Determination of protein-protein interactions at the single-molecule level using optical tweezers.

Biomolecular interactions are at the base of all physical processes within living organisms; the study of these interactions has led to the development of a plethora of different methods. Among these, single-molecule (in singulo) experiments have become relevant in recent years because these studies can give insight into mechanisms and interactions that are hidden for ensemble-based (in multiplo) methods. The focus of this review is on optical tweezer (OT) experiments, which can be used to apply and measure mechanical forces in molecular systems. OTs are based on optical trapping, where a laser is used to exert a force on a dielectric bead; and optically trap the bead at a controllable position in all three dimensions. Different experimental approaches have been developed to study protein­protein interactions using OTs, such as: (1) refolding and unfolding in trans interaction where one protein is tethered between the beads and the other protein is in the solution; (2) constant force in cis interaction where each protein is bound to a bead, and the tension is suddenly increased. The interaction may break after some time, giving information about the lifetime of the binding at that tension. And (3) force ramp in cis interaction where each protein is attached to a bead and a ramp force is applied until the interaction breaks. With these experiments, parameters such as kinetic constants (koff, kon), affinity values (KD), energy to the transition state ΔG≠, distance to the transition state Δx≠ can be obtained. These parameters characterize the energy landscape of the interaction. Some parameters such as distance to the transition state can only be obtained from force spectroscopy experiments such as those described here.

Improved Bounds on Ultralight Scalar Dark Matter in the Radio-Frequency Range.

We present a search for fundamental constant oscillations in the range 20 kHz-100 MHz that may arise within models for ultralight dark matter (UDM). Using two independent optical-spectroscopy apparatuses, we achieve up to ×1000 greater sensitivity in the search relative to previous work [D. Antypas et al., Phys. Rev. Lett. 123, 141102 (2019).PRLTAO0031-900710.1103/PhysRevLett.123.141102]. We report no observation of UDM and thus constrain respective couplings to electrons and photons within the investigated UDM particle mass range 8×10^{-11}-4×10^{-7} eV. The constraints significantly exceed previously set bounds from atomic spectroscopy and, as we show, may surpass in future experiments those provided by equivalence-principle (EP) experiments in a specific case regarding the combination of UDM couplings probed by the EP experiments.

Search for Axionlike Dark Matter Using Solid-State Nuclear Magnetic Resonance.

We report the results of an experimental search for ultralight axionlike dark matter in the mass range 162-166 neV. The detection scheme of our Cosmic Axion Spin Precession Experiment is based on a precision measurement of ^{207}Pb solid-state nuclear magnetic resonance in a polarized ferroelectric crystal. Axionlike dark matter can exert an oscillating torque on ^{207}Pb nuclear spins via the electric dipole moment coupling g_{d} or via the gradient coupling g_{aNN}. We calibrate the detector and characterize the excitation spectrum and relaxation parameters of the nuclear spin ensemble with pulsed magnetic resonance measurements in a 4.4 T magnetic field. We sweep the magnetic field near this value and search for axionlike dark matter with Compton frequency within a 1 MHz band centered at 39.65 MHz. Our measurements place the upper bounds |g_{d}|<9.5×10^{-4} GeV^{-2} and |g_{aNN}|<2.8×10^{-1} GeV^{-1} (95% confidence level) in this frequency range. The constraint on g_{d} corresponds to an upper bound of 1.0×10^{-21} e cm on the amplitude of oscillations of the neutron electric dipole moment and 4.3×10^{-6} on the amplitude of oscillations of CP-violating θ parameter of quantum chromodynamics. Our results demonstrate the feasibility of using solid-state nuclear magnetic resonance to search for axionlike dark matter in the neV mass range.

Search for Axionlike Dark Matter with a Liquid-State Nuclear Spin Comagnetometer.

We report the results of a search for axionlike dark matter using nuclear magnetic resonance (NMR) techniques. This search is part of the multifaceted Cosmic Axion Spin Precession Experiment program. In order to distinguish axionlike dark matter from magnetic fields, we employ a comagnetometry scheme measuring ultralow-field NMR signals involving two different nuclei (^{13}C and ^{1}H) in a liquid-state sample of acetonitrile-2-^{13}C (^{13}CH_{3}CN). No axionlike dark matter signal was detected above the background. This result constrains the parameter space describing the coupling of the gradient of the axionlike dark matter field to nucleons to be g_{aNN}<6×10^{-5} GeV^{-1} (95% confidence level) for particle masses ranging from 10^{-22} eV to 1.3×10^{-17} eV, improving over previous laboratory limits for masses below 10^{-21} eV. The result also constrains the coupling of nuclear spins to the gradient of the square of the axionlike dark matter field, improving over astrophysical limits by orders of magnitude over the entire range of particle masses probed.

Stochastic fluctuations of bosonic dark matter.

