Direct observation of the wrapping/unwrapping of ssDNA around/from a SWCNT at the single-molecule level: towards tuning the binding mode and strength

Nanoscale ◽  
2018 ◽  
Vol 10 (39) ◽  
pp. 18586-18596 ◽  
Author(s):  
Zhandong Li ◽  
Yu Song ◽  
Aisen Li ◽  
Weiqing Xu ◽  
Wenke Zhang
Keyword(s):  
Direct Observation ◽  
Single Molecule ◽  
Force Spectroscopy ◽  
Binding Mode ◽  
Single Molecule Force Spectroscopy ◽  
Single Molecule Level ◽  
Long Chain

AFM-based single-molecule force spectroscopy is employed to quantify the interactions between long-chain ssDNA and SWCNT and monitor the dynamic wrapping/unwrapping processes of ssDNA around/from the CNT.

scholarly journals Resolving dual binding conformations of cellulosome cohesin-dockerin complexes using single-molecule force spectroscopy

eLife ◽  
2015 ◽  
Vol 4 ◽  
Author(s):  
Markus A Jobst ◽  
Lukas F Milles ◽  
Constantin Schoeler ◽  
Wolfgang Ott ◽  
Daniel B Fried ◽  
...  
Keyword(s):  
Single Molecule ◽  
Molecular Conformation ◽  
Bacterial Species ◽  
Force Spectroscopy ◽  
Binding Mode ◽  
Site Directed Mutagenesis ◽  
Binding Modes ◽  
Single Molecule Force Spectroscopy ◽  
Vast Number ◽  
Knock Out

Receptor-ligand pairs are ordinarily thought to interact through a lock and key mechanism, where a unique molecular conformation is formed upon binding. Contrary to this paradigm, cellulosomal cohesin-dockerin (Coh-Doc) pairs are believed to interact through redundant dual binding modes consisting of two distinct conformations. Here, we combined site-directed mutagenesis and single-molecule force spectroscopy (SMFS) to study the unbinding of Coh:Doc complexes under force. We designed Doc mutations to knock out each binding mode, and compared their single-molecule unfolding patterns as they were dissociated from Coh using an atomic force microscope (AFM) cantilever. Although average bulk measurements were unable to resolve the differences in Doc binding modes due to the similarity of the interactions, with a single-molecule method we were able to discriminate the two modes based on distinct differences in their mechanical properties. We conclude that under native conditions wild-type Doc from Clostridium thermocellum exocellulase Cel48S populates both binding modes with similar probabilities. Given the vast number of Doc domains with predicteddual binding modes across multiple bacterial species, our approach opens up newpossibilities for understanding assembly and catalytic properties of a broadrange of multi-enzyme complexes.

Polypeptide-Solvent Interactions Measured by Single Molecule Force Spectroscopy

2005 ◽  
Vol 898 ◽  
Author(s):  
Alexei Valiaev ◽  
Dong Woo Lim ◽  
Ashutosh Chilkoti ◽  
Scott Schmidler ◽  
Stefan Zauscher
Keyword(s):  
Single Molecule ◽  
Chemical Properties ◽  
Force Spectroscopy ◽  
Hydrophobic Hydration ◽  
Peptide Sequence ◽  
Segment Length ◽  
Single Molecule Force Spectroscopy ◽  
Single Molecule Level ◽  
Solvent Quality ◽  
Stimulus Responsive

AbstractStimulus-responsive biomolecules have attracted a large research interest because of their potential application in various areas such as drug delivery, actuators and sensing devices at the nanoscale. Using single-molecule force spectroscopy (SMFS) we studied elastin-like polypeptides (ELPs). These stimulus-responsive polypeptides undergo an inverse temperature transition, accompanied by a large conformational change, when the solvent quality is changed by increasing the temperature or by addition of salt. Understanding the relationship between peptide sequence and mechanisms of force generation can provide a route to engineer ELPs with desirable mechano-chemical properties. Here we studied the effect of solvent quality and type of guest residue on the mechanical properties of ELPs on the single-molecule level. We used a statistical approach to estimate polymer elasticity parameters from model fits to the data. With this approach we were able to resolve small changes in the Kuhn segment length distributions associated with different molecular architectures. We then show that these mechanical differences likely arise from differences in the hydrophobic hydration of sidegoups, in line with recent predictions from molecular dynamics simulations.

