High-resolution imaging of the cellular world in recent years has underpinned a revolution in high-content volume data accumulation resulting in a new understanding of cell organization and behaviour. Amongst the highlights of microscopy developments in cellular imaging has been the emergence of new correlative imaging modalities that incorporate Soft X-ray Tomography (SXT) of cryopreserved...
PAL-XFEL operates user beamtime for various scientific studies related to physics, chemistry, and biology since 2017. It especially provides XFEL pulses in a very high quality for the timing jitter and stability [1, 2]. To unveil the macromolecular structures at room temperature and nearly atomic resolution, we run the serial femtosecond crystallography (SFX) science program at the NCI...
Coherent X-ray diffractive imaging (CXDI) of single particles at X-ray free-electron lasers (XFEL) is a method to determine structure. Single particles are injected sequentially at unknown, random orientations into the intense XFEL beam and noisy diffraction patterns are measured, known as diffraction before destruction.[1] We orient these patterns using the expand, maximize and compress (EMC)...
The human middle ear hosts the three auditory ossicles, which ensure sound transmission from the environment to the inner ear through impedance matching. Unlike for long bones, the ossification of the human hearing bones is completed shortly after birth, and only little ossicular remodeling of the bone has been observed afterwards[1-4]. Nevertheless, studies have shown that the overall...
Objectives: Trephine bur is the most common and effective instrument used in the biopsy of bone tissue to evaluate the results of bone regeneration procedures. Trephine bur can be mounted on the rotating instrument to obtain the regenerated tissue in a cylindrical shape. However, in the process of separating the new bone tissue from the trephine bur after tissue harvest, a physical force may...
Breast cancer is the leading cause of cancer death in women worldwide [1]. In these patients, more than 90% of breast cancer-related deaths are caused not by the primary tumor, but by their metastases at distant sites. Metastasis is an extraordinarily complex process, entailing tumor cells to acquire a set of features that allow them to develop new foci of the disease. Systemic changes in the...
Autumn 2023 will see the next major release of the CCP4 software suite. Following the, largely, successful update from python2 to python3 for the 8.0 series, 8.1 will use a python 3.9 base. Among the step changes is the move to DIALS 3.13+ {1] with an updated graphical user interface, DUI2, greater coot scripting from Paul Emsley [2], the introduction of webCoot (code name moorhen) [3], plus...
Water is essential for all life forms on the planet, yet after thousands of years in which it has been an abundant resource, the situation is drastically changing to the point where water scarcity has become one of the greatest threats of the 21st century (1). Membrane filtration technologies are able to provide reliable filtered water qualities and a low footprint meanwhile presenting a high...
Many metal complexes are widely known for their activity in biological systems. In addition to the compounds occurring naturally in the human body, metal ions are also required for their role as pharmaceuticals as well as diagnostic agents. Due to the increasing number of cancer cases in the world, research into new anti-tumor drugs containing metal ions is particularly important. Therefore,...
Visualize the subcellar structures within cells is important to understand biological phenomena in details for biomedical research. Microscopy plays and important role to fulfill this demand. Among all the microscopy techniques, transmission electron microscopy (TEM) and fluorescence microscopy are two major imaging modalities to explore the cellular structures. Fluorescence microscopy can...
SARS-CoV-2, the causative agent of the COVID-19 pandemic, has speeded its spread across the globe immediately after its emergence in China in December 2019. Since then, a coordinated and tireless race for developing simple, less invasive, cheap, highly accurate, and able to be applied in large-scale tests to supply the huge demand of governments to detect infected persons and plan effective...
We discuss recent work on making use of deep-learning-based protein structure prediction programs with the CCP4 Software Suite. These programs include AlphaFold2 [1] and OpenFold [2], which use multiple-sequence alignments as input, and ESM-Fold [3], which uses embeddings from protein Language Models. We have developed an adapter script that allows running these programs via a unified...
