Multivalent interactions of the disordered regions of XLF and XRCC4 foster robust cellular NHEJ and drive the formation of ligation-boosting condensates in vitro.

In mammalian cells, DNA double-strand breaks are predominantly repaired by non-homologous end joining (NHEJ). During repair, the Ku70-Ku80 heterodimer (Ku), X-ray repair cross complementing 4 (XRCC4) in complex with DNA ligase 4 (X4L4) and XRCC4-like factor (XLF) form a flexible scaffold that holds the broken DNA ends together. Insights into the architectural organization of the NHEJ scaffold and its regulation by the DNA-dependent protein kinase catalytic subunit (DNA-PKcs) were recently obtained by single-particle cryo-electron microscopy analysis. However, several regions, especially the C-terminal regions (CTRs) of the XRCC4 and XLF scaffolding proteins, have largely remained unresolved in experimental structures, which hampers the understanding of their functions. Here we used magnetic resonance techniques and biochemical assays to comprehensively characterize the interactions and dynamics of the XRCC4 and XLF CTRs at residue resolution. We show that the CTRs of XRCC4 and XLF are intrinsically disordered and form a network of multivalent heterotypic and homotypic interactions that promotes robust cellular NHEJ activity. Importantly, we demonstrate that the multivalent interactions of these CTRs lead to the formation of XLF and X4L4 condensates in vitro, which can recruit relevant effectors and critically stimulate DNA end ligation. Our work highlights the role of disordered regions in the mechanism and dynamics of NHEJ and lays the groundwork for the investigation of NHEJ protein disorder and its associated condensates inside cells with implications in cancer biology, immunology and the development of genome-editing strategies.

Small-molecule autocatalysis drives compartment growth, competition and reproduction.

Sustained autocatalysis coupled to compartment growth and division is a key step in the origin of life, but an experimental demonstration of this phenomenon in an artificial system has previously proven elusive. We show that autocatalytic reactions within compartments-when autocatalysis, and reactant and solvent exchange outpace product exchange-drive osmosis and diffusion, resulting in compartment growth. We demonstrate, using the formose reaction compartmentalized in aqueous droplets in an emulsion, that compartment volume can more than double. Competition for a common reactant (formaldehyde) causes variation in droplet growth rate based on the composition of the surrounding droplets. These growth rate variations are partially transmitted after selective division of the largest droplets by shearing, which converts growth-rate differences into differences in droplet frequency. This shows how a combination of properties of living systems (growth, division, variation, competition, rudimentary heredity and selection) can arise from simple physical-chemical processes and may have paved the way for the emergence of evolution by natural selection.

Comprehensive analysis of relaxation decays from high-resolution relaxometry.

Relaxometry consists in measuring relaxation rates over orders of magnitude of magnetic fields to probe motions of complex systems. High-resolution relaxometry (HRR) experiments can be performed on conventional high-field NMR magnets equipped with a sample shuttle. During the experiment, the sample shuttle transfers the sample between the high-field magnetic center and a chosen position in the stray field for relaxation during a variable delay, thus using the stray field as a variable field. As the relaxation delay occurs outside of the probe, HRR experiments cannot rely on the control of cross-relaxation pathways, which is standard in high-field relaxation pulse sequences. Thus, decay rates are not pure relaxation rates, which may impair a reliable description of the dynamics. Previously, we took into account cross-relaxation effects in the analysis of high-resolution relaxometry data by applying a correction factor to relaxometry decay rates in order to estimate relaxation rates. These correction factors were obtained from the iterative simulation of the relaxation decay while the sample lies outside of the probe and a preceding analysis of relaxation rates which relies on the approximation of a priori multi-exponential decays by mono-exponential functions. However, an analysis protocol matching directly experimental and simulated relaxometry decays should be more self consistent and more generally applicable as it can accommodate deviations from mono-exponential decays. Here, we introduce Matching INtensities for the Optimization of Timescales and Amplitudes of motions Under Relaxometry (MINOTAUR), a framework for the analysis of high-resolution relaxometry that takes as input the intensity decays at all fields. This approach uses the full relaxation matrix to calculate intensity decays, allowing complex relaxation pathways to be taken into account. Therefore, it eliminates the need for a correction of decay rates and for fitting multi-exponential decays with mono-exponential functions. The MINOTAUR software is designed as a flexible framework where relaxation matrices and spectral density functions corresponding to various models of motions can be defined on a case-by-case basis. The agreement with our previous analyses of protein side-chain dynamics from carbon-13 relaxation is excellent, while providing a more robust analysis tool. We expect MINOTAUR to become the tool of choice for the analysis of high-resolution relaxometry.

