Category: Brazilian Synchrotron Light Laboratory (LNLS)

CNPEM study reveals novel enzyme mechanism with potential for biofuels and biotechnology

CNPEM study reveals novel enzyme mechanism with potential for biofuels and biotechnology

The new discovery will aid in the development of more efficient and sustainable technologies for bioenergy generation

A study led by researchers from the Brazilian Center for Research in Energy and Materials (CNPEM), located in Campinas (SP), has identified a novel molecular mechanism that explains how enzymes degrade beta-glucans, a class of carbohydrates found in fungi, algae, and plants, with great relevance for industrial and energy applications. The research involved approximately 18 collaborators from the LNBR (Brazilian Biorenewables National Laboratory) and the LNLS (Brazilian Synchrotron Light Laboratory), both part of CNPEM, in addition to external researchers from Unicamp and universities in Spain and Canada.

Published in the scientific journal Nature Communications, the work describes, for the first time, a process called processive catalysis applied to the breakdown of these compounds. In this mechanism, the enzyme acts continuously on the same molecular chain, without detaching itself after each stage of the reaction, which makes the process more efficient.

According to researcher Mariana Morais, one of the study coordinators, the work utilized various techniques and equipment at CNPEM, including directed mutagenesis techniques and kinetic analyses. The research also included high-resolution X-ray crystallography experiments conducted at Sirius, CNPEM’s particle accelerator, as well as computer simulations carried out on the Santos Dumont supercomputer, at the National Laboratory for Scientific Computing (LNCC).

“This integration allowed for the observation, at the atomic level, of all stages of the enzymatic process, from substrate recognition to product release and the restart of the catalytic cycle”, says Morais.

Read more on the CNPEM website

Image: Representation of the enzyme forming a catalytic tunnel that enables interaction with the beta-glucan chain and its continuous processing

Sapoti: X-ray microscopy’s new frontier at Sirius

Sapoti: X-ray microscopy’s new frontier at Sirius

Designed to achieve resolutions on the order of 1 nanometer, the Sapoti station of the Carnaúba beamline combines cryogenics, ultra-high vacuum, and cutting-edge mechatronics engineering to reveal structures at the atomic scale

Sapoti (Scanning Analysis by PtychO for Tomographic Imaging) is one of the two experimental stations of the Carnaúba beamline at Sirius. The facility is one of the most sophisticated and challenging stations ever developed at the Brazilian accelerator. Its goal is to achieve resolutions on the order of 1 nanometer in coherent X-ray imaging and tomography, a performance that places it among the world’s most precise instruments in synchrotron light-based microscopy.  

The experimental stations of the Carnaúba beamline

The Carnaúba beamline operates in the 2.05 to 15 keV energy range, and was designed to perform simultaneous measurements with multiple X-ray analytical techniques, including diffraction, spectroscopy, fluorescence, and luminescence, as well as two- and three-dimensional imaging. It is the longest line at Sirius and uses a highly bright beam from an undulator, exploring the full potential for coherence and intensity that a fourth-generation synchrotron light source can provide.

Its infrastructure houses two complementary experimental stations. The Tarumã station was designed for in situ, in vivo (with plants), and cryogenic experiments, operating in an open environment with high flexibility for different types of samples. Sapoti operates in ultra-high vacuum and cryogenic conditions, which ensures even greater thermal and mechanical stability, leading to better spatial resolutions, as well as better conditions for experiments at the lower energy limit.

Read more on the Sirius website

Image: Part of the Carnaúba beamline’s infrastructure at Sirius. The beamline features two experimental stations located 136 and 142 m from the X-ray source, a vertically polarized undulator

Credit: Sirius

The role of lichens in the evolutionary process of life on Earth

The role of lichens in the evolutionary process of life on Earth

Measurements carried out in several beamlines of Sirius provided strong evidence for the classification of the fossil Spongiophyton nanum as a lichen, suggesting a strong contribution of these organisms to the process of evolution of life in terrestrial environments.

A broad international effort involving several research institutions brought together experts from Brazil, Australia, the United States, the United Kingdom and France to unravel a great enigma in the history of the evolution of life on Earth. The research, which was featured on the cover of the journal Science Advances, demonstrated that the organism Spongiophyton nanum was, in fact, one of the oldest and most widely distributed lichens in Earth’s history. 

