Staring at a Protein: Ensemble and Single-Molecule Investigations on Protein-Folding Dynamics

2011 ◽  
pp. 1-22
Author(s):  
Satoshi Takahashi ◽  
Kiyoto Kamagata
Keyword(s):  
Protein Folding ◽  
Single Molecule ◽  
Folding Dynamics

SpyTag/SpyCatcher Tether as a Fingerprint and Force Marker for Single-Molecule Force Spectroscopy Experiments

Nanoscale ◽  
2021 ◽  
Author(s):  
Zilong Guo ◽  
Haiyan Hong ◽  
Hao Sun ◽  
Xiaofeng Zhang ◽  
Chen-Xu Wu ◽  
...  
Keyword(s):  
Protein Folding ◽  
Single Molecule ◽  
Force Spectroscopy ◽  
Single Molecule Force Spectroscopy ◽  
Receptor Interactions ◽  
Folding Dynamics

Single molecule force spectroscopy has emerged as a powerful tool to study protein folding dynamics, ligand-receptor interactions, and various mechanobiological processes. High force precision does not necessarily lead to high...

scholarly journals Non-Markovian modeling of protein folding

2021 ◽  
Vol 118 (31) ◽  
pp. e2023856118
Author(s):  
Cihan Ayaz ◽  
Lucas Tepper ◽  
Florian N. Brünig ◽  
Julian Kappler ◽  
Jan O. Daldrop ◽  
...  
Keyword(s):  
Protein Folding ◽  
Single Molecule ◽  
Md Simulations ◽  
Reaction Coordinate ◽  
Generalized Langevin Equation ◽  
Folding Dynamics ◽  
Α Helix ◽  
Friction Function ◽  
Explicit Water ◽  
Unfolding Kinetics

We extract the folding free energy landscape and the time-dependent friction function, the two ingredients of the generalized Langevin equation (GLE), from explicit-water molecular dynamics (MD) simulations of the α-helix forming polypeptide alanine9 for a one-dimensional reaction coordinate based on the sum of the native H-bond distances. Folding and unfolding times from numerical integration of the GLE agree accurately with MD results, which demonstrate the robustness of our GLE-based non-Markovian model. In contrast, Markovian models do not accurately describe the peptide kinetics and in particular, cannot reproduce the folding and unfolding kinetics simultaneously, even if a spatially dependent friction profile is used. Analysis of the GLE demonstrates that memory effects in the friction significantly speed up peptide folding and unfolding kinetics, as predicted by the Grote–Hynes theory, and are the cause of anomalous diffusion in configuration space. Our methods are applicable to any reaction coordinate and in principle, also to experimental trajectories from single-molecule experiments. Our results demonstrate that a consistent description of protein-folding dynamics must account for memory friction effects.

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