Multivalent interactions of the disordered regions of XLF and XRCC4 foster robust cellular NHEJ and drive the formation of ligation-boosting condensates in vitro.

In mammalian cells, DNA double-strand breaks are predominantly repaired by non-homologous end joining (NHEJ). During repair, the Ku70/80 heterodimer (Ku), XRCC4 in complex with DNA Ligase 4 (X4L4), and XLF form a flexible scaffold that holds the broken DNA ends together. Insights into the architectural organization of the NHEJ scaffold and its regulation by the DNA-dependent protein kinase catalytic subunit (DNA-PKcs) have recently been obtained by single-particle cryo-electron microscopy analysis. However, several regions, especially the C-terminal regions (CTRs) of the XRCC4 and XLF scaffolding proteins, have largely remained unresolved in experimental structures, which hampers the understanding of their functions. Here, we used magnetic resonance techniques and biochemical assays to comprehensively characterize the interactions and dynamics of the XRCC4 and XLF CTRs at atomic resolution. We show that the CTRs of XRCC4 and XLF are intrinsically disordered and form a network of multivalent heterotypic and homotypic interactions that promotes robust cellular NHEJ activity. Importantly, we demonstrate that the multivalent interactions of these CTRs led to the formation of XLF and X4L4 condensates in vitro which can recruit relevant effectors and critically stimulate DNA end ligation. Our work highlights the role of disordered regions in the mechanism and dynamics of NHEJ and lays the groundwork for the investigation of NHEJ protein disorder and its associated condensates inside cells with implications in cancer biology, immunology and the development of genome editing strategies.

Various facets of intermolecular transfer of phase coherence by nuclear dipolar fields.

It has long been recognized that dipolar fields can mediate intermolecular transfer of phase coherence from abundant solvent to sparse solute spins. Generally, the dipolar field has been considered while acting during prolonged free-precession delays. Recently, we have shown that transfer can also occur during suitable uninterrupted radio frequency pulse trains that are used for total correlation spectroscopy. Here, we will expand upon the latter work. First, analytical expressions for the evolution of the solvent magnetization under continuous irradiation and the influence of the dipolar field are derived. These expressions facilitate the simulations of the transfer process. Then, a pulse sequence for the retrieval of high-resolution spectra in inhomogeneous magnetic fields is described, along with another sequence to detect a transfer from an intermolecular double-quantum coherence. Finally, various schemes are discussed where the magnetization is modulated by a combination of multiple selective radio frequency pulses and pulsed field gradients in different directions. In these schemes, the magnetization is manipulated in such a way that the dipolar field, which originates from a single-spin species, can be decomposed into two components. Each component originates from a part of the magnetization that is modulated in a different direction. Both can independently, but simultaneously, mediate an intermolecular transfer of phase coherence.

Long-lived states of methylene protons in achiral molecules.

In nuclear magnetic resonance (NMR), the lifetimes of long-lived states (LLSs) are exquisitely sensitive to their environment. However, the number of molecules where such states can be excited has hitherto been rather limited. Here, it is shown that LLSs can be readily excited in many common molecules that contain two or more neighboring CH2 groups. Accessing such LLSs does not require any isotopic enrichment, nor does it require any stereogenic centers to lift the chemical equivalence of CH2 protons. LLSs were excited in a variety of metabolites, neurotransmitters, vitamins, amino acids, and other molecules. One can excite LLSs in several different molecules simultaneously. In combination with magnetic resonance imaging, LLSs can reveal a contrast upon noncovalent binding of ligands to macromolecules. This suggests new perspectives to achieve high-throughput parallel drug screening by NMR.