The researchers used multiple beamlines from Sirius — CNPEM’s synchrotron light source — during the investigations, employing advanced imaging and characterization techniques using synchrotron light, making it possible to reveal microstructures and chemical signatures preserved in fossils with very high resolution. The work also included experiments at other large international facilities, such as Diamond Light Source and Advanced Photon Source.

Read more on the LNLS website

Image: Artistic reconstruction of Spongiophyton nanum during the Early Devonian period in the polar environments of the Paraná Basin. Image from “The rise of lichens during the colonization of terrestrial environments”

Credit: Science Advances, 2024. Available at: https://www.science.org/doi/10.1126/sciadv.adw7879

New strategy combines techniques to study intracellular transport of nanoparticles

New strategy combines techniques to study intracellular transport of nanoparticles

Research led by CNPEM scientists reveals intracellular movement of nanoparticles coated with a protein corona. The technique employed in the study will be available at the Sibipiruna beamline, which is dedicated to research on BSL-4 pathogens.

Researchers from the Brazilian Center for Research in Energy and Materials (CNPEM), in collaboration with institutions in Brazil, the United Kingdom and the United States, have demonstrated a new strategy to monitor the intracellular trajectory of nanoparticles. The study was one of the cover features for the journal Small in June 2025, and combined different high-resolution microscopy techniques to observe how these particles move around in the cellular environment over time.

The research used advanced microscopy resources from the Nanotechnology National Laboratory (LNNano) and Sirius facilities, and included a technique not yet available at the center, X-ray cryotomography. Measurements were obtained using a beamline with characteristics similar to the future Sibipiruna line, which will be part of Project Orion. The resulting data verified the use of this technique in cryogenic conditions, as well as its ability to reveal cellular structures smaller than the viruses that will be studied in the future laboratory complex. 

The approach made it possible to identify the migration of nanoparticles to the perinuclear region of cells and fusion of the vesicles that transport them, without the use of contrast agents. The results overcome common limitations in studies of this type, and offer a promising tool for understanding how nanomaterials behave in complex biological systems.  

Nanoparticles and the challenge of cell internalization

Nanoparticles have been widely studied for their potential in biomedical applications such as controlled release of medications, diagnostic imaging and targeted therapy. But these applications still face major obstacles, especially with regard to detailed understanding of the mechanisms through which these particles are internalized and move within cells. 

The formation of the protein corona, a layer of biomolecules that adsorbs onto the surface of nanoparticles when they come into contact with biological fluids, is a good example of the complexity involved in investigating the mechanisms of internalization and intracellular transit. This layer significantly alters the physical and chemical properties of the particles, influencing their stability and interaction with different cell types. Understanding the behavior of these nanoparticles in the intracellular environment consequently requires approaches that take into account both cell dynamics and the variability introduced by the corona’s composition. 

Despite advances in characterization techniques, most studies offer only specific or static views of the internalization process; it is generally not possible to distinguish between particles absorbed at different times, or to follow their precise location within the cell over time. This study conducted by CNPEM researchers proposes an alternative approach intended to overcome these obstacles through an experimental strategy that employs different imaging methods, providing a broader analysis that extracts the best from each technique. 

A new approach to studying cell dynamics

The researchers proposed a protocol based on a short period of cell exposure, followed by complete removal of the unabsorbed nanoparticles and cryopreservation of the cells after different time intervals (0, 2, and 24 hours). Nanoparticle internalization by the cells was then evaluated using wide-field fluorescence microscopy, and showed progressive migration to the perinuclear region. 

“Previous studies investigating the internalization process of nanoparticles also used cells that were fixed after different time intervals but incubated continuously. As a result of this method, nanoparticles internalized at the beginning of the incubation period cannot be distinguished from those internalized at the end. The alternative method we are proposing avoids this problem and facilitates analysis of the sequence of events and changes associated with the cell internalization process,” explains Mateus Cardoso, an author of the article and researcher at the Synchrotron Light National Laboratory (LNLS), which is part of CNPEM. 