Structure solution of membrane bound proteins remains a significant challenge. These targets, such as potentially druggable GPCRs, represent ~3% of the X-ray diffraction structures in the PDB. Crystallisation often requires the use of lipid cubic phase (LCP) to maintain the hydrophobic environment, protein stability and promote crystallisation. Membrane protein LCP crystals are generally...
The biomolecular SAS community of users has grown sharply since the 1990’s with increased ease of access and innovation in instrumentation and analysis tools. With this growth, SAS methods have become attractive to main-stream structural biologists who traditionally have relied almost exclusively on high-resolution, data-rich techniques. Key to this development have been the modelling tools...
Biochemical processes at lipid membranes are essential for all living organisms and can be influenced by the interaction of proteins with lipid interfaces [1-2]. Hence, the effects of protein adsorption at such surfaces are important for understanding the organisms’ biochemistry, for current issues in the pharmaceutical industry and for bio- and nanotechnology [3-5].
We studied the adsorption...
More than a third of all proteins contain metal ions [1] with crucial roles in stabilizing structure or enabling a specific function. Identifying metal ion-binding sites is important for understanding the biological functions of proteins and further helps in designing potent therapeutics.
Membrane proteins have important roles to play in shuttling a variety of ligands and ions across...
Introduction: Osteoarthritis (OA) is a debilitating joint disease affecting the middle-aged and elderly population, characterized by the progressive degeneration of cartilage and other joint tissues (1). Since the mechanisms are not fully understood, there is a need for non-destructive, high-resolution methods to identify structural changes in different disease stages. Phase-contrast...
Recently the world has been ravaged by the outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). SARS-CoV-2 belongs to the Coronaviridae family, Coronaviruses (CoVs) are positive-sense single-stranded RNA viruses with a 5′ Cap and a 3′ poly-A tail that may infect both human beings and animals. SARS-CoV-2 maturation, replication, and invasion all rely on the viral...
Wax physisorption kinetics with FTIR (WPK-FTIR) imaging provides a glycol-histopathological imaging analysis for differentiating the abnormal glycosylation within medical tissue sections and cell lines, utilizing n-alkanes (n-CnH2n+2) with varied carbon number (CN) from 20 to 34 and beeswax as wax adsorbents for targeting similar longitudinal length of glycans of glycoconjugates anchoring in...
Introduction: The recovery of the collagen structure following Achilles tendon rupture is poor, resulting in high risk for re-ruptures (1). The loading environment affects the mechanical properties of healing tendons but knowledge regarding how it affects regeneration of the tendon structure is still limited. This study characterizes the effect of reduced in vivo loading on the regenerating 3D...
Here we present Moorhen, a next-generation client-side web-based application for the visualisation and manipulation of molecules in structure determination and analysis.
Recent developments in the field of cloud-based computing have enabled a rapid increase in the range of crystallographic tools available on the web, which crystallographers can use without the need for installing software...
Mineral nutrients are taken up by plants through their root network, therefore if additional nutrient is required, this is today applied to the soil in vast quantities. From this, the crops take up only a minor fraction [1]. We are researching the possibility to apply nutrients through foliar fertilization, developing nanoparticles (NPs) as vessels to deliver the fertilizer through the leaf...
The High-Performance Macromolecular Crystallography beamline (MX3) will be capable of providing high-flux, microfocus X-rays for small and weakly diffracting protein crystals. The beamline has an energy range from 10-15 keV with beam sizes at sample from 2x2 to 40x40 microns with flux up to 1.3e14 ph/s (at 13 keV). The beamline will provide three modes of data collection: goniometer (standard...
Lund Protein Production Platform (LP3, www.lu.se/lp3) is a cross-faculty expert center and user facility of Lund University (LU). As such, we provide services and make equipment available in the areas of recombinant protein production, crystallization, biophysical characterization, and structure determination. We also act as the LU node of a new national distributed research infrastructure for...
