Relaxation mechanisms of multi-quantum coherences in the Zeeman structure of atomic Cs trapped in solid He

This paper extends our previous work on near-degenerate magnetic resonance transitions in alkali ground states involving the simultaneous absorption of multiple radio-frequency quanta. New experimental results with an improved spectral resolution were obtained with cesium atoms trapped in the cubic phase of a helium crystal. The main objective of the paper is a theoretical study of the influence of stochastic perturbations of given multipole orders on the various multi-photon coherences. Algebraic and numerical results for perturbations of both dipolar and quadrupolar symmetry are presented. The present experimental resolution does not yet allow us to distinguish between these two most likely relaxation mechanisms. Nonetheless, the experimental spectra are very well described when allowing in the calculations for a magnetic field inhomogeneity of 2×10-

Multi-photon processes in the Zeeman structure of atomic Cs trapped in solid helium

We report magnetic resonance experiments with optical detection performed on cesium atoms trapped in a crystalline Hematrix. Multi-photon transitions, i.e., processes in which several radio-frequency photons are absorbed simultaneously in a given hyperfine Zeeman multiplet of the ground state, were the central topic of these studies. The long relaxation times of spin coherences of Cs in solid He allow such transitions to be spectrally resolved in fields as low as 1mT. We observed all allowed multi-photon transitions up to the ΔM=8 transition in the F=4 state. We compare the experimental spectra with theoretical spectra obtained from numerical solutions of the Liouville equation that include optical pumping and the interaction with the static and oscillating fields. Multi-photon transitions may find applications in magnetometry, suppress systematic effects in EDM experiments, and allow the study of relaxation phenomena in doped He crystals. The demonstration of these features is still hindered by inhomogeneous line broadenin

Disordered RNA chaperones can enhance nucleic acid folding via local charge screening

This work is licensed under a Creative Commons Attribution 4.0 International License.RNA chaperones are proteins that aid in the folding of nucleic acids, but remarkably, many of these proteins are intrinsically disordered. How can these proteins function without a well-defined three-dimensional structure? Here, we address this question by studying the hepatitis C virus core protein, a chaperone that promotes viral genome dimerization. Using single-molecule fluorescence spectroscopy, we find that this positively charged disordered protein facilitates the formation of compact nucleic acid conformations by acting as a flexible macromolecular counterion that locally screens repulsive electrostatic interactions with an efficiency equivalent to molar salt concentrations. The resulting compaction can bias unfolded nucleic acids towards folding, resulting in faster folding kinetics. This potentially widespread mechanism is supported by molecular simulations that rationalize the experimental findings by describing the chaperone as an unstructured polyelectrolyte.Swiss National Science FoundationEuropean Molecular Biology OrganizationIntramural Research Program of the NIDDK at the National Institutes of Healt

The inverted free energy landscape of an intrinsically disordered peptide by simulations and experiments

The free energy landscape theory has been very successful in rationalizing the folding behaviour of globular proteins, as this representation provides intuitive information on the number of states involved in the folding process, their populations and pathways of interconversion. We extend here this formalism to the case of the A\u3b240 peptide, a 40-residue intrinsically disordered protein fragment associated with Alzheimer's disease. By using an advanced sampling technique that enables free energy calculations to reach convergence also in the case of highly disordered states of proteins, we provide a precise structural characterization of the free energy landscape of this peptide. We find that such landscape has inverted features with respect to those typical of folded proteins. While the global free energy minimum consists of highly disordered structures, higher free energy regions correspond to a large variety of transiently structured conformations with secondary structure elements arranged in several different manners, and are not separated from each other by sizeable free energy barriers. From this peculiar structure of the free energy landscape we predict that this peptide should become more structured and not only more compact, with increasing temperatures, and we show that this is the case through a series of biophysical measurements

Precision and accuracy of single-molecule FRET measurements - a multi-laboratory benchmark study

Single-molecule Förster resonance energy transfer (smFRET) is increasingly being used to determine distances, structures, and dynamics of biomolecules in vitro and in vivo. However, generalized protocols and FRET standards to ensure the reproducibility and accuracy of measurements of FRET efficiencies are currently lacking. Here we report the results of a comparative blind study in which 20 labs determined the FRET efficiencies (E) of several dye-labeled DNA duplexes. Using a unified, straightforward method, we obtained FRET efficiencies with s.d. between ±0.02 and ±0.05. We suggest experimental and computational procedures for converting FRET efficiencies into accurate distances, and discuss potential uncertainties in the experiment and the modeling. Our quantitative assessment of the reproducibility of intensity-based smFRET measurements and a unified correction procedure represents an important step toward the validation of distance networks, with the ultimate aim of achieving reliable structural models of biomolecular systems by smFRET-based hybrid methods

The FRET-based structural dynamics challenge -- community contributions to consistent and open science practices

Single-molecule Förster resonance energy transfer (smFRET) has become a mainstream technique for probing biomolecular structural dynamics. The rapid and wide adoption of the technique by an ever-increasing number of groups has generated many improvements and variations in the technique itself, in methods for sample preparation and characterization, in analysis of the data from such experiments, and in analysis codes and algorithms. Recently, several labs that employ smFRET have joined forces to try to bring the smFRET community together in adopting a consensus on how to perform experiments and analyze results for achieving quantitative structural information. These recent efforts include multi-lab blind-tests to assess the accuracy and precision of smFRET between different labs using different procedures, the formal assembly of the FRET community and development of smFRET procedures to be considered for entries in the wwPDB. Here we delve into the different approaches and viewpoints in the field. This position paper describes the current "state-of-the field", points to unresolved methodological issues for quantitative structural studies, provides a set of 'soft recommendations' about which an emerging consensus exists, and a list of resources that are openly available. To make further progress, we strongly encourage 'open science' practices. We hope that this position paper will provide a roadmap for newcomers to the field, as well as a reference for seasoned practitioners