Read more on CNPEM website

Image: FFibroblasts after incubation with silica nanoparticles in the presence of bovine serum albumin (BSA). Wide-field fluorescence microscopy image. (Image adapted from Galdino et al., Small, 2024, https://doi.org/10.1002/smll.202409065)

Enzyme discovered from Brazilian biodiversity can revolutionize bio-refineries

Enzyme discovered from Brazilian biodiversity can revolutionize bio-refineries

Unprecedented enzyme class prospected in Brazilian soil can increase biorefinery efficiency and accelerate the sustainable production of energy and chemicals

A new enzyme class discovered in Brazilian soil represents one of the main advances in recent decades in the field of sustainable production of energy and chemicals. This enzyme is capable of accelerating the cellulose breakdown, a critical process in the production of bioenergy and biochemicals. This discovery, published in the journal Nature, was led by researchers from CNPEM (Brazilian Center for Research in Energy and Materials, in Campinas) in a partnership with researchers from INRAE (French National Research Institute for Agriculture, Food and Environment, at Aix Marseille University) and Technical University of Denmark (DTU).

This enzyme was identified from the genetic material of a microbial community found in biomass residues collected in Brazilian soils. Its novel mechanism of action, combined with the ability to generate its own co-substrate, makes it a powerful tool for plant biomass deconstruction.

“This discovery changes the paradigm of cellulose degradation in nature and has the potential to revolutionize biorefineries”, says CNPEM researcher Mario Murakami, responsible for leading the studies. “With CelOCE, we can envision new routes for bioenergy, biochemicals and biomaterials production from plant biomass, contributing to a bio-based, low-carbon and circular economy.”

CelOCE (Cellulose Oxidative Cleaving Enzyme) improves efficiency in breaking down biomass into glucose, an essential step to convert this raw material into bioenergy and biochemicals. This research spanned from bioprospection in nature to an industrially relevant scale, with validation at the CNPEM pilot plant.

Data under industrial conditions have shown that, when used together with enzymes already used in the industry, CelOCE increased the amount of glucose released by up to 21% from agro-industrial residues. This means higher productivity and less waste in the industrial process.

According to ANP (Brazilian National Agency for Petroleum, Natural Gas and Biofuels) data, Brazil produced 43 billion ethanol liters in 2023. With this discovery, production can increase by billions of liters, using agro-industrial residues such as sugarcane bagasse, corn straw, wood and other crops, without needing to expand planting areas. However, the exact volume of this increase cannot yet be determined, as it depends on the amount of residues that will be used for ethanol production.

The research was carried out by a multidisciplinary team of scientists from CNPEM and international institutions from countries such as France and Denmark. According to CNPEM’s General Director, Antonio José Roque da Silva, the combination of advanced techniques available at the Center, including X-ray crystallography at Sirius, Brazil’s particle accelerator, and genetic engineering with CRISPR-Cas9, was essential to unravel  CelOCE’s unprecedented mechanism. “This work exemplifies the potential opened up by the integration and synergy between CNPEM’s different scientific competencies”, highlights the institution’s General Director.

Read more on CNPEM website

Possible green solution for manganese-contaminated soils

Possible green solution for manganese-contaminated soils

Manganese (Mn) is an essential micronutrient for plants, but at high concentrations, it can become toxic. However, Eucalyptus tereticornis appears to be remarkably tolerant to Mn, even at levels well above those that would cause harm to other plant species. The mechanism(s) underlying this ability were not understood based on scientific literature. From a study that monitored the Mn absorption in these plants, published in the Journal of Hazardous Materials, researchers from the Department of Plant Biology at the State University of Campinas (Unicamp) and from The Brazilian Synchrotron Light Laboratory (LNLS), from the Brazilian Center for Research in Energy and Materials (CNPEM), demonstrated how E. tereticornis can tolerate and detoxify high levels of Mn in its environment.  

The article, entitled “Tissue-level distribution and speciation of foliar manganese in Eucalyptus tereticornis by µ-SXRF and µ-XANES shed light on its detoxification mechanisms” led by Vinicius H. De Oliveira at Unicamp, presents the locations in the plant organism where Mn is accumulated, in what forms this element is assimilated, and even elucidates some of the mechanisms responsible for this ability to tolerate high concentrations of the metal used by E. tereticornis. This characteristic could be explored for environmental remediation purposes, particularly in contaminated soils.  

