Approach of Serial Crystallography

Radiation damage and cryogenic sample environment are an experimental limitation observed in the traditional X-ray crystallography technique. However, the serial crystallography (SX) technique not only helps to determine structures at room temperature with minimal radiation damage, but it is also a useful tool for profound understanding of macromolecules. Moreover, it is a new tool for time-resolved studies. Over the past 10 years, various sample delivery techniques and data collection strategies have been developed in the SX field. It also has a wide range of applications in instruments ranging from the X-ray free electron laser (XFEL) facility to synchrotrons. The importance of the various approaches in terms of the experimental techniques and a brief review of the research carried out in the field of SX has been highlighted in this editorial.

Learning to Fold RNAs in Linear Time

RNA secondary structure is helpful for understanding RNA’s functionality, thus accurate prediction systems are desired. Both thermodynamics-based models and machine learning-based models have been used in different prediction systems to solve this problem. Compared to thermodynamics-based models, machine learning-based models can address the inaccurate measurement of thermodynamic parameters due to experimental limitation. However, the existing methods for training machine learning-based models are still expensive because of their cubic-time inference cost. To overcome this, we present a linear-time machine learning-based folding system, using recently proposed approximate folding tool LinearFold as inference engine, and structured SVM (sSVM) as training algorithm. Furthermore, to remedy non-convergence of naive sSVM with inexact search inference, we introduce a max violation update strategy. The training speed of our system is 41× faster than CONTRAfold on a diverse dataset for one epoch, and 14× faster than MXfold on a dataset with longer sequences. With the learned parameters, our system improves the accuracy of LinearFold, and is also the most accurate system among selected folding tools, including CONTRAfold, Vienna RNAfold and MXfold.

Nuclear structure in the neutron-deficient Sn nuclei TKEL effects on lifetime measurements

The presence of seniority-like isomers along the Z = 50 isotopic chain have been an experimental limitation to the investigation of the electromagnetic properties of the low-lying states in the light Sn nuclei. Combining a multi-nucleon transfer reaction with the Recoil-Distance Doppler-Shift technique, the lifetimes of the 21+ and 41+ excited states have been directly measured in the neutron-deficient 106, 108Sn isotopes for the very first time. The emitted γ rays were detected by the AGATA array, while the reactionproducts were uniquely identified by the VAMOS++ magnetic spectrometer. The control of the direct feeding of the statesby gating on the Total Kinetic Energy Loss, together with the unique capabilities of the two spectrometers, was crucial for the measurementin 108Sn.

Structure of the 30S ribosomal decoding complex at ambient temperature

ABSTRACTThe ribosome translates nucleotide sequences of messenger RNA to proteins through selection of cognate transfer RNA according to the genetic code. To date, structural studies of ribosomal decoding complexes yielding high-resolution data have predominantly relied on experiments performed at cryogenic temperatures. New lightsources like the X-ray free electron laser (XFEL) have enabled data collection from macromolecular crystals at ambient temperature. Here, we report an X-ray crystal structure of the Thermus thermophilus 30S ribosomal subunit decoding complex to 3.45 Å resolution using data obtained at ambient temperature at the Linac Coherent Light Source (LCLS). We find that this ambient-temperature structure is largely consistent with existing cryogenic-temperature crystal structures, with key residues of the decoding complex exhibiting similar conformations, including adenosine residues 1492 and 1493. Minor variations were observed, namely an alternate conformation of cytosine 1397 near the mRNA channel and the A-site. Our serial crystallography experiment illustrates the amenability of ribosomal microcrystals to routine structural studies at ambient temperature, thus overcoming a long-standing experimental limitation.

The Use of Connected Masks for Reconstructing the Single Particle Image from X-Ray Diffraction Data. III. Maximum-Likelihood Based Strategies to Select Solution of the Phase Problem

The main experimental limitation of biological crystallography is associated with the need to prepare the object under study in the form of a single crystal. New powerful X-ray sources, namely free-electron X-ray lasers, makes it possible to raise the question of the determination of the structure of isolated biological macromolecules and their complexes in practice. An additional advantage of working with isolated particles is the possibility to obtain information about scattering in all directions, and not only in those limited by the Laue-Bragg diffraction conditions. This significantly facilitates the solution of the phase problem of X-ray diffraction analysis. This paper is devoted to two lines of development of the method for solving the phase problem, proposed earlier by the authors, which is based on the random scanning of the configuration space of potential solutions of the phase problem. The paper suggests a new criterion for the selection of "candidates" for solving the phase problem in the process of scanning. It involves the maximization of statistical likelihood, and its effectiveness is shown in test calculations. The second line concerns the choice of the optimal scanning strategy. It is shown that the gradual expansion of the set of experimental data used in the work allows obtaining solutions of a higher quality than those obtained with all available data included into the work simultaneously from the beginning.

