Glycosylation Site Prediction

Our algorithm predicts short linear functional motifs in proteins using only sequence information. Statistical models for short linear functional motifs in proteins are built using the database of short sequence fragments taken from proteins in the current release of the Swiss-Prot database. Those segments are confirmed by experiments to have single-residue post-translational modification. The sensitivities of the classification for various types of short linear motifs are in the range of 70%. The query protein sequence is dissected into short overlapping fragments. All segments are represented as vectors. Each vector is then classified by a machine learning algorithm (Support Vector Machine) as potentially modifiable or not. The resulting list of plausible post-translational sites in the query protein is returned to the user. We also present a study of the human protein kinase C family as a biological application of our method.

The complexation of alkynes to form dicobalt hexacarbonyl derivatives facilitates the formation, under acid catalysis, of highly stabilized propargylic cations whose reaction with nucleophiles to form propargylic compounds, currently known as the Nicholas reaction, has found ample use in organic synthesis. This transformation has shown to be particularly useful when applied to carbohydrate derivatives. In this chapter, we provide a brief overview on this subject pioneered by early contributions from Isobe's research group. Thus, carbohydrate-derived dicobalt hexacarbonyl complexes have been used in the epimerization of C-alkynyl glycosides, pyranose ring-opening nucleophile trapping reactions, pyranose ring-opening ring-recyclization leading to medium-sized oxacycles, glycosylation strategies, C-glycosylation and pyranose to carbocycle transformations among others. Finally, contributions from our research group focusing on the synthetic applications of Ferrier-Nicholas cations are also presented.

Our algorithm predicts short linear functional motifs in proteins using only sequence information. Statistical models for short linear functional motifs in proteins are built using the database of short sequence fragments taken from proteins in the current release of the Swiss-Prot database. Those segments are confirmed by experiments to have single-residue post-translational modification. The sensitivities of the classification for various types of short linear motifs are in the range of 70%. The query protein sequence is dissected into short overlapping fragments. All segments are represented as vectors. Each vector is then classified by a machine learning algorithm (Support Vector Machine) as potentially modifiable or not. The resulting list of plausible post-translational sites in the query protein is returned to the user. We also present a study of the human protein kinase C family as a biological application of our method.

Histone H3 is amongst the most evolutionarily conserved proteins, and is located along with histone 2A, 2B and 4 in the core of the nucleosome. The N-terminal tails of the histone protrude the chromatin structure and become accessible to various enzymes for post translational modifications (PTMs). Phosphorylation of H3 has been found to have an impact on progression of the cell cycle, especially during mitosis. Another equally abundant PTM is the glycosylation at serine/threonine by O-GlcNAc (O-linked glycosylation) that occurs on the same or neighboring Ser or Thr residues, which also are accessible to kinases (Yin Yang sites). O-GlcNAc is added by O-GlcNAc transferase (OGT), and is found exclusively in the nucleus or cytoplasm of the cell. By using computational methods like Netphos 2.0 and Yinoyang 1.2 we found that OGT, Aurora B kinase and OGT, Death-associated protein (DAP)like kinase, work together in a Yin Yang way, and thereby control specific checkpoints during mitosis. Bioinformatics tool, thus, are very helpful to elucidate the function of the protein by predicting the PTMs in proteins.

The reaction of glycals containing good leaving groups with aromatic vinyl azides to give α- C-glycosyl amides in good yields is described. Various vinyl azides with different groups undergo the reaction smoothly. In these reactions, an iminodiazonium intermediate is generated by the attack of the vinyl azide onto the glycal under Lewis acid conditions. This undergoes Schmidt-type denitrogenative 1,2-migration to form a nitrilium ion, which, upon hydrolysis, gives the desired C-glycosyl amide.

Spectral analysis 3-16 Copies of 1 H, 13 C NMR and 2D spectras. 17-71 General information: 1 H and 13 C NMR spectra were recorded on 400 and 500 MHz spectrometers with TMS as the internal standard. Chemical shifts are expressed in parts per million (δ ppm). Silica gel coated aluminium plates were used for TLC. The products were

Large number of proteins in vivo perform multiple functions. The post-translational modifications induce conformational, more often transitory, changes in most of the cytoplasmic and nuclear proteins, which result in the regulation of diverse functions including signal transduction cascade. The O-β-GlcNAc modification on Ser/Thr has been described as dynamic as phosphorylation and interplay between the two modifications at the same or neighboring residue(s) can result in diverse functional regulation of proteins. Assessing temporary functional changes due to transitory protein structural changes in vivo is difficult. Computer assisted predictions of modification potential of proteins direct possible functional changes and help design experiments to verify these possible multiple functionality of proteins. In this study using computer-assisted techniques functional changes of epidermal growth factor receptor (EGFR) were investigated due to O-GlcNAc and phosphorylation modifications of EGFR-protein.

The reaction of glycals containing good leaving groups with aromatic vinyl azides to give α- C-glycosyl amides in good yields is described. Various vinyl azides with different groups undergo the reaction smoothly. In these reactions, an iminodiazonium intermediate is generated by the attack of the vinyl azide onto the glycal under Lewis acid conditions. This undergoes Schmidt-type denitrogenative 1,2-migration to form a nitrilium ion, which, upon hydrolysis, gives the desired C-glycosyl amide.

