A Network of Conformational Transitions Revealed by Molecular Dynamics Simulations of the Binary Complex of Escherichia coli 6-Hydroxymethyl-7,8-dihydropterin Pyrophosphokinase with MgATP

Biochemistry ◽  
2016 ◽  
Vol 55 (49) ◽  
pp. 6931-6939 ◽  
Author(s):  
Kaifu Gao ◽  
Ya Jia ◽  
Minghui Yang
Keyword(s):  
Escherichia Coli ◽  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Conformational Transitions ◽  
Binary Complex ◽  
Dynamics Simulations

Peptides design based on transmembrane Escherichia coli ’ s OmpA protein through molecular dynamics simulations in water–dodecane interfaces

2016 ◽  
Vol 68 ◽  
pp. 216-223 ◽  
Author(s):  
Sonia M. Aguilera-Segura ◽  
Vanessa Núñez Vélez ◽  
Luke Achenie ◽  
Oscar Álvarez Solano ◽  
Rodrigo Torres ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Ompa Protein ◽  
Dynamics Simulations

scholarly journals Comment on ‘Valid molecular dynamics simulations of human hemoglobin require a surprisingly large box size’

2019 ◽  
Author(s):  
Vytautas Gapsys ◽  
Bert L. de Groot
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Size Dependence ◽  
Conformational Transitions ◽  
Human Hemoglobin ◽  
Order Of Magnitude ◽  
The Stability ◽  
Dynamics Simulations ◽  
T State

AbstractA recent molecular dynamics investigation into the stability of hemoglobin concluded that the unliganded protein is only stable in the T state when a solvent box is used in the simulations that is ten times larger than what is usually employed. Here, we express three main concerns about that study. In addition, we show that with an order of magnitude more statistics, the reported box size dependence is not reproducible. Overall, no significant effects on the kinetics or thermodynamics of conformational transitions were observed.

scholarly journals Comment on 'Valid molecular dynamics simulations of human hemoglobin require a surprisingly large box size'

eLife ◽  
2019 ◽  
Vol 8 ◽  
Author(s):  
Vytautas Gapsys ◽  
Bert L de Groot
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Size Dependence ◽  
Conformational Transitions ◽  
Human Hemoglobin ◽  
Order Of Magnitude ◽  
The Stability ◽  
Dynamics Simulations ◽  
T State

A recent molecular dynamics investigation into the stability of hemoglobin concluded that the unliganded protein is only stable in the T state when a solvent box is used in the simulations that is ten times larger than what is usually employed (El Hage et al., 2018). Here, we express three main concerns about that study. In addition, we find that with an order of magnitude more statistics, the reported box size dependence is not reproducible. Overall, no significant effects on the kinetics or thermodynamics of conformational transitions were observed.

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