Structural insights into plasmalemma vesicle-associated protein (PLVAP): Implications for vascular endothelial diaphragms and fenestrae.

In many organs, small openings across capillary endothelial cells (ECs) allow the diffusion of low-molecular weight compounds and small proteins between the blood and tissue spaces. These openings contain a diaphragm composed of radially arranged fibers, and current evidence suggests that a single-span type II transmembrane protein, plasmalemma vesicle-associated protein-1 (PLVAP), constitutes these fibers. Here, we present the three-dimensional crystal structure of an 89-amino acid segment of the PLVAP extracellular domain (ECD) and show that it adopts a parallel dimeric alpha-helical coiled-coil configuration with five interchain disulfide bonds. The structure was solved using single-wavelength anomalous diffraction from sulfur-containing residues (sulfur SAD) to generate phase information. Biochemical and circular dichroism (CD) experiments show that a second PLVAP ECD segment also has a parallel dimeric alpha-helical configuration-presumably a coiled coil-held together with interchain disulfide bonds. Overall, ~2/3 of the ~390 amino acids within the PLVAP ECD adopt a helical configuration, as determined by CD. We also determined the sequence and epitope of MECA-32, an anti-PLVAP antibody. Taken together, these data lend strong support to the model of capillary diaphragms formulated by Tse and Stan in which approximately ten PLVAP dimers are arranged within each 60- to 80-nm-diameter opening like the spokes of a bicycle wheel. Passage of molecules through the wedge-shaped pores is presumably determined both by the length of PLVAP-i.e., the long dimension of the pore-and by the chemical properties of amino acid side chains and N-linked glycans on the solvent-accessible faces of PLVAP.

Impact of Cyclic Error on Absolute Distance Measurement Based on Optical Frequency Combs.

Absolute distance measurements based on optical frequency combs (OFCs) have greatly promoted advances in both science and technology, owing to the high precision, large non-ambiguity range (NAR), and a high update rate. However, cyclic error, which is extremely difficult to eliminate, reduces the linearity of measurement results. In this study, we quantitatively investigated the impact of cyclic error on absolute distance measurement using OFCs based on two types of interferometry: synthetic wavelength interferometry and single-wavelength interferometry. The numerical calculations indicate that selecting a suitable reference path length can minimize the impact of cyclic error when combining the two types of interferometry. Recommendations for selecting an appropriate synthetic wavelength to address the tradeoff between achieving a large NAR and minimizing the risk of failure when combining the two methods are provided. The results of this study are applicable not only in absolute distance measurements but also in other applications based on OFCs, such as surface profile, vibration analysis, etc.

Radiation damage to biological samples: still a pertinent issue.

An understanding of radiation damage effects suffered by biological samples during structural analysis using both X-rays and electrons is pivotal to obtain reliable molecular models of imaged molecules. This special issue on radiation damage contains six papers reporting analyses of damage from a range of biophysical imaging techniques. For X-ray diffraction, an in-depth study of multi-crystal small-wedge data collection single-wavelength anomalous dispersion phasing protocols is presented, concluding that an absorbed dose of 5 MGy per crystal was optimal to allow reliable phasing. For small-angle X-ray scattering, experiments are reported that evaluate the efficacy of three radical scavengers using a protein designed to give a clear signature of damage in the form of a large conformational change upon the breakage of a disulfide bond. The use of X-rays to induce OH radicals from the radiolysis of water for X-ray footprinting are covered in two papers. In the first, new developments and the data collection pipeline at the NSLS-II high-throughput dedicated synchrotron beamline are described, and, in the second, the X-ray induced changes in three different proteins under aerobic and low-oxygen conditions are investigated and correlated with the absorbed dose. Studies in XFEL science are represented by a report on simulations of ultrafast dynamics in protic ionic liquids, and, lastly, a broad coverage of possible methods for dose efficiency improvement in modalities using electrons is presented. These papers, as well as a brief synopsis of some other relevant literature published since the last Journal of Synchrotron Radiation Special Issue on Radiation Damage in 2019, are summarized below.