Histone H3 is amongst the most evolutionarily conserved proteins, and is located along with histone 2A, 2B and 4 in the core of the nucleosome. The N-terminal tails of the histone protrude the chromatin structure and become accessible to various enzymes for post translational modifications (PTMs). Phosphorylation of H3 has been found to have an impact on progression of the cell cycle, especially during mitosis. Another equally abundant PTM is the glycosylation at serine/threonine by O-GlcNAc (O-linked glycosylation) that occurs on the same or neighboring Ser or Thr residues, which also are accessible to kinases (Yin Yang sites). O-GlcNAc is added by O-GlcNAc transferase (OGT), and is found exclusively in the nucleus or cytoplasm of the cell. By using computational methods like Netphos 2.0 and Yinoyang 1.2 we found that OGT, Aurora B kinase and OGT, Death-associated protein (DAP)like kinase, work together in a Yin Yang way, and thereby control specific checkpoints during mitosis. Bioinformatics tool, thus, are very helpful to elucidate the function of the protein by predicting the PTMs in proteins.

DNA sequence, containing all genetic traits is not a functional entity. Instead, it is transferred to protein sequences by transcription and translation processes. This protein sequence takes on a 3D structure later, which is a functional unit and can manage biological interactions using the information encoded in DNA. Every life process one can figure is undertaken by proteins with specific functional responsibilities. Consequently protein function prediction is a momentous task in bioinformatics. Protein function can be elucidated from its structure. Protein secondary structure prediction has attracted great attention since it’s the input feature of many bioinformatics problems. The variety of proposed computational methods for protein secondary structure prediction is very extensive. Nevertheless they couldn’t achieve much due to the existing obstacles such as abstruse protein data patterns, noise, class imbalance and high dimensionality of encoding schemes of amino acid sequence...

Detailed knowledge of the three-dimensional (3D) structure of a protein is essential for the proper understanding of its function(s) that could be modified through posttranslational modifications (PTMs). Among these PTMs, alterations of serine/threonine residues of a protein through phosphorylation and O-glycosylation are extremely dynamic and could modulate the functions of a protein by affecting their 3D structure. Potential of a protein for certain PTMs could be evaluated through computer-based methods. Erythropoietin (EPO) is a multifunctional protein that primarily regulates red blood cell production and is also involved in other nonhematopoietic functions; for example, EPO also has cardioprotective and neuroprotective effects. In this study, multifunctional EPO behavior has been revealed based on transient modifications of its receptor. In this study, PTMs of erythropoietin receptor (EPO-R) were predicted using neural network tools, and the possible effects of these modifications are suggested. Phosphorylation and O-glycosylation at serine 380 and 444 of the cytoplasmic domain of EPO-R seem to have an antagonistic role in controlling signaling events induced by EPO. O-glycosylation at threonine 423 might hinder β-TrCP (a ubiquitin ligase) binding, which ubiquitinates at K 428, and ultimately results in the recycling of EPO-R, thus increasing EPO sensitivity. In contrast, the phosphorylated form of the same residue inhibits the recycling of EPO-R and thereby decreases the EPO sensitivity. Additionally, the interplay of O-glycosylation modification at serine 478 and phosphorylation at tyrosine 479 might help in controlling the duration of EPO-induced signaling.

HCV is a leading cause of hepatocellular carcinoma and cirrhosis all over the world. Claudins belong to family of tight junction's proteins that are responsible for establishing barriers for controlling the flow of molecules around cells. For therapeutic strategies, regulation of viral entry into the host cells holds a lot of promise. During HCV infection claudin-1 is highly expressed in liver and believed to be associated with HCV virus entry after HCV binding with or without co-receptor CD81. The claudin-1 assembly with tight junctions is regulated by post translational modifications. During claudins assembly and disassembly with tight junctions, phosphorylation is required at C-terminal tail. In cellular proteins, interplay between phosphorylation and O-β-GlcNAc modification is believed to be functional switch, but it is very difficult to monitor these functional and vibrant changes in vivo. Netphos 2.0 and Disphos 1.3 programs were used for potential phosphorylation; NetPhos...

Synapsin I (SynI) is the most abundant brain phosphoprotein present at presynaptic terminals that regulates neurotransmitter release, clustering of synaptic vesicles (SVs) at active zones, and stimulates synaptogenesis and neurite outgrowth.

Spectral analysis 3-16 Copies of 1 H, 13 C NMR and 2D spectras. 17-71 General information: 1 H and 13 C NMR spectra were recorded on 400 and 500 MHz spectrometers with TMS as the internal standard. Chemical shifts are expressed in parts per million (δ ppm). Silica gel coated aluminium plates were used for TLC. The products were

Abstract-Predicting implantation outcomes of invitro fertilization (IVF) embryos is critical for the success of the treatment. We have applied Naive Bayes classifier to an original IVF dataset in order to discriminate embryos according to implantation potentials. The dataset we analyzed represents an imbalanced distribution of positive and negative instances. In order to deal with the problem of imbalance, we examined the effects of over sampling the minority class, under sampling the majority class and adjustment of the decision threshold on the classification performance. We have used features of Receiver Operating Characteristics (ROC) curves in the evaluation of experiments. Our results revealed that it is possible to obtain optimum True Positive and False Positive Rates simply by adjusting the decision threshold. Under-sampling experiments show that we can achieve same prediction performance with less data as well as 736 embryo samples.

