and Akt activation-mediated cell proliferation and cell cycle progression in myoblasts.

[Mitochondrial G12630A variation is associated with statin-induced myalgia in Chinese patients with coronary artery disease]

OBJECTIVE

To identify mitochondrial gene variants associated with statin-induced myalgia in Chinese patients with coronary artery disease (CHD).

METHODS

This study was conducted in a cohort of 403 patients with CHD receiving rosuvastatin therapy, among whom 341 patients had complete follow-up data concerning myalgia and 389 patients had documented measurements of plasma creatine kinase (CK) level. All these patients underwent genetic analysis using GSA chip for detecting mitochondria gene variants associated with myalgia. A logistic regression model was used to assess the association between 69 mitochondrial single-nucleotide polymorphisms (SNPs) and myopathy in 341 patients. The impact of these mutation sites on CK levels in 389 patients was evaluated by linear regression analysis.

RESULTS

G12630A variant was identified to correlate with an increased risk of myalgia in CHD patients (OR: 8.689, 95% CI: 1.586-47.6; P=0.01273), but CK levels did not differ significantly between patients with different genotypes of G12630A (P > 0.05). SNPs at T12285C and A13105G were found to significantly correlate with CK levels in these patients (P < 0.05).

CONCLUSIONS

Mitochondrial G12630A variation is associated with statin-induced myalgia in patients with CHD, indicating the necessity of different treatment strategies for patients who carry this risk allele.

Molecular docking investigation of the amantadine binding to the enzymes upregulated or downregulated in Parkinson's disease

Parkinson's disease (PD) is a progressive neurodegenerative disease. Levodopa in combination with amantadine has a demonstrated efficacy in motility impairment. An extensive investigation of some enzymes described to be upregulated or downregulated in PD was made - adenylate kinase (AK), adenine phosphoribosyltransferase (APRT), ectonucleoside triphosphate diphosphohydrolase 1 (ENTPD1), nucleoside-diphosphate kinase 3 (NDK3), purine nucleoside phosphorylase 1 (PNP1), and ecto-5'-nucleotidase (NT5E). Also, creatine kinase (CK) was included in the study because it is one of the main enzymes involved in the regulation of the nucleotide ratio in energy metabolism. To date, there is no proven link between amantadine treatment of PD and these enzymes. Because there are many AKs isoforms modified in PD, the AK was the first investigated. The molecular docking experiments allow the analysis of the selective binding of amantadine - unionized (with -NH₂ group) and ionized form (with -NH₃ ⁺ group) - to the AKs' isoforms implicated in PD. Using available X-ray 3D structures of human AKs in closed-conformation, it was demonstrated that there are notable differences between the interactions of the two forms of amantadine for the zebrafish AK1 (5XZ2), human AK2 (2C9Y), human AK5 (2BWJ), and AK from B.stearothermophilus. The cytosolic human AK1 and human AK2 mostly interact with ionized amantadine by AMP binding residues. The human AK5 interaction with ionized amantadine does not involve the residues from the catalytic site. Among other enzymes tested in the present study, APRT revealed the best results in respect of binding amantadine ionized form. The results offer a new perspective for further investigation of the connections between amantadine treatment of PD and some enzymes involved in purine metabolism.