Color Index of Transformer Oil: A Low-Cost Measurement Approach Using Ultraviolet-Blue Laser.

The color of transformer oil can be one of the first indicators determining the quality of the transformer oil and the condition of the power transformer. The current method of determining the color index (CI) of transformer oil utilizes a color comparator based on the American Society for Testing and Materials (ASTM) D1500 standard, which requires a human observer, leading to human error and a limited number of samples tested per day. This paper reports on the utilization of ultra violet-blue laser at 405- and 450-nm wavelengths to measure the CI of transformer oil. In total, 20 transformer oil samples with CI ranging from 0.5 to 7.5 were measured at optical pathlengths of 10 and 1 mm. A linear regression model was developed to determine the color index of the transformer oil. The equation was validated and verified by measuring the output power of a new batch of transformer oil samples. Data obtained from the measurements were able to quantify the CI accurately with root-mean-square errors (RMSEs) of 0.2229 for 405 nm and 0.4129 for 450 nm. This approach shows the commercialization potential of a low-cost portable device that can be used on-site for the monitoring of power transformers.

Crystal structure of the periplasmic sensor domain of histidine kinase VbrK suggests indirect sensing of ß-lactam antibiotics.

Bacterial two-component regulatory systems (TCS) play important roles in sensing environmental stimuli and responding to them by regulating gene expression. VbrK/VbrR, a TCS in Vibrio parahaemolyticus, confers resistance to ß-lactam antibiotics through activating a ß-lactamase gene. Its periplasmic sensor domain was previously suggested to detect ß-lactam antibiotics by direct binding. Here, we report a crystal structure of the periplasmic sensing domain of VbrK (VbrKSD) using sulfur-based single-wavelength anomalous diffraction (S-SAD) phasing. Contrary to most bacterial sensor domains which form dimers, we show that VbrKSD is a monomer using size exclusion chromatography coupled with multi-angle light scattering. This observation is also supported by molecular dynamics simulations. To quantify the binding affinity of ß-lactam antibiotics to VbrKSD, we performed isothermal titration calorimetry and other biophysical analyses. Unexpectedly, VbrKSD did not show any significant binding to ß-lactam antibiotics. Therefore, we propose that the detection of ß-lactam antibiotics by VbrK is likely to be indirect via an as yet unidentified mechanism.

Structural and biochemical insights into the catalytic mechanisms of two insect chitin deacetylases of the carbohydrate esterase 4 family.

Insect chitin deacetylases (CDAs) catalyze the removal of acetyl groups from chitin and modify this polymer during its synthesis and reorganization. CDAs are essential for insect survival and therefore represent promising targets for insecticide development. However, the structural and biochemical characteristics of insect CDAs have remained elusive. Here, we report the crystal structures of two insect CDAs from the silk moth Bombyx mori: BmCDA1, which may function in cuticle modification, and BmCDA8, which may act in modifying peritrophic membranes in the midgut. Both enzymes belong to the carbohydrate esterase 4 (CE4) family. Comparing their overall structures at 1.98-2.4 Å resolution with those from well-studied microbial CDAs, we found that two unique loop regions in BmCDA1 and BmCDA8 contribute to the distinct architecture of their substrate-binding clefts. These comparisons revealed that both BmCDA1 and BmCDA8 possess a much longer and wider substrate-binding cleft with a very open active site in the center than the microbial CDAs, including VcCDA from Vibrio cholerae and ArCE4A from Arthrobacter species AW19M34-1. Biochemical analyses indicated that BmCDA8 is an active enzyme that requires its substrates to occupy subsites 0, +1, and +2 for catalysis. In contrast, BmCDA1 also required accessory proteins for catalysis. To the best of our knowledge, our work is the first to unveil the structural and biochemical features of insect proteins belonging to the CE4 family.

