Understanding the molecular basis of MK2–p38α signaling complex assembly: insights into protein–protein interaction by molecular dynamics and free energy studies

2012 ◽  
Vol 8 (8) ◽  
pp. 2106 ◽  
Author(s):  
Ying Yang ◽  
Huanxiang Liu ◽  
Xiaojun Yao
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Protein Interaction ◽  
Molecular Basis ◽  
Complex Assembly ◽  
Protein Protein Interaction ◽  
Signaling Complex

scholarly journals Molecular Basis of a Million-Fold Affinity Maturation Process in a Protein–Protein Interaction

2011 ◽  
Vol 411 (2) ◽  
pp. 321-328 ◽  
Author(s):  
Daniel A. Bonsor ◽  
Sandra Postel ◽  
Brian G. Pierce ◽  
Ningyan Wang ◽  
Penny Zhu ◽  
...  
Keyword(s):  
Protein Interaction ◽  
Molecular Basis ◽  
Affinity Maturation ◽  
Maturation Process ◽  
Protein Protein Interaction

scholarly journals Thermodynamic Measures of Human Brain Development from Fetal Stage to Adulthood

2019 ◽  
Author(s):  
Edward A. Rietman ◽  
Sophie Taylor ◽  
Hava T. Siegelmann ◽  
Marco Cavaglia ◽  
Jack A. Tuszynski
Keyword(s):  
Free Energy ◽  
Brain Development ◽  
Gibbs Free Energy ◽  
Protein Interaction ◽  
Brain Regions ◽  
Protein Interaction Networks ◽  
Interaction Networks ◽  
Protein Protein Interaction ◽  
Protein Protein Interaction Networks ◽  
The Brain

AbstractThis paper analyzes the data obtained from tissue samples of the human brains containing protein expression values. The data have been processed for their thermodynamic measure in terms of the Gibbs free energy of the corresponding protein-protein interaction networks. We have investigated the functional dependence of the Gibbs free energies on age and found consistent trends for most of the 16 main brain areas. The peak of the Gibbs energy values is found at birth with a trend toward plateauing at the age of maturity. We have also compared the data for males and females and uncovered functional differences for some of the brain regions.Significance StatementIn this paper we briefly outline the theoretical basis for a novel analysis of brain development in terms of a thermodynamic measure (Gibbs free energy) for the corresponding protein-protein interaction networks. We analyzed the overall developmental patterns for Gibbs free energy as a function of age across all brain regions. Of particular note was the significant upward trend in the fetal stages, which is generally followed by a sharp dip at birth and a plateau at maturity. We then compared the trends for female and male samples. A crossover pattern was observed for most of the brain regions, where the Gibbs free energy of the male samples were lower than the female samples at prenatal and neonatal ages, but higher at ages 8-40.

scholarly journals Investigation of the Josephin Domain Protein-Protein Interaction by Molecular Dynamics

PLoS ONE ◽  
2014 ◽  
Vol 9 (9) ◽  
pp. e108677 ◽  
Author(s):  
Marco A. Deriu ◽  
Gianvito Grasso ◽  
Ginevra Licandro ◽  
Andrea Danani ◽  
Diego Gallo ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Protein Interaction ◽  
Protein Protein Interaction ◽  
Domain Protein

GPU Accelerated Molecular Dynamics Simulations for Protein-Protein Interaction of Ankyrin Complex

2014 ◽  
Vol 156 (1) ◽  
pp. 137-146 ◽  
Author(s):  
Kanchanok Kodchakorn ◽  
Supaporn Dokmaisrijan ◽  
Wei Lim Chong ◽  
Apirak Payaka ◽  
Tanchanok Wisitponchai ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Protein Interaction ◽  
Protein Protein Interaction ◽  
Accelerated Molecular Dynamics ◽  
Dynamics Simulations
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