According to LNLS Soil Science Advisor, Dr. Dean Hesterberg, one of the article’s authors, it is not just the total Mn concentration that is important for understanding contaminated soils. “In acidic soils and especially under reducing redox conditions, manganese minerals are more soluble, which generally increases Mn availability for plant uptake. This can impact plants, which mainly absorb dissolved Mn. And, in Brazil, there are many acidic soils”, says Hesterberg.  

Synchrotron radiation imaging techniques

To gain evidence of how eucalyptus tolerates Mn-rich soils, researchers mapped the Mn distribution within Eucalyptus tereticornis leaves over time. This was possible through advanced techniques available at the Carnaúba beamline of the electron accelerator and synchrotron light generator, Sirius. The techniques used in the work included synchrotron micro scanning X-ray fluorescence imaging (µ-SXRF) and micro X-ray Absorption Near-Edge Structure (µ-XANES) spectroscopy.

Both use synchrotron radiation, a type of light released when electrons are accelerated to speeds very close to that of light. This usually happens by making them travel in a circular path, through strong magnetic fields, as is the case with the Sirius machine. Synchrotron light is incredibly bright and tunable over a wide range of wavelengths. In this way, the Carnaúba beamline uses light at X-ray wavelengths produced by the Sirius accelerator.

µ-SXRF

The synchrotron micro scanning X-ray fluorescence imaging (µ-SXRF) technique is used to investigate the elemental distribution and composition of materials on a microscopic scale. Fluorescence occurs because when materials are exposed to X-rays, atoms in the sample are excited and emit secondary (or fluorescent) X-rays when de-excited. The energy of these emissions serves as a fingerprint of each chemical element. This allows scientists to identify and quantify the composition of the studied material.  

LNLS/CNPEM researcher Dr. Carlos Alberto Pérez, one of the study’s authors, explains a little about how the technique works. “The µ-SXRF works based on X-ray optical equipment. The equipment has a monochromator, a crystal that defines a specific energy for the sample excitation. Another part of the equipment is the nanofocusing of this monochromatic light. This way, an X-ray beam that is about 100 times smaller than a human hair is created”.  

Through this beam of light, researchers are able to scan the sample, point by point, which generates an image with thousands of pixels. X-ray fluorescence is emitted as the beam hits each of these points. At the end, the pixels are computed using a program to generate an image, called elemental map. 

Elemental maps can be constructed for several specific chemical elements. In the case of the research published in the Journal of Hazardous Materials, the group of scientists assembled the elemental map of Mn in eucalyptus tissues. Thus, they were able to compare the presence of Mn in the plant’s leaf tissues, when it grew with an abundance of Mn and when it grew with normal amounts of the metal.  

μ-XANES

Micro-X-Ray Absorption Near Edge Structure (μ-XANES) spectroscopy, in turn, is used to probe the chemical state and electronic structure of specific elements in a sample. It is a sub-technique of X-ray Absorption Spectroscopy (analysis of how a sample absorbs X-rays), focusing on the energy band near the absorption edge of the element being studied. That is why the technique’s name brings the term ‘near the edge’.  

Hesterberg says that “unlike µ-SXRF, which is a fixed energy and scanning technique, µ-XANES is a variable energy technique. The absorption edge region is where there is a large increase in X-ray absorption by the sample”.  

Analysis of the edge region made it possible to discover the manganese oxidation state, that is, whether the element was in the form Mn²⁺, Mn³⁺ or Mn⁴⁺. Therefore, the technique allowed the researchers to understand if the manganese was in an oxidized form, or in a mineral state, and what coordinating atoms are likely around it. This means understanding what strategies eucalyptus uses to detoxify itself from the metal.  

Read more on CNPEM website

Image: Detectors around a sample being measured at the Sirius’ Carnaúba beamline.

XPCS as a powerful tool for nanoparticles analysis in complex biological media

XPCS as a powerful tool for nanoparticles analysis in complex biological media

An article published by CNPEM researchers was featured on the Nano Letters scientific journal’s cover and explores how the X-ray Photon Correlation Spectroscopy (XPCS) technique can distinguish protein corona formation from nanoparticle aggregation in complex biological media.