Rational Design of IR820- and Ce6-Based Versatile Micelle for Single NIR Laser-Induced Imaging and Dual-Modal Phototherapy.

Phototherapy as a promising cancer diagnostic and therapeutic strategy has aroused extensive attention. However, single-wavelength near-infrared (NIR) light-triggered combinational treatment of photothermal therapy (PTT) and photodynamic therapy (PDT) is still a great challenge. Herein, a multifunctional micelle activated by a single-wavelength laser for simultaneous PTT and PDT as well as fluorescence imaging is developed. Briefly, new indocyanine green (IR820) is conjugated to d-α-tocopheryl polyethylene glycol 1000 succinate (TPGS) via the linker 6-aminocaproic acid, and then, chlorin e6 (Ce6) is encapsulated into the micelles formed by TPGS-IR820 conjugates to fabricate TPGS-IR820/Ce6 micelles. As the well-designed TPGS-IR820 conjugate shares a similar peak absorption wavelength with Ce6, this micelle can be applied with a single NIR laser (660 nm). The stable micelles exhibit excellent photothermal conversion efficiency in vitro and in vivo as well as high singlet oxygen generation capacity in tumor cells. After efficient cellular internalization, the as-prepared micelles display outstanding anticancer activity upon single NIR laser irradiation in vitro and in vivo. Furthermore, TPGS-IR820/Ce6 micelles show negligible systemic toxicity. The highly safe and effective TPGS-IR820/Ce6 micelles can offer an innovative strategy to construct single NIR light-induced PTT and PDT combined phototherapy nanoplatforms via suitable modification of organic phototherapeutic agents.

Development of a dose-limiting data collection strategy for serial synchrotron rotation crystallography.

Serial crystallography, in which single-shot diffraction images are collected, has great potential for protein microcrystallography. Although serial femtosecond crystallography (SFX) has been successfully demonstrated, limited beam time prevents its routine use. Inspired by SFX, serial synchrotron crystallography (SSX) has been investigated at synchrotron macromolecular crystallography beamlines. Unlike SFX, the longer exposure time of milliseconds to seconds commonly used in SSX causes radiation damage. However, in SSX, crystals can be rotated during the exposure, which can achieve efficient coverage of the reciprocal space. In this study, mercury single-wavelength anomalous diffraction (Hg-SAD) phasing of the luciferin regenerating enzyme (LRE) was performed using serial synchrotron rotation crystallography. The advantages of rotation and influence of dose on the data collected were evaluated. The results showed that sample rotation was effective for accurate data collection, and the optimum helical rotation step depended on multiple factors such as multiplicity and partiality of reflections, exposure time per rotation angle and the contribution from background scattering. For the LRE microcrystals, 0.25° was the best rotation step for the achievable resolution limit, whereas a rotation step larger than or equal to 1° was favorable for Hg-SAD phasing. Although an accumulated dose beyond 1.1 MGy caused specific damage at the Hg site, increases in resolution and anomalous signal were observed up to 3.4 MGy because of a higher signal-to-noise ratio.

SAD phasing: History, current impact and future opportunities.

Single wavelength anomalous diffraction (SAD) can trace its beginnings to the early 1950s. Researchers at the time recognized that SAD offers some unique features that might be advantageous for crystallographic phasing, despite the fact that at that time recording accurate SAD data was problematic. In this review we will follow the trail from those early days, highlighting key advances in the field and interpreting them in terms on how they stimulated continued phasing development that produced the theoretical foundation for the routine macromolecular structure determination by SAD today. The technological advances over the past three decades in both hardware and software, which played a significant role in making SAD phasing a 'first choice method', will also be described.

Structural analyses of the CRISPR protein Csc2 reveal the RNA-binding interface of the type I-D Cas7 family.

