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Biomolecules, Volume 3, Issue 2 (June 2013), Pages 270-350

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Research

Jump to: Review

Open AccessArticle Overcoming Challenges and Opening New Opportunities in Glycoproteomics
Biomolecules 2013, 3(2), 270-286; doi:10.3390/biom3020270
Received: 20 February 2013 / Revised: 14 March 2013 / Accepted: 15 March 2013 / Published: 26 March 2013
Cited by 3 | PDF Full-text (1972 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Glycoproteomics has emerged as a prime area of interest within the field of proteomics because glycoproteins have been shown to function as biomarkers for disease and as promising therapeutic targets. A significant challenge in the study of glycoproteins is the fact that [...] Read more.
Glycoproteomics has emerged as a prime area of interest within the field of proteomics because glycoproteins have been shown to function as biomarkers for disease and as promising therapeutic targets. A significant challenge in the study of glycoproteins is the fact that they are expressed in relatively low abundance in cells. In response, various enrichment methods have been developed to improve the detection of glycoproteins. One such method involves their capture via oxidation of their glycan chains and covalent attachment with hydrazide resins which, when catalyzed by PNGase F, release N-linked glycans and convert the glycosite Asn to Asp; this conversion is identifiable with LC/ESI-MS/MS as a corresponding increase of 0.984 Da in molecular weight. The present study builds on this body of work, providing evidence of three additional strategies that improve glycoprotein identification: (1) use of a high resolution mass spectrometer—the Q Exactive MS—which delivers 2–3 times more glycoprotein identifications than a low resolution MS; (2) optimization of instrument settings and database search parameters to reduce misidentification of N-linked glycopeptides to ~1 percent; and (3) labeling glycopeptides with 18O during PNGase F treatment to locate N-linked glycosites within peptides containing multiple N-linked sequons. Full article
(This article belongs to the Special Issue Challenges in Glycan, Glycoprotein and Proteoglycan Research)
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Open AccessArticle The Roles of Sphingosine Kinase 1 and 2 in Regulating the Metabolome and Survival of Prostate Cancer Cells
Biomolecules 2013, 3(2), 316-333; doi:10.3390/biom3020316
Received: 9 May 2013 / Revised: 3 June 2013 / Accepted: 4 June 2013 / Published: 10 June 2013
Cited by 4 | PDF Full-text (343 KB) | HTML Full-text | XML Full-text
Abstract
We have previously shown that treatment of androgen-sensitive LNCaP cells with the sphingosine kinase (SK) inhibitor SKi (2-(p-hydroxyanilino)-4-(p-chlorophenyl)thiazole) induces the proteasomal degradation of two N-terminal variants of SK1 (SK1a and SK1b), increases C22:0-ceramide and diadenosine 5′,5′′′-P1 [...] Read more.
We have previously shown that treatment of androgen-sensitive LNCaP cells with the sphingosine kinase (SK) inhibitor SKi (2-(p-hydroxyanilino)-4-(p-chlorophenyl)thiazole) induces the proteasomal degradation of two N-terminal variants of SK1 (SK1a and SK1b), increases C22:0-ceramide and diadenosine 5′,5′′′-P1,P3-triphosphate (Ap3A) and reduces S1P levels, and promotes apoptosis. We have now investigated the effects of three SK inhibitors (SKi, (S)-FTY720 vinylphosphonate, and (R)-FTY720 methyl ether) on metabolite and sphingolipid levels in androgen-sensitive LNCaP and androgen-independent LNCaP-AI prostate cancer cells. The 51 kDa N-terminal variant of SK1 (SK1b) evades the proteasome in LNCaP-AI cells, and these cells do not exhibit an increase in C22:0-ceramide or Ap3A levels and do not undergo apoptosis in response to SKi. In contrast, the SK inhibitor (S)-FTY720 vinylphosphonate induces degradation of SK1b in LNCaP-AI, but not in LNCaP cells. In LNCaP-AI cells, (S)-FTY720 vinylphosphonate induces a small increase in C16:0-ceramide levels and cleavage of polyADPribose polymerase (indicative of apoptosis). Surprisingly, the level of S1P is increased by 7.8- and 12.8-fold in LNCaP and LNCaP-AI cells, respectively, on treatment with (S)-FTY720 vinylphosphonate. Finally, treatment of androgen-sensitive LNCaP cells with the SK2-selective inhibitor (R)-FTY720 methyl ether increases lysophosphatidylinositol levels, suggesting that SK2 may regulate lyso-PI metabolism in prostate cancer cells. Full article
(This article belongs to the Special Issue Sphingolipids and Bioactive Lipids)
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Review

