scholarly journals Mutations in the phosphorylation sites of SARS-CoV-2 encoded nucleocapsid protein and structure model of sequestration by protein 14-3-3

2020 ◽  
Vol 532 (1) ◽  
pp. 134-138 ◽  
Author(s):  
H.Y. Lim Tung ◽  
Pierre Limtung
Keyword(s):  
Nucleocapsid Protein ◽  
Phosphorylation Sites ◽  
Structure Model

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 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

scholarly journals Identification of phosphorylation sites in the nucleocapsid protein (N protein) of SARS-coronavirus

2007 ◽  
Vol 268 (2-3) ◽  
pp. 296-303 ◽  
Author(s):  
Liang Lin ◽  
Jianmin Shao ◽  
Maomao Sun ◽  
Jinxiu Liu ◽  
Gongjin Xu ◽  
...  
Keyword(s):  
Nucleocapsid Protein ◽  
Phosphorylation Sites ◽  
Sars Coronavirus ◽  
N Protein

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.

Fast calibration of CBED patterns for quantitative analysis

1993 ◽  
Vol 51 ◽  
pp. 674-675
Author(s):  
M.A. Gribelyuk ◽  
M. Rühle
Keyword(s):  
Reciprocal Lattice ◽  
Accurate Determination ◽  
Incident Beam ◽  
Crystal Thickness ◽  
Structure Model ◽  
Beam Direction ◽  
Transmitted Beam ◽  
Reciprocal Vector ◽  
On Line

A new method is suggested for the accurate determination of the incident beam direction K, crystal thickness t and the coordinates of the basic reciprocal lattice vectors V1 and V2 (Fig. 1) of the ZOLZ plans in pixels of the digitized 2-D CBED pattern. For a given structure model and some estimated values Vest and Kest of some point O in the CBED pattern a set of line scans AkBk is chosen so that all the scans are located within CBED disks.The points on line scans AkBk are conjugate to those on A0B0 since they are shifted by the reciprocal vector gk with respect to each other. As many conjugate scans are considered as CBED disks fall into the energy filtered region of the experimental pattern. Electron intensities of the transmitted beam I0 and diffracted beams Igk for all points on conjugate scans are found as a function of crystal thickness t on the basis of the full dynamical calculation.

Specificity determinants of phosphoprotein phosphatases controlling kinetochore functions

2020 ◽  
Vol 64 (2) ◽  
pp. 325-336 ◽  
Author(s):  
Dimitriya H. Garvanska ◽  
Jakob Nilsson
Keyword(s):  
Spindle Assembly Checkpoint ◽  
Activity Level ◽  
Phosphorylation Sites ◽  
Binding Affinities ◽  
Mitotic Kinases ◽  
Anaphase Onset ◽  
Phosphoprotein Phosphatases ◽  
Linear Motifs ◽  
Temporal And Spatial ◽  
Kinetochore Function

Abstract Kinetochores are instrumental for accurate chromosome segregation by binding to microtubules in order to move chromosomes and by delaying anaphase onset through the spindle assembly checkpoint (SAC). Dynamic phosphorylation of kinetochore components is key to control these activities and is tightly regulated by temporal and spatial recruitment of kinases and phosphoprotein phosphatases (PPPs). Here we focus on PP1, PP2A-B56 and PP2A-B55, three PPPs that are important regulators of mitosis. Despite the fact that these PPPs share a very similar active site, they target unique ser/thr phosphorylation sites to control kinetochore function. Specificity is in part achieved by PPPs binding to short linear motifs (SLiMs) that guide their substrate specificity. SLiMs bind to conserved pockets on PPPs and are degenerate in nature, giving rise to a range of binding affinities. These SLiMs control the assembly of numerous substrate specifying complexes and their position and binding strength allow PPPs to target specific phosphorylation sites. In addition, the activity of PPPs is regulated by mitotic kinases and inhibitors, either directly at the activity level or through affecting PPP–SLiM interactions. Here, we discuss recent progress in understanding the regulation of PPP specificity and activity and how this controls kinetochore biology.

Prediction of root damaging during mechanical shaking of fruit trees

2014 ◽  
Vol 10 (1) ◽  
pp. 1-15
Author(s):  
Z. Láng
Keyword(s):  
Field Experiments ◽  
Calculated Data ◽  
Fruit Trees ◽  
List Type ◽  
Structure Model ◽  
Root Damage ◽  
Set Up ◽  
Simple Tree ◽  
The Given ◽  
Cherry Trees

The possible effect of shaker harvest on root damage of 10-year-old cherry trees was studied on a simple tree structure model. The model was composed of elastic trunk and rigid main roots, the ends of which were connected to the surrounding soil via springs and dumping elements. Equations were set up to be able to calculate the relation between shaking height on the trunk and strain in the roots. To get the data for root break and their elongation at different shaking heights on the trunk, laboratory and field experiments were carried out on cherry trees and on their roots. Having evaluated the measured and calculated data it could be concluded that root damage is to be expected even at 3.6% strain and the risk of it increases with increased trunk amplitudes, i.e.with the decrease of shaking heightat smaller stem diameters (i.e. in younger plantation), andif the unbalanced mass of the shaker machine is too large for the given tree size.

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