Detailed knowledge of the three-dimensional (3D) structure of a protein is essential for the proper understanding of its function(s) that could be modified through posttranslational modifications (PTMs). Among these PTMs, alterations of serine/threonine residues of a protein through phosphorylation and O-glycosylation are extremely dynamic and could modulate the functions of a protein by affecting their 3D structure. Potential of a protein for certain PTMs could be evaluated through computer-based methods. Erythropoietin (EPO) is a multifunctional protein that primarily regulates red blood cell production and is also involved in other nonhematopoietic functions; for example, EPO also has cardioprotective and neuroprotective effects. In this study, multifunctional EPO behavior has been revealed based on transient modifications of its receptor. In this study, PTMs of erythropoietin receptor (EPO-R) were predicted using neural network tools, and the possible effects of these modifications are suggested. Phosphorylation and O-glycosylation at serine 380 and 444 of the cytoplasmic domain of EPO-R seem to have an antagonistic role in controlling signaling events induced by EPO. O-glycosylation at threonine 423 might hinder β-TrCP (a ubiquitin ligase) binding, which ubiquitinates at K 428, and ultimately results in the recycling of EPO-R, thus increasing EPO sensitivity. In contrast, the phosphorylated form of the same residue inhibits the recycling of EPO-R and thereby decreases the EPO sensitivity. Additionally, the interplay of O-glycosylation modification at serine 478 and phosphorylation at tyrosine 479 might help in controlling the duration of EPO-induced signaling.

Detailed knowledge of the three-dimensional (3D) structure of a protein is essential for the proper understanding of its function(s) that could be modified through posttranslational modifications (PTMs). Among these PTMs, alterations of serine/threonine residues of a protein through phosphorylation and O-glycosylation are extremely dynamic and could modulate the functions of a protein by affecting their 3D structure. Potential of a protein for certain PTMs could be evaluated through computer-based methods. Erythropoietin (EPO) is a multifunctional protein that primarily regulates red blood cell production and is also involved in other nonhematopoietic functions; for example, EPO also has cardioprotective and neuroprotective effects. In this study, multifunctional EPO behavior has been revealed based on transient modifications of its receptor. In this study, PTMs of erythropoietin receptor (EPO-R) were predicted using neural network tools, and the possible effects of these modifications are suggested. Phosphorylation and O-glycosylation at serine 380 and 444 of the cytoplasmic domain of EPO-R seem to have an antagonistic role in controlling signaling events induced by EPO. O-glycosylation at threonine 423 might hinder β-TrCP (a ubiquitin ligase) binding, which ubiquitinates at K 428, and ultimately results in the recycling of EPO-R, thus increasing EPO sensitivity. In contrast, the phosphorylated form of the same residue inhibits the recycling of EPO-R and thereby decreases the EPO sensitivity. Additionally, the interplay of O-glycosylation modification at serine 478 and phosphorylation at tyrosine 479 might help in controlling the duration of EPO-induced signaling.

HCV is a leading cause of hepatocellular carcinoma and cirrhosis all over the world. Claudins belong to family of tight junction's proteins that are responsible for establishing barriers for controlling the flow of molecules around cells. For therapeutic strategies, regulation of viral entry into the host cells holds a lot of promise. During HCV infection claudin-1 is highly expressed in liver and believed to be associated with HCV virus entry after HCV binding with or without co-receptor CD81. The claudin-1 assembly with tight junctions is regulated by post translational modifications. During claudins assembly and disassembly with tight junctions, phosphorylation is required at C-terminal tail. In cellular proteins, interplay between phosphorylation and O-b-GlcNAc modification is believed to be functional switch, but it is very difficult to monitor these functional and vibrant changes in vivo. Netphos 2.0 and Disphos 1.3 programs were used for potential phosphorylation; NetPhosK 1.0 and KinasePhos for kinase prediction; and YinOYang 1.2 and OGPET to predict possible O-glycosylation sites. We also identified Yin Yang sites that may have potential for O-b-GlcNAc and phosphorylation interplay at same Ser/Thr residues. We for the first time proposed that alternate phosphorylation and O-b-GlcNAc modification on Ser 192, Ser 205, Ser 206; and Thr 191 may provide an on/off switch to regulate assembly of claudin-1 at tight junctions. In addition these phosphorylation sites may be targeted by novel chemotherapeutic agents to prevent phosphorylation lead by HCV viral entry complex.

