scholarly journals Mapping In Vivo O-Glycoproteome Using Site-specific Extraction of O-linked glycopeptides (EXoO)

2018 ◽  
Author(s):  
Weiming Yang ◽  
Minghui Ao ◽  
Yingwei Hu ◽  
Qing Kay Li ◽  
Hui Zhang
Keyword(s):  
Large Scale ◽  
Human Kidney ◽  
Clinical Diagnostics ◽  
Protein Glycosylation ◽  
Major Type ◽  
Site Specific ◽  
Detailed Structural Analysis ◽  
Glycosylation Sites ◽  
Definition Of

AbstractProtein glycosylation is one of the most abundant post-translational modifications. However, detailed analysis ofin vivoO-linked glycosylation, a major type of protein glycosylation, has been severely impeded by the scarcity of suitable methodologies. Here, we present a chemoenzymatic method for the site-specificextractionofO-linked glycopeptides (EXoO), which enabled the unambiguous mapping of over 3,000 O-linked glycosylation sites and definition of their glycans on over 1,000 proteins in human kidney tissues, T cells and serum. This large-scale localization of O-linked glycosylation sites nearly doubles the number of previously identified sites, demonstrating that EXoO is the most effective method to-date for defining the site-specific O-linked glycoproteome in different types of sample. Detailed structural analysis of the sites identified revealed conserved motifs and topological orientations facing extracellular space, the cell surface, the lumen of the ER and the Golgi. EXoO was also able to reveal significant differences in thein vivoO-linked glycoproteome of tumor and normal kidney tissues pointing to its broader use in clinical diagnostics and therapeutics.

scholarly journals Capturing site-specific heterogeneity with large-scale N-glycoproteome analysis

2019 ◽  
Author(s):  
Nicholas M. Riley ◽  
Alexander S. Hebert ◽  
Michael S. Westphall ◽  
Joshua J. Coon
Keyword(s):  
Large Scale ◽  
Electron Transfer Dissociation ◽  
Protein Glycosylation ◽  
Analytical Challenge ◽  
Post Translational Modification ◽  
Structural Domains ◽  
Site Specific ◽  
Future Studies ◽  
Site Heterogeneity ◽  
Degree Of Heterogeneity

ABSTRACTProtein glycosylation is a highly important, yet a poorly understood protein post-translational modification. Thousands of possible glycan structures and compositions create potential for tremendous site heterogeneity and analytical challenge. A lack of suitable analytical methods for large-scale analyses of intact glycopeptides has ultimately limited our abilities to both address the degree of heterogeneity across the glycoproteome and to understand how it contributes biologically to complex systems. Here we show that N-glycoproteome site-specific microheterogeneity can be captured via large-scale glycopeptide profiling with methods enabled by activated ion electron transfer dissociation (AI-ETD), ultimately characterizing 1,545 N-glycosites (>5,600 unique N-glycopeptides) from mouse brain tissue. Moreover, we have used this large-scale glycoproteomic data to develop several new visualizations that will prove useful for analyzing intact glycopeptides in future studies. Our data reveal that N-glycosylation profiles can differ between subcellular regions and structural domains and that N-glycosite heterogeneity manifests in several different forms, including dramatic differences in glycosites on the same protein.

Complexity and Modularity of MAPK Signaling Networks

2013 ◽  
pp. 676-689
Author(s):  
George V. Popescu ◽  
Sorina C. Popescu
Keyword(s):  
Large Scale ◽  
Mapk Signaling ◽  
Mitogen Activated Protein Kinase ◽  
Signaling Networks ◽  
Mapk Cascades ◽  
Mitogen Activated Protein ◽  
Computational Modeling And Simulation ◽  
Definition Of

Signaling through mitogen-activated protein kinase (MAPK) cascades is a conserved and fundamental process in all eukaryotes. This chapter reviews recent progress made in the identification of components of MAPK signaling networks using novel large scale experimental methods. It also presents recent landmarks in the computational modeling and simulation of the dynamics of MAPK signaling modules. The in vitro MAPK signaling network reconstructed from predicted phosphorylation events is dense, supporting the hypothesis of a combinatorial control of transcription through selective phosphorylation of sets of transcription factors. Despite the fact that additional co-factors and scaffold proteins may regulate the dynamics of signal transduction in vivo, the complexity of MAPK signaling networks supports a new model that departs significantly from that of the classical definition of a MAPK cascade.

