Mechanisms of Nanonewton Mechanostability in a Protein Complex Revealed by Molecular Dynamics Simulations and Single-Molecule Force Spectroscopy

Journal of the American Chemical Society ◽

10.1021/jacs.9b06776 ◽

2019 ◽

Vol 141 (37) ◽

pp. 14752-14763 ◽

Author(s):

Rafael C. Bernardi ◽

Ellis Durner ◽

Constantin Schoeler ◽

Klara H. Malinowska ◽

Bruna G. Carvalho ◽

...

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Single Molecule ◽

Protein Complex ◽

Force Spectroscopy ◽

Single Molecule Force Spectroscopy ◽

Dynamics Simulations

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

Langmuir ◽

10.1021/la305157p ◽

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

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Using steered molecular dynamics simulations and single-molecule force spectroscopy to guide the rational design of biomimetic modular polymeric materials

Polymer ◽

10.1016/j.polymer.2008.06.047 ◽

2008 ◽

Vol 49 (18) ◽

pp. 3892-3901 ◽

Author(s):

Dora L. Guzmán ◽

Jason T. Roland ◽

Harindar Keer ◽

Yen Peng Kong ◽

Thorsten Ritz ◽

...

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Single Molecule ◽

Rational Design ◽

Force Spectroscopy ◽

Polymeric Materials ◽

Steered Molecular Dynamics ◽

Single Molecule Force Spectroscopy ◽

Dynamics Simulations

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

Langmuir ◽

10.1021/acs.langmuir.7b03011 ◽

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

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

Chemical Communications ◽

10.1039/d0cc00714e ◽

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.

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Single Molecule Force Spectroscopy and Steered Molecular Dynamics Simulations Reveal the Mechanical Design of the Third FnIII Domain of Tenascin-C

Biophysical Journal ◽

10.1016/j.bpj.2008.12.3389 ◽

2009 ◽

Vol 96 (3) ◽

pp. 641a

Author(s):

Qing Peng ◽

Shulin Zhuang ◽

Meijia Wang ◽

Yi Cao ◽

Yuanai Khoo ◽

...

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Single Molecule ◽

Mechanical Design ◽

Force Spectroscopy ◽

Steered Molecular Dynamics ◽

Single Molecule Force Spectroscopy ◽

The Third ◽

Fniii Domain ◽

Dynamics Simulations

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Single-Molecule Force Spectroscopy and Molecular Dynamics Simulations Reveals Complex Folding Landscape and its Potential Role in Amyloid Fibril Formation in a PDZ Domain

Biophysical Journal ◽

10.1016/j.bpj.2018.11.249 ◽

2019 ◽

Vol 116 (3) ◽

pp. 38a

Author(s):

Ha H. Truong ◽

Susan Marqusee

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Single Molecule ◽

Potential Role ◽

Amyloid Fibril ◽

Fibril Formation ◽

Single Molecule Force Spectroscopy ◽

Amyloid Fibril Formation ◽

Dynamics Simulations

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Probing Protein Folding Landscape by Using Combined Force Spectroscopy and Molecular Dynamics Simulations

Biophysical Journal ◽

10.1016/j.bpj.2017.11.2284 ◽

2018 ◽

Vol 114 (3) ◽

pp. 412a

Author(s):

Ha H. Truong ◽

Susan Marqusee

Keyword(s):

Molecular Dynamics ◽

Protein Folding ◽

Molecular Dynamics Simulations ◽

Force Spectroscopy ◽

Dynamics Simulations

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Molecular dynamics simulations of RNA: Anin silico single molecule approach

Biopolymers ◽

10.1002/bip.20620 ◽

2007 ◽

Vol 85 (2) ◽

pp. 169-184 ◽

Author(s):

S. Elizabeth McDowell ◽

Nad'a Špačková ◽

Jiří Šponer ◽

Nils G. Walter

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Single Molecule ◽

Dynamics Simulations

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An Integrative Approach to Single-Molecule FRET Spectroscopy and Molecular Dynamics Simulations for the Study of Intrinsically Disordered Proteins

Biophysical Journal ◽

10.1016/j.bpj.2019.11.906 ◽

2020 ◽

Vol 118 (3) ◽

pp. 143a

Author(s):

Mahmoud Moradi

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Single Molecule ◽

Intrinsically Disordered Proteins ◽

Disordered Proteins ◽

Integrative Approach ◽

Intrinsically Disordered ◽

Single Molecule Fret ◽

Dynamics Simulations

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The complex folding behavior of HIV-1-protease monomer revealed by optical-tweezer single-molecule experiments and molecular dynamics simulations

Biophysical Chemistry ◽

10.1016/j.bpc.2014.08.001 ◽

2014 ◽

Vol 195 ◽

pp. 32-42 ◽

Author(s):

M. Caldarini ◽

P. Sonar ◽

I. Valpapuram ◽

D. Tavella ◽

C. Volonté ◽

...

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Single Molecule ◽

Optical Tweezer ◽

Dynamics Simulations ◽

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