scholarly journals Mechanical Unfolding of Ensemble Biomolecular Structures by Shear Force

2021 ◽  
Author(s):  
Changpeng Hu ◽  
Sagun Jonchhe ◽  
Pravin Pokhrel ◽  
Deepak Karna ◽  
Hanbin Mao
Keyword(s):  
Single Molecule ◽  
Shear Force ◽  
Force Spectroscopy ◽  
Single Molecule Force Spectroscopy ◽  
Single Molecule Level

Mechanical unfolding of biomolecular structures has been exclusively performed at the single-molecule level by single-molecule force spectroscopy (SMFS) techniques. Here we transformed sophisticated mechanical investigations on individual molecules into a...

scholarly journals Single Molecule Force Spectroscopy Reveals Two-Domain Binding Mode of Pilus-1 Tip Protein RrgA of Streptococcus pneumoniae to Fibronectin

ACS Nano ◽  
2018 ◽  
Vol 12 (1) ◽  
pp. 549-558 ◽  
Author(s):  
Tanja D. Becke ◽  
Stefan Ness ◽  
Raimund Gürster ◽  
Arndt F. Schilling ◽  
Anne-Marie di Guilmi ◽  
...  
Keyword(s):  
Streptococcus Pneumoniae ◽  
Single Molecule ◽  
Force Spectroscopy ◽  
Binding Mode ◽  
Single Molecule Force Spectroscopy

scholarly journals Ultrahigh Adhesion Force Between Silica-Binding Peptide SB7 and Glass Substrate Studied by Single-Molecule Force Spectroscopy and Molecular Dynamic Simulation

2020 ◽  
Vol 8 ◽  
Author(s):  
Xiaoxu Zhang ◽  
Jialin Chen ◽  
Enci Li ◽  
Chunguang Hu ◽  
Shi-Zhong Luo ◽  
...  
Keyword(s):  
Single Molecule ◽  
Glass Surface ◽  
Silica Surface ◽  
Adhesion Force ◽  
Force Spectroscopy ◽  
Dynamics Simulation ◽  
Single Molecule Force Spectroscopy ◽  
Binding Peptide ◽  
Single Molecule Level ◽  
Arginine Residues

Many proteins and peptides have been identified to effectively and specifically bind on certain surfaces such as silica, polystyrene and titanium dioxide. It is of great interest, in many areas such as enzyme immobilization, surface functionalization and nanotechnology, to understand how these proteins/peptides bind to solid surfaces. Here we use single-molecule force spectroscopy (SMFS) based on atomic force microscopy to directly measure the adhesion force between a silica-binding peptide SB7 and glass surface at single molecule level. SMFS results show that the adhesion force of a single SB7 detaching from the glass surface distributes in two populations at ~220 pN and 610 pN, which is higher than the unfolding forces of most mechanically stable proteins and the unbinding forces of most stable protein-protein interactions. Molecular dynamics simulation reveals that the electrostatic interactions between positively charged arginine residues and the silica surface dominates the binding of SB7 on silica. Our study provides experimental evidence and molecular mechanism at the single-molecule level for the SB7-based immobilization of proteins on silica-based surface, which is able to withstand high mechanical forces, making it an ideal fusion tag for silica surface immobilization or peptide-base adhesive materials.

scholarly journals Single Molecule Force Spectroscopy of Siloxanes

2021 ◽  
Vol 714 (3) ◽  
pp. 032023
Author(s):  
Ling Chen ◽  
Liya Yang ◽  
Chunxia Wang ◽  
Ting Zhu
Keyword(s):  
Single Molecule ◽  
Force Spectroscopy ◽  
Single Molecule Force Spectroscopy

Interaction of chloramphenicol with titin I27 probed using single-molecule force spectroscopy

2021 ◽  
Author(s):  
Jyoti Yadav ◽  
Yashwant Kumar ◽  
Gayathri S. Singaraju ◽  
Shivprasad Patil
Keyword(s):  
Single Molecule ◽  
Force Spectroscopy ◽  
Single Molecule Force Spectroscopy
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