HCV is a leading cause of hepatocellular carcinoma and cirrhosis all over the world. Claudins belong to family of tight junction's proteins that are responsible for establishing barriers for controlling the flow of molecules around cells. For therapeutic strategies, regulation of viral entry into the host cells holds a lot of promise. During HCV infection claudin-1 is highly expressed in liver and believed to be associated with HCV virus entry after HCV binding with or without co-receptor CD81. The claudin-1 assembly with tight junctions is regulated by post translational modifications. During claudins assembly and disassembly with tight junctions, phosphorylation is required at C-terminal tail. In cellular proteins, interplay between phosphorylation and O-b-GlcNAc modification is believed to be functional switch, but it is very difficult to monitor these functional and vibrant changes in vivo. Netphos 2.0 and Disphos 1.3 programs were used for potential phosphorylation; NetPhosK 1.0 and KinasePhos for kinase prediction; and YinOYang 1.2 and OGPET to predict possible O-glycosylation sites. We also identified Yin Yang sites that may have potential for O-b-GlcNAc and phosphorylation interplay at same Ser/Thr residues. We for the first time proposed that alternate phosphorylation and O-b-GlcNAc modification on Ser 192, Ser 205, Ser 206; and Thr 191 may provide an on/off switch to regulate assembly of claudin-1 at tight junctions. In addition these phosphorylation sites may be targeted by novel chemotherapeutic agents to prevent phosphorylation lead by HCV viral entry complex.

InCl 3 has been used for the first time as a mediator for the C-glycosylation of per- O -acetylglycals with allyltrimethylsilane, and the reactions proceeded to give products in good-to-excellent yield and in high diastereoselectivity. The 1,5-anti diastereoselectivity in the allylation of 3,4,6-tri- O -acetyl-1,5-anhydro-2-deoxy- d - arabino -hex-1-enitol and 3,4-di- O -acetyl-1,5-anhydro-2,6-dideoxy- l - arabino -hex-1-enitol and the 1,4-anti diastereoselectivity with 3,4-di- O -acetyl-1,5-anhydro-2-deoxy- d - erythro -pent-1-enitol are in the range 80–90%, whereas 3,4,6-tri- O -acetyl-1,5-anhydro-2-deoxy- d - lyxo -hex-1-enitol furnished exclusively the corresponding C -α- d -galactopyranosyl compound.

HCV is a leading cause of hepatocellular carcinoma and cirrhosis all over the world. Claudins belong to family of tight junction's proteins that are responsible for establishing barriers for controlling the flow of molecules around cells. For therapeutic strategies, regulation of viral entry into the host cells holds a lot of promise. During HCV infection claudin-1 is highly expressed in liver and believed to be associated with HCV virus entry after HCV binding with or without co-receptor CD81. The claudin-1 assembly with tight junctions is regulated by post translational modifications. During claudins assembly and disassembly with tight junctions, phosphorylation is required at C-terminal tail. In cellular proteins, interplay between phosphorylation and O-b-GlcNAc modification is believed to be functional switch, but it is very difficult to monitor these functional and vibrant changes in vivo. Netphos 2.0 and Disphos 1.3 programs were used for potential phosphorylation; NetPhosK 1.0 and KinasePhos for kinase prediction; and YinOYang 1.2 and OGPET to predict possible O-glycosylation sites. We also identified Yin Yang sites that may have potential for O-b-GlcNAc and phosphorylation interplay at same Ser/Thr residues. We for the first time proposed that alternate phosphorylation and O-b-GlcNAc modification on Ser 192, Ser 205, Ser 206; and Thr 191 may provide an on/off switch to regulate assembly of claudin-1 at tight junctions. In addition these phosphorylation sites may be targeted by novel chemotherapeutic agents to prevent phosphorylation lead by HCV viral entry complex.

HCV is a leading cause of hepatocellular carcinoma and cirrhosis all over the world. Claudins belong to family of tight junction's proteins that are responsible for establishing barriers for controlling the flow of molecules around cells. For therapeutic strategies, regulation of viral entry into the host cells holds a lot of promise. During HCV infection claudin-1 is highly expressed in liver and believed to be associated with HCV virus entry after HCV binding with or without co-receptor CD81. The claudin-1 assembly with tight junctions is regulated by post translational modifications. During claudins assembly and disassembly with tight junctions, phosphorylation is required at C-terminal tail. In cellular proteins, interplay between phosphorylation and O-b-GlcNAc modification is believed to be functional switch, but it is very difficult to monitor these functional and vibrant changes in vivo. Netphos 2.0 and Disphos 1.3 programs were used for potential phosphorylation; NetPhosK 1.0 and KinasePhos for kinase prediction; and YinOYang 1.2 and OGPET to predict possible O-glycosylation sites. We also identified Yin Yang sites that may have potential for O-b-GlcNAc and phosphorylation interplay at same Ser/Thr residues. We for the first time proposed that alternate phosphorylation and O-b-GlcNAc modification on Ser 192, Ser 205, Ser 206; and Thr 191 may provide an on/off switch to regulate assembly of claudin-1 at tight junctions. In addition these phosphorylation sites may be targeted by novel chemotherapeutic agents to prevent phosphorylation lead by HCV viral entry complex.

Bromination of glycals with tribromides formed in situ from bromine and different bromide salts in dichloromethane (DCM) or acetonitrile (AN) was found to give predominantly the products of anti addition of bromine from the C-6 side in high yields. The same selectivity, which was much higher compared to bromination with bromine alone, was achieved in bromination of these substrates by anodic generation of bromine from the same salts.