Numerous theories extending beyond the standard model of particle physics predict the existence of bosons that could constitute dark matter. In the standard halo model of galactic dark matter, the velocity distribution of the bosonic dark matter field defines a characteristic coherence time τc. Until recently, laboratory experiments searching for bosonic dark matter fields have been in the regime where the measurement time T significantly exceeds τc, so null results have been interpreted by assuming a bosonic field amplitude Φ0 fixed by the average local dark matter density. Here we show that experiments operating in the T ≪ τc regime do not sample the full distribution of bosonic dark matter field amplitudes and therefore it is incorrect to assume a fixed value of Φ0 when inferring constraints. Instead, in order to interpret laboratory measurements (even in the event of a discovery), it is necessary to account for the stochastic nature of such a virialized ultralight field. The constraints inferred from several previous null experiments searching for ultralight bosonic dark matter were overestimated by factors ranging from 3 to 10 depending on experimental details, model assumptions, and choice of inference framework.

Search for topological defect dark matter with a global network of optical magnetometers.

Ultralight bosons such as axion-like particles are viable candidates for dark matter. They can form stable, macroscopic field configurations in the form of topological defects that could concentrate the dark matter density into many distinct, compact spatial regions that are small compared with the Galaxy but much larger than the Earth. Here we report the results of the search for transient signals from the domain walls of axion-like particles by using the global network of optical magnetometers for exotic (GNOME) physics searches. We search the data, consisting of correlated measurements from optical atomic magnetometers located in laboratories all over the world, for patterns of signals propagating through the network consistent with domain walls. The analysis of these data from a continuous month-long operation of GNOME finds no statistically significant signals, thus placing experimental constraints on such dark matter scenarios.

Structural characterization of the saxitoxin-targeting APTSTX1 aptamer using optical tweezers and molecular dynamics simulations.

Optical tweezers have enabled the exploration of picoNewton forces and dynamics in single-molecule systems such as DNA and molecular motors. In this work, we used optical tweezers to study the folding/unfolding dynamics of the APTSTX1-aptamer, a single-stranded DNA molecule with high affinity for saxitoxin (STX), a lethal neurotoxin. By measuring the transition force during (un)folding processes, we were able to characterize and distinguish the conformational changes of this aptamer in the presence of magnesium ions and toxin. This work was supported by molecular dynamics (MD) simulations to propose an unfolding mechanism of the aptamer-Mg+2 complex. Our results are a step towards the development of new aptamer-based STX sensors that are potentially cheaper and more sensitive than current alternatives.

Constraints on bosonic dark matter from ultralow-field nuclear magnetic resonance.

The nature of dark matter, the invisible substance making up over 80% of the matter in the universe, is one of the most fundamental mysteries of modern physics. Ultralight bosons such as axions, axion-like particles, or dark photons could make up most of the dark matter. Couplings between such bosons and nuclear spins may enable their direct detection via nuclear magnetic resonance (NMR) spectroscopy: As nuclear spins move through the galactic dark-matter halo, they couple to dark matter and behave as if they were in an oscillating magnetic field, generating a dark-matter-driven NMR signal. As part of the cosmic axion spin precession experiment (CASPEr), an NMR-based dark-matter search, we use ultralow-field NMR to probe the axion-fermion "wind" coupling and dark-photon couplings to nuclear spins. No dark matter signal was detected above background, establishing new experimental bounds for dark matter bosons with masses ranging from 1.8 × 10-16 to 7.8 × 10-14 eV.

Single-molecule measurements of the effect of force on Thy-1/αvß3-integrin interaction using nonpurified proteins.

Thy-1 and αvß3 integrin mediate bidirectional cell-to-cell communication between neurons and astrocytes. Thy-1/αvß3 interactions stimulate astrocyte migration and the retraction of neuronal prolongations, both processes in which internal forces are generated affecting the bimolecular interactions that maintain cell-cell adhesion. Nonetheless, how the Thy-1/αvß3 interactions respond to mechanical cues is an unresolved issue. In this study, optical tweezers were used as a single-molecule force transducer, and the Dudko-Hummer-Szabo model was applied to calculate the kinetic parameters of Thy-1/αvß3 dissociation. A novel experimental strategy was implemented to analyze the interaction of Thy-1-Fc with nonpurified αvß3-Fc integrin, whereby nonspecific rupture events were corrected by using a new mathematical approach. This methodology permitted accurately estimating specific rupture forces for Thy-1-Fc/αvß3-Fc dissociation and calculating the kinetic and transition state parameters. Force exponentially accelerated Thy-1/αvß3 dissociation, indicating slip bond behavior. Importantly, nonspecific interactions were detected even for purified proteins, highlighting the importance of correcting for such interactions. In conclusion, we describe a new strategy to characterize the response of bimolecular interactions to forces even in the presence of nonspecific binding events. By defining how force regulates Thy-1/αvß3 integrin binding, we provide an initial step towards understanding how the neuron-astrocyte pair senses and responds to mechanical cues.