Transfer of phase coherence by the dipolar field in total correlation liquid state nuclear magnetic resonance spectroscopy.

In this work, it is shown that radio-frequency pulse trains designed for total correlation nuclear magnetic resonance spectroscopy can mediate inter-molecular transfer of phase coherence from one spin species to another by the dipolar field. In contrast to previous studies (where short pulses interleaved with long free precession delays were used), here the transverse component of the dipolar field plays an important role. The transfer is so efficient that signal intensities close to those of a single pulse experiment can be achieved. The results are rationalized by numerical simulations that take into account relaxation and diffusion.

Unexpected Acid-Triggered Formation of Reversibly Photoswitchable Stenhouse Salts from Donor-Acceptor Stenhouse Adducts.

Donor-acceptor Stenhouse adducts (DASAs) are reversibly photoswitchable dyes, which are able to interconvert between a red/NIR absorbing triene-like state and a colorless cyclic state. Although optically attractive for multiple applications, their low solubility and lack of photoswitching in water impede their use in aqueous environments. We developed water-soluble DASAs based on indoline as donor and methyl, or trifluoromethyl, pyrazolone-based acceptors. In acetonitrile, photophysical analysis and photochemical studies, accounted with a three-state kinetic model, confirmed the reversible photoswitching mechanism previously proposed. In water, the colorless cyclic state is a thermodynamic sink at neutral pH values. In contrast, in acidic conditions, we observed a fast scrambling of DASAs' end-group resulting in the in situ formation of Stenhouse salts (StS), which are in turn capable of reversible photoswitching. We believe that this unexpected result is of interest not only for the future design of DASAs with improved stability, but also for further development and applications of StS as photoswitchable probes.

Effects of Microwave Gating on Nuclear Spin Echoes in Dynamic Nuclear Polarization.

Dipolar or quadrupolar echoes allow one to observe undistorted powder patterns, in contrast to simple Fourier transformations of free induction decays (FIDs). In this work, the buildup of proton polarization due to dynamic nuclear polarization (DNP) is monitored by observing echoes rather than FIDs. When the microwave irradiation is interrupted during the buildup of DNP, the electrons relax back to their Boltzmann distribution at high fields (B0 = 6.7 T) and low temperatures 1.2 < Tsample < 4.0 K, so that dipolar flip-flop-flip terms involving two electrons and one proton become largely ineffective as a mechanism of proton decoherence. This leads to a prolongation of the nuclear coherence lifetime T2'(1H). The increase in T2'(1H) leads to transient surges of the amplitudes of spin echoes. Conversely, transient slumps of spin echoes are observed when the microwave irradiation is switched back on, due to a shortening of nuclear coherence lifetimes.

A Direct NMR Method To Measure Self-Diffusion Coefficients in Liquids by Monitoring Diffusing Molecules through One-Dimensional Imaging.

Diffusion processes can be followed directly by recording one-dimensional images of a selected slice at variable intervals after selective inversion of the magnetization. The resulting diffusion coefficients of H2 O and DMSO are consistent with earlier studies at different temperatures, obtained by monitoring the attenuation of NMR signals as a function of the gradient amplitude in gradient echo sequences.

Radiation damping strongly perturbs remote resonances in the presence of homonuclear mixing.

In this work, it is experimentally shown that the weak oscillating magnetic field (known as the "radiation damping" field) caused by the inductive coupling between the transverse magnetization of nuclei and the radio frequency circuit perturbs remote resonances when homonuclear total correlation mixing is applied. Numerical simulations are used to rationalize this effect.

Detection of Metabolite-Protein Interactions in Complex Biological Samples by High-Resolution Relaxometry: Toward Interactomics by NMR.