Reversible posttranslational modification (PTM) plays a very important role in biological process by changing properties of proteins. As many proteins are multiply modified by PTMs, cross talk of PTMs is becoming an intriguing topic and draws much attention. Currently, lots of evidences suggest that the PTMs work together to accomplish a specific biological function. However, both the general principles and underlying mechanism of PTM crosstalk are elusive. In this study, by using large-scale datasets we performed evolutionary conservation analysis, gene ontology enrichment, motif extraction of proteins with cross talk of O-GlcNAcylation and phosphorylation cooccurring on the same residue. We found that proteins with in situ O-GlcNAc/Phos cross talk were significantly enriched in some specific gene ontology terms and no obvious evolutionary pressure was observed. Moreover, 3 functional motifs associated with O-GlcNAc/Phos sites were extracted. We further used sequence features and GO features to predict O-GlcNAc/Phos cross talk sites based on phosphorylated sites and O-GlcNAcylated sites separately by the use of SVM model. The AUC of classifier based on phosphorylated sites is 0.896 and the other classifier based on GlcNAcylated sites is 0.843. Both classifiers achieved a relatively better performance compared with other existing methods.

Post-translational modifications provide the proteins with the possibility to perform functions in addition to those determined by their primary sequence. However, analysis of multifunctional protein structures in the environment of cells and body fluids is made especially difficult by the presence of other interacting proteins. Bioinformatics tools are therefore helpful to predict protein multifunctionality through the identification of serine and threonine residues wherein the hydroxyl group is likely to become modified by phosphorylation or glycosylation. Moreover, serines and threonines where both modifications are likely to occur can also be predicted (YinYang sites), to suggest further functional versatility. Structural modifications of hydroxyl groups of P-, E-, and L-selectins have been predicted and possible functions resulting from such modifications are proposed. Functional changes of the three selectins are based on the assumption that transitory and reversible protein modifications by phosphate and O-GlcNAc cause specific conformational changes and generate binding sites for other proteins. The computer-assisted prediction of glycosylation and phosphorylation sites in selectins should be helpful to assess the contribution of dynamic protein modifications in selectin-mediated inflammatory responses and cell-cell adhesion processes that are difficult to determine experimentally.

Bromination of glycals with tribromides formed in situ from bromine and different bromide salts in dichloromethane (DCM) or acetonitrile (AN) was found to give predominantly the products of anti addition of bromine from the C-6 side in high yields. The same selectivity, which was much higher compared to bromination with bromine alone, was achieved in bromination of these substrates by anodic generation of bromine from the same salts.

InCl 3 has been used for the first time as a mediator for the C-glycosylation of per-O-acetylglycals with allyltrimethylsilane, and the reactions proceeded to give products in good-to-excellent yield and in high diastereoselectivity. The 1,5-anti diastereoselectivity in the allylation of 3,4,6-triO -acetyl-1,5-anhydro-2-deoxy-D-arabino-hex-1-enitol and 3,4-di-O-acetyl-1,5-anhydro-2,6-dideoxy-L-arabino-hex-1-enitol and the 1,4-anti diastereoselectivity with 3,4-di-O-acetyl-1,5-anhydro-2-deoxy-D-erythro-pent-1-enitol are in the range 80-90%, whereas 3,4,6-triO -acetyl-1,5anhydro-2-deoxy-D-lyxo-hex-1-enitol furnished exclusively the corresponding C-aD -galactopyranosyl compound.

Large number of proteins in vivo perform multiple functions. The post-translational modifications induce conformational, more often transitory, changes in most of the cytoplasmic and nuclear proteins, which result in the regulation of diverse functions including signal transduction cascade. The O-β-GlcNAc modification on Ser/Thr has been described as dynamic as phosphorylation and interplay between the two modifications at the same or neighboring residue(s) can result in diverse functional regulation of proteins. Assessing temporary functional changes due to transitory protein structural changes in vivo is difficult. Computer assisted predictions of modification potential of proteins direct possible functional changes and help design experiments to verify these possible multiple functionality of proteins. In this study using computer-assisted techniques functional changes of epidermal growth factor receptor (EGFR) were investigated due to O-GlcNAc and phosphorylation modifications of EGFR-protein.

Post-translational modifications (PTMs) of proteins induce structural and functional changes that are most often transitory and difficult to follow and investigate in vivo. In silico prediction procedures for PTMs are very valuable to foresee and define such transitory changes responsible for the multifunctionality of proteins. Epidermal growth factor receptor (EGFR) is such a multifunctional transmembrane protein with intrinsic tyrosine kinase activity that is regulated primarily by ligand-stimulated transphosphorylation of dimerized receptors. In human EGFR, potential phosphorylation sites on Ser, Thr and Tyr residues including five autophosphorylation sites on Tyr were investigated using in silico procedures. In addition to phosphorylation, O-GlcNAc modifications and interplay between these two modifications was also predicted. The interplay of phosphorylation and O-GlcNAc modification on same or neighboring Ser/Thr residues is termed as Yin Yang hypothesis and the interplay sites are named as Yin Yang sites. Amongst these modification sites, one residue is localized in the juxtamembrane (Thr 654) and two are found in the catalytic domain (Ser 1046/1047) of the EGFR. We propose that, when EGFR is O-GlcNAc modified on Thr 654, EGFR may be transferred from early to late endosomes, whereas when EGFR is O-GlcNAc modified on Ser 1046/1047 desensitization of the receptor may be prevented. These findings suggest a complex interplay between phosphorylation and O-Glc-NAc modification resulting in modulation of EGFR's functionality.

