Deciphering complex dynamics of water counteraction around secondary structural elements of allosteric protein complex: Case study of SAP-SLAM system in signal transduction cascade

2018 ◽  
Vol 148 (4) ◽  
pp. 045102
Author(s):  
Sudipta Samanta ◽  
Sanchita Mukherjee
Keyword(s):  
Signal Transduction ◽  
Protein Complex ◽  
Complex Dynamics ◽  
Complex Case ◽  
Structural Elements ◽  
Signal Transduction Cascade ◽  
Secondary Structural Elements ◽  
Allosteric Protein

PROTEIN STRUCTURE PREDICTION USING GAS PHASE MOLECULAR DYNAMICS SIMULATION: EOTAXIN-3 CYTOKINE AS A CASE STUDY

2012 ◽  
Vol 09 ◽  
pp. 193-198 ◽  
Author(s):  
NURUL BAHIYAH AHMAD KHAIRUDIN ◽  
HABIBAH A WAHAB
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Hydrogen Bonds ◽  
Gas Phase ◽  
Structure Prediction ◽  
Dominant Role ◽  
Dynamics Simulation ◽  
Structural Elements ◽  
Secondary Structural Elements

In the current work, the structure of the enzyme CC chemokine eotaxin-3 (1G2S) was chosen as a case study to investigate the effects of gas phase on the predicted protein conformation using molecular dynamics simulation. Generally, simulating proteins in the gas phase tend to suffer from various drawbacks, among which excessive numbers of protein-protein hydrogen bonds. However, current results showed that the effects of gas phase simulation on 1G2S did not amplify the protein-protein hydrogen bonds. It was also found that some of the hydrogen bonds which were crucial in maintaining the secondary structural elements were disrupted. The predicted models showed high values of RMSD, 11.5 Å and 13.5 Å for both vacuum and explicit solvent simulations, respectively, indicating that the conformers were very much different from the native conformation. Even though the RMSD value for the in vacuo model was slightly lower, it somehow suffered from lower fraction of native contacts, poor hydrogen bonding networks and fewer occurrences of secondary structural elements compared to the solvated model. This finding supports the notion that water plays a dominant role in guiding the protein to fold along the correct path.

scholarly journals Parametric Analysis of the Shear Lag Effect in Tube Structural Systems of Tall Buildings

2020 ◽  
Vol 11 (1) ◽  
pp. 278
Author(s):  
Ivan Hafner ◽  
Anđelko Vlašić ◽  
Tomislav Kišiček ◽  
Tvrtko Renić
Keyword(s):  
Parametric Analysis ◽  
Numerical Models ◽  
Tall Buildings ◽  
Structural Systems ◽  
Structural Elements ◽  
Structural System ◽  
Shear Lag ◽  
Shear Lag Effect ◽  
Lag Effect ◽  
Secondary Structural Elements

Horizontal loads such as earthquake and wind are considered dominant loads for the design of tall buildings. One of the most efficient structural systems in this regard is the tube structural system. Even though such systems have a high resistance when it comes to horizontal loads, the shear lag effect that is characterized by an incomplete and uneven activation of vertical elements may cause a series of problems such as the deformation of internal panels and secondary structural elements, which cumulatively grow with the height of the building. In this paper, the shear lag effect in a typical tube structure will be observed and analyzed on a series of different numerical models. A parametric analysis will be conducted with a great number of variations in the structural elements and building layout, for the purpose of giving recommendations for an optimal design of a tube structural system.

scholarly journals Effect of blast loading and resulting progressive failure of a cable-stayed bridge

2021 ◽  
Vol 3 (3) ◽  
Author(s):  
Ravi Mudragada ◽  
S. S. Mishra
Keyword(s):  
Progressive Failure ◽  
Blast Resistance ◽  
Progressive Collapse ◽  
Building Structures ◽  
Structural Elements ◽  
Blast Loads ◽  
Cable Stayed Bridge ◽  
Bridge Performance ◽  
Cable Stayed Bridges

AbstractMany researchers have carried out experimental and numerical investigations to examine building structures’ response to explosive loads. Studies of bridges subjected to blast loads are limited. Hence, in this study, we present a case study on a cable-stayed bridge, namely, Charles River Cable-Stayed Bridge-Boston, to assess its robustness and resistance against the progressive collapse resulting from localized failure due to blast loads. Three different blast scenarios are considered to interpret the bridge performance to blast loads. To monitor the progressive failure mechanisms of the structural elements due to blast, pre-defined plastic hinges are assigned to the bridge deck. The results conclude that the bridge is too weak to sustain the blast loads near the tower location, and the progressive collapse is inevitable. Hence, to preserve this cable-stayed bridge from local and global failure, structural components should be more reinforced near the tower location. This case study helps the designer better understand the need for blast resistance design of cable-stayed bridges.

scholarly journals Stability charts based on the finite element method for underground cavities in soft carbonate rocks: validation through case-study applications

