Single-molecule force spectroscopy of protein folding

R Petrosyan, A Narayan, MT Woodside - Journal of Molecular Biology, 2021 - Elsevier
The use of force probes to induce unfolding and refolding of single molecules through the
application of mechanical tension, known as single-molecule force spectroscopy (SMFS) …

[HTML][HTML] Folding and functions of knotted proteins

STD Hsu - Current Opinion in Structural Biology, 2023 - Elsevier
Topologically knotted proteins have entangled structural elements within their native
structures that cannot be disentangled simply by pulling from the N-and C-termini …

The mechanical bond in biological systems

SR Beeren, CT McTernan, F Schaufelberger - Chem, 2023 - cell.com
The field of mechanically interlocked molecules (MIMs) has advanced rapidly in recent
years, with much work focused on their use in materials, sensing, and catalysis. However …

De novo design of knotted tandem repeat proteins

LA Doyle, B Takushi, RD Kibler, LF Milles… - Nature …, 2023 - nature.com
De novo protein design methods can create proteins with folds not yet seen in nature. These
methods largely focus on optimizing the compatibility between the designed sequence and …

AlphaFold predicts novel human proteins with knots

AP Perlinska, WH Niemyska, BA Gren… - Protein …, 2023 - Wiley Online Library
The fact that proteins can have their chain formed in a knot is known for almost 30 years.
However, as they are not common, only a fraction of such proteins is available in the Protein …

Sampling molecular conformations and dynamics in a multiuser virtual reality framework

M O'Connor, HM Deeks, E Dawn, O Metatla… - Science …, 2018 - science.org
We describe a framework for interactive molecular dynamics in a multiuser virtual reality
(VR) environment, combining rigorous cloud-mounted atomistic physics simulations with …

Stereoselective synthesis of a composite knot with nine crossings

L Zhang, AJ Stephens, AL Nussbaumer… - Nature Chemistry, 2018 - nature.com
The simultaneous synthesis of a molecular nine-crossing composite knot that contains three
trefoil tangles of the same handedness and a 9 7 3 link (a type of cyclic [3] catenane …

Mechanical strength of RNA knot in Zika virus protects against cellular defenses

M Zhao, MT Woodside - Nature Chemical Biology, 2021 - nature.com
Unusual knot-like structures recently discovered in viral exoribonuclease-resistant RNAs
(xrRNAs) prevent digestion by host RNases to create subgenomic RNAs enhancing …

[HTML][HTML] Interactive molecular dynamics in virtual reality from quantum chemistry to drug binding: An open-source multi-person framework

MB O'Connor, SJ Bennie, HM Deeks… - The Journal of …, 2019 - pubs.aip.org
As molecular scientists have made progress in their ability to engineer nanoscale molecular
structure, we face new challenges in our ability to engineer molecular dynamics (MD) and …

On folding of entangled proteins: knots, lassos, links and θ-curves

JI Sulkowska - Current opinion in structural biology, 2020 - Elsevier
Around 6% of protein structures deposited in the PDB are entangled, forming knots,
slipknots, lassos, links, and θ-curves. In each of these cases, the protein backbone weaves …