Mapping and chemical characterization of post-translational modifications (PTMs) in proteins are critical to understand the regulatory mechanisms involving modified proteins and their role in disease. Neurofibromatosis type 1 (NF-1) is an autosomal dominantly inherited disorder, where NF1 mutations usually result in a reduced level of the tumor suppressor protein, neurofibromin (NF). NF is a multifunctional cytoplasmic protein that regulates microtubule dynamics and participates in several signaling pathways, particularly the RAS signaling pathway. NF is a Ras GTPase-activating protein (GAP) that prevents oncogenesis by converting GTP-Ras to GDP-Ras. This function of NF is regulated by phosphorylation. Interplay of phosphorylation with O-GlcNAc modification on the same or vicinal Ser/Thr residues, the Yin Yang sites, is well known in cytoplasmic and nuclear proteins. The dynamic aspects of PTMs and their interplay being difficult to follow in vivo, we undertook this in silico work to predict and define the possible role of Yin Yang sites in NF-1. Interplay of phosphorylation and O-GlcNAc modification is proposed as a mechanism controlling the Ras signaling pathway.

Reactions of 2,3,4,6-tetra-O-acetyl-ct-D-glucopyranosyl bromide (3) with chromium(II)L complexes (L = EDTA, NTA` IDA, GLY, MAL) in neutral (5 < pH < 7) aqueous DMF gave 3,4,6-triO -acetyl-l,5anhydro-2-deoxy-D-arabino-hex-l-elfitol (13) in 70-90% yields and >95% purity. Complexes of Cr(lI) with L = EDTA, NTA were similarly efficient with 2,3,4,6-tetra-O-acetyl-ct-D-glucopyranosyl chloride (2) in furnishing glucal 13, while with L = IDA, GLY, MAL hydrolysis of 2 could not be suppressed. Under the same conditions [Cra(EDTA)] 2" also efficiently gave the corresponding glycals 14-19 from 2,3,4,6-tetra-O-benzoyl-(4) and 2,3,4,6-tetra-O-pivaloyl-ct-D-glucopyranosyl bromide (5), per-O-acetylated ct-D-galactopyranosyl chloride (6) and bromide (7), Ot-D-mannopyranosyl chloride ($), ct-D-xylopyranosyl chloride (9), and bromide (10), 13-Darabinopyranosyl bromide (11), and ot-L-rhanmopyranosyl chloride (12).

ÐTitanocene(III) chloride and zirconcene(III) chloride are effective and mild reagents for radical generation in organic synthesis. In carbohydrate chemistry, these species are useful for the conversion of glycosyl halides to glycals, and for the stereospeci®c preparation of C-glycosides. In all cases, the 1-glycosyl radical is an active intermediate, generated by reaction of carbohydrate substrates with the organometallic.

Mapping and chemical characterization of post-translational modifications (PTMs) in proteins are critical to understand the regulatory mechanisms involving modified proteins and their role in disease. Neurofibromatosis type 1 (NF-1) is an autosomal dominantly inherited disorder, where NF1 mutations usually result in a reduced level of the tumor suppressor protein, neurofibromin (NF). NF is a multifunctional cytoplasmic protein that regulates microtubule dynamics and participates in several signaling pathways, particularly the RAS signaling pathway. NF is a Ras GTPase-activating protein (GAP) that prevents oncogenesis by converting GTP-Ras to GDP-Ras. This function of NF is regulated by phosphorylation. Interplay of phosphorylation with O-GlcNAc modification on the same or vicinal Ser/Thr residues, the Yin Yang sites, is well known in cytoplasmic and nuclear proteins. The dynamic aspects of PTMs and their interplay being difficult to follow in vivo, we undertook this in silico work to predict and define the possible role of Yin Yang sites in NF-1. Interplay of phosphorylation and O-GlcNAc modification is proposed as a mechanism controlling the Ras signaling pathway.

Post-translational modifications (PTMs) of proteins induce structural and functional changes that are most often transitory and difficult to follow and investigate in vivo. In silico prediction procedures for PTMs are very valuable to foresee and define such transitory changes responsible for the multifunctionality of proteins. Epidermal growth factor receptor (EGFR) is such a multifunctional transmembrane protein with intrinsic tyrosine kinase activity that is regulated primarily by ligand-stimulated transphosphorylation of dimerized receptors. In human EGFR, potential phosphorylation sites on Ser, Thr and Tyr residues including five autophosphorylation sites on Tyr were investigated using in silico procedures. In addition to phosphorylation, O-GlcNAc modifications and interplay between these two modifications was also predicted. The interplay of phosphorylation and O-GlcNAc modification on same or neighboring Ser/Thr residues is termed as Yin Yang hypothesis and the interplay sites are named as Yin Yang sites. Amongst these modification sites, one residue is localized in the juxtamembrane (Thr 654) and two are found in the catalytic domain (Ser 1046/1047) of the EGFR. We propose that, when EGFR is O-GlcNAc modified on Thr 654, EGFR may be transferred from early to late endosomes, whereas when EGFR is O-GlcNAc modified on Ser 1046/1047 desensitization of the receptor may be prevented. These findings suggest a complex interplay between phosphorylation and O-Glc-NAc modification resulting in modulation of EGFR's functionality.

