Current Proteomics - Volume 16, Issue 2, 2019

Background: To date, there is no x-ray crystallography or structures from nuclear magnetic resonance (NMR) on royal jelly proteins available in the online data banks. In addition, characterization of proteins in royal jelly is not fully accomplished to date. Although new investigations unravel novel proteins in royal jelly, the majority of a protein family is present in high amounts (80-90%). Objective: In this review, we attempted to predict the three-dimensional structure of royal jelly proteins (especially the major royal jelly proteins) to allow visualization of the four protein surface properties (aromaticity, hydrophobicity, ionizability and (hydrogen (H)-bond) by using bioinformatics tools. Furthermore, we gathered the information on available therapeutic activities of crude royal jelly and its proteins. Methods: For protein modeling, prediction and analysis, the Phyre2 web portal systematically browsed in which the modeling mode was intensive. On the other side, to build visualized understanding of surface aromaticity, hydrophobicity, ionizability and H-bond of royal jelly proteins, the Discovery Studio 4.1 (Accelrys Software Inc.) was used. Results: Our in silico study confirmed that all proteins treasure these properties, including aromaticity, hydrophobicity, ionizability and (hydrogen (H)-bond. Another finding was that newly discovered proteins in royal jelly do not belong to the major royal jelly protein group. Conclusion: In conclusion, the three dimensional structure of royal jelly proteins along with its major characteristics were successfully elucidated in this review. Further studies are warranted to elucidate the detailed physiochemical properties and pharmacotherapeutics of royal jelly proteins.

Background: In the era of modern microbiology, several methods are available for identification and typing of bacteria, including whole genome sequencing. However, in microbiological laboratories or hospitals where genomic based molecular typing methods and/or trained manpower are unavailable, whole cell protein profiling using sodium dodecyl sulfate polyacrylamide gel electrophoresis might be a useful alternative/supplementary method for bacterial identification, strain typing and epidemiology. Whole cell protein profiling by SDS-PAGE is based on the principle that under standard growth conditions, a bacterial strain expresses the same set of proteins, the pattern of which can be used for bacterial identification. Objective: The objective of this review is to assess the current status of whole cell protein profiling by SDS-PAGE and its advantages and constraints for bacterial identification and typing. Results and Conclusion: Several earlier and recent studies prove the potential and utility of this technique as an adjunct or supplementary method for bacterial identification, strain typing and epidemiology. There is no denying the fact that utility of this technique as an adjunct or supplementary method for bacterial identification and typing has already been demonstrated and its practical applications need to be evaluated further.

Background: Neuropsychiatric systemic lupus erythematosus or NPSLE, as its name suggests, refers to the neurological and psychiatric manifestations of Systemic Lupus Erythematosus (SLE). In clinical practice, it is often difficult to reach an accurate diagnosis, as this disease presents differently in different patients, and the available diagnostic tests are often not specific enough. Objectives: The aim of this study was to search for proteomic biomarkers in cerebrospinal fluid that could be proposed as diagnostic aids for this disease. Methods: The proteomic profile of cerebrospinal fluid samples of 19 patients with NPSLE, 12 patients with SLE and no neuropsychiatric manifestation (SLEnoNP), 6 patients with neuropsychiatric symptoms but no SLE (NPnoSLE), 5 with Other Autoimmune Disorders without neuropsychiatric manifestations (OADs), and 4 Healthy Controls (HC), were obtained by two-dimensional gel electrophoresis and compared using ImageMaster Platinum 7.0 software. Results: The comparative analysis of the different study groups revealed three proteins of interest that were consistently over-expressed in NPSLE patients. These were identified by mass spectrometry as albumin (spot 16), haptoglobin (spot 160), and beta-2 microglobulin (spot 161). Conclusion: This work is one of the few proteomic studies of NPSLE that uses cerebrospinal fluid as the biological sample. Albumin has previously been proposed as a potential biomarker of rheumatoid arthritis and SLE, which is coherent with these results; but this is the first report of haptoglobin and beta-2 microglobulin in NPSLE, although haptoglobin has been associated with increased antibody production and beta-2 microglobulin with lupus nephritis.

Objective: Transplantation is the preferred treatment for patients with end-stage liver diseases. However, in clinical practice, functional preservation of the liver is a major concern before the transplantation. Although various protective solutions are used (in combination with hypothermia), the functional preservation time for liver is still limited to hours. We analyzed the preservation medium to detect the proteins released from the liver during storage period. Material/Methods: Samples were collected from the pre-transplant preservation mediums of 23 liver donors. For all donors, the cases involved Donation after Brain Death (DBD). 2D-PAGE and LCMSMS methodologies were used to detect the proteins and peptides from the preservation mediums. Results: A total of 198 proteins originating from the liver were detected. Conclusion: The data provide valuable insights into biomarkers that may be used to evaluate organ injury, functional status, and suitability for transplantation. Additionally, the findings could be valuable for the development of new strategies for effective preservation of solid organs prior to transplantation.