The innovative work, carried out at Sirius, expands analysis capacity in nanomedicine and highlights the XPCS potential to characterize nanoparticle interactions in biological environments in real time, providing a valuable resource for nanobiotechnology research and new biomedical materials development. 

The innovative nanoparticles applications in biomedicine

Nanoparticles are tiny structures, with dimensions generally between 1 and 100 nanometers. Due to its size, they can interact with cells, proteins and molecules in a highly precise way, which allows driven delivery of medicines and therapeutic agents. This allows, for example, for cancer treatments to be more effective, by releasing drugs directly into tumor cells, minimizing side effects on healthy tissues.

Furthermore, nanoparticles can be designed for responding to specific stimuli, such as pH, temperature or biological signs, allowing a controlled release of medicines only when necessary.

In the diagnosis area, nanoparticles offer new ways ​​to prematurely detect diseases. They can be linked to specific biomarkers that bind to molecular targets, making it easier to identify cancerous cells or the presence of viruses and bacteria, for example. 

The interaction between nanoparticles and proteins in biological systems

These applications, however, are conditioned to a predictable behavior of these nanoparticles in complex biological systems. In some cases, by coming into contact with biological fluids, such as blood, a protein coating can be formed around nanoparticles, a phenomenon known in biomedicine by the English term “protein corona”. 

This happens because nanoparticles attract proteins present in the biological environment, forming a “corona” or “crown” around its surface. The formation of this protein corona strongly influences how do nanoparticles interact with cells and tissues in the organism, which can affect its efficacy and safety in medical applications, such as drug therapies, diagnostics, and vaccine development. 

For these reasons, studying the protein corona formation and characteristics is crucial for the development of nanoparticles that are safe and effective for biomedical use. 

Limitations of optical techniques for analyzing these samples

Optical techniques, such as Fluorescence Correlation Spectroscopy (FCS) and Dynamic Light Scattering (DLS), face significant limitations when analyzing nanoparticles in complex biological environments. One of the main limitations is the need for diluted and transparent samples, which makes it difficult to analyze nanoparticles in highly concentrated media, such as blood and body fluids. In complex media, particles and biomolecules can interfere with light propagation, causing spreading and excessive absorption, which compromises the accuracy of nanoparticle size and concentration measurements. 

Furthermore, optical techniques rely on nanoparticle specific properties, which limits its application to particles that present these specific characteristics. For example, in the FCS case, it is necessary that nanoparticles show fluorescence in order to be detected, restricting the technique’s use to fluorescent materials. This is one of the limitations that makes optical techniques less suitable to characterize nanoparticles under realistic conditions and in real time, as in unprocessed samples of biological fluids. 

XPCS: A powerful technique for nanoparticles analysis in complex media

The X-ray Photon Correlation Spectroscopy (XPCS) technique appears as a good alternative by offering significant advantages for nanoparticle analysis in complex biological environments, overcoming many of the optical techniques limitations. One of its main advantages is the ability to analyze highly concentrated and complex samples, such as blood and other bodily fluids, without need for dilution or transparency.

Read more on CNPEM website

A powerful tool for nanoparticles analysis in complex biological media

A powerful tool for nanoparticles analysis in complex biological media

An article published by CNPEM researchers was featured on the Nano Letters scientific journal’s cover and explores how the X-ray Photon Correlation Spectroscopy (XPCS) technique can distinguish protein corona formation from nanoparticle aggregation in complex biological media.

The innovative work, carried out at Sirius, expands analysis capacity in nanomedicine and highlights the XPCS potential to characterize nanoparticle interactions in biological environments in real time, providing a valuable resource for nanobiotechnology research and new biomedical materials development. 

The innovative nanoparticles applications in biomedicine

Nanoparticles are tiny structures, with dimensions generally between 1 and 100 nanometers. Due to its size, they can interact with cells, proteins and molecules in a highly precise way, which allows driven delivery of medicines and therapeutic agents. This allows, for example, for cancer treatments to be more effective, by releasing drugs directly into tumor cells, minimizing side effects on healthy tissues.

