scholarly journals Slow Transition Path Times Reveal a Complex Folding Barrier in a Designed Protein

2020 ◽  
Vol 8 ◽  
Author(s):  
Alexander Mehlich ◽  
Jie Fang ◽  
Benjamin Pelz ◽  
Hongbin Li ◽  
Johannes Stigler
Keyword(s):  
Optical Tweezers ◽  
Single Molecule ◽  
De Novo ◽  
High Energy ◽  
Transition Path ◽  
Barrier Crossing ◽  
Designed Proteins ◽  
Transition Barrier ◽  
Millisecond Range ◽  
Transition Times

De-novo designed proteins have received wide interest as potential platforms for nano-engineering and biomedicine. While much work is being done in the design of thermodynamically stable proteins, the folding process of artificially designed proteins is not well-studied. Here we used single-molecule force spectroscopy by optical tweezers to study the folding of ROSS, a de-novo designed 2x2 Rossmann fold. We measured a barrier crossing time in the millisecond range, much slower than what has been reported for other systems. While long transition times can be explained by barrier roughness or slow diffusion, we show that isotropic roughness cannot explain the measured transition path time distribution. Instead, this study shows that the slow barrier crossing of ROSS is caused by the population of three short-lived high-energy intermediates. In addition, we identify incomplete and off-pathway folding events with different barrier crossing dynamics. Our results hint at the presence of a complex transition barrier that may be a common feature of many artificially designed proteins.

scholarly journals Real-time assembly of an artificial virus elucidated at the single-particle level

2019 ◽  
Author(s):  
Margherita Marchetti ◽  
Douwe Kamsma ◽  
Ernesto Cazares Vargas ◽  
Armando Hernandez García ◽  
Paul van der Schoot ◽  
...  
Keyword(s):  
Real Time ◽  
Optical Tweezers ◽  
Single Molecule ◽  
Single Particle ◽  
Self Assembly ◽  
De Novo ◽  
Particle Growth ◽  
Single Particle Tracking ◽  
Contour Length ◽  
Assembly Pathways

AbstractWhile the structure of a variety of viruses has been resolved at atomistic detail, their assembly pathways remain largely elusive. Key unresolved issues in assembly are the nature of the critical nucleus starting particle growth, the subsequent self-assembly reaction and the manner in which the viral genome is compacted. These issues are difficult to address in bulk approaches and are effectively only accessible by tracking the dynamics of assembly of individual particles in real time, as we show here. With a combination of single-molecule techniques we study the assembly into rod-shaped virus-like particles (VLPs) of artificial capsid polypeptides, de-novo designed previously. Using fluorescence optical tweezers we establish that oligomers that have pre-assembled in solution bind to our DNA template. If the oligomer is smaller than a pentamer, it performs one-dimensional diffusion along the DNA, but pentamers and larger oligomers are essentially immobile and nucleate VLP growth. Next, using real-time multiplexed acoustic force spectroscopy, we show that DNA is compacted in regular steps during VLP growth. These steps, of ∼30 nm of DNA contour length, fit with a DNA packaging mechanism based on helical wrapping of the DNA around the central protein core of the VLP. By revealing how real-time, single particle tracking of VLP assembly lays bare nucleation and growth principles, our work opens the doors to a new fundamental understanding of the complex assembly pathways of natural virus particles.

scholarly journals Lasing at the nanoscale: coherent emission of surface plasmons by an electrically driven nanolaser

Nanophotonics ◽  
2020 ◽  
Vol 9 (12) ◽  
pp. 3965-3975 ◽  
Author(s):  
Dmitry Yu. Fedyanin ◽  
Alexey V. Krasavin ◽  
Aleksey V. Arsenin ◽  
Anatoly V. Zayats
Keyword(s):  
Data Storage ◽  
Surface Plasmon ◽  
Single Molecule ◽  
Optical Communication ◽  
Surface Plasmon Polariton ◽  
High Energy ◽  
Photonic Devices ◽  
Sensing Applications ◽  
Diverse Application ◽  
Plasmon Polariton

AbstractPlasmonics offers a unique opportunity to break the diffraction limit of light and bring photonic devices to the nanoscale. As the most prominent example, an integrated nanolaser is a key to truly nanoscale photonic circuits required for optical communication, sensing applications and high-density data storage. Here, we develop a concept of an electrically driven subwavelength surface-plasmon-polariton nanolaser, which is based on a novel amplification scheme, with all linear dimensions smaller than the operational free-space wavelength λ and a mode volume of under λ3/30. The proposed pumping approach is based on a double-heterostructure tunneling Schottky barrier diode and gives the possibility to reduce the physical size of the device and ensure in-plane emission so that the nanolaser output can be naturally coupled to a plasmonic or nanophotonic waveguide circuitry. With the high energy efficiency (8% at 300 K and 37% at 150 K), the output power of up to 100 μW and the ability to operate at room temperature, the proposed surface plasmon polariton nanolaser opens up new avenues in diverse application areas, ranging from ultrawideband optical communication on a chip to low-power nonlinear photonics, coherent nanospectroscopy, and single-molecule biosensing.

Slow magnetic relaxation in dinuclear dysprosium and holmium phenoxide bridged complexes: a Dy2 single molecule magnet with a high energy barrier

2021 ◽  
Author(s):  
Matilde Fondo ◽  
Julio Corredoira-Vázquez ◽  
Ana M. Garcia-Deibe ◽  
Jesus Sanmartin Matalobos ◽  
Silvia Gómez-Coca ◽  
...  
Keyword(s):  
Crystal Structures ◽  
Single Molecule ◽  
Energy Barrier ◽  
Magnetic Relaxation ◽  
High Energy ◽  
Single Molecule Magnet ◽  
High Energy Barrier ◽  
Slow Magnetic Relaxation

Dinuclear [M(H3L1,2,4)]2 (M = Dy, Dy2; M = Ho, Ho2) complexes were isolated from an heptadentate aminophenol ligand. The crystal structures of Dy2·2THF, and the pyridine adducts Dy2·2Py and Ho2·2Py,...

scholarly journals Optical tweezers in single-molecule biophysics

2021 ◽  
Vol 1 (1) ◽  
Author(s):  
Carlos J. Bustamante ◽  
Yann R. Chemla ◽  
Shixin Liu ◽  
Michelle D. Wang
Keyword(s):  
Optical Tweezers ◽  
Single Molecule ◽  
Single Molecule Biophysics

Molecular Motors: Force and Movement Generated by Single Myosin II Molecules

Physiology ◽  
2002 ◽  
Vol 17 (5) ◽  
pp. 213-218 ◽  
Author(s):  
Caspar Rüegg ◽  
Claudia Veigel ◽  
Justin E. Molloy ◽  
Stephan Schmitz ◽  
John C. Sparrow ◽  
...  
Keyword(s):  
Optical Tweezers ◽  
Single Molecule ◽  
Molecular Motors ◽  
Molecular Motor ◽  
Myosin Ii ◽  
Force Production ◽  
Myosin Isoforms ◽  
Single Molecule Level ◽  
Recent Developments ◽  
Muscle Myosin

Muscle myosin II is an ATP-driven, actin-based molecular motor. Recent developments in optical tweezers technology have made it possible to study movement and force production on the single-molecule level and to find out how different myosin isoforms may have adapted to their specific physiological roles.

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