scholarly journals Quantum and All-Atom Molecular Dynamics Simulations of Protonation and Divalent Ion Binding to Phosphatidylinositol 4,5-Bisphosphate (PIP2)

2013 ◽  
Vol 117 (28) ◽  
pp. 8322-8329 ◽  
Author(s):  
David R. Slochower ◽  
Peter J. Huwe ◽  
Ravi Radhakrishnan ◽  
Paul A. Janmey
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Ion Binding ◽  
Dynamics Simulations

scholarly journals Quantum and All-Atom Molecular Dynamics Simulations of Protonation and Divalent Ion Binding to Phosphatidylinositol 4,5-Bisphosphate (PIP2)

2013 ◽  
Vol 104 (2) ◽  
pp. 79a
Author(s):  
David R. Slochower ◽  
Peter J. Huwe ◽  
Ryan Bradley ◽  
Ravi Radhakrishnan ◽  
Paul A. Janmey
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Ion Binding ◽  
Dynamics Simulations

Molecular Dynamics Simulations of Metal Ion Binding to the His-tag Motif

2005 ◽  
Vol 52 (6) ◽  
pp. 1281-1290 ◽  
Author(s):  
Chin-Wen Chen ◽  
Hsuan-Liang Liu ◽  
Jin-Chung Lin ◽  
Yih Ho
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Metal Ion ◽  
Ion Binding ◽  
Metal Ion Binding ◽  
His Tag ◽  
Dynamics Simulations

scholarly journals Investigation of Ion Binding in Chlorite Dismutases by Means of Molecular Dynamics Simulations

Biochemistry ◽  
2014 ◽  
Vol 53 (29) ◽  
pp. 4869-4879 ◽  
Author(s):  
Axel Sündermann ◽  
Maria M. Reif ◽  
Stefan Hofbauer ◽  
Christian Obinger ◽  
Chris Oostenbrink
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Ion Binding ◽  
Dynamics Simulations

scholarly journals Ion Binding to a Mammalian Sodium/Proton Exchanger Membrane Protein from Molecular Dynamics Simulations

2021 ◽  
Vol 120 (3) ◽  
pp. 105a
Author(s):  
Chenou Zhang ◽  
Ricky Sexton ◽  
Iven Winkelmann ◽  
Rei Matsuoka ◽  
Pascal Meier ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Membrane Protein ◽  
Molecular Dynamics Simulations ◽  
Ion Binding ◽  
Sodium Proton Exchanger ◽  
Dynamics Simulations

How calcium ion binding induces the conformational transition of the calmodulin N-terminal domain—an atomic level characterization

2019 ◽  
Vol 21 (36) ◽  
pp. 19795-19804 ◽  
Author(s):  
Likun Zhao ◽  
Luhua Lai ◽  
Zhuqing Zhang
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Calcium Ion ◽  
Conformational Transition ◽  
Atomic Level ◽  
Ion Binding ◽  
Terminal Domain ◽  
Calcium Ion Binding ◽  
Dynamics Simulations ◽  
Conformation Transition

The Ca2+ binding and triggering conformation transition of nCaM were detected in unbiased molecular dynamics simulations.

scholarly journals Analyzing ion distributions around DNA

2014 ◽  
Vol 42 (12) ◽  
pp. 8138-8149 ◽  
Author(s):  
Richard Lavery ◽  
John H. Maddocks ◽  
Marco Pasi ◽  
Krystyna Zakrzewska
Keyword(s):  
Molecular Dynamics ◽  
Nucleic Acid ◽  
Molecular Dynamics Simulations ◽  
Dna Conformation ◽  
Ion Binding ◽  
Dna Oligomers ◽  
Cartesian Space ◽  
Ion Distributions ◽  
Dynamics Simulations ◽  
Convergence Sequence

Abstract We present a new method for analyzing ion, or molecule, distributions around helical nucleic acids and illustrate the approach by analyzing data derived from molecular dynamics simulations. The analysis is based on the use of curvilinear helicoidal coordinates and leads to highly localized ion densities compared to those obtained by simply superposing molecular dynamics snapshots in Cartesian space. The results identify highly populated and sequence-dependent regions where ions strongly interact with the nucleic and are coupled to its conformational fluctuations. The data from this approach is presented as ion populations or ion densities (in units of molarity) and can be analyzed in radial, angular and longitudinal coordinates using 1D or 2D graphics. It is also possible to regenerate 3D densities in Cartesian space. This approach makes it easy to understand and compare ion distributions and also allows the calculation of average ion populations in any desired zone surrounding a nucleic acid without requiring references to its constituent atoms. The method is illustrated using microsecond molecular dynamics simulations for two different DNA oligomers in the presence of 0.15 M potassium chloride. We discuss the results in terms of convergence, sequence-specific ion binding and coupling with DNA conformation.

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