Protein-Protein Association in Polymer Solutions: From Dilute to Semidilute to Concentrated

AbstractIn a typical cell, proteins function in the crowded cytoplasmic environment where 30% of the space is occupied by macromolecules of varying size and nature. This environment may be simulated in vitro using synthetic polymers. Here, we followed the association and diffusion rates of TEM1-β-lactamase (TEM) and the β-lactamase inhibitor protein (BLIP) in the presence of crowding agents of varying molecular mass, from monomers (ethylene glycol, glycerol, or sucrose) to polymeric agents such as different polyethylene glycols (PEGs, 0.2–8 kDa) and Ficoll. An inverse linear relation was found between translational diffusion of the proteins and viscosity in all solutions tested, in accordance with the Stokes-Einstein (SE) relation. Conversely, no simple relation was found between either rotational diffusion rates or association rates (kon) and viscosity. To assess the translational diffusion-independent steps along the association pathway, we introduced a new factor, α, which corrects the relative change in kon by the relative change in solution viscosity, thus measuring the deviations of the association rates from SE behavior. We found that these deviations were related to the three regimes of polymer solutions: dilute, semidilute, and concentrated. In the dilute regime PEGs interfere with TEM-BLIP association by introducing a repulsive force due to solvophobic preferential hydration, which results in slower association than predicted by the SE relation. Crossing over from the dilute to the semidilute regime results in positive deviations from SE behavior, i.e., relatively faster association rates. These can be attributed to the depletion interaction, which results in an effective attraction between the two proteins, winning over the repulsive force. In the concentrated regime, PEGs again dramatically slow down the association between TEM and BLIP, an effect that does not depend on the physical dimensions of PEGs, but rather on their mass concentration. This is probably a manifestation of the monomer-like repulsive depletion effect known to occur in concentrated polymer solutions. As a transition from moderate to high crowding agent concentration can occur in the cellular milieu, this behavior may modulate protein association in vivo, thereby modulating biological function

Higher-Order Photon Statistics as a New Tool to Reveal Hidden Excited States in a Plasmonic Cavity

Among the best known quantities obtainable from photon correlation measurements are the $g^{(m)}$~correlation functions. Here, we introduce a new procedure to evaluate these correlation functions based on higher-order factorial cumulants $C_{\text{F},m}$ which integrate over the time dependence of the correlation functions, i.e., summarize the available information at different time spans. In a systematic manner, the information content of higher-order correlation functions as well as the distribution of photon waiting times is taken into account. Our procedure greatly enhances the sensitivity for probing correlations and, moreover, is robust against a limited counting efficiency and time resolution in experiment. It can be applied even in case $g^{(m)}$ is not accessible at short time spans. We use the new evaluation scheme to analyze the photon emission of a plasmonic cavity coupled to a single quantum dot. We derive criteria which must hold if the system can be described by a generic Jaynes-Cummings model. A violation of the criteria can be explained by the presence of an additional excited quantum dot state.Comment: 10 pages manuscript + 9 pages supporting informatio

Complex plasmon-exciton dynamics revealed through quantum dot light emission in a nanocavity

Plasmonic cavities can confine electromagnetic radiation to deep sub-wavelength regimes. This facilitates strong coupling phenomena to be observed at the limit of individual quantum emitters. Here, we report an extensive set of measurements of plasmonic cavities hosting one to a few semiconductor quantum dots. Scattering spectra show Rabi splitting, demonstrating that these devices are close to the strong coupling regime. Using Hanbury Brown and Twiss interferometry, we observe non-classical emission, allowing us to directly determine the number of emitters in each device. Surprising features in photoluminescence spectra point to the contribution of multiple excited states. Using model simulations based on an extended Jaynes-Cummings Hamiltonian, we find that the involvement of a dark state of the quantum dots explains the experimental findings. The coupling of quantum emitters to plasmonic cavities thus exposes complex relaxation pathways and emerges as an unconventional means to control dynamics of quantum states.S.N.G. thanks the Government of Israel for a Planning and Budgeting Committee Fel-lowship. G.H. is the incumbent of the Hilda Pomeraniec Memorial Professorial Chair.R.E., T.N. and J.A. acknowledge funding from projects FIS2016-80174-P and PID2019-107432GB-I00 of the Spanish Ministry of Science, Innovation and Universities MICINN,as well as funding from grant IT1164-19 for consolidated groups of the Basque Uni-versity, through the Department of Universities of the Basque Government. This projectreceived partial support from the European Union’s Horizon 2020 research and inno-vation programme under grant agreement no. 861950, project POSEIDON, and grantagreement no. 810626, project SINNCE. We thank Garnett W. Bryant and PeterNordlander for stimulating discussion

