Current Proteomics - Volume 11, Issue 3, 2014

The NADPH-dependent reduction of glucose reaction that is catalyzed by Aldose Reductase (AR) follows a sequential ordered kinetic mechanism in which the co-factor NADPH binds to the enzyme prior to the aldehyde substrate. The kinetic/structural experiments have found a conformational change involving a hinge-like movement of a surface loop (residues 213-224) which is anticipated to take place upon the binding of the diphosphate moiety of NADPH. The reorientation of this loop, expected to permit the release of NADP+, represents the rate-limiting step of the catalytic mechanism. This study reveals: 1) The Translation/Libration/Screw (TLS) analysis of absolute B-factors of apo AR crystal structures indicates that the 212-224 loop might move as a rigid group. 2) Residues that make the flexible loop slide in the AR binary and ternary complexes. 3) The normalized B-factors separate this segment into three differnt clusters with fewer residues.

Plant protein is seldom studied by researchers, particularly from the roots of Eurycoma longifolia. This is mainly due to the minute amount of plant protein and low sample recovery of protein extraction from the recalcitrant tissues. However, plant protein could be the bioactive constituent for numerous biological activities which have been proven scientifically and practicing traditionally. Therefore, four extraction methods ranging from simple maceration (water extraction without and with detergent, Triton X-100) to buffer-assisted precipitation approaches (phenol-SDS and TCAacetone) were carried out to extract plant protein from the roots of E. longifolia harvested from Pahang and Perak, Malaysia. The results showed that water extraction produced lower yield (0.1% w/w), but higher protein content (13-29 mg/g pellet) than precipitation methods. The higher protein content in water extraction method also produced higher number of protein spots (5-6), and better resolution of the polyacrylamide gel image. The mass peptide fragments revealed that mostly mitochondrial proteins were detected due to the plant cell lysis by the non-ionic detergent, Triton X-100. On the other hand, hydrophobic proteins with higher molecular size (46-51 kDa) were only found in the phenol-SDS and TCAacetone precipitation methods. The findings conclude that different extraction methods produced different kinds of plant proteins.

Proteomics has advanced and identified various plasma proteins that may be implicated in lesions in brains from neurodegenerative individuals. Apolipoprotein E and amyloid beta are amongst the many candidate proteins identified in common neurodegenerative disorders with effects by diet and nutriproteomics on the interactions of apo E and amyloid beta. The purpose of this review paper is to specify the role of proteins and lipoproteins and their effects on hepatic amyloid beta clearance that are important to brain amyloidosis. In recent and historical research provided in various research papers the blood brain barrier (BBB) is abnormal in neurodegenerative disease and proteins and oxidized lipids leak across the BBB. The improved scientific understanding of apo E/amyloid beta interactions identifies modulations in protein structure and lipid:protein interactions induced by nutrients and has become important to peripheral amyloid beta metabolism. Hepatic acute phase proteins induced by diet, inflammation and oxidative stress are connected to the pathophysiology of neurotoxic diseases. Oxidative stress induced by high cholesterol diets can cause electrostatic alterations in amyloid oligomers accompanied with alterations in oxidized lipids and acute phase proteins. Recent progress in proteomics with relevance to Alzheimer’s disease has led to the identification of acute phase proteins and include pentraxins that regulate or reduce amyloid beta sizes that are related to membrane permeability and disruption. In this review research papers identify acute phase biomarkers that are involved in the alterations of amyloid beta oligomers in obesity and diabetes with increased BBB permeability and central nervous system disorders.

Tanshinone IIA is the major active ingredient of Salviae miltiorrhizae extract, and has been widely used in China for the treatment of cardiovascular and cerebrovascular diseases. We have identified proteins modulated by Tanshinone IIA during the formation of macrophage-derived foam cells to uncover its anti-atherosclerotic mechanism. Low density lipoprotein (LDL) isolated from hyperlipidemia patients, designated as HP-LDL. HP-LDL (80 μg/mL for 24 h) can improve the total cholesterol and the proportion of cholesterol ester in the RAW264.7 macrophage and transform it into foam cell, which can be inhibited by Tanshinone IIA (20 μg/mL, 24 h). Two-dimensional electrophoresis and matrixassisted laser desorption ionization time-of-flight mass spectrometry were used to analysis and identify the proteins differentially expressed after Tanshinone IIA treatment of HP-LDL induced RAW264.7 macrophage transformation into foam cell. Fifteen proteins have been identified, which involved the different cellular functions, such as regulation of cytosolic calcium concentration, oxidative stress, inflammation, cell proliferation and differentiation, and lipid metabolism. This provides new insight into the anti-atherosclerotic mechanism of Tanshinone IIA.

