SAXS – Lightsources.org

How the cheese-noodle principle could help counter Alzheimer’s

2025/11/212025/11/21

Researchers at the Paul Scherrer Institute PSI have clarified how spermine – a small molecule that regulates many processes in the body’s cells – can guard against diseases such as Alzheimer’s and Parkinson’s: it renders certain proteins harmless by acting a bit like cheese on noodles, making them clump together. This discovery could help combat such diseases. The study has now been published in the journal Nature Communications.

Our life expectancy keeps rising – and as it does, age-related illnesses, including neurodegenerative diseases such as Alzheimer’s and Parkinson’s, become increasingly common. These diseases are caused by accumulations in the brain of harmful protein structures consisting of incorrectly folded amyloid proteins. Their shape is reminiscent of fibres or spaghetti. To date, there is no effective therapy to prevent or eliminate such accumulations.

Yet a naturally occurring molecule in the body called spermine offers hope. In experiments, researchers led by study leader Jinghui Luo, in the Center for Life Sciences at the Paul Scherrer Institute PSI, have discovered that this substance is capable of extending the life span of small nematode worms, improving their mobility in old age, and strengthening the powerhouses of their cells – the mitochondria. Specifically, the researchers observed how spermine helps the body’s immune system eliminate nerve-damaging accumulations of amyloid proteins.

The new findings could serve as a basis for developing novel therapies for such diseases.

A central mediator of cellular processes

Spermine is a vital substance for the organism. It belongs to the so-called polyamines, which are relatively small organic molecules. Spermine, first discovered more than 150 years ago, is named after the seminal fluid, as it is found in particularly high concentrations there. But it also occurs in many other cells of the body – especially those that are active and capable of dividing.

Spermine promotes cell mobility and activity and controls numerous processes. Above all, it interacts with the nucleic acids of the genome, regulating the expression of genes and their conversion into proteins. This ensures that cells can properly grow and divide and ultimately die. Spermine is also central to an important cellular process called biomolecular condensation: In this process, certain macromolecules, such as proteins and nucleic acids, segregate and collect within the cell in a droplet-like form, so that important reactions can take place there.

In connection with neurodegenerative diseases such as Alzheimer’s or Parkinson’s, there has previously been evidence that spermine can protect nerve cells and alleviate age-related memory loss. Lacking until now, however, has been a more precise understanding of how spermine intervenes in nerve-damaging processes – understanding that might make it possible to derive medical benefits from it.

Assisting cellular waste removal

Jinghui Luo’s group has now investigated this in more detail. In addition to optical microscopy, the researchers also used the SAXS scattering technique at PSI’s Swiss Light Source SLS to shed light on the molecular dynamics of these processes. The investigations were conducted both in a glass capillary (in vitro) and in a living organism (in vivo). The nematode C. elegans served as a model organism.

Read more on the PSI website

Image: Jinghui Luo is a researcher at the Center for Life Sciences at the Paul Scherrer Institute PSI. He studies accumulations of so-called amyloid proteins, which lead to nerve damage in the brain. His research aims to help mitigate neurodegenerative diseases such as Alzheimer’s and Parkinson’s in the long term.

Credit: © Paul Scherrer Institute PSI/Markus Fischer

From Sequence to Structure: A Fast Track for RNA Modeling

2025/05/152025/05/15

In Biology 101, we learn that RNA is a single, ribbon-like strand of base pairs that is copied from our DNA then read like a recipe to build a protein. But there’s more to the story. Some RNA strands fold into complex shapes that allow them to drive cellular processes like gene regulation and protein synthesis, or catalyze biochemical reactions. We know that these active molecules, called non-coding RNAs, are present in all life forms, yet we’re just starting to understand their many roles – and how they can be harnessed for applications in environmental science, agriculture, and medicine.

To study – and potentially modify – the functions of non-coding RNAs, we need to determine their structure. Scientists from Lawrence Berkeley National Laboratory (Berkeley Lab) and the Hebrew University of Jerusalem have developed a streamlined process that predicts the structure of an RNA molecule down to the atomic level. Members of the research community can come to Berkeley Lab’s Advanced Light Source (ALS) user facility knowing nothing more than the molecule’s nucleotide sequence and get a structure, or they can do it themselves using the team’s open-source software.

“We were looking at the bigger picture with structure prediction, like how we can go from A to Z rather than working on A, B, and D. That’s what we try to do at Berkeley Lab, make it user friendly,” said Michal Hammel, a staff scientist in Berkeley Lab’s Molecular Biophysics and Integrated Bioimaging (MBIB) division. Hammel co-developed the process, called SOlution Conformation PrEdictor for RNA (SCOPER), with MBIB colleague Scott Classen and Hebrew University collaborators Dina Schneidman-Duhovny and Edan Patt.