Complexity and Modularity of MAPK Signaling Networks

2011 ◽  
pp. 355-368 ◽  
Author(s):  
George V. Popescu ◽  
Sorina C. Popescu
Keyword(s):  
Large Scale ◽  
Mapk Signaling ◽  
Mitogen Activated Protein Kinase ◽  
Signaling Networks ◽  
Mapk Cascades ◽  
Mitogen Activated Protein ◽  
Computational Modeling And Simulation ◽  
Definition Of

Signaling through mitogen-activated protein kinase (MAPK) cascades is a conserved and fundamental process in all eukaryotes. This chapter reviews recent progress made in the identification of components of MAPK signaling networks using novel large scale experimental methods. It also presents recent landmarks in the computational modeling and simulation of the dynamics of MAPK signaling modules. The in vitro MAPK signaling network reconstructed from predicted phosphorylation events is dense, supporting the hypothesis of a combinatorial control of transcription through selective phosphorylation of sets of transcription factors. Despite the fact that additional co-factors and scaffold proteins may regulate the dynamics of signal transduction in vivo, the complexity of MAPK signaling networks supports a new model that departs significantly from that of the classical definition of a MAPK cascade.

Purification of the Antihemophilic Factor by Gel Filtration on Agarose

1969 ◽  
Vol 22 (03) ◽  
pp. 577-583 ◽  
Author(s):  
M.M.P Paulssen ◽  
A.C.M.G.B Wouterlood ◽  
H.L.M.A Scheffers
Keyword(s):  
Factor Viii ◽  
Plasma Proteins ◽  
Large Scale ◽  
Gel Filtration ◽  
Large Scale Preparation ◽  
Scale Preparation ◽  
Antihemophilic Factor

SummaryFactor VIII can be isolated from plasma proteins, including fibrinogen by chromatography on agarose. The best results were obtained with Sepharose 6B. Large scale preparation is also possible when cryoprecipitate is separated by chromatography. In most fractions containing factor VIII a turbidity is observed which may be due to the presence of chylomicrons.The purified factor VIII was active in vivo as well as in vitro.

The Effect of Active Site-inhibited Factor VIIa on Tissue Factor-initiated Coagulation Using Platelets before and after Aspirin Administration

1997 ◽  
Vol 78 (04) ◽  
pp. 1202-1208 ◽  
Author(s):  
Marianne Kjalke ◽  
Julie A Oliver ◽  
Dougald M Monroe ◽  
Maureane Hoffman ◽  
Mirella Ezban ◽  
...  
Keyword(s):  
Tissue Factor ◽  
Active Site ◽  
Large Scale ◽  
Thrombin Generation ◽  
Factor Viia ◽  
Dependent Manner ◽  
Antithrombotic Agent ◽  
Before And After ◽  
Ic50 Values

SummaryActive site-inactivated factor VIIa has potential as an antithrombotic agent. The effects of D-Phe-L-Phe-L-Arg-chloromethyl ketone-treated factor VIla (FFR-FVIIa) were evaluated in a cell-based system mimicking in vivo initiation of coagulation. FFR-FVIIa inhibited platelet activation (as measured by expression of P-selectin) and subsequent large-scale thrombin generation in a dose-dependent manner with IC50 values of 1.4 ± 0.8 nM (n = 8) and 0.9 ± 0.7 nM (n = 7), respectively. Kd for factor VIIa binding to monocytes ki for FFR-FVIIa competing with factor VIIa were similar (11.4 ± 0.8 pM and 10.6 ± 1.1 pM, respectively), showing that FFR-FVIIa binds to tissue factor in the tenase complex with the same affinity as factor VIIa. Using platelets from volunteers before and after ingestion of aspirin (1.3 g), there were no significant differences in the IC50 values of FFR-FVIIa [after aspirin ingestion, the IC50 values were 1.7 ± 0.9 nM (n = 8) for P-selectin expression, p = 0.37, and 1.4 ± 1.3 nM (n = 7) for thrombin generation, p = 0.38]. This shows that aspirin treatment of platelets does not influence the inhibition of tissue factor-initiated coagulation by FFR-FVIIa, probably because thrombin activation of platelets is not entirely dependent upon expression of thromboxane A2.