Upon pathogen invasion, bacteria and archaea activate an RNA-interference-like mechanism termed CRISPR (clustered regularly interspaced short palindromic repeats). A large family of Cas (CRISPR-associated) proteins mediates the different stages of this sophisticated immune response. Bioinformatic studies have classified the Cas proteins into families, according to their sequences and respective functions. These range from the insertion of the foreign genetic elements into the host genome to the activation of the interference machinery as well as target degradation upon attack. Cas7 family proteins are central to the type I and type III interference machineries as they constitute the backbone of the large interference complexes. Here we report the crystal structure of Thermofilum pendens Csc2, a Cas7 family protein of type I-D. We found that Csc2 forms a core RRM-like domain, flanked by three peripheral insertion domains: a lid domain, a Zinc-binding domain and a helical domain. Comparison with other Cas7 family proteins reveals a set of similar structural features both in the core and in the peripheral domains, despite the absence of significant sequence similarity. T. pendens Csc2 binds single-stranded RNA in vitro in a sequence-independent manner. Using a crosslinking - mass-spectrometry approach, we mapped the RNA-binding surface to a positively charged surface patch on T. pendens Csc2. Thus our analysis of the key structural and functional features of T. pendens Csc2 highlights recurring themes and evolutionary relationships in type I and type III Cas proteins.

DNA nanoflowers for multiplexed cellular imaging and traceable targeted drug delivery.

We present a facile approach to make aptamer-conjugated FRET (fluorescent resonance energy transfer) nanoflowers (NFs) through rolling circle replication for multiplexed cellular imaging and traceable targeted drug delivery. The NFs can exhibit multi-fluorescence emissions by a single-wavelength excitation as a result of the DNA matrix covalently incorporated with three dye molecules able to perform FRET. Compared with the conventional DNA nanostructure assembly, NF assembly is independent of template sequences, avoiding the otherwise complicated design of DNA building blocks assembled into nanostructures by base-pairing. The NFs were uniform and exhibited high fluorescence intensity and excellent photostability. Combined with the ability of traceable targeted drug delivery, these colorful DNA NFs provide a novel system for applications in multiplex fluorescent cellular imaging, effective screening of drugs, and therapeutic protocol development.

Crystal structure of blue laccase BP76, a unique termite suicidal defense weapon.

Aging workers of the termite Neocapritermes taracua can defend their colony by sacrificing themselves by body rupture, mixing the externally stored blue laccase BP76 with hydroquinones to produce a sticky liquid rich in toxic benzoquinones. Here, we describe the crystal structure of BP76 isolated from N. taracua in its native form. The structure reveals several stabilization strategies, including compact folding, glycosylation, and flexible loops with disulfide bridges and tight dimer interface. The remarkable stability of BP76 maintains its catalytic activity in solid state during the lifespan of N. taracua workers, providing old workers with an efficient defensive weapon to protect their colony.

A modified phase-retrieval algorithm to facilitate automatic de novo macromolecular structure determination in single-wavelength anomalous diffraction.

The success of experimental phasing in macromolecular crystallography relies primarily on the accurate locations of heavy atoms bound to the target crystal. To improve the process of substructure determination, a modified phase-retrieval algorithm built on the framework of the relaxed alternating averaged reflection (RAAR) algorithm has been developed. Importantly, the proposed algorithm features a combination of the π-half phase perturbation for weak reflections and enforces the direct-method-based tangent formula for strong reflections in reciprocal space. The proposed algorithm is extensively demonstrated on a total of 100 single-wavelength anomalous diffraction (SAD) experimental datasets, comprising both protein and nucleic acid structures of different qualities. Compared with the standard RAAR algorithm, the modified phase-retrieval algorithm exhibits significantly improved effectiveness and accuracy in SAD substructure determination, highlighting the importance of additional constraints for algorithmic performance. Furthermore, the proposed algorithm can be performed without human intervention under most conditions owing to the self-adaptive property of the input parameters, thus making it convenient to be integrated into the structural determination pipeline. In conjunction with the IPCAS software suite, we demonstrated experimentally that automatic de novo structure determination is possible on the basis of our proposed algorithm.