A paper describing SCOPER was recently published in Biophysical Journal.

Historically, it has ranged between difficult to impossible to accurately determine the three-dimensional atomic blueprint of a folded RNA because they rarely convert into a neat crystalline form to be imaged with X-ray crystallography. And because the twists and folds of the RNA strand move around as the molecule functions, there are actually multiple correct structures.

In recent years, artificial intelligence (AI) tools like AlphaFold have become very accurate at generating protein structure predictions based on amino acid sequence, making life a lot easier for scientists worldwide and greatly accelerating the pace of drug discovery. These algorithms have been expanded to RNA structures, but the accuracy remains middling. Getting a reliable model currently involves combining the outputs of multiple computational tools and imaging data. It’s a long process, and still fraught with uncertainty.

SCOPER has simplified it significantly. Say you want to study a new RNA: First, put the nucleotide sequence into one of the open-source, AI-based structure prediction tools available today. Then, take your sample to a small angle X-ray scattering (SAXS) facility for characterization. Better yet, let Hammel and his colleagues at the ALS’s SAXS beamline get that data for you.

Take the SAXS data and predicted structures, and put them through SCOPER’s pipeline. The first step uses an existing program to generate possible flexible arrangements of the RNA from the predicted static structures. Next, a new machine learning program, developed and trained on existing atomic structures by Patt, refines the structures by adding the placements of magnesium ions. Inside cells, positively charged magnesium ions interact with negatively charged RNAs to keep them folded stably. Their presence also helps elucidate structure when using SAXS.

Next, SCOPER generates simulated SAXS data representing the theoretical structures and compares them with the real-world SAXS data to determine which structure is correct.

Read more on ALS website

Image: These renderings show RNA structures that were used to evaluate the accuracy of the new SCOPER process. The AI-generated initial structure predictions based on sequence (blue) is pictured with the refined predicted structure generated by SCOPER (red), which includes the placement of magnesium ions (violet).

Credit: Michal Hammel/Berkeley Lab

Cross-β Structure – a Core Building Block for Streptococcus mutans Functional Amyloids

2020/06/302020/08/24

Most amyloids¹ are misfolded proteins, having enormous variety in native structures. Pathological amyloids are implicated in diseases including Alzheimer’s disease and many others. They are characterized by long, unbranched fibrillar structure, enhanced birefringence on binding Congo red dye, and cross-β structure – β-strands running approximately perpendicular to the fibril axis, forming long β-sheets running in the direction of the axis. Fiber diffraction patterns from amyloids are marked by strong intensity at about 4.8 Å in the meridional direction (parallel to the fibril axis), corresponding to the separation of strands in a β-sheet, and in many cases broader but distinct equatorial intensity at about 10 Å. The 10 Å intensity (whose position may vary considerably) comes from the distance between stacked β-sheets. This stacking is characteristic of the many amyloids formed by small peptides, including peptide fragments of larger amyloidogenic proteins. While some authors have required the 10 Å intensity to characterize an amyloid, it is not strictly necessary, since architecturally more complex examples have been found of Congo-red-staining fibrils with cross-β structure, but without the stacked-sheet structure, and consequently without the 10 Å intensity on the equator.

Amyloids do not always stem from protein misfolding. Organisms across all kingdoms utilize functional amyloids in numerous biological processes. Bacteria are no exception. Bacterial amyloids contribute to biofilm formation and stability. Tooth decay is the most common infectious disease in the world. A major etiologic agent, Streptococcus mutans, is a quintessential biofilm dweller that produces at least three different amyloid-forming proteins, adhesins P1 and WapP, and the cell density and competence regulator Smu_63c². The naturally occurring truncation derivatives of P1 and WapA, C123 and AgA, represent the amyloidogenic moieties, and a new paradigm of Gram-positive bacterial adhesins is emerging of adhesins having dual functions in monomeric and amyloid forms. While each S. mutans protein possesses considerable β-sheet structure, the tertiary structures of each protein are quite different (Fig. 1). This study further characterized S. mutans amyloids and addressed the ongoing debate regarding the underlying structure and assembly of bacterial amyloids including speculation that they are structurally dissimilar from better-characterized amyloids.

Read more on the SSRL website

Image: Crystal or predicted 3D structures of S. mutans C123 (left), AgA (center), and Smu_63c (right).

A fast and precise look into fibre-reinforced composites

2019/11/122019/11/18

Researchers at the Paul Scherrer Institute PSI have improved a method for small angle X-ray scattering (SAXS) to such an extent that it can now be used in the development or quality control of novel fibre-reinforced composites.

