Single-molecule interaction force measurements of catechol analog monomers and synthesis of adhesive polymer using the results

2016 ◽  
Vol 48 (6) ◽  
pp. 715-721 ◽  
Author(s):  
Shougo Kinugawa ◽  
Siqian Wang ◽  
Shu Taira ◽  
Akihiko Tsuge ◽  
Daisaku Kaneko
Keyword(s):  
Single Molecule ◽  
Interaction Force ◽  
Force Measurements ◽  
Molecule Interaction

scholarly journals Rational design of protein-specific folding modifiers

2020 ◽  
Author(s):  
Anirban Das ◽  
Anju Yadav ◽  
Mona Gupta ◽  
R Purushotham ◽  
Vishram L. Terse ◽  
...  
Keyword(s):  
Single Molecule ◽  
Rational Design ◽  
Resonance Energy Transfer ◽  
Resonance Energy ◽  
Force Measurements ◽  
Folding Nucleus ◽  
Dynamics Simulations ◽  
General Method

AbstractProtein folding can go wrong in vivo and in vitro, with significant consequences for the living cell and the pharmaceutical industry, respectively. Here we propose a general design principle for constructing small peptide-based protein-specific folding modifiers. We construct a ‘xenonucleus’, which is a pre-folded peptide that resembles the folding nucleus of a protein, and demonstrate its activity on the folding of ubiquitin. Using stopped-flow kinetics, NMR spectroscopy, Förster Resonance Energy transfer, single-molecule force measurements, and molecular dynamics simulations, we show that the ubiquitin xenonucleus can act as an effective decoy for the native folding nucleus. It can make the refolding faster by 33 ± 5% at 3 M GdnHCl. In principle, our approach provides a general method for constructing specific, genetically encodable, folding modifiers for any protein which has a well-defined contiguous folding nucleus.

scholarly journals Resolving the Dynamic Non-Covalent Interaction inside Membrane Protein Channel by Single-Molecule Interaction Spectrum

2018 ◽  
Author(s):  
Meng-Yin Li ◽  
Yi-Lun Ying ◽  
Xi-Xin Fu ◽  
Jie Yu ◽  
Shao-Chuang Liu ◽  
...  
Keyword(s):  
Membrane Protein ◽  
Single Molecule ◽  
Ionic Current ◽  
Md Simulations ◽  
Energy Spectra ◽  
Membrane Channels ◽  
Non Covalent Interactions ◽  
Protein Channels ◽  
Covalent Interactions ◽  
Molecule Interaction

Millions of years of evolution have produced membrane protein channels capable of efficiently moving ions across the cell membrane. The underlying fundamental mechanisms that facilitate these actions greatly contribute to the weak non-covalent interactions. However, uncovering these dynamic interactions and its synergic network effects still remains challenging in both experimental techniques and molecule dynamics (MD) simulations. Here, we present a rational strategy that combines MD simulations and frequency-energy spectroscopy to identify and quantify the role of non-covalent interactions in carrier transport through membrane protein channels, as encoded in traditional single channel recording or ionic current. We employed wild-type aerolysin transporting of methylcytosine and cytosine as a model to explore the dynamic ionic signatures with non-stationary and non-linear frequency analysis. Our data illuminate that methylcytosine experiences strong non-covalent interactions with the aerolysin nanopore at Region 1 around R220 than cytosine, which produces characteristic frequency-energy spectra. Furthermore, we experimentally validate the obtained hypothesis from frequency-energy spectra by designing single-site mutation of K238G which creates significantly enhanced non-covalent interactions for the recognition of methylcytosine. The frequency-energy spectrum of ions flowing inside membrane channels constitutes a single-molecule interaction spectrum, which bridges the gap between traditional ionic current recording and the MD simulations, facilitating the qualitative and quantitive description of the non-covalent interactions inside membrane channels.

scholarly journals Biophysical characterization of DNA binding from single molecule force measurements

2010 ◽  
Vol 7 (3) ◽  
pp. 299-341 ◽  
Author(s):  
Kathy R. Chaurasiya ◽  
Thayaparan Paramanathan ◽  
Micah J. McCauley ◽  
Mark C. Williams
Keyword(s):  
Dna Binding ◽  
Single Molecule ◽  
Force Measurements ◽  
Biophysical Characterization

Joining forces: integrating the mechanical and optical single molecule toolkits

2014 ◽  
Vol 5 (5) ◽  
pp. 1680-1697 ◽  
Author(s):  
Monique J. Jacobs ◽  
Kerstin Blank
Keyword(s):  
Fluorescence Detection ◽  
Single Molecule ◽  
Materials Science ◽  
Force Measurements

Combining single molecule force measurements with fluorescence detection opens up exciting new possibilities for the characterization of mechanoresponsive molecules in Biology and Materials Science.

scholarly journals Single molecule force measurements of perlecan/HSPG2: A key component of the osteocyte pericellular matrix

2016 ◽  
Vol 50 ◽  
pp. 27-38 ◽  
Author(s):  
Sithara S. Wijeratne ◽  
Jerahme R. Martinez ◽  
Brian J. Grindel ◽  
Eric W. Frey ◽  
Jingqiang Li ◽  
...  
Keyword(s):  
Single Molecule ◽  
Pericellular Matrix ◽  
Force Measurements

scholarly journals Free Energy of Membrane Protein Unfolding Derived from Single-Molecule Force Measurements

2007 ◽  
Vol 93 (3) ◽  
pp. 930-937 ◽  
Author(s):  
Johannes Preiner ◽  
Harald Janovjak ◽  
Christian Rankl ◽  
Helene Knaus ◽  
David A. Cisneros ◽  
...  
Keyword(s):  
Free Energy ◽  
Membrane Protein ◽  
Single Molecule ◽  
Protein Unfolding ◽  
Force Measurements

scholarly journals Solvent-molecule interaction induced gating of charge transport through single-molecule junctions

2020 ◽  
Vol 65 (11) ◽  
pp. 944-950 ◽  
Author(s):  
Zheng Tang ◽  
Songjun Hou ◽  
Qingqing Wu ◽  
Zhibing Tan ◽  
Jueting Zheng ◽  
...  
Keyword(s):  
Charge Transport ◽  
Single Molecule ◽  
Solvent Molecule ◽  
Single Molecule Junctions ◽  
Molecule Interaction
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