Characterizing the hippocampal theta’s response to carbachol; using a complete septo-hippocampal preparation

The present study describes the pharmacological analysis of the effects of carbachol, a cholinergic agonist, on hippocampal theta activity. Knowing that this activity is critically related to cognitive function and altered in patients with neurodegeneration, pharmacological efforts aiming to directly modulate hippocampal theta activity becomes of central importance. In a recently developed complete septo-hippocampal preparation, carbachol elicited significant theta power enhancement with 1 μM. Concentrations under 1 μM and over 2 μM carbachol caused significant reduction in the power of hippocampal theta activity. Carbachol effects were completely blocked with the cholinergic antagonist scopolamine. At the experimental level, it is the first time the direct action of a cholinergic agonist is evaluated in the septo-hippocampal pathway completely isolated. However, carbachol as a cholinergic agonist is a drug with a certain level of nonspecific response. That is why to correct this experimental limitation, we used scopolamine (cholinergic antagonist) which allowed us to corroborate the effects on the cholinergic pathway. In summary, electrophysiological assays demonstrated an effective concentration range of carbachol specifically modulating hippocampal theta activity.

Characterizing the hippocampal theta’s response to carbachol; using a complete septo-hippocampal preparation

The present study describes the pharmacological analysis of the effects of carbachol, a cholinergic agonist, on hippocampal theta activity. Knowing that this activity is critically related to cognitive function and altered in patients with neurodegeneration, pharmacological efforts aiming to directly modulate hippocampal theta activity becomes of central importance. In a recently developed complete septo-hippocampal preparation, carbachol elicited significant theta power enhancement with 1 μM. Concentrations under 1 μM and over 2 μM carbachol caused significant reduction in the power of hippocampal theta activity. Carbachol effects were completely blocked with the cholinergic antagonist scopolamine. At the experimental level, it is the first time the direct action of a cholinergic agonist is evaluated in the septo-hippocampal pathway completely isolated. However, carbachol as a cholinergic agonist is a drug with a certain level of nonspecific response. That is why to correct this experimental limitation, we used scopolamine (cholinergic antagonist) which allowed us to corroborate the effects on the cholinergic pathway. In summary, electrophysiological assays demonstrated an effective concentration range of carbachol specifically modulating hippocampal theta activity.

Functional characterization of a ClC transporter by solid-supported membrane electrophysiology

EcClC, a prokaryotic member of the ClC family of chloride channels and transporters, works as coupled H+/Cl− exchanger. With a known structure and the possibility of investigating its behavior with different biochemical and biophysical techniques, the protein has become an important model system for the family. Although many aspects of its function have been previously characterized, it was difficult to measure transport on the same sample under different environmental conditions. To overcome this experimental limitation, we have studied EcClC by solid-supported membrane electrophysiology. The large transport-related transient currents and a simple way of relating transport rates to the measured signal have allowed a thorough investigation of ion selectivity, inhibition, and the dependence of transport on changes in ion concentration and pH. Our results confirm that the protein transports larger anions with about similar rates, whereas the smaller fluoride is not a substrate. We also show that 4,4′-diisothiocyano-2,2’-stilbenedisulfonic acid (DIDS), a known inhibitor of other anion transport protein, irreversibly inhibits EcClC from the intracellular side. The chloride dependence shows an apparent saturation at millimolar concentrations that resembles a similar behavior in eukaryotic ClC channels. Our experiments have also allowed us to quantify the pH dependence of transport. EcClC shows a strong activation at low pH with an apparent pKa of 4.6. The pronounced pH dependence is lost by the mutation of a conserved glutamate facing the extracellular solution that was previously shown to be an acceptor for transported protons, whereas it is largely retained by the mutation of an equivalent residue at the intracellular side. Our results have provided a quantitative basis for the transport behavior of EcClC, and they will serve as a reference for future investigations of novel electrogenic transporters with still-uncharacterized properties.