This means that in the future, such materials can be investigated not only with X-rays from especially powerful sources such as the Swiss Light Source SLS, but also with those from conventional X-ray tubes. The researchers have published their results in the journal Nature Communications.
Novel fibre-reinforced composites are becoming increasingly important as stable and lightweight materials. One example of this type of composite is carbon fibre reinforced polymers (CFRP), which are used in aircraft construction or in the construction of Formula 1 racing cars and sports bicycles. The properties of these materials depend to a large extent on how the tiny fibres are aligned and how they are arranged and embedded in the surrounding material, influencing the mechanical, optical, or electromagnetic behaviour of the composites.

To investigate the fibre’s orientation in such composites, researchers must look inside them. One could use small angle X-ray scattering (SAXS), exploiting the fact that X-rays are scattered when they penetrate matter. The resulting scattering pattern can then be used to obtain information about the interior of a sample and potentially the orientation of the fibres. However, the common SAXS methods have the disadvantage of being quite slow: It can take up to several hours to scan centimetre-sized specimens with the required resolution.

Image: Matias Kagias (left) and Marco Stampanoni in front of the apparatus with which they examined the composites using the newly developed X-ray method. Both hold one of the workpieces that have been X-rayed.
Credit: Paul Scherrer Institute/Mahir Dzambegovic

17 meter long detector chamber delivered to CoSAXS

2019/05/142019/05/15

The experimental techniques used at the CoSAXS beamline will use a huge vacuum vessel with possibilities to accommodate two in-vacuum detectors in the SAXS/WAXS geometry.

A major milestone was reached for the CoSAXS project when this vessel was recently delivered, installed and tested.
The main method that will be used at the CoSAXS beamline is called Small Angle X-ray Scattering (SAXS). By detecting the scattered rays coming from the sample at shallow angles, less than 4° typically, it is possible to learn about the size, shape, and orientation of the small building blocks that make up different samples and how this structure gives these materials their properties. The materials to be studied can come from various sources and in diverse states, for example, plastics from packaging, food and how it is processed or proteins in solution which can be used as drugs.
The “co” in CoSAXS stands for coherence, a quality of the synchrotron light optimized at the MAX IV machine, that loosely could be translated as laser-likeness. In the specific case of X-ray Photon Correlation Spectroscopy (XPCS), it lets the researchers not only measure the structure of the building blocks in the sample but also their dynamics – how they change in time.

A shape-induced orientation phase within 3D nanocrystal solids

2018/09/202018/09/20

Designing nanocrystal (NC) materials aims at obtaining superlattices that mimic the atomic structure of crystalline solids. In such atomic systems, spatially anisotropic orbitals determine the crystalline lattice type. Similarly, in NC systems the building block anisotropy defines the order of the final solid: here, the NC shape governs the final superlattice structure. Yet, in contrast to atomic systems, NC shape-anisotropy induces not only positional, but also orientational order, ranging from full rotational disorder to a stable, fixed alignment of all NCs. This orientational relation is of special interest, as it determines to what extent atomically coherent connections between NCs are possible, thereby enabling complete wave function delocalization within the NC solid.
In addition to predicting the final NC orientation and position structure, the realization of NC materials demands a controllable fabrication process such that the designed order can be produced. Generally, such highly ordered NC superstructures are achieved through solvent evaporation induced self‐assembly on hard substrates. For applications where the 2D nature of this substrates process is limiting, nonsolvent into solvent diffusion, a technique commonly used to grow single crystals of dissolved molecules, is an attractive option. However, the precise influence of self-assembly parameters on the final superlattice outcome remains unknown. In this work, the researchers posed two closely related questions regarding the design of novel free-standing NC materials: (i) how can the NC self-assembly process be controlled to yield highly ordered free-standing supercrystals and (ii) what is the detailed positional and orientational order within the NC solid? A multidisciplinary team of collaborators, including the Austrian Small Angle X-ray Scattering (SAXS) beamline at Elettra, approached this challenge by a combined experimental and computational strategy.

Image: Self‐assembly of 3D colloidal supercrystals built from faceted 20 nm Bi nanocrystals is studied by mens of in-situ synchrotron X‐ray scattering, combined with Monte Carlo simulations.