Furthermore, nanoparticles can be designed for responding to specific stimuli, such as pH, temperature or biological signs, allowing a controlled release of medicines only when necessary.

In the diagnosis area, nanoparticles offer new ways ​​to prematurely detect diseases. They can be linked to specific biomarkers that bind to molecular targets, making it easier to identify cancerous cells or the presence of viruses and bacteria, for example. 

The interaction between nanoparticles and proteins in biological systems

These applications, however, are conditioned to a predictable behavior of these nanoparticles in complex biological systems. In some cases, by coming into contact with biological fluids, such as blood, a protein coating can be formed around nanoparticles, a phenomenon known in biomedicine by the English term “protein corona”. 

This happens because nanoparticles attract proteins present in the biological environment, forming a “corona” or “crown” around its surface. The formation of this protein corona strongly influences how do nanoparticles interact with cells and tissues in the organism, which can affect its efficacy and safety in medical applications, such as drug therapies, diagnostics, and vaccine development. 

For these reasons, studying the protein corona formation and characteristics is crucial for the development of nanoparticles that are safe and effective for biomedical use. 

Read more on LNLS website

Image: Schematic representation of a functionalized SiO2 nanoparticle

SRI 2025 in Brazil and Lightsources.org Poster Prize 2024 winner

SRI 2025 in Brazil and Lightsources.org Poster Prize 2024 winner

During SRI 2024, Brazil was chosen to host the next edition of the conference, scheduled for 2027. The decision was made among Brazil, Canada, and South Korea, countries that had expressed interest in hosting the international event.

Held for more than 40 years, the SRI aims to anticipate the latest ideas and trends in synchrotron instrumentation, with a view to sharing technical and scientific knowledge and advancing the field as a whole.

Science Poster Prize

LNLS/CNPEM engineer Renan Geraldes received the main prize for his poster, which presented the charging chamber of the cryogenic nanoprobe at the Sapoti experimental station on the Carnaúba beamline at Sirius.

“In addition to the invitations to present received by the editing team and the choice of Brazil as the next host, the awarding of a work also symbolizes and concretizes, in a way, the recognition of the space occupied by Sirius within the synchrotron community,” says Renan Geraldes.

Read more on LNLS website

Image: NLS/CNPEM engineer Renan Geraldes received the main prize for his poster, which presented the charging chamber of the cryogenic nanoprobe at the Sapoti experimental station on the Carnaúba beamline at Sirius.

Ptychographic computed X-ray tomography reveals structure of porous membranes on the nano scale

Ptychographic computed X-ray tomography reveals structure of porous membranes on the nano scale

Article published in Communications Materials presents significant findings and discusses the possibilities offered by this technique combined with synchrotron light sources

Porous materials play key roles in a variety of contexts, from transporting water and nutrients in biological systems to storing oil and water in reservoirs of rock. And synthetic polymer membranes are essential to separation processes, as in the case of chromatography. They have well-established applications in water desalination, hemodialysis, and gas separation, and these uses are expanding into processes that filter out pollutants from contaminated water. Their benefits include energy efficiency, smaller carbon footprint, and compact design that provides a large area of membrane in a small volume.

Membranes that can fulfill technological objectives have complex porous structures that ensure the required selectivity, mechanical stability, and characteristics for rapid transport; the effectiveness and performance of these membranes is defined by characteristics such as porosity and interconnectivity, which can be particularly difficult to measure when they are brought down to the nano scale.

The limitations of electron microscopy and advantages of ptychographic X-ray computed tomography

Techniques such as scanning electron microscopy (SEM), atomic force microscopy (AFM), and transmission electron microscopy (TEM) have helped scientists better understand the transport mechanisms in these applications and develop membranes for different purposes. But even though they are powerful, these techniques also have significant limitations: the samples must be dehydrated and covered with a metallic layer, and must also remain in a vacuum during analysis, which can affect the structure of these membranes and hinder analysis under near-real conditions.

Furthermore, when the pores of the material reach the nano scale, the total sample volume must be significantly reduced in order to attain the resolution necessary for analysis. Within this context, X-ray tomography has emerged as a good alternative. This method not only offers non-destructive visualization, but samples can be analyzed in ambient conditions with significantly larger total sample volumes.