Metabolomics, the systematic investigation of metabolites in biological fluids, cells, or tissues, reveals essential information about metabolism and diseases. Metabolites have functional roles in a myriad of biological processes, as substrates and products of enzymatic reactions but also as cofactors and regulators of large numbers of biochemical mechanisms. These functions involve interactions of metabolites with macromolecules. Yet, methods to systematically investigate these interactions are still scarce to date. In particular, there is a need for techniques suited to identify and characterize weak metabolite-macromolecule interactions directly in complex media such as biological fluids. Here, we introduce a method to investigate weak interactions between metabolites and macromolecules in biological fluids. Our approach is based on high-resolution NMR relaxometry and does not require any invasive procedure or separation step. We show that we can detect interactions between small and large molecules in human blood serum and quantify the size of the complex. Our work opens the way for investigations of metabolite (or other small molecules)-protein interactions in biological fluids for interactomics or pharmaceutical applications.

Theoretical and computational framework for the analysis of the relaxation properties of arbitrary spin systems. Application to high-resolution relaxometry.

A wide variety of nuclear magnetic resonance experiments rely on the prediction and analysis of relaxation processes. Recently, innovative approaches have been introduced where the sample travels through a broad range of magnetic fields in the course of the experiment, such as dissolution dynamic nuclear polarization or high-resolution relaxometry. Understanding the relaxation properties of nuclear spin systems over orders of magnitude of magnetic fields is essential to rationalize the results of these experiments. For example, during a high-resolution relaxometry experiment, the absence of control of nuclear spin relaxation pathways during the sample transfers and relaxation delays leads to systematic deviations of polarization decays from an ideal mono-exponential decay with the pure longitudinal relaxation rate. These deviations have to be taken into account to describe quantitatively the dynamics of the system. Here, we present computational tools to (1) calculate analytical expressions of relaxation rates for a broad variety of spin systems and (2) use these analytical expressions to correct the deviations arising in high-resolution relaxometry experiments. These tools lead to a better understanding of nuclear spin relaxation, which is required to improve the sensitivity of many pulse sequences, and to better characterize motions in macromolecules.

An easy-to-implement combinatorial approach involving an activity-based assay for the discovery of a peptidyl copper complex mimicking superoxide dismutase.

A combinatorial approach using a one-bead-one-compound method and a screening based on a SOD-activity assay was set up for the discovery of an efficient peptidyl copper complex. The complex exhibited good stability constants, suitable redox potentials and excellent intrinsic activity. This complex was further assayed in cells for its antioxidant properties and showed beneficial effects when cells were subjected to oxidative stress.

Orientation-Dependent Proton Relaxation of Water Molecules Trapped in Solids: Crystallites with Long-Lived Magnetization.

The longitudinal spin-lattice relaxation properties of water molecules trapped in a static powdered polycrystalline sample of barium chlorate monohydrate are investigated by means of solid-state 1H NMR spectroscopy. Different portions of the inhomogeneous Pake pattern that are associated with crystallites at different orientations with respect to the external magnetic field show either a mono- or a biexponential recovery. At high field (9.4 T), the chemical shift anisotropy is the main interaction that is responsible for the inhomogeneity of the relaxation rates. A theoretical description of rapid two-site hopping about the H-O-H bisector in the framework of Liouville space agrees very well with the experimental evidence. Numerical simulations predict a distribution of monoexponential time constants associated with individual single-crystal orientations. Overlapping signals give rise to biexponential recovery. This is confirmed experimentally by 1H NMR spectra of static single crystals.

Cross-term Splittings Due to the Orientational Inequivalence of Proton Magnetic Shielding Tensors: Do Water Molecules Trapped in Crystals Hop or Tunnel?

Water molecules trapped in crystals of barium chlorate monohydrate have been investigated by magic-angle spinning (MAS) proton NMR spectroscopy in the temperature range 110-300 K. At high temperatures, a single spinning sideband pattern is observed. Below 150 K, however, two interleaved spinning sideband manifolds appear, with distinct centerbands that do not coincide with the average isotropic chemical shift seen at high temperatures. This hitherto unknown "cross-term splitting" results from the interplay of the homonuclear dipole-dipole coupling and two anisotropic proton shielding tensors that have identical principal components but nonequivalent orientations. The resulting cross terms cannot be averaged out by rotation about the magic angle. The analysis of the exchange-induced broadening, coalescence, and narrowing of the cross-term splitting in MAS spectra allows one to estimate the rate of exchange of the two protons between 140 and 190 K. The experimental data is compared with 2H and 1H NMR studies of the same sample reported in the literature. Density functional theory methods are utilized to estimate the thermal activation energy for a 2-fold hopping process of proton exchange about the H-O-H bisector. The Bell-Limbach model allows one to take into account contributions due to incoherent quantum tunneling in the low-temperature regime.

