Structure Model Analysis of the Effects of Mutations in the Phosphorylation Sites of SARS-CoV-2 Encoded Nucleocapsid Protein

2020 ◽  
Vol 3 (1) ◽  
pp. 023-030
Author(s):  
Pierre Limtung ◽  
HY Lim Tung
Keyword(s):  
Binding Energy ◽  
Nucleocapsid Protein ◽  
Thermodynamic Calculation ◽  
Model Analysis ◽  
Structure Modeling ◽  
Phosphorylation Sites ◽  
Structure Model ◽  
Rich Domain ◽  
Recognition Sites ◽  
Stability Energy

Mutations in several phosphorylation sites within the phosphorylation rich domain of SARS-COV-2 Nucleocapsid protein (NCp), including serines 186, 197 and 202, and adjacent arginine 203 and glycine 204 have been described and have been proposed to prevent the binding and sequestration of NCp by Protein 14-3-3. Structure modeling and thermodynamic calculation show that mutations of phosphorylation sites, phospho-serines 186, 197 and 202 to phenylalanine, leucine and asparagine, and phosphorylation recognition sites, arginine/glycine 203/204 to lysine/arginine or lysine/threonine resulted in signifi cant destabilization of the NCp-14-3-3 complex by causing a decrease in Stability Energy (ΔGstability energy) and Binding Energy (ΔΔGbinding energy). These results evidenced that mutations in NCp underlie a mechanism to bypass sequestration by Protein 14-3-3 which would result in enhanced dimerization of NCp, and replication, transcription and packaging of the SARS-COV-2 genome

scholarly journals Structure Model Analysis Of Phosphorylation Dependent Binding And Sequestration Of SARS-COV-2 Encoded Nucleocapsid Protein By Protein 14-3-3

2020 ◽  
Author(s):  
Pierre Limtung ◽  
H.Y. Lim Tung
Keyword(s):  
Binding Energy ◽  
Nucleocapsid Protein ◽  
Energy Difference ◽  
Model Analysis ◽  
Cellular Mechanism ◽  
Structure Model ◽  
Calculated Binding Energy ◽  
Binding Energy Difference ◽  
The Stability ◽  
Stability Energy

AbstractPhosphorylation of serines 197 and 206 of SARS-COV-2 Nucleocapsid protein (NCp) enhanced the stability and binding efficiency and sequestration of NCp to Protein 14-3-3 by increasing the Stability Energy (ΔGstability energy) and Binding Energy (ΔΔGbinding energy) from ~545 Kcal/mol to ~616 Kcal/mol, and from 108 Kcal/mol to ~228 Kcal/mol respectively. The calculated Binding Energy Difference (ΔΔGbinding energy difference) between dephospho-NCp-14-3-3 complex and phospho-NCp-13-3-3 complex was ~72 Kcal/mol. Phosphorylations of serines 186, 197, 202 and 206, and threonines 198 and 205 NCp also caused an increase in the Stability Energy (ΔGstability energy) and Binding Energy (ΔΔGbinding energy) from ~545 Kcal/mol to ~617, 616, 583, 580, 574, 564 and 566 Kcal/mol and from ~108 Kcal/mol to ~228, 216, 184, 188, 184, 174 and 112 Kcal/mol respectively. Phosphorylation of NCp on serines 197 and 206 caused a decrease in Stability Energy and Binding Energy from ~698 Kcal/mol to 688 Kcal/mol, and from ~91 Kcal/mol to ~82 Kcal/mol for the dimerization of NCp. These results support the existence of a phosphorylation dependent cellular mechanism to bind and sequester NCp.

scholarly journals Systematic Matter and Binding-Energy Distributions from a Dispersive Optical Model Analysis

2020 ◽  
Vol 125 (10) ◽  
Author(s):  
C. D. Pruitt ◽  
R. J. Charity ◽  
L. G. Sobotka ◽  
M. C. Atkinson ◽  
W. H. Dickhoff
Keyword(s):  
Binding Energy ◽  
Optical Model ◽  
Model Analysis ◽  
Energy Distributions ◽  
Optical Model Analysis

scholarly journals Identification of mouse hepatitis coronavirus A59 nucleocapsid protein phosphorylation sites

2007 ◽  
Vol 126 (1-2) ◽  
pp. 139-148 ◽  
Author(s):  
Tiana C. White ◽  
Zhengping Yi ◽  
Brenda G. Hogue
Keyword(s):  
Protein Phosphorylation ◽  
Nucleocapsid Protein ◽  
Phosphorylation Sites

Identification of the rapamycin-sensitive phosphorylation sites within the Ser/Thr-rich domain of the yeast Npr1 protein kinase