Conventional X-ray tomography, which analyzes different absorption in different parts of a sample, faces challenges related to resolution limits when analyzing less dense materials (such as membranes). But as new fourth-generation synchrotron light sources have recently come online and ptychographic X-ray tomography has been developed, images of these materials can be obtained with nanometric resolution.

Ptychographic X-ray computed tomography (PXCT) is a powerful phase-contrast imaging technique that uses a series of two-dimensional projections of the object from different angles to reconstruct its three-dimensional structure in high resolution, revealing information about porosities and interconnectivity.

Read more on CNPEM website

Sirius helps reveal previously unknown process of maturation for key protein in SARS-CoV-2 replication

Sirius helps reveal previously unknown process of maturation for key protein in SARS-CoV-2 replication

Researchers at USP in São Carlos combined cutting-edge technologies and demonstrated that a molecule targeted by medications behaves differently than previously theorized.

A group of researchers from the University of São Paulo in São Carlos has just presented their findings from research indicating a new understanding of the maturation process and how inhibitors act upon the Mpro protein, an essential component in the life cycle of the Sars-CoV-2 virus and the target of various efforts to develop medications to treat Covid-19. Their results appear in an article entitled “An in-solution snapshot of SARS-COV-2 main protease maturation process and inhibition,” published in the journal Nature Communications (https://doi.org/10.1038/s41467-023-37035-5).

Mpro is an abbreviation for main protease, because of its importance to the virus. Today, two medications are available which interact with this molecule to treat covid-19. Still, some of the processes in this protein’s activity are not yet entirely understood, and this was the object of the study undertaken at Sirius.

As part of the role it plays in the life cycle of the Sars-CoV-2 virus, Mpro undergoes a series of modifications until it reaches its final form. Part of this process had already been described by the group from São Carlos, directed by Professor Glaucius Oliva.

André Godoy, who led the group, was one of the first external users of Sirius, the cutting- synchrotron light source planned and built by the Brazilian Center for Research in Energy and Materials (CNPEM), an organization overseen by the Ministry of Science, Technology and Innovation (MCTI).

In September 2020 he brought approximately 200 crystals containing proteins from the Sars-CoV-2 virus for analysis in the Manacá beamline, which was developed for experiments involving X-ray diffraction crystallography. “The Manacá beamline was the first research station to open at Sirius, as the result of a task-force effort at the CNPEM to support research exploring molecular mechanisms related to covid-19. This is one of the publications that resulted from this effort,” explains Harry Westfahl, Director of the Brazilian Synchrotron Light National Laboratory (LNLS).

Read more on the LNLS website

Image: Cryomicroscopy map of the Mpro dimer interacting with the N-terminal. Image obtained from analyses conducted at Diamond and Sirius by the USP São Carlos group

New biocatalyst could more efficiently split water molecules

New biocatalyst could more efficiently split water molecules

Experiment carried out on Sirius shed light on reaction fundamental to the production of hydrogen fuel


A recent experiment at Sirius, the Brazilian synchrotron light source at the Brazilian Center for Research in Energy and Materials (CNPEM) in Campinas, São Paulo (see Pesquisa FAPESP issue 269) showed how a certain biological catalyst can more efficiently split water molecules (H2O) using electrolysis. This reaction, an electrochemical process that uses electricity to break down water into the elements that comprise it, is very significant because it produces not only oxygen but also hydrogen, considered the fuel of the future by many specialists because it does not emit any polluting gases when it is utilized (see Pesquisa FAPESP issue 314).

“We discovered that when some enzymes present in nature like bilirubin oxidase (BOD) are manipulated in the lab, they can accelerate the reaction to split water,” states chemist Frank Nelson Crespilho, a professor at the University of São Paulo’s São Carlos Institute of Chemistry (IQSC-USP) who led the study. “We didn’t know why this happened; thanks to new equipment developed specifically for Sirius, we were able to observe how this enzyme, BOD, behaves during the process of oxidation in water. We found that the copper atoms within it are relevant to this reaction.”