Protein Production Sweden (PPS; www.gu.se/pps) is a new national research infrastructure established in 2022 and focused on the production and purification of protein reagents for Swedish researchers, both from academia and commercial entities. Well-established protein production platforms from five universities (the University of Gothenburg (host), Karolinska Institutet, KTH Royal Institute...
At the Photon Factory macromolecular crystallography beamlines, sample exchange system PAM and PAM-HC have been installed and operated by the Structural Biology Research Centre. Most of the samples are brought in by Uni-puck, and information of the samples in the Uni-puck is described in the sample list file corresponding to each Uni-puck. The Uni-puck is automatically recognized by the sample...
The sphingosine-1-phosphate (S1P) is a bioactive lysophospholipid that acts through five different subtypes of G protein coupled S1P receptors (S1PRs) - S1P1-5. S1P5 affects many cellular processes such as division, migration and survival. To date, several drugs (such as fingolimod [1], siponimod [2] and ozanimod [3]) have been developed for the treatment of multiple sclerosis, Crohn's disease...
Non-structural protein 10 (nsp10) and nsp16 are part of the SARS-CoV-2 viral RNA replication complex. Nsp16 exhibits methyltransferase activity needed for mRNA capping and is active in heterodimeric complexes with the enzymatic inert nsp10. The inactivation of this complex interferes severely with viral replication, making it a promising drug target against COVID-19. As only limited...
The fourth-generation synchrotron radiation light source has the outstanding advantages such as low divergence and high brightness,facilitating high spatial and energy resolution X-ray spectroscopy studies and the detection of “light-in-light-out” photon-hungry spectroscopy. The proposed high-resolution soft X-ray spectroscopy beamlines of Shenzhen Industrial Light Source (SILF) will set up...
The Covid-19 pandemic resulted in the release of the new class of vaccine products- the mRNA vaccines. These consist of synthetic mRNA strands packed in lipid nano particle (LNP) that deliver the mRNA to the cells, initiate antigen production and lastly result in immune protection. The function of mRNA in vivo depends on effective, safe and stable delivery to allow cellular uptake and RNA...
Group A Streptococcus (GAS) is a strict human pathogen renowned for its highly aggressive destruction of host tissues that can lead to life-threatening diseases including streptococcal toxic shock syndrome and necrotizing fasciitis. GAS possesses a unique pathogenic trait to enhance its virulence by utilizing the synergism of two secreted toxins, Streptolysin O (SLO) and NAD+-glycohydrolase...
Cryo-soft X-ray tomography (SXT) with full-field transmission microscopy is a new growing synchrotron-based technique, which is developed to image 3D complete frozen cells at Taiwan Photon Source TPS 24A beamline in National Synchrotron Radiation Research Center (NSRRC)[1]. To avoid the radiation damage, bio-samples have to be frozen in liquid ethane condition and transferred to be imaged by...
Biological Small Angle Scattering is a technique that is widely used to characterize samples of biomolecules in solution. Despite thousands of data sets generated every year, only a fraction of them is published, and even a smaller fraction is presented in a way that results can be reproduced, and unbiased conclusions can be drawn. A reporting guideline, specifically targeted for structural...
Serine hydroxymethyltransferase (SHMT) is a pyridoxal-5’-phosphate (PLP) dependent enzyme that catalyzes the tetrahydrofolate (THF)-dependent cleavage of L-Ser to form glycine and 5,10-methylene-THF. This reaction is significant for its role in the biosynthesis of thymidine and purines, as well as the methyl group of methionine by providing single carbon units to one-carbon metabolism. Human...
In recent years, bio-resorbable magnesium implants have gained interest as treatment options for bone fractures. Their advantages include their mechanical properties, their excellent immunological response during healing, and the reduced need for a second intervention to remove the implant. In this study, we wanted to understand the behavior of bone around Mg biodegradable implants and the...