2008 ◽  
Vol 22 (23) ◽  
pp. 3743-3753 ◽  
Author(s):  
Stefan Gander ◽  
Debora Bonenfant ◽  
Patrick Altermatt ◽  
Dietmar E. Martin ◽  
Simon Hauri ◽  
...  
Keyword(s):  
Protein Kinase ◽  
Phosphorylation Sites ◽  
Rich Domain

Methods of Fault Modeling by Well-to-Seismic Integration

2015 ◽  
Vol 733 ◽  
pp. 178-181
Author(s):  
Peng Yan Wang ◽  
Yao Hua Li ◽  
Ze Yu Li
Keyword(s):  
Seismic Data ◽  
Digital Simulation ◽  
Fault Modeling ◽  
Geological Structure ◽  
Fault Model ◽  
Structure Modeling ◽  
Structure Model ◽  
Important Work ◽  
Body Checking ◽  
Property Modeling

Geological structure model is the foundation of the sedimentary faces modeling, property modeling and digital simulation, which includes the horizon model and fault model. Fault model which is accorded with underground conditions plays an important role in the structure modeling, so it would be an important work to build the fault model perfectly with the seismic and logging data. This paper take the fault modeling of C84-6 well area in Chaoyanggou field as an example, building the fault model by four methods of ‘Projection of polygon’ ‘Correction of depth domain seismic body’ ‘Checking by overlooking’ ‘Correction of breakpoints’ by the software of Petrel. The fault model which is built by integrating logging and seismic data can be the skeleton to build the final geological structure model, and those methods mentioned in this paper has been applied to the modeling work in some adjacent areas at present.

Study on Topic Tree-Based Topic Structure Modeling

2014 ◽  
Vol 687-691 ◽  
pp. 1320-1323
Author(s):  
Yin Fei Huang ◽  
Qian Chen ◽  
Shu Han Yuan ◽  
Dong Dong Lv ◽  
Qi Zhang
Keyword(s):  
Probability Theory ◽  
Simulation Experiment ◽  
Structure Modeling ◽  
Structure Model ◽  
Time And Space ◽  
Kl Divergence ◽  
News Corpus ◽  
Topic Structure

The topic tree-based topic structure model is proposed using five-tuple and probability theory of ontology. Vocabularies in the glossary are presented with leaf nodes of the topic tree. The results of simulation experiment on real news corpus eventually show that the topic similarity of sym-KL divergence could construct a topic tree more accurately and dig the potential semantic topic characteristics of time and space more deeply in the text stream compared with other flat topic structure models.

Three Dimensional Fine Structure Modeling of Haqian1 Wellblock, in Northern Dzungaria Basin, China

2013 ◽  
Vol 734-737 ◽  
pp. 488-492
Author(s):  
Chen Qiang Dong ◽  
Fang Ding ◽  
Wei Wei Ren
Keyword(s):  
Three Dimensional ◽  
Fault Model ◽  
Structure Modeling ◽  
Good Prospect ◽  
Geological Model ◽  
Structure Model ◽  
Geological Modeling ◽  
Geological Exploration ◽  
3D Geological Modeling ◽  
Set Up

Haqian wellblock has a very good prospect in Dzungaria Basin, as it developed many faults and some formations are truncated, the development situation of it is very complicated, in this paper, we applied 3D geological modeling method which is one of the most important technology methods in describing the underground development situation, to illustrate the intricate structure. This geological model involved computer modeling and visualization of geological fault in 3D, the type of data of geological faults based on geological exploration is analyzed, after the fault model and horizon model are built, a whole structure model is finally set up.

Effects of Mo(Ni) on Valence Electron Structures of TiC/Fe Cermets

2008 ◽  
Vol 368-372 ◽  
pp. 1119-1122 ◽  
Author(s):  
Zheng Guang Zou ◽  
Yi Wu ◽  
Fei Long ◽  
Wen Wu Xu ◽  
Dong Ye Yao
Keyword(s):  
Binding Energy ◽  
Electron Density ◽  
Valence Electron ◽  
Electron Cloud ◽  
Metal Phase ◽  
Structure Model ◽  
Electron Theory ◽  
Ceramic Phase ◽  
Empirical Electron Theory

Based on the empirical electron theory (EET) of solids and molecules, the valence electron structures (VESs) of TiC-Mo(Ni)-Fe system were calculated by building proper structure model. The results indicate that additives of Mo and Ni improve the interface conjunction factors of the cermets in different ways. By adding Mo, the VESs of the ceramic phase are improved for the formation of the rim phase (Ti1-xMox)C, which leads to the enhancement of the interface conjunction, while the improvement of the VESs on metal phase by adding Ni is due to the formation of the Fe100-yNiy. Mo and Ni additives increase the interface electron density of cermets, that is, the adding of the Mo and Ni enhance the overlapping grade of the electron cloud on interface and increase the binding energy of the interface, which is propitious to the wettability. The best wettability was found at x=0.5 or y=30.

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