Crespilho expects this advance to pave the way for science to get inspiration from the part of the enzyme that accelerated the reaction. “It is important for us to recognize the important regions of BOD, since today synthetic chemists that work in materials production can copy and synthesize this part of the enzyme in the laboratory. This will make the catalyst much more affordable, with a much broader range of potential applications,” he adds. Most of the catalysts used in this process utilize noble metals like platinum and iridium, making large-scale application unfeasible due to the cost involved. An article describing the experiment written by Crespilho’s team, which includes the researchers Graziela Sedenho, Rafael Colombo, Thiago Bertaglia, and Jessica Pacheco, was published in October in the journal Advanced Energy Materials. Scientists from the Brazilian Synchrotron Light National Laboratory (LNLS) also participated in the study.

Read more on the LNLS website

Image: Researcher manipulates electrochemical cell used in experiment

Researchers investigate the origins of superconductivity

Researchers investigate the origins of superconductivity

The first scientific paper published with data obtained at the EMA beamline studied the relationship between skutterudite’s superconducting properties and the distance between their atoms.

In Brazil, about 7.5% of the electricity produced is lost in transmission and distribution. This happens because the materials that make up these systems are not perfect electrical conductors and dissipate part of the energy, for example, in the form of heat. Similarly, even though electric cars are much more efficient than combustion-engine vehicles, they can still lose up to 15 percent of their energy during the charging process.

Thus, the challenges of achieving sustainable development lie not only in the availability of abundant, clean, and cheap energy, but also in the development of new, efficient, and low-cost energy transport and storage systems.

In turn, these new systems require research into new materials with special properties, such as superconducting materials. Superconductivity is the property that allows certain materials to conduct electric current without resistance and therefore without energy loss. Currently, however, a major limitation for the large-scale use of superconducting materials is their need to be kept at very low temperatures, close to absolute zero (-273.15°C), which requires their association with large cooling infrastructures. In these conditions, superconductors have applications in MRI machines and other high-performance medical equipment, as well as in scientific research equipment, such as the super-magnets used in particle accelerators.

Although superconductivity has been known for more than a century, its origin is still a matter of intense debate in the scientific community. Why do certain materials exhibit superconductivity while others do not? Once this is known, it will be possible to build materials that are superconducting even under ambient temperature and pressure conditions, allowing a true technological revolution, not only in the transmission and storage of energy but also in all kinds of electrical equipment in everyday life.

The movement of electrons without resistance along a superconducting material is understood so far to be possible by the union of two electrons (called Cooper pairs) that, with the help of a deformation in the material’s lattice (called a phonon), can overcome Coulombian repulsion and start moving as a single particle.

The question to which there is still no satisfactory answer is: what makes these electrons want to come together in pairs? Among the various hypotheses, one possibility is that this phenomenon would be connected to the distance between the atoms in the superconducting material.

Thus, in research published in the journal Materials, researchers from the Brazilian Center for Research in Energy and Materials (CNPEM), and collaborators from Germany, investigated two materials (LaPt4Ge12 and PrPt4Ge12) whose crystalline structure is known as skutterudite to test the hypothesis that superconductivity would be related to the distance between the atoms of the material. This was the first scientific paper published with data obtained at the EMA beamline of CNPEM’s synchrotron light source Sirius.

Read more on the LNLS website

Capybara gut holds valuable enzymes for biotechnology

Capybara gut holds valuable enzymes for biotechnology

Study elucidates unprecedented processes of herbivore metabolism involved in the efficient degradation of plant fibers

A group of researchers from the Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), an organization supervised by the Brazilian Ministry of Science, Technology and Innovations (MCTI), has published in the journal Nature Communications a study that explores some of the most modern resources of current science to reveal unprecedented and valuable details of the capybara’s digestive process.

The capybara, the largest rodent on the planet, is known for its ability to degrade very efficiently the biomass it consumes, but the details of the animal’s microbiota metabolism that contribute to this characteristic have not yet been elucidated. Researcher Mario Murakami recalls that, in Brazil, this animal is used to eating sugarcane. “Since Brazilian biodiversity is an invaluable source of biotechnological solutions, our hypothesis was that the microorganisms inhabiting capybaras’ intestines have, throughout evolution, developed highly effective molecular strategies for the degradation and use of this biomass of great industrial and economic importