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

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 ◽  
Pdz Domain ◽  
Fibril Formation ◽  
Single Molecule Force Spectroscopy ◽  
Amyloid Fibril Formation ◽  
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.

scholarly journals Molecular dynamics simulations of mechanical failure in polymorphic arrangements of amyloid fibrils containing structural defects

2013 ◽  
Vol 4 ◽  
pp. 429-440 ◽  
Author(s):  
Hlengisizwe Ndlovu ◽  
Alison E Ashcroft ◽  
Sheena E Radford ◽  
Sarah A Harris
Keyword(s):  
Mechanical Properties ◽  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Amyloid Fibrils ◽  
Amyloid Fibril ◽  
Steered Molecular Dynamics ◽  
Mechanical Failure ◽  
Structural Defects ◽  
Dynamics Simulations

We examine how the different steric packing arrangements found in amyloid fibril polymorphs can modulate their mechanical properties using steered molecular dynamics simulations. Our calculations demonstrate that for fibrils containing structural defects, their ability to resist force in a particular direction can be dominated by both the number and molecular details of the defects that are present. The simulations thereby suggest a hierarchy of factors that govern the mechanical resilience of fibrils, and illustrate the general principles that must be considered when quantifying the mechanical properties of amyloid fibres containing defects.

scholarly journals Molecular dynamics simulations of RNA: Anin silico single molecule approach

Biopolymers ◽  
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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