Background and Objective: Antimycin A (AntA) is a potent Electron Transport System (ETS) inhibitor exerting its effect through inhibiting the transfer of the electrons by binding to the quinone reduction site of the cytochrome bc1 complex (Complex III), which is known to be impaired in Huntington’s Disease (HD). The current studies were undertaken to investigate the effect of complex III inhibition in the SH-SY5Y cell line to delineate the molecular and cellular processes, which may play a role in the pathogenesis of HD. Method: We treated SH-SY5Y neuroblastoma cells with AntA in order to establish an in vitro mitochondrial dysfunction model for HD. Differential proteome analysis was performed by the nLCMS/ MS system. Protein expression was assessed by western blot analysis. Results: Thirty five differentially expressed proteins as compared to the vehicle-treated controls were detected. Functional pathway analysis indicated that proteins involved in ubiquitin-proteasomal pathway were up-regulated in AntA-treated SH-SY5Y neuroblastoma cells and the ubiquitinated protein accumulation was confirmed by immunoblotting. We found that Prothymosin α (ProT α) was downregulated. Furthermore, we demonstrated that nuclear factor erythroid 2-related factor 2 (Nrf2) protein expression was co-regulated with ProT α expression, hence knockdown of ProT α in SH-SY5Y cells decreased Nrf2 protein level. Conclusion: Our findings suggest that complex III impairment might downregulate ubiquitinproteasome function and NRF2/Keap1 antioxidant response. In addition, it is likely that downregulation of Nrf2 is due to the decreased expression of ProT α in AntA-treated SH-SY5Y cells. Our results could advance the understanding of mechanisms involved in neurodegenerative diseases.

Objective: The aim of the present study was to build protein profiles of untreated breast cancer patients of invasive ductal carcinoma grade II at tissue level in Pakistani population and to compare 2-D profiles of breast tumor tissues with matched normal tissues in order to evaluate for variations of proteins among them. Materials & Methods: Breast tissue profiles were made after polytron tissue lysis and rehydrated proteins were further characterized by using two-dimensional gel electrophoresis. On the basis of isoelectric point (pI) and molecular weight, proteins were identified by online tool named Siena 2-D database and their identification was further confirmed by using MALDI-TOF. Results: Among identified spots, 10 proteins were found to be differentially expressed i.e.; COX5A, THIO, TCTP, HPT, SODC, PPIA, calreticulin (CRT), HBB, albumin and serotransferrin. For further investigation, CRT was selected. The level of CRT in tumors was found to be significantly higher than in normal group (p < 0.05). The increased expression of CRT level in tumor was statistically significant (p = 0.010) at a 95% confidence level (p <0.05) as analyzed by Mann-Whitney. CRT was found distinctly expressed in high amount in tumor tissue as compared to their matched normal tissues. Conclusion: It has been concluded that CRT expression could discriminate between normal tissue and tumor tissue so it might serve as a possible candidate for future studies in cancer diagnostic markers.

Background: Microbial remediation is an ecologically safe alternative to controlling environmental pollution caused by toxic aromatic compounds including azo dyes. Marine bacteria show excellent potential as agents of bioremediation. However, a lack of understanding of the entailing mechanisms of microbial degradation often restricts its wide-scale and effective application. Objective: To understand the changes in a bacterial proteome profile during azo dye decolorization. Method: In this study, we tested a Gram-negative bacterium, Shewanella seohaensis NIODMS14 isolated from an estuarine environment and grown in three different azo dyes (Reactive Black 5 (RB5), Reactive Green 19 (RG19) and Reactive Red 120 (RR120)). The unlabeled bacterial protein samples extracted during the process of dye decolorization were subject to mass spectrometry. Relative protein quantification was determined by comparing the resultant MS/MS spectra for each protein. Results: Maximum dye decolorization of 98.31% for RB5, 91.49% for RG19 and 97.07% for RR120 at a concentration of 100 mg L-1 was observed. The liquid chromatography-mass spectrometry - Quadrupole Time of Flight (LCMS-QToF) analysis revealed that as many as 29 proteins were up-regulated by 7 hours of growth and 17 by 24 hours of growth. Notably, these were common across the decolorized solutions of all three azo dyes. In cultures challenged with the azo dyes, the major class of upregulated proteins was cellular oxidoreductases and an alkyl hydroperoxide reductase (SwissProt ID: A9KY42). Conclusion: The findings of this study on the bacterial proteome profiling during the azo dye decolorization process are used to highlight the up-regulation of important proteins that are involved in energy metabolism and oxido-reduction pathways. This has important implications in understanding the mechanism of azo dye decolorization by Shewanella seohaensis.