pH-Dependent Stability of a Decalysine α-Helix Studied by Explicit-Solvent Molecular Dynamics Simulations at Constant pH

2004 ◽  
Vol 108 (35) ◽  
pp. 13551-13559 ◽  
Author(s):  
Ulf Börjesson ◽  
Philippe H. Hünenberger
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Constant Ph ◽  
Explicit Solvent ◽  
Ph Dependent ◽  
Α Helix ◽  
Dynamics Simulations

scholarly journals Probing the Accuracy of Explicit Solvent Constant pH Molecular Dynamics Simulations for Peptides

2020 ◽  
Vol 16 (4) ◽  
pp. 2561-2569 ◽  
Author(s):  
Plamen Dobrev ◽  
Sahithya Phani Babu Vemulapalli ◽  
Nilamoni Nath ◽  
Christian Griesinger ◽  
Helmut Grubmüller
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Constant Ph ◽  
Explicit Solvent ◽  
Dynamics Simulations ◽  
Constant Ph Molecular Dynamics

scholarly journals Probing the Accuracy of Explicit Solvent Constant pH Molecular Dynamics Simulations for Peptides

2020 ◽  
Vol 118 (3) ◽  
pp. 140a
Author(s):  
Plamen N. Dobrev ◽  
Sahithya Vemulapalli ◽  
Nilamoni Nath ◽  
Christian Griesinger ◽  
Helmut Grubmueller
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Constant Ph ◽  
Explicit Solvent ◽  
Dynamics Simulations ◽  
Constant Ph Molecular Dynamics

scholarly journals Correction to “Probing the Accuracy of Explicit Solvent Constant pH Molecular Dynamics Simulations for Peptides”

2020 ◽  
Vol 16 (7) ◽  
pp. 4753-4753
Author(s):  
Plamen Dobrev ◽  
Sahithya Phani Babu Vemulapalli ◽  
Nilamoni Nath ◽  
Christian Griesinger ◽  
Gerrit Groenhof ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Constant Ph ◽  
Explicit Solvent ◽  
Dynamics Simulations ◽  
Constant Ph Molecular Dynamics

scholarly journals pH-Dependent cooperativity and existence of a dry molten globule in the folding of a miniprotein BBL

2018 ◽  
Vol 20 (5) ◽  
pp. 3523-3530 ◽  
Author(s):  
Zhi Yue ◽  
Jana Shen
Keyword(s):  
Molecular Dynamics ◽  
Energy Barrier ◽  
Molten Globule ◽  
Free Energy Barrier ◽  
Molten Globule State ◽  
Constant Ph ◽  
Ph Dependent ◽  
Dynamics Simulations ◽  
Constant Ph Molecular Dynamics ◽  
Folding Free Energy

Constant pH molecular dynamics simulations of BBL reveals negligible folding free energy barrier that is pH dependent and a sparsely populated dry molten globule state.

An α-helix mimetic oligopyridylamide, ADH-31, modulates Aβ42 monomer aggregation and destabilizes protofibril structures: insights from molecular dynamics simulations

2020 ◽  
Vol 22 (48) ◽  
pp. 28055-28073
Author(s):  
Anupamjeet Kaur ◽  
Deepti Goyal ◽  
Bhupesh Goyal
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Helical Conformation ◽  
Aβ Peptide ◽  
Α Helix ◽  
Dynamics Simulations

The molecular dynamics simulations highlighted that ADH-31 inhibited Aβ42 aggregation by constraining Aβ peptide into helical conformation and destabilized Aβ42 trimer as well as protofibril structures.

Prediction of aqueous free energies of solvation using coupled QM and MM explicit solvent simulations

2020 ◽  
Vol 22 (15) ◽  
pp. 8021-8034
Author(s):  
Daniel Sadowsky ◽  
J. Samuel Arey
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Free Energies ◽  
Explicit Solvent ◽  
Dynamics Simulations ◽  
Ionic Solutes

A method based on molecular dynamics simulations which employ two distinct levels of theory is proposed and tested for the prediction of Gibbs free energies of solvation for non-ionic solutes in water.

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