Mapping and chemical characterization of post-translational modifications (PTMs) in proteins are critical to understand the regulatory mechanisms involving modified proteins and their role in disease. Neurofibromatosis type 1 (NF-1) is an autosomal dominantly inherited disorder, where NF1 mutations usually result in a reduced level of the tumor suppressor protein, neurofibromin (NF). NF is a multifunctional cytoplasmic protein that regulates microtubule dynamics and participates in several signaling pathways, particularly the RAS signaling pathway. NF is a Ras GTPase-activating protein (GAP) that prevents oncogenesis by converting GTP-Ras to GDP-Ras. This function of NF is regulated by phosphorylation. Interplay of phosphorylation with O-GlcNAc modification on the same or vicinal Ser/Thr residues, the Yin Yang sites, is well known in cytoplasmic and nuclear proteins. The dynamic aspects of PTMs and their interplay being difficult to follow in vivo, we undertook this in silico work to predict and define the possible role of Yin Yang sites in NF-1. Interplay of phosphorylation and O-GlcNAc modification is proposed as a mechanism controlling the Ras signaling pathway.

Post-translational modifications provide the proteins with the possibility to perform functions in addition to those determined by their primary sequence. However, analysis of multifunctional protein structures in the environment of cells and body fluids is made especially difficult by the presence of other interacting proteins. Bioinformatics tools are therefore helpful to predict protein multifunctionality through the identification of serine and threonine residues wherein the hydroxyl group is likely to become modified by phosphorylation or glycosylation. Moreover, serines and threonines where both modifications are likely to occur can also be predicted (YinYang sites), to suggest further functional versatility. Structural modifications of hydroxyl groups of P-, E-, and L-selectins have been predicted and possible functions resulting from such modifications are proposed. Functional changes of the three selectins are based on the assumption that transitory and reversible protein modifications by phosphate and O-GlcNAc cause specific conformational changes and generate binding sites for other proteins. The computer-assisted prediction of glycosylation and phosphorylation sites in selectins should be helpful to assess the contribution of dynamic protein modifications in selectin-mediated inflammatory responses and cell-cell adhesion processes that are difficult to determine experimentally.

Functional switches are often regulated by dynamic protein modifications. Assessing protein functions, in vivo, and their functional switches remains still a great challenge in this age of development. An alternative methodology based on in silico procedures may facilitate assessing the multifunctionality of proteins and, in addition, allow predicting functions of those proteins that exhibit their functionality through transitory modifications. Extensive research is ongoing to predict the sequence of protein modification sites and analyze their dynamic nature. This study reports the analysis performed on phosphorylation, Phospho.ELM (version 3.0) and glycosylation, OGlycBase (version 6.0) data for mining association patterns utilizing a newly developed algorithm, MAPRes. This method, MAPRes (Mining Association Patterns among preferred amino acid residues in the vicinity of amino acids targeted for post-translational modifications), is based on mining association among significantly preferred amino acids of neighboring sequence environment and modification sites themselves. Association patterns arrived at by association pattern/rule mining were in significant conformity with the results of different approaches. However, attempts to analyze substrate sequence environment of phosphorylation sites catalyzed for Tyr kinases and the sequence data for O-GlcNAc modification were not successful, due to the limited data available. Using the MAPRes algorithm for developing an association among PTM site with its vicinal amino acids is a valid method with many potential uses: this is indeed the first method ever to apply the association pattern mining technique to protein post-translational modification data.

Post-translational modifications (PTMs) of proteins induce structural and functional changes that are most often transitory and difficult to follow and investigate in vivo. In silico prediction procedures for PTMs are very valuable to foresee and define such transitory changes responsible for the multifunctionality of proteins. Epidermal growth factor receptor (EGFR) is such a multifunctional transmembrane protein with intrinsic tyrosine kinase activity that is regulated primarily by ligand-stimulated transphosphorylation of dimerized receptors. In human EGFR, potential phosphorylation sites on Ser, Thr and Tyr residues including five autophosphorylation sites on Tyr were investigated using in silico procedures. In addition to phosphorylation, O-GlcNAc modifications and interplay between these two modifications was also predicted. The interplay of phosphorylation and O-GlcNAc modification on same or neighboring Ser/Thr residues is termed as Yin Yang hypothesis and the interplay sites are named as Yin Yang sites. Amongst these modification sites, one residue is localized in the juxtamembrane (Thr 654) and two are found in the catalytic domain (Ser 1046/1047) of the EGFR. We propose that, when EGFR is O-GlcNAc modified on Thr 654, EGFR may be transferred from early to late endosomes, whereas when EGFR is O-GlcNAc modified on Ser 1046/1047 desensitization of the receptor may be prevented. These findings suggest a complex interplay between phosphorylation and O-Glc-NAc modification resulting in modulation of EGFR's functionality.