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Open AccessReview Single Nucleotide Polymorphisms Associated with MicroRNA Regulation
Biomolecules 2013, 3(2), 287-302; doi:10.3390/biom3020287
Received: 2 March 2013 / Revised: 22 March 2013 / Accepted: 27 March 2013 / Published: 9 April 2013
Cited by 11 | PDF Full-text (235 KB) | HTML Full-text | XML Full-text
Abstract
Since the discovery of microRNA (miRNA), the polymorphisms that affect miRNA regulation had been extensively investigated by many independent studies. Recently, researchers utilized bioinformatics and statistical approaches for genome-wide analysis on the human polymorphisms that reside in the miRNA genes, targets, and/or [...] Read more.
Since the discovery of microRNA (miRNA), the polymorphisms that affect miRNA regulation had been extensively investigated by many independent studies. Recently, researchers utilized bioinformatics and statistical approaches for genome-wide analysis on the human polymorphisms that reside in the miRNA genes, targets, and/or genes involved in miRNA processing. In this review, we will give an overview about the important findings of these studies from three perspectives: architecture of the polymorphisms within miRNAs or their targets, potential functional consequences of the polymorphisms on miRNA processing or targeting, and the associations of the polymorphisms with miRNA or target gene expression. The results of the previous studies demonstrated the signatures of natural selections on the miRNA genes and their targets, and proposed a collection of potentially functional, expression-associated, and/or positively selected polymorphisms that are promising for further investigations. In the meantime, a few useful resources about the polymorphic miRNA regulation have been developed and the different features of these databases were discussed in this review. Though recent research had benefited from these comprehensive studies and resources, there were still gaps in our knowledge about the polymorphisms involved in miRNA regulation, and future investigations were expected to address these questions. Full article
(This article belongs to the Special Issue Non-coding RNA)
Open AccessReview Sphingosine 1-Phosphate and Cancer: Lessons from Thyroid Cancer Cells
Biomolecules 2013, 3(2), 303-315; doi:10.3390/biom3020303
Received: 19 April 2013 / Revised: 3 May 2013 / Accepted: 6 May 2013 / Published: 14 May 2013
Cited by 3 | PDF Full-text (385 KB) | HTML Full-text | XML Full-text
Abstract
Sphingomyelin is found in the cell membrane of all eukaryotic cells, and was for a long time considered merely as a structural component. However, during the last two decades, metabolites of sphingomyelin, especially sphingosine 1-phosphate (S1P), have proven to be physiologically significant [...] Read more.
Sphingomyelin is found in the cell membrane of all eukaryotic cells, and was for a long time considered merely as a structural component. However, during the last two decades, metabolites of sphingomyelin, especially sphingosine 1-phosphate (S1P), have proven to be physiologically significant regulators of cell function. Through its five different G protein-coupled receptors, S1P regulates a wide array of cellular processes, ranging from stimulating cellular proliferation and migration, to the inhibition of apoptosis and induction of angiogenesis and modulation of cellular calcium homeostasis. Many of the processes regulated by S1P are important for normal cell physiology, but may also induce severe pathological conditions, especially in malignancies like cancer. Thus, understanding S1P signaling mechanisms has been the aim of a multitude of investigations. Great interest has also been shown in understanding the action of sphingosine kinase (SphK), i.e., the kinase phosphorylating sphingosine to S1P, and the interactions between S1P and growth factor signaling. In the present review, we will discuss recent findings regarding the possible importance of S1P and SphK in the etiology of thyroid cancer. Although clinical data is still scarce, our in vitro findings suggest that S1P may function as a “double-edged sword”, as the receptor profile of thyroid cancer cells largely determines whether S1P stimulates or blocks cellular migration. We will also discuss the interactions between S1P- and VEGF-evoked signaling, and the importance of a S1P1-VEGF receptor 2 complex in thyroid cancer cells. Full article
(This article belongs to the Special Issue Sphingolipids and Bioactive Lipids)
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Open AccessReview Angling for Uniqueness in Enzymatic Preparation of Glycosides
Biomolecules 2013, 3(2), 334-350; doi:10.3390/biom3020334
Received: 4 May 2013 / Revised: 23 May 2013 / Accepted: 3 June 2013 / Published: 13 June 2013
Cited by 4 | PDF Full-text (348 KB) | HTML Full-text | XML Full-text
Abstract
In the early days of biocatalysis, limitations of an enzyme modeled the enzymatic applications; nowadays the enzyme can be engineered to be suitable for the process requirements. This is a general bird’s-eye view and as such cannot be specific for articulated situations [...] Read more.
In the early days of biocatalysis, limitations of an enzyme modeled the enzymatic applications; nowadays the enzyme can be engineered to be suitable for the process requirements. This is a general bird’s-eye view and as such cannot be specific for articulated situations found in different classes of enzymes or for selected enzymatic processes. As far as the enzymatic preparation of glycosides is concerned, recent scientific literature is awash with examples of uniqueness related to the features of the biocatalyst (yield, substrate specificity, regioselectivity, and resistance to a particular reaction condition). The invention of glycosynthases is just one of the aspects that has thrust forward the research in this field. Protein engineering, metagenomics and reaction engineering have led to the discovery of an expanding number of novel enzymes and to the setting up of new bio-based processes for the preparation of glycosides. In this review, new examples from the last decade are compiled with attention both to cases in which naturally present, as well as genetically inserted, characteristics of the catalysts make them attractive for biocatalysis. Full article
(This article belongs to the Special Issue Enzymes and Their Biotechnological Applications) Print Edition available
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