CONCEPT OF THE IMPROVEMENT OF A KEY PUBLIC SPACE (USING THE EXAMPLE OF «ALLEY OF ARCHITECTS», VORONEZH)

2020 ◽  
pp. 97-109
Author(s):  
С. Л. Подвальный ◽  
О. А. Сотникова ◽  
Я. А. Золотухина
Keyword(s):  
Urban Environment ◽  
Public Space ◽  
Large Scale ◽  
Economic Value ◽  
Ecological Condition ◽  
Territory Design ◽  
Definition Of ◽  
The City ◽  
Modern Technologies ◽  
Intensive Growth

Постановка задачи. В настоящее время формирование современной комфортной городской среды приобретает особое социально-экономическое значение и выдвигается в число приоритетных государственных масштабных программ. В связи с этим необходимо разработать концепцию благоустройства ключевого общественного пространства, а именно: определить основные и сопутствующие функции данной территории, создать эскизное предложение проекта благоустройства с учетом всех необходимых норм и стандартов, внедрить современные технологии. Результаты. Выполнен эскизный дизайн-проект «Аллеи архитекторов» по ул. Орджоникидзе г. Воронеж, включающий в себя основные элементы по зонированию территории, проектированию акцентных объектов и внедрению инновационных технологий «умного города», позволяющих повысить уровень комфорта горожан. Выводы. Благоустройство населенных мест приобретает особое значение в условиях дискомфорта среды. С выполнением комплекса мероприятий, направленных на благоустройство, и с внедрением современных технологий значительно улучшается экологическое состояние, внешний облик города. Оздоровление и модернизация среды, которая окружает человека в городе, благотворно влияет на психофизическое состояние, что особенно важно в период интенсивного роста городов. Statement of the problem. Currently the formation of the modern comfortable urban environment is gaining a special social and economic value and moving forward in the priorities of state large-scale programs. The purpose of development of the concept of improvement of public space is definition of the main and accompanying functions of this territory, design of the outline offer of the project of improvement considering all necessary norms and standards and implementation of modern technologies. Results. The conceptual project of “Alley of Architects” includes the basic elements of territory zoning, design of accent objects and implementation of technologies of a “smart-city”. These elements allow one to increase the level of comfort of inhabitants. Conclusions. Improvement of the inhabited places is of particular importance in the conditions of discomfort of the environment. Carrying out a complex of the actions directed to gardening and improvement, introducing modern technologies, the ecological condition, the physical appearance of the city considerably improves. Improvement and modernization of the environment which surrounds the person in the city influences a psychophysical state well that especially important during intensive growth of the cities.

Site Specific Incorporation of Amino Acid Analogues into Proteins In Vivo

2000 ◽  
Author(s):  
Anne K. Kowal ◽  
Caroline Kohrer ◽  
Uttam L. RajBhandary
Keyword(s):  
Amino Acid ◽  
Site Specific ◽  
Amino Acid Analogues

Bottlenecks in the Implementation of On-Site Wastewater Treatment Plants on a Large Scale in The Netherlands

1990 ◽  
Vol 22 (3-4) ◽  
pp. 291-298
Author(s):  
Frits A. Fastenau ◽  
Jaap H. J. M. van der Graaf ◽  
Gerard Martijnse
Keyword(s):  
Wastewater Treatment ◽  
The Netherlands ◽  
Large Scale ◽  
Wastewater Treatment Plants ◽  
Housing Stock ◽  
Research Work ◽  
Field Research ◽  
Domestic Wastewater ◽  
Research Programme ◽  
Definition Of

More than 95 % of the total housing stock in the Netherlands is connected to central sewerage systems and in most cases the wastewater is treated biologically. As connection to central sewerage systems has reached its economic limits, interest in on-site treatment of the domestic wastewater of the remaining premises is increasing. A large scale research programme into on-site wastewater treatment up to population equivalents of 200 persons has therefore been initiated by the Dutch Ministry of Housing, Physical Planning and Environment. Intensive field-research work did establish that the technological features of most on-site biological treatment systems were satisfactory. A large scale implementation of these systems is however obstructed in different extents by problems of an organisational, financial and/or juridical nature and management difficulties. At present research is carried out to identify these bottlenecks and to analyse possible solutions. Some preliminary results are given which involve the following ‘bottlenecks':-legislation: absence of co-ordination and absence of a definition of ‘surface water';-absence of subsidies;-ownership: divisions in task-setting of Municipalities and Waterboards; divisions involved with cost-sharing;-inspection; operational control and maintenance; organisation of management;-discharge permits;-pollution levy;-sludge disposal. Final decisions and practical elaboration of policies towards on-site treatment will have to be formulated in a broad discussion with all the authorities and interest groups involved.

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