Current Proteomics - Volume 5, Issue 2, 2008

Quantitative structure - activity relationships (QSAR) is a well established ligand-based approach to drug design. It correlates changes in the chemical structure of a series of compounds with changes in their biological activities. Peptides of equal length which bind to a certain protein are an excellent target for QSAR. In the present review, we summarize our experience in QSAR studies of peptides acting as T-cell epitopes. T-cell epitopes are protein fragments presented on the cell surface which afford the immune system the opportunity to detect and respond to both intracellular and extracellular pathogens. Epitope-based vaccines are a new generation of vaccines with lower side effects. The process of antigen presentation, which includes proteasome cleavage, TAP and MHC binding, has been modeled and analyzed by QSAR. Derived QSAR models are highly predictive, allowing us to design and test in vitro MHC superbinders. All models have been implemented in servers for in silico prediction of MHC binders and T-cell epitopes. In practice, better initial in silico prediction leads to improved subsequent experimental research on epitope-based vaccines.

In this review we describe the effects of methionine sulfoxide reductase A (MsrA) ablation in mouse tissues on the expression of various mRNAs and proteins, with an emphasis on brain tissues. Initially, the expression / activity levels of preselected proteins relevant to the methionine sulfoxide reductase system in various tissues are discussed (the list of proteins contains: thioredoxin, thioredoxin reductase, methionine sulfoxide reductase B, glucose-6-phosphate dehydrogenase, gluthathione peroxidase, selenoprotein P, and cysteine dioxygenase). Additionally, the consequences from lack of MsrA on protein oxidation (carbonylation and methionine oxidation) are evaluated. Finally, newly generated unpublished data is presented on genomic and proteomic analyses, compared between MsrA-/- and wild-type control brains. The gathered information is sorted out into three major protein groups that are linked to: 1) oxidative stress / apoptosis / degradation; 2) neuroregulation; and 3) signal transduction / transcription / elongation factors. In summary, the importance and relevance of MsrA in protecting against the development and progression of neurodegenerative diseases is reviewed.

Disease specific proteins are highly valuable as clinical biomarkers, which can be used in early diagnosis, monitoring disease progressions and evaluating therapies. The identification and characterization of protein biomarkers in different physiological and pathological sources of interest under diverse milieu represent a key area of clinical proteomics. However, owing to the inherent complexities and the large dynamic ranges of proteins, there are many practical issues and challenges in discovering the low-abundance, disease-specific biomarkers from heterogeneous tissues and biofluids. Thus, an integrated approach for selective protein pre-fractionation, purification and separation, is necessary to detect low-abundant biomarkers in proteomics research. This review will summarize recent advancements in clinical sample preparation for removing high abundant proteins, as well as the improved two-dimensional gel electrophoresis- and mass spectrometry-based technologies for resolving low-abundant proteins. We will also elaborate the proteomic strategies for targeting protein sub-populations with special interests, such as high molecular weight protein complexes, membrane or its associated proteins, and organelle specific proteins etc. We will emphasize the use of these strategies to interrogate the current proteomic researches in clinical biomarker discovery.

Antibody immobilization is of considerable interest for miscellaneous fields of interest, e.g. detecting biomarkers in cancer diagnostics, e.g. prostate specific antigen (PSA) for prostate cancer and pathogens like Escherichia coli, a foodborne pathogen. For this purpose, specific antibody captures are required and all of them should guarantee highest reproducibility and capacity possible. Especially in clinical applications very complex and specific immunoassays are needed. However, the complexity of pinning antibodies necessitates particular methods concerning the immobilization technique itself- because of their structure and specificity- and of course the analyzing methods. Glass, polymers, gold and even fullerene beads have been used as carriers, treated with various spacers and activation steps within the last few years. Furthermore, considerable attention is drawn to the regeneration of matrices and their capabilities for further antibody attachment. Commonly applied verification tools for the detection of the trapped antibodies include impedance spectroscopy (IS), atomic fluorescence microscopy (AFM), electrophoresis (EP), enzyme linked immunosorbent assays (ELISA), quartz crystal microbalance (QCM) and infrared spectroscopy (IR). Matrix assisted laser desorption/ionization-time-offlight mass spectrometry (MALDI-TOF/MS) is also a useful tool for proving the success of new antibody fixing procedures. Immobilization techniques have been improved concerning their reproducibility, binding capacity and high specificity. In this review, recent developments of antibody (Ab) immobilization are summarized, the individual applications are mentioned, advantages and disadvantages are discussed in detail.

Among eukaryotic organisms a vast majority of Box H/ACA ribonucleoproteins (RNPs) are responsible for the post-transcriptional introduction of pseudouridine (Ψ) into ribosomal RNAs (rRNA) and spliceosomal small nuclear RNAs (snRNA), thus influencing protein translation and pre-mRNA splicing, respectively. Additionally, a few distinct Box H/ACA RNPs are involved in the processing of rRNA, and the stabilization of vertebrate telomerase RNA. Thus, whether directly or indirectly, Box H/ACA RNPs impact major steps of gene expression, as well as play a role in maintaining genome integrity. Box H/ACA RNPs each consist of a unique Box H/ACA RNA and a set of four common core proteins. While the RNA component is responsible for dictating site-specificity, the four core proteins impact numerous aspects of RNP function including both stability and catalytic potential. Interestingly, mutations have been identified in the core proteins of the Box H/ACA RNP, resulting in a rare inherited bone marrow failure syndrome referred to as dyskeratosis congenita. This review discusses our current understanding of the roles of the protein components of the Box H/ACA RNP, and provides a framework to understand how mutations in the Box H/ACA RNP contribute to disease pathology.

Research on the effects of exposure of micro-organisms to high hydrostatic pressure (HHP) has grown in the last decade. The main foci have been to understand adaptation to life in the deep ocean and the HHP stress response. Amongst other effects, HHP interferes with the cellular membrane structure, increasing the order of lipid molecules especially in the vicinity of proteins, leading to decreased membrane fluidity. Protein structure may also be affected by pressure, disturbing polymerization, folding and the activity. HHP also inhibits protein synthesis, one of the most piezosensitive cellular functions. Ribosome disassembly contributes to this inhibition. RNA synthesis is maintained at pressures at which DNA and protein synthesis are completely inhibited. A number of these responses overlap with responses to other forms of stress, particularly cold stress. Microarray analysis of micro-organisms has identified numerous genes upregulated after exposure to high pressure. However, many of these genes code for proteins of unknown function. Corresponding proteomic analyses detect very few proteins synthesized as a result of such exposure. The review high lights the need for future research to understand the complex pathways involved in the response to HHP.