A highly efficient and mild glycosylation reaction between 3,4-O-carbonate glycal and N-tosyl functionalized aliphatic and aromatic amines via palladium-catalyzed decarboxylative allylation is disclosed. A wide range of highly functionalized 2,3-unsaturated β-N-glycosides are furnished in good to excellent yields and complete regioselectivity and stereoselectivity. In addition, applications of the glycosyl sulfonamides as the precursor to assemble functional derivatives have also been explored, including glycosylation, dihydroxylation, and nucleophilic addition to the N-glycosides.

Hepatitis C virus (HCV) is one of the leading causes of liver diseases. Several host factors that facilitate the attachment and entry of HCV have been discovered, of which human occludin seems to be the most promising. Studies have shown that activity of occludin is dependent upon its phosphorylation status, and that during HCV infection deregulation of phosphorylated occludin collectively leads to a reduction in tight junction (TJ) integrity of hepatocytes and favors HCV entry. However, detailed information of the posttranslational modifications (PTMs) of occludin still remains largely unknown. In addition to phosphorylation, serine/threonine residues of several proteins are also regulated by a unique type of modification known as O-β-glycosylation and this crosstalk serves as a functional switch. To identify the O-β-glycosylation potential and how interplay between phosphorylation and O-β-glycosylation can be exploited for the inhibition of HCV entry, here we report a computationa...

Impaired insulin signaling has been thought of as important step in both Alzheimer&#39;s disease (AD) and type 2 diabetes mellitus (T2DM). Posttranslational modifications (PTMs) regulate functions and interaction of insulin with insulin receptors substrates (IRSs) and activate insulin signaling downstream pathways via autophosphorylation on several tyrosine (TYR) residues on IRSs. Two important insulin receptor substrates 1 and 2 are widely expressed in human, and alternative phosphorylation on their serine (Ser) and threonine (Thr) residues has been known to block the Tyr phosphorylation of IRSs, thus inhibiting insulin signaling and promoting insulin resistance. Like phosphorylation, O-glycosylation modification is important PTM and inhibits phosphorylation on same or neighboring Ser/Thr residues, often called Yin Yang sites. Both IRS-1 and IRS-2 have been shown to be O-glycosylated; however exact sites are not determined yet. In this study, by using neuronal network based predict...

HCV is a leading cause of hepatocellular carcinoma and cirrhosis all over the world. Claudins belong to family of tight junction's proteins that are responsible for establishing barriers for controlling the flow of molecules around cells. For therapeutic strategies, regulation of viral entry into the host cells holds a lot of promise. During HCV infection claudin-1 is highly expressed in liver and believed to be associated with HCV virus entry after HCV binding with or without co-receptor CD81. The claudin-1 assembly with tight junctions is regulated by post translational modifications. During claudins assembly and disassembly with tight junctions, phosphorylation is required at C-terminal tail. In cellular proteins, interplay between phosphorylation and O-b-GlcNAc modification is believed to be functional switch, but it is very difficult to monitor these functional and vibrant changes in vivo. Netphos 2.0 and Disphos 1.3 programs were used for potential phosphorylation; NetPhosK 1.0 and KinasePhos for kinase prediction; and YinOYang 1.2 and OGPET to predict possible O-glycosylation sites. We also identified Yin Yang sites that may have potential for O-b-GlcNAc and phosphorylation interplay at same Ser/Thr residues. We for the first time proposed that alternate phosphorylation and O-b-GlcNAc modification on Ser 192, Ser 205, Ser 206; and Thr 191 may provide an on/off switch to regulate assembly of claudin-1 at tight junctions. In addition these phosphorylation sites may be targeted by novel chemotherapeutic agents to prevent phosphorylation lead by HCV viral entry complex.

A simple Pd(OAc) 2 catalyzed strategy for the synthesis of sugar-fused indolines from 2-N-oxalylamido-2-deoxy-C-aryl glycosides is reported by utilizing N-oxalylamido group as an auxiliary via C(sp 2)-H/NeH Activation. The reaction is successfully applied on glucose as well as galactose derived differently substituted 2-N-oxalylamido-2-deoxy-C-aryl glycosides to give sugar-fused indolines in moderate to good yields. The utility of this strategy in the synthesis of sugar-fused indoles is also described.

We have developed a new catalyst system comprising AuCl 3 6 and phenylacetylene that promotes the Ferrier rearrangement of glycals and 2-acetoxymethylglycals with different nucleophiles, and also the O-glycosylation of 1-O-acetyl sugars to obtain a variety of useful glycosides at room tem-

In this article, we focus on the synthesis of aryl C-glycosides via Heck coupling. It is organized based on the type of structures used in the assembly of the C-glycosides (also called C-nucleosides) with the following subsections: pyrimidine C-nucleosides, purine C-nucleosides, and monocyclic, bicyclic, and tetracyclic C-nucleosides. The reagents and conditions used for conducting the Heck coupling reactions are discussed. The subsequent conversion of the Heck products to the corresponding target molecules and the application of the target molecules are also described.