Exploring the Folding Pattern of a Polymer Chain in a Single Crystal by Combining Single-Molecule Force Spectroscopy and Steered Molecular Dynamics Simulations

Langmuir ◽  
2013 ◽  
Vol 29 (12) ◽  
pp. 3853-3857 ◽  
Author(s):  
Yu Song ◽  
Wei Feng ◽  
Kai Liu ◽  
Peng Yang ◽  
Wenke Zhang ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Single Crystal ◽  
Molecular Dynamics Simulations ◽  
Polymer Chain ◽  
Single Molecule ◽  
Force Spectroscopy ◽  
Steered Molecular Dynamics ◽  
Single Molecule Force Spectroscopy ◽  
Folding Pattern ◽  
Dynamics Simulations

Single Molecule Force Spectroscopy and Molecular Dynamics Simulations as a Combined Platform for Probing Protein Face-Specific Binding

Langmuir ◽  
2017 ◽  
Vol 33 (41) ◽  
pp. 10851-10860 ◽  
Author(s):  
Kartik Srinivasan ◽  
Suvrajit Banerjee ◽  
Siddharth Parimal ◽  
Lars Sejergaard ◽  
Ronen Berkovich ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Single Molecule ◽  
Specific Binding ◽  
Force Spectroscopy ◽  
Single Molecule Force Spectroscopy ◽  
Dynamics Simulations

Verification of sortase for protein conjugation by single-molecule force spectroscopy and molecular dynamics simulations

2020 ◽  
Vol 56 (28) ◽  
pp. 3943-3946
Author(s):  
Fang Tian ◽  
Guoqiang Li ◽  
Bin Zheng ◽  
Yutong Liu ◽  
Shengchao Shi ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Single Molecule ◽  
Force Spectroscopy ◽  
Md Simulations ◽  
Protein Conjugation ◽  
Single Molecule Force Spectroscopy ◽  
Closed Conformation ◽  
Dynamics Simulations

SMFS and MD simulations revealed a closed conformation and a decreased stability of sortase-mediated polyprotein I27 when a linker with a high content of glycine is used.

How strong are hydrogen bonds in the peptide model?

2020 ◽  
Vol 22 (3) ◽  
pp. 1392-1399
Author(s):  
Jakub Dąbrowski ◽  
Wiesław Nowak ◽  
Arkadiusz Ptak
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bonds ◽  
Molecular Dynamics Simulations ◽  
Force Spectroscopy ◽  
Steered Molecular Dynamics ◽  
Dynamic Force ◽  
Dynamic Force Spectroscopy ◽  
Dynamics Simulations

We provide a methodology based on the steered molecular dynamics simulations and dynamic force spectroscopy calculations to determine the kinetic and energetic characteristics of hydrogen bonds.

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