Nanoparticles form supercrystals under pressure

2018/09/062018/09/10

Investigations at Diamond may lead to easier ways to synthesise nanoparticle supercrystals

Self-assembly and crystallisation of nanoparticles (NPs) is generally a complex process, based on the evaporation or precipitation of NP-building blocks. Obtaining high-quality supercrystals is slow, dependent on forming and maintaining homogenous crystallisation conditions. Recent studies have used applied pressure as a homogeneous method to induce various structural transformations and phase transitions in pre-ordered nanoparticle assemblies. Now, in work recently published in the Journal of Physical Chemistry Letters, a team of German researchers studying solutions of gold nanoparticles coated with poly(ethylene glycol)- (PEG-) based ligands has discovered that supercrystals can be induced to form rapidly within the whole suspension.

Figure: 2D SAXS patterns of PEG-coated gold nanoparticles (AuNP) with 2 M CsCl added at different pressures. Left: 1 bar; Middle: 4000 bar; Right: After pressure release at 1 bar. The scheme on top illustrates the structural assembly of the coated AuNPs at different pressures: At 1 bar, the particle ensemble is in an amorphous, liquid state. Upon reaching the crystallization pressure, face-centred cubic crystallites are formed by the AuNPs. After pressure release, the AuNPs return to the liquid state.

Microfluidic mixing chips can reveal how biomolecules interact

2018/07/312018/09/05

Christopher Flynn, a fourth year student majoring in Physics and Mathematics at Fort Lewis College, and a SUnRiSE student at Cornell this summer, is contributing to the design of microfluidic mixing chips which could significantly enhance our understanding of proteins and living cells.

Microfluidic mixing chips are used by scientists to analyze biological molecules. They have small channels in which biological solutions, usually solutions of protein, are mixed. Biological small angle x-ray solution scattering (BioSAXS) is then used to study how these biomolecules change under different conditions, for example when they mix with hormones and drugs or when they interact with other biomolecules. These observations can help further our understanding of how cells function.

With the intention of opening a door to the inner workings of cells, Flynn and Gillilan are continuing the work of Gillilan’s former postdoctoral student, Jesse Hopkins, who started a project on microfluidic chips more than two years ago. Hopkins was working on fabricating chips that could be used to observe molecular interactions and structural changes on a millisecond scale.

While Hopkins successfully designed almost every aspect of the chip, he was unable to get the final x-ray transparent window fixed on the chip without it leaking. Flynn’s main task over the summer is to resolve this. He creates chips in the Cornell NanoScale Science and Technology Facility (CNF), using techniques including photolithography and lamination. The chips have different layers, the faulty transparent window being in one of the last. After the first few layers of the chips are made, Flynn uses them to investigate different possibilities for the window. He expects to test these windows by pumping liquids through the chips, and if they have been fit successfully, to compare any results to computer simulations that Hopkins had developed.

Image: Richard Gillilan and Topher Flynn. The channels of the mixing chips are 30 microns wide, 500 microns deep.; a difficult feat but important feature of the chip.

Understanding how alkaline treatment affects bamboo

2018/05/14

In China, bamboo is a symbol of longevity and vitality, able to survive the hardest natural conditions and remain green all year round. In a storm, bamboo stems bend but do not break, representing the qualities of durability, strength, flexibility and resilience¹.

Bamboo is a traditional construction material in Asia. Its strength and flexibility arise from its hollow stems (‘culms’) made from distinct material components. The solid outer shell of the culm is made primarily from longitudinal fibres. A higher density at the outer wall makes it stronger than the inner regions, and results in remarkable stiffness and flexural strength. Running through the centre of bamboo stem are parenchyma cells that store and channel the plant’s nutrients.

At the micro-/nano-scale both the fibres and the matrix contain cellulose nano-fibrils of the same type. However, the structural arrangement of the two materials result in contrasting mechanical properties. Individual fibres may reach a strength of 900 MPa, whilst the matrix can only resist about 50 MPa. There is also a considerable difference in their elastic properties, with the fibres being much stiffer than the matrix.

Bamboo is often treated with alkaline solutions, to modify these properties. Alkaline treatments can turn this rapidly renewable and low-cost resource into soft textiles, and extract fibres to be used in composite materials or as biomass for fuel.

Image: Dr Enrico Salvati on the B16 beamline at Diamond.

Inscuteable: No longer inscrutable

2018/04/09

The structure and function of a controller of stem cell division

An important complex forming the core of the cell division apparatus in stem cells has been imaged using the Macromolecular Crystallography beamlines, I04 and I04-1 at Diamond Light Source. As recently reported in Nature Communications, the spindle orientation protein known as LGN bound to an adapter protein known as Inscuteable in a tetrameric arrangement, which drove asymmetric stem cell division.

Stem cells are undifferentiated cells that have the capacity to differentiate into specialised cells. In a developing embryo, stem cells are the foundation of all other cells, whereas in adults, they can aid repair by replenishing lost tissue. To ensure a physiological balance between differentiated and undifferentiated cells, stem cells undergo asymmetric division to give rise to an identical daughter stem cell and a differentiated cell.