Epigenetic mechanisms orchestrate inheritable concerted networks essential for chromatin remodeling. Molecular interplays include post-translational modifications to histones, DNA methylation, activity of small non coding RNAs, govern activation and silencing of gene expression and define the molecular basis of pluripotency, reprogramming, early human development and differentiation. The implications of epigenetic regulation in maintaining stem cell fate determination are well known. Thus: (i) embryonic stem cells (ESCs) seem to employ selected histone modification mechanisms for maintaining pluripotency and for the activation of multipotency programs; (ii) induced pluripotent stem cells, while recapitulating the overall features of the ESCs epigenome, express differences in DNA methylation; (iii) the lineage-restricted process of adult mesenchymal stem cell differentiation involves epigenetic regulation and consists of a unique pattern of DNA methylation and histone modifications; (iv) the epigenetic profiles of adult stem cells correlate with a more restricted differentiation potential as compared to ESCs. This review will discuss the role of epigenetic regulation in pluripotency, stemness and cell fate specification, taking advantage of recent discoveries showing that mass spectrometry and proteomics are become indispensable tools in epigenetic research.

The large collection of mutated genes in the cancer genome mapping onto a reduced set of signalling pathways highlights the paramount importance of signalling pathways in cancer therapeutics. Signalling proteins operate through a large and complex network associated with cell properties and ultimately reprogrammed in order to implement the known hallmark capabilities in cancer cells. Overall the underlying connection between signalling networks and the hallmarks of cancer may be considered as an organising principle that fixes the framework for understanding the remarkable diversity of this disease. There is a growing body of evidence suggesting that drug polypharmacology is the rule rather than the exception to overtake the limited success obtained in clinical treatment of cancer. Further the need for multi-target approaches, the combination between network pharmacology and polypharmacology is shifting the specific targeted drugs paradigm. In this novel systemic paradigm the dysregulated signalling networks themselves emerge as a class of targetable entities. Diverse cancer types and even a heterogeneous cellular population within a cancer type may exhibit heterogeneity in their signalling networks. We review these emerging trends in the field of computational and systems biology to achieve a more effective and safer control of cancer.

Background: Stigmatic and stylar proteins play a pivotal role in plant reproduction during pollination and fertilization. Methods: Total proteins from kiwifruit (Actinidia. Arguta L.) stigmatic and stylar have been extracted in our present study at two time points, before pollination and 10 h after pollination. Further, proteins were characterized and identified using fluorescence differential in-gel electrophoresis (DIGE), matrix-assisted laser-desorption / ionization Time of Fight / Time of Fight (MALDI-TOF / TOF), and bioinformatics technology. Meanwhile, the growth of kiwifruit pollen tubes in the style was observed under a fluorescence microscope. Ten hours after pollination, most pollen tubes reached the bottom of the kiwifruit style. Results: Twenty-four protein spots showed significantly differential expressions (ratio > 2.5) by using DeCyder 6.5 (Amersham Bioscience) analysis in our study. Of these 24 proteins, 18 proteins were specifically investigated through MALDI-TOF / TOF. Of these 18 proteins, eight protein candidates (spot No. 958, 1022, 1025, 968, 1088, 1058, 1087, and 1081) belong to the actinidin family, two of them (spot No. 911 and 907) belong to chitinase, and four protein spots belong to proline dehydrogenase (spot No. 1336), glutathione S-transferase (spot No. 1106), ATP synthase (spot No. 1100), and L-galactose-1-phosphate phosphatase (spot No. 977). The remaining four candidates (spot No. 895, 903, 1378, and 1345) are hypothetical proteins. Among these 18 significantly differentially expressed protein spots, six were up-regulated while 12 were down-regulated, when compared with stigmatic and stylar proteins before pollination. Conclusion: Most of the identified proteins may play an important role during kiwifruit pollination. But their putative functions during this stage remain to be further investigated.