Deep-learning map segmentation for protein X-ray crystallographic structure determination.

When solving a structure of a protein from single-wavelength anomalous diffraction X-ray data, the initial phases obtained by phasing from an anomalously scattering substructure usually need to be improved by an iterated electron-density modification. In this manuscript, the use of convolutional neural networks (CNNs) for segmentation of the initial experimental phasing electron-density maps is proposed. The results reported demonstrate that a CNN with U-net architecture, trained on several thousands of electron-density maps generated mainly using X-ray data from the Protein Data Bank in a supervised learning, can improve current density-modification methods.

Combining crystallography and EPR: crystal and solution structures of the multidomain cochaperone DnaJ.

Hsp70 chaperones assist in a large variety of protein-folding processes in the cell. Crucial for these activities is the regulation of Hsp70 by Hsp40 cochaperones. DnaJ, the bacterial homologue of Hsp40, stimulates ATP hydrolysis by DnaK (Hsp70) and thus mediates capture of substrate protein, but is also known to possess chaperone activity of its own. The first structure of a complete functional dimeric DnaJ was determined and the mobility of its individual domains in solution was investigated. Crystal structures of the complete molecular cochaperone DnaJ from Thermus thermophilus comprising the J, GF and C-terminal domains and of the J and GF domains alone showed an ordered GF domain interacting with the J domain. Structure-based EPR spin-labelling studies as well as cross-linking results showed the existence of multiple states of DnaJ in solution with different arrangements of the various domains, which has implications for the function of DnaJ.

Single-wavelength sO2 measurement based on Grüneisen-relaxation photoacoustic effect.

The photoacoustic effect-based sO2 measurement is attracting more and more attention due to its non-invasiveness and accuracy. Compared with the linear dual-wavelength method, the sO2 measurement based on single-wavelength excitation can be potentially applied with simplified system construction. However, the single-wavelength methods proposed in previous studies decreases the safety or lacks the in-depth resolution. This paper proposes a novel single-wavelength method based on the Grüneisen-relaxation (GR) nonlinear effects. It avoids the high fluence excitation with maintaining in-depth resolution and obtains the signals in hundreds of nanoseconds, simultaneously improving the safety and detection speed. The construction of a single laser source for GR effect generation makes the system stable. The sO2 quantification results of blood samples have a good consistency with the reference values. Our work provides a safer and faster measurement method, and a stable system, to promote its application in the clinical area.

A single-wavelength excited NIR fluorescence probe for distinguishing GSH/H2S and Cys/Hcy in living cells and zebrafish through separated dual-channels.

Biothiols and hydrogen sulfide, as critical sulfur-containing reactive substances, serve essential functions in various human pathological processes, making it challenging to simultaneously distinguish them due to their similar reactivity and structures (-SH). Here, we rationalized the development of a single-wavelength excitation near-infrared (NIR) fluorescence probe, FC-NBD, for distinguishing GSH/H2S and Cys/Hcy by separated fluorescence dual channels. In this probe, FC-NBD, composed of coumarin-benzopyrylium derivatives linked with nitro benzoxadiazole (NBD) via ether bonds, could quantitatively and selectively distinguish GSH/H2S and Cys/Hcy with a low limit of detection (LOD) of 0.199/0.177 µM and 0.106/0.076 µM, respectively. As expected, under single-wavelength excitation (470 nm), FC-NBD demonstrated distinctly separable green and NIR fluorescence emissions towards Cys/Hcy at 550 and 660 nm, but only exhibited a noticeable NIR fluorescence emission towards GSH/H2S at 660 nm. Moreover, FC-NBD could simultaneously visualize and discriminate GSH/H2S and Cys/Hcy in living cells as well as zebrafish through green and NIR channels at a single excitation wavelength.