Asymmetric division occurs when there is an unequal segregation of cellular contents. For this to occur, the line of division of the cell (known as the axis) must be carefully positioned. The stem cells use polarity proteins, such as Par3, to determine the location of this axis, and then proteins such as LGN and Inscuteable (Insc) help to align the mitotic spindle to the axis of polarity.

Despite the importance of such a process, little is known about the interactions between the proteins. Dr Marina Mapelli, Group Leader at the European Institute of Oncology in Milan and Dr Simone Culurgioni, Post-Doctoral Research Associate here at Diamond, along with scientists from the Italian Institute of Technology, plus the European Molecular Biology Laboratory in Grenoble set out to solve the crystal structure of LGN bound to Insc. They saw that the proteins were intertwined in a fascinating tetrameric arrangement and found that Insc alone had impressive anti-proliferative properties.

Figure : On the left, a stem cell orienting (movement highlighted by the red arrow) its mitotic spindle (in green) in order to partition its cellular components (in pink and yellow) unequally in the two daughter cells; one is retaining the stem state (in pink) and the other one is committed to differentiate (in yellow). On the right, the structure of Insc:LGN complex governing this asymmetric cell division process. Insc:LGN complex assembles in highly stable intertwinned tetrameric structure (Insc in blue and purple, LGN in yellow and orange respectively
Entire image here.

Major upgrade of the NCD beamline

2018/03/132018/03/16

The NCD beamline, now NCD-SWEET, devoted to Small Angle and Wide Angle X-ray Scattering (SAXS, WAXS), is offering users further experimental possibilities and higher quality data.

The SAXS beamline of ALBA has gone through a major upgrade in 2017. Upgraded items in the SAXS WAXS experimental techniques (SWEET) involve a new monochromator system, a new photon counting detector (Pilatus 1M), a new sample table with an additional rotating stage, and a beam conditioning optics with µ-focus and GISAXS options.

The original double crystal monochromator (DCM) has been replaced by a channel-cut silicon (1 1 1), improving the beam stability at sample position up to 0.9% and 0.4% of the beam size horizontally and vertically, respectivelly.

>Read more on the ALBA website

Figure: Vertical beam profile with the Be lenses into the beam (Horizontal axis unit is mm). The plot is the derivative of an edge scan along the vertical direction. The horizontal beam profile shows a gaussian shape as well.

Modifications to novel non-fullerene small molecule acceptor in organic thin film

2018/03/112018/03/16

… for solar cells demonstrates improved power conversion efficiency.

Scientists from the Imperial College London, Monash University, CSIRO, and King Abdullah University of Science and Technology have reported an organic thin film for solar cells with a non-fullerene small molecule acceptor that achieved a power conversion efficiency of just over 13 per cent.

By replacing phenylalkyl side chains in indacenodithieno[3,2-b]thiophene-based non-fullerene acceptor (ITIC) with simple linear chains to form C8-ITIC, they improved the photovoltaic performance of the material.

C8-ITIC was blended with a fluorinated analog of the donor polymer PBDB-T to form bulk-heterojunction thin films.

The research was recently published in Advanced Materials.

Dr Xuechen Jiao of McNeill Research Group at Monash University carried out grazing incidence wide angle X-ray scattering (GIWAXS) measurements at the Australian Synchrotron to gain morphological information on pure and blended thin films.

“By changing the chemical structure of the organic compound, a promising boost in efficiency was successfully achieved in an already high-performing organic solar cells” said Jiao.

Hijacker parasite blocked from infiltrating blood

2018/01/052018/04/25

A major international collaboration led by Melbourne researchers has discovered that the world’s most widespread malaria parasite infects humans by hijacking a protein the body cannot live without.

The researchers were then able to successfully develop antibodies that disabled the parasite from carrying out this activity.
The study, led by the Walter and Eliza Hall Institute’s Associate Professor Wai-Hong Tham and Dr Jakub Gruszczyk, found that the deadly malaria parasite Plasmodium vivax (P. vivax) causes infection through latching onto the human transferrin receptor protein, which is crucial for iron delivery into the body’s young red blood cells.

Published today in Science, the discovery has solved a mystery that researchers have been grappling with for decades.
The MX and SAXS beamline staff at the Australian Synchrotron assisted with data collection.

Associate Professor Tham, who is also a HHMI-Wellcome International Research Scholar, said the collective efforts of teams from Australia, New Zealand, Singapore, Thailand, United Kingdom, United States, Brazil and Germany had brought the world closer to a potential effective vaccine against P.vivax malaria.