Complex plasmon-exciton dynamics revealed through quantum dot light emission in a nanocavity

Plasmonic cavities can confine electromagnetic radiation to deep sub-wavelength regimes. This facilitates strong coupling phenomena to be observed at the limit of individual quantum emitters. Here, we report an extensive set of measurements of plasmonic cavities hosting one to a few semiconductor quantum dots. Scattering spectra show Rabi splitting, demonstrating that these devices are close to the strong coupling regime. Using Hanbury Brown and Twiss interferometry, we observe non-classical emission, allowing us to directly determine the number of emitters in each device. Surprising features in photoluminescence spectra point to the contribution of multiple excited states. Using model simulations based on an extended Jaynes-Cummings Hamiltonian, we find that the involvement of a dark state of the quantum dots explains the experimental findings. The coupling of quantum emitters to plasmonic cavities thus exposes complex relaxation pathways and emerges as an unconventional means to control dynamics of quantum states.S.N.G. thanks the Government of Israel for a Planning and Budgeting Committee Fel-lowship. G.H. is the incumbent of the Hilda Pomeraniec Memorial Professorial Chair.R.E., T.N. and J.A. acknowledge funding from projects FIS2016-80174-P and PID2019-107432GB-I00 of the Spanish Ministry of Science, Innovation and Universities MICINN,as well as funding from grant IT1164-19 for consolidated groups of the Basque Uni-versity, through the Department of Universities of the Basque Government. This projectreceived partial support from the European Union’s Horizon 2020 research and inno-vation programme under grant agreement no. 861950, project POSEIDON, and grantagreement no. 810626, project SINNCE. We thank Garnett W. Bryant and PeterNordlander for stimulating discussion

Vacuum Rabi splitting of a dark plasmonic cavity mode revealed by fast electrons

Recent years have seen a growing interest in strong coupling between plasmons and excitons, as a way to generate new quantum optical testbeds and influence chemical dynamics and reactivity. Strong coupling to bright plasmonic modes has been achieved even with single quantum emitters. Dark plasmonic modes fare better in some applications due to longer lifetimes, but are difficult to probe as they are subradiant. Here, we apply electron energy loss (EEL) spectroscopy to demonstrate that a dark mode of an individual plasmonic bowtie can interact with a small number of quantum emitters, as evidenced by Rabi-split spectra. Coupling strengths of up to 85meV place the bowtie-emitter devices at the onset of the strong coupling regime. Remarkably, the coupling occurs at the periphery of the bowtie gaps, even while the electron beam probes their center. Our findings pave the way for using EEL spectroscopy to study exciton-plasmon interactions involving non-emissive photonic modes

FRET-based dynamic structural biology: Challenges, perspectives and an appeal for open-science practices

Single-molecule FRET (smFRET) has become a mainstream technique for studying biomolecular structural dynamics. The rapid and wide adoption of smFRET experiments by an ever-increasing number of groups has generated significant progress in sample preparation, measurement procedures, data analysis, algorithms and documentation. Several labs that employ smFRET approaches have joined forces to inform the smFRET community about streamlining how to perform experiments and analyze results for obtaining quantitative information on biomolecular structure and dynamics. The recent efforts include blind tests to assess the accuracy and the precision of smFRET experiments among different labs using various procedures. These multi-lab studies have led to the development of smFRET procedures and documentation, which are important when submitting entries into the archiving system for integrative structure models, PDB-Dev. This position paper describes the current ‘state of the art’ from different perspectives, points to unresolved methodological issues for quantitative structural studies, provides a set of ‘soft recommendations’ about which an emerging consensus exists, and lists openly available resources for newcomers and seasoned practitioners. To make further progress, we strongly encourage ‘open science’ practices