Advances in single-scan time-encoding magnetic resonance imaging.

Time-encoding MRI is a single-scan method that uses traditional k-encoding only in one direction. In the orthogonal "time-encoding" direction, a string of echoes appears in an order that depends on the position of the corresponding spin packets. In one variant of time-encoding, this is achieved by using a series of selective pulses and appropriate gradients in both k-encoding and time-encoding directions. Although time-encoding offers some advantages over traditional single-scan Fourier methods such as echo planar imaging (EPI), the original time-encoding sequence also has some drawbacks that limit its applications. In this work, we show how one can improve several aspects of the original time-encoding sequence. By using an additional gradient pulse one can change the order in which the echoes appear, leading to identical echo times for all echoes, and hence to a uniform signal attenuation due to transverse relaxation and a reduction in average signal attenuation due to diffusion. By rearranging positive and negative gradients one can reduce the switching rate of the gradients. Furthermore, we show how one can implement time-encoding sequences in an interleaved fashion in order to reduce signal attenuation due to transverse relaxation and diffusion, while increasing the spatial resolution.

Structure and Dynamics of an Intrinsically Disordered Protein Region That Partially Folds upon Binding by Chemical-Exchange NMR.

Many intrinsically disordered proteins (IDPs) and protein regions (IDRs) engage in transient, yet specific, interactions with a variety of protein partners. Often, if not always, interactions with a protein partner lead to partial folding of the IDR. Characterizing the conformational space of such complexes is challenging: in solution-state NMR, signals of the IDR in the interacting region become broad, weak, and often invisible, while X-ray crystallography only provides information on fully ordered regions. There is thus a need for a simple method to characterize both fully and partially ordered regions in the bound state of IDPs. Here, we introduce an approach based on monitoring chemical exchange by NMR to investigate the state of an IDR that folds upon binding through the observation of the free state of the protein. Structural constraints for the bound state are obtained from chemical shifts, and site-specific dynamics of the bound state are characterized by relaxation rates. The conformation of the interacting part of the IDR was determined and subsequently docked onto the structure of the folded partner. We apply the method to investigate the interaction between the disordered C-terminal region of Artemis and the DNA binding domain of Ligase IV. We show that we can accurately reproduce the structure of the core of the complex determined by X-ray crystallography and identify a broader interface. The method is widely applicable to the biophysical investigation of complexes of disordered proteins and folded proteins.

Susceptibility contrast by echo shifting in spatially encoded single-scan MRI.

To overcome the effects of static field inhomogeneities, single-scan hybrid imaging techniques that use k-space encoding in one direction and spatial encoding in the other have been shown to be superior to traditional imaging techniques based on full k-space encoding. Like traditional imaging methods, hybrid methods can be implemented in different ways that favor different sources of contrast. So far, little attention appears to have been paid to these aspects. By modifying an established hybrid imaging sequence called Rapid Acquisition by Sequential Excitation and Refocusing (RASER) so as to obtain Echo-Shifted RASER sequences, we show that by shifting spin echoes one can tune the contrast due to inhomogeneous T decay.

The effects of molecular diffusion in spatially encoded magnetic resonance imaging.

In spatially encoded MRI, the signal is acquired sequentially for different coordinates. In particular for single-scan acquisitions in inhomogeneous fields, spatially encoded methods improve the image quality compared to traditional k-space encoding. Previously, much attention has been paid in order to homogenize T2 losses across the sample. In this work, we investigate the effects of diffusion on the image quality in spatially encoded MRI. We show that losses due to diffusion are often not uniform along the spatially encoded dimension, and how to adapt spatially encoded sequences in order to obtain uniformly diffusion-weighted images.