scholarly journals Conformational Switching between Protein Substates Studied with 2D IR Vibrational Echo Spectroscopy and Molecular Dynamics Simulations

2010 ◽  
Vol 114 (51) ◽  
pp. 17187-17193 ◽  
Author(s):  
Sayan Bagchi ◽  
Dayton G. Thorpe ◽  
Ian F. Thorpe ◽  
Gregory A. Voth ◽  
M. D. Fayer
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Conformational Switching ◽  
2D Ir ◽  
Dynamics Simulations ◽  
Vibrational Echo

scholarly journals 2D IR spectra of cyanide in water investigated by molecular dynamics simulations

2013 ◽  
Vol 139 (5) ◽  
pp. 054506 ◽  
Author(s):  
Myung Won Lee ◽  
Joshua K. Carr ◽  
Michael Göllner ◽  
Peter Hamm ◽  
Markus Meuwly
Keyword(s):  
Molecular Dynamics ◽  
Ir Spectra ◽  
Molecular Dynamics Simulations ◽  
2D Ir ◽  
Dynamics Simulations

Ultrafast Dynamics of Myoglobin without the Distal Histidine:  Stimulated Vibrational Echo Experiments and Molecular Dynamics Simulations

2005 ◽  
Vol 109 (35) ◽  
pp. 16959-16966 ◽  
Author(s):  
Ilya J. Finkelstein ◽  
Anne Goj ◽  
Brian L. McClain ◽  
Aaron M. Massari ◽  
Kusai A. Merchant ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Ultrafast Dynamics ◽  
Dynamics Simulations ◽  
Vibrational Echo

Water Dynamics:  Vibrational Echo Correlation Spectroscopy and Comparison to Molecular Dynamics Simulations

2004 ◽  
Vol 108 (7) ◽  
pp. 1107-1119 ◽  
Author(s):  
John B. Asbury ◽  
Tobias Steinel ◽  
C. Stromberg ◽  
S. A. Corcelli ◽  
C. P. Lawrence ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Correlation Spectroscopy ◽  
Water Dynamics ◽  
Dynamics Simulations ◽  
Vibrational Echo

Lanthanide-dependent coordination interactions in lanmodulin: a 2D IR and molecular dynamics simulations study

2021 ◽  
Author(s):  
Emily R Featherston ◽  
Stephanie Liu ◽  
Joseph Cotruvo ◽  
Carlos Baiz
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Lanthanide Ions ◽  
Selective Binding ◽  
2D Ir ◽  
Biological Importance ◽  
Structural Principles ◽  
Dynamics Simulations

The biological importance of lanthanides, and the early lanthanides (La3+-Nd3+) in particular, has only recently been recognized, and the structural principles underlying selective binding of lanthanide ions in biology are...

scholarly journals PAGE4 and Conformational Switching: Insights from Molecular Dynamics Simulations and Implications for Prostate Cancer

2018 ◽  
Vol 430 (16) ◽  
pp. 2422-2438 ◽  
Author(s):  
Xingcheng Lin ◽  
Susmita Roy ◽  
Mohit Kumar Jolly ◽  
Federico Bocci ◽  
Nicholas P. Schafer ◽  
...  
Keyword(s):  
Prostate Cancer ◽  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Conformational Switching ◽  
Dynamics Simulations

scholarly journals PAGE4 and Conformational Switching: Insights from Molecular Dynamics Simulations and Implications for Prostate Cancer

2018 ◽  
Author(s):  
Xingcheng Lin ◽  
Susmita Roy ◽  
Mohit Kumar Jolly ◽  
Federico Bocci ◽  
Nicholas Schafer ◽  
...  
Keyword(s):  
Prostate Cancer ◽  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Molecular Model ◽  
Coarse Grained ◽  
Activator Protein 1 ◽  
Conformational Switching ◽  
Interacting Protein ◽  
Oscillatory Dynamics ◽  
Dynamics Simulations

AbstractProstate-Associated Gene 4 (PAGE4) is a disordered protein implicated in the progression of prostate cancer. PAGE4 can be phosphorylated at two residue sites by Homeodomain-Interacting Protein Kinase 1 (HIPK1) to facilitate its binding to the Activator Protein-1 (AP-1) transcription factor. In contrast, a further hyperphosphorylation of PAGE4 by CDC-Like Kinase 2 (CLK2) reduces its binding affinity to AP-1, thus affecting the androgen receptor (AR) activity. Both SAXS and smFRET experiments have shown a structural expansion of PAGE4 upon hyperphosphorylation and a significant increase in size at its N-terminal half than that at its C-terminus. To understand the molecular mechanism underlying this structural transition, we performed a series of constant temperature molecular dynamics simulations using Atomistic AWSEM — a multi-scale molecular model combining detailed atomistic and coarse-grained simulation approaches. Our simulations show that electrostatic interaction drives a transient formation of an N-terminal loop, which causes the change in size for different phosphorylated forms of PAGE4. Phosphorylation also changes the preference of secondary structure formation of PAGE4, which signifies a transition between states that display different degree of disorder. Finally, we construct a mechanism-based mathematical model that allows us to capture the interactions of different forms of PAGE4 with AP-1 and AR, a key therapeutic target in prostate cancer. Our model predicts intracellular oscillatory dynamics of HIPK1-PAGE4, CLK2-PAGE4 and AR activity, indicating phenotypic heterogeneity in an isogenic cell population. Thus, conformational switching among different forms of PAGE4 may potentially affect the efficiency of therapeutic targeting of AR.

The Influence of Aqueous versus Glassy Solvents on Protein Dynamics:  Vibrational Echo Experiments and Molecular Dynamics Simulations

2005 ◽  
Vol 127 (41) ◽  
pp. 14279-14289 ◽  
Author(s):  
Aaron M. Massari ◽  
Ilya J. Finkelstein ◽  
Brian L. McClain ◽  
Anne Goj ◽  
Xin Wen ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Protein Dynamics ◽  
Dynamics Simulations ◽  
Vibrational Echo
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