Current Proteomics - Volume 14, Issue 1, 2017

Soybean is a widely cultivated crop and it serves as a major source of protein and vegetable oil. The growth and yield of soybean are markedly affected by adverse environmental conditions including abiotic and biotic stresses. Nanoparticles (NPs), which are the materials with specific size ranging from 1 to 100 nm, are used in agricultural products on a large scale. NPs cause differential growth effects on plants depending on their sizes, plant species/growth phase, and stress conditions. The current knowledge of NPs effects on plant growth is increasing; while the understanding of the underlying mechanisms and metabolisms involved is limited. In this review, characteristic aspects of plant NPs interaction are summarized. In addition, the morphological and molecular mechanisms mediated by NPs on soybean are addressed. Furthermore, the impact of NPs on the nutritional quality of plants is discussed. Continued advances of NPs on soybean proteomics are expected to contribute towards better understanding of the plant responses under various conditions.

Peptide drugs have received more attention as potential next-generation drugs or drug leads. Such attention is primarily due to the higher target selectivities and efficiencies of peptide drugs. Moreover, peptide drugs typically have lower accumulation rates and toxicities. Although peptide drugs have advanced significantly in the 21^st century, two bottlenecks (disadvantages) primarily hinder peptide drug research and development compared to small molecule drugs. One bottleneck is the identification of a valuable peptide in a complicated pool of crude products; the other bottleneck is the ability to prepare sufficient amounts of peptides for preclinical or clinical trials. This review discusses important methodologies for addressing these two bottlenecks.

Objective: Non-alcoholic fatty liver disease (NAFLD) is the most common chronic liver disease and becoming an important public health concern in the world. However, the molecular mechanism of the pathogenesis in NAFLD is still unclear. Method: In this study, in vitro model of NAFLD was established and differential expression of proteins in this cellular model was investigated by using proteomic technique. Result: By using two-dimensional polyacrylamide gel electrophoresis, approximately 650 proteins were separated and sixteen were found to be significantly affected by oleic acid compared to the untreated control. Among them, eight were upregulated and other eight were downregulated. These proteins were successfully identified with peptide mass fingerprinting using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) after in-gel trypsin digestion. The results showed that these proteins are involved in transcription regulation (53.4%), metabolic process (13.3%), cytoskeleton (20%), and cellular signaling transduction (13.3%), respectively. Conclusion: It is suggested that the pathogenesis of NAFLD is associated with the differential expression of some functional proteins. These proteins may provide potential targets for future mechanistic studies concerning the development and prevention of NAFLD.

Background: Aggregation of Human α-synuclein protein into well-ordered amyloid fibrils is critical at the onset of Parkinson’s disease (PD), a progressive and irreversible neurodegenerative disorder. In the recent past, the importance of tyrosine residues in the fibrillation process of α-synuclein has been highlighted but their definite role in the early events of fibrillation is not clear. Objective: To understand the role of Tyr residues on the early events of α-synuclein fibrillation process. Methodology: We have used the all the atom molecular dynamics simulation and investigated the conformational dynamics of wild-type (WT) and the three modelled Tyr mutants (Y39A, Y133A, and Y (125,133,136) A) of α-synuclein. Results: Among the WT and the mutants, we observed Y(125, 133, 136)A and Y133A to have lesser number of hydrophobic contacts between the residues in the N- and C-terminal regions, exhibiting a differing folding pattern and conformation that has the ability to delay the aggregation propensity of α-synuclein. We also found that Tyr residue at position 133 is primarily important to drive the intramolecular interactions and subsequent fibrillation process. Conclusion: Therefore, our findings in this study suggest that targeting the Tyr residue at the position 133 may provide better solution to significant delay in the early stage of aggregation in α- synuclein.