Multivariate estimation of substructure amplitudes for a single-wavelength anomalous diffraction experiment.

To determine a substructure from single-wavelength anomalous diffraction (SAD) data using Patterson or direct methods, the substructure-factor amplitude (|Fa|) is first estimated. Currently, the absolute value of the Bijvoet difference is widely used as an estimate of |Fa| values for SAD data. Here, an equation is derived from multivariate statistics and tested that takes into account the correlation between the observed positive (F+) and negative (F-) Friedel pairs and Fa along with measurement errors in the observed data. The multivariate estimation of |Fa| has been implemented in a new program, Afro. Results on over 180 test cases show that Afro provides a higher correlation to the final substructure-factor amplitudes (calculated from the refined, final substructures) than the Bijvoet differences and improves the robustness of direct-methods substructure detection.

Cell-Membrane Coated Nanoparticles for Tumor Delineation and Qualitative Estimation of Cancer Biomarkers at Single Wavelength Excitation in Murine and Phantom Models.

Real-time guidance through fluorescence imaging improves the surgical outcomes of tumor resections, reducing the chances of leaving positive margins behind. As tumors are heterogeneous, it is imperative to interrogate multiple overexpressed cancer biomarkers with high sensitivity and specificity to improve surgical outcomes. However, for accurate tumor delineation and ratiometric detection of tumor biomarkers, current methods require multiple excitation wavelengths to image multiple biomarkers, which is impractical in a clinical setting. Here, we have developed a biomimetic platform comprising near-infrared fluorescent semiconducting polymer nanoparticles (SPNs) with red blood cell membrane (RBC) coating, capable of targeting two representative cell-surface biomarkers (folate, αυß3 integrins) using a single excitation wavelength for tumor delineation during surgical interventions. We evaluate our single excitation ratiometric nanoparticles in in vitro tumor cells, ex vivo tumor-mimicking phantoms, and in vivo mouse xenograft tumor models. Favorable biological properties (improved biocompatibility, prolonged blood circulation, reduced liver uptake) are complemented by superior spectral features: (i) specific fluorescence enhancement in tumor regions with high tumor-to-normal tissue (T/NT) ratios in ex vivo samples and (ii) estimation of cell-surface tumor biomarkers with single wavelength excitation providing insights about cancer progression (metastases). Our single excitation, dual output approach has the potential to differentiate between the tumor and healthy regions and simultaneously provide a qualitative indicator of cancer progression, thereby guiding surgeons in the operating room with the resection process.

Simultaneous Discrimination of Cys/Hcy and GSH With Simple Fluorescent Probe Under a Single-Wavelength Excitation and its Application in Living Cells, Tumor Tissues, and Zebrafish.

Owing to the important physiological sits of biothiols (Cys, Hcy, and GSH), developing accurate detection methods capable of qualitative and quantitative analysis of biothiols in living systems is needed for understanding the biological profile of biothiols. In this work, we have designed and synthesized a 4'-hydroxy-[1,1'-biphenyl]-4-carbonitrile modified with NBD group-based fluorescent probe, BPN-NBD, for sensitive detection of Cys/Hcy and GSH by dual emission signals via a single-wavelength excitation. BPN-NBD exhibited an obvious blue fluorescence (λmaxem = 475 nm) upon the treatment with GSH and reacted with Cys/Hcy to give a mixed blue-green fluorescence (λmaxem = 475 and 545 nm). Meanwhile, BPN-NDB performed sufficient selectivity, rapid detection (150 s), high sensitivity (0.011 µM for Cys, 0.015 µM for Hcy, and 0.003 µM for GSH) and could work via a single-wavelength excitation to analytes and had the ability to image Cys/Hcy from GSH in living MCF-7 cells, tumor tissues, and zebrafish by exhibiting different fluorescence signals. Overall, this work provided a powerful tool for thiols visualization in biological and medical applications.