2019 ◽  
Vol 19 (10) ◽  
pp. 2079-2095 ◽  
Author(s):  
Michele Perrotti ◽  
Piernicola Lollino ◽  
Nunzio Luciano Fazio ◽  
Mario Parise
Keyword(s):  
Finite Element ◽  
Safety Margin ◽  
Structural Elements ◽  
The Finite Element Method ◽  
Geometrical Features ◽  
Overall Stability ◽  
Underground Cavities ◽  
The Stability ◽  
Rock Mechanical Properties

Abstract. The stability of man-made underground cavities in soft rocks interacting with overlying structures and infrastructures represents a challenging problem to be faced. Based upon the results of a large number of parametric two-dimensional (2-D) finite-element analyses of ideal cases of underground cavities, accounting for the variability both cave geometrical features and rock mechanical properties, specific charts have been recently proposed in the literature to assess at a preliminary stage the stability of the cavities. The purpose of the present paper is to validate the efficacy of the stability charts through the application to several case studies of underground cavities, considering both quarries collapsed in the past and quarries still stable. The stability graphs proposed by Perrotti et al. (2018) can be useful to evaluate, in a preliminary way, a safety margin for cavities that have not reached failure and to detect indications of predisposition to local or general instability phenomena. Alternatively, for sinkholes that already occurred, the graphs may be useful in identifying the conditions that led to the collapse, highlighting the importance of some structural elements (as pillars and internal walls) on the overall stability of the quarry system.

In Silico Genetic Robustness Analysis of Secondary Structural Elements in the miRNA Gene

2008 ◽  
Vol 67 (5) ◽  
pp. 560-569 ◽  
Author(s):  
Wenjie Shu ◽  
Ming Ni ◽  
Xiaochen Bo ◽  
Zhiqiang Zheng ◽  
Shengqi Wang
Keyword(s):  
In Silico ◽  
Mirna Gene ◽  
Robustness Analysis ◽  
Structural Elements ◽  
Genetic Robustness ◽  
Secondary Structural Elements

RNA viruses and the mitogenic Raf/MEK/ERK signal transduction cascade

2008 ◽  
Vol 389 (10) ◽  
Author(s):  
Stephan Pleschka
Keyword(s):  
Signal Transduction ◽  
Rna Viruses ◽  
Rna Virus ◽  
Cell Metabolism ◽  
Mitogen Activated Protein Kinase ◽  
Erk Signaling ◽  
Control Center ◽  
Signal Transduction Cascade ◽  
Host Interaction ◽  
Differentiation And Proliferation

AbstractThe Raf/MEK/ERK signal transduction cascade belongs to the mitogen-activated protein kinase (MAPK) cascades. Raf/MEK/ERK signaling leads to stimulus-specific changes in gene expression, alterations in cell metabolism or induction of programmed cell death (apoptosis), and thus controls cell differentiation and proliferation. It is induced by extracellular agents, including pathogens such as RNA viruses. Many DNA viruses are known to induce cellular signaling via this pathway. As these pathogens partly use the DNA synthesis machinery for their replication, they aim to drive cells into a proliferative state. In contrast, the consequences of RNA virus-induced Raf/MEK/ERK signaling were less clear for a long time, but since the turn of the century the number of publications on this topic has rapidly increased. Research on this virus/host-interaction will broaden our understanding of its relevance in viral replication. This important control center of cellular responses is differently employed to support the replication of several important human pathogenic RNA viruses including influenza, Ebola, hepatitis C and SARS corona viruses.

Wounded Because of Religion: Identifying the Components of Gender-Specific Religious Persecution of Christians

2021 ◽  
Vol 38 (1) ◽  
pp. 119-141
Author(s):  
Helene Fisher ◽  
Elizabeth Lane Miller ◽  
Christof Sauer
Keyword(s):  
Central African Republic ◽  
Complex Dynamics ◽  
Holistic Approach ◽  
Christian Women ◽  
Religious Persecution ◽  
The World ◽  
Gender Specific ◽  
The Church ◽  
Insight Into

Abstract Emerging understanding of gender-specific religious persecution in some of the world’s most difficult countries for Christians offers timely insight into complex dynamics in which the church and missions have too often been unwittingly complicit due to limited visibility of the components contributing to these wounds. Fresh research into these deeply wounding global phenomena stands as both a warning and a pointer towards an avenue for effective ministrations by churches and Christian ministries that are working in the most severely affected areas of the world. Drawing on the latest trends identified by World Watch Research, outcomes of the Consultation for Christian Women under Pressure for their Faith, a contemporary case study from Central African Republic, and a biblical narrative, we will explore practical opportunities for a holistic approach to bring preparedness, healing, and restoration for communities under severe pressure for their Christian faith.

A novel protein complex involved in signal transduction possessing similarities to 26S proteasome subunits

1998 ◽  
Vol 12 (6) ◽  
pp. 469-478 ◽  
Author(s):  
Michael Seeger ◽  
Regine Kraft ◽  
Katherine Ferrell ◽  
Dawadschargal Bech‐Otschir ◽  
Renate Dumdey ◽  
...  
Keyword(s):  
Signal Transduction ◽  
Protein Complex ◽  
26S Proteasome ◽  
Proteasome Subunits ◽  
Novel Protein
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