Background: Low temperature is a serious environmental factor that affects plant growth and cultivation. As one of the most popular fruit crop in the world, grapevine exhibited much difference in cold stress tolerance of different cultivars. Objective: To understand the cold tolerance mechanism in grapevine and provide certain proteomics data may contribute to its breeding for enhancement of cold tolerance. Method: In this study, iTRAQ-based comparative proteomic analysis was conducted to identify cold-response proteins in two grape cultivars including a cold-resistant grape cultivar (Vitis amurensis) and a cold-sensitive grape cultivar (Vitis vinifera cv. Muscat of Hamburg). Results: Totally, 532 and 264 proteins were differentially expressed in Va and M, respectively, with 91 overlapping proteins. Compared to the control, most of these proteins exhibited down-regulated at 12 h, then up-regulated at 24 h, and decreased again at 48 h under cold treatment. Among these differentially expressed proteins, those involved in metabolic process, cellular process, single-organism process and response to stimuli were the most abundant group. Conclusion: Based on these findings, we proposed that proteins involved in photosynthesis, starch and sucrose metabolism, response to stimuli (such as glycine-rich RNA-binding protein, calmodulin, WSI18 protein etc.), signal transduction may play important roles for grape to resist cold stress. These results provide new insight to understand the cold tolerance mechanism in grapevine and may contribute to its breeding for enhancement of cold tolerance.

Objectives: Bio-informatics methodologies have made possible to profile the global composition of tissue or organelle at a specific point or under particular developmental or disease state. In schizophrenia, research has extensively focused on identification of the alterations associated with gene and protein expression profiling. An additional target of the present study is the assorted mechanisms by which post-translational modifications can regulate these functions. As phosphorylation, s-nitrosylation and glycosylation are the familiar post-translational modification; the phosphorylation offers a foremost regulatory system due to the high variability in the protein structure, particularly flanking amino acid residues, the reliable prediction of these sites still remains a vital issue. Post-translational modifications modulate protein's cellular function critically involved in cell signaling and regulatory mechanisms in the molecular context. The gene mutations greatly influence these modification sites and believed as a disease biomarker. Methods: The present study illustrates Insilico analysis approach to predict possible posttranslational modifications in dopamine receptor D2 (DRD2) protein in previously identified G-T mutation in the 310 bp Taq1A receptor gene sequence in the Pakistani schizophrenic patients as compared to normal healthy controls. Results: The significant changes were observed, particularly the down-regulation in phosphorylation and glycosylation sites in G-T mutated sequence of the schizophrenic patient as compared to healthy controls. However, no change observed in nitrosylation sites in both groups, suggests that this downregulation or loss of modification target sites may be associated with the disease consequences. Conclusion: Current study expressed remarkable results that propose unique possibilities to investigate post-translational modifications at gene / protein level could further enhance understanding towards the biological function that altered during schizophrenia progression.

Background: Lung cancer is one of the most common causes of cancer-related mortality, and its incidence is increasing steadily worldwide. NSCLC represents approximately 83% of lung cancer cases, including different subtypes, among clinically histological lung cancer types. Materials and Methods: In this study, we aimed to identify proteome level differences between NSCLC tumor and tumor-adjacent non-tumor tissue samples using gel-based comparative proteomics. Additionally, proteins were classified using PANTHER, protein-protein interactions were mapped by STRING, and also, the top canonical pathway was identified using IPA network system. Western blot was used for validation the proteomics findings. Results: A total of 40 protein spots were successfully identified by MALDI-TOF/TOF, and 33 proteins were found differentially expressed, of which 27 proteins were up-regulated, whereas, 6 proteins were down-regulated in NSCLC tumor tissues. Conclusion: These findings show that proteome level differences between NSCLC tumor and nontumor tissue samples.

Background: The Pekin duck, bred from the mallard (Anas platyrhynchos) in china, is one of the most famous meat duck species in the world. However, it is more sensitive to heat stress than Muscovy duck, which is believed to have originated in South America. Objective: This study aims to uncover the temperature-dependent proteins of two duck species using comparative proteomic approach. Methods: we performed the comparative proteomic analysis based on the previous methods and focused on α-enolase, an enzyme previously shown to change in response to high temperatures, but in a species-dependent manner. We also performed a semi-quantification assay of α-enolase mRNA in these two duck species. Results: Gene expression levels and enzymatic activity for α-enolase (ENO1) were both upregulated in Muscovy ducks and downregulated in Pekin ducks. A comparison of cloned amino acid sequences showed 21 base pair differences in the ENO1 between Pekin and Muscovy ducks, corresponding to five different amino acids between protein sequences. Sites 171 and 173 were polymorphic for Pro/Cys in α-enolase in Pekin ducks and Leu/Val in Muscovy ducks, respectively. Conclusion: The moieties L171P and V173C were located at the top of β-sheets depending on the three-dimensional structure of α-enolase, which may have a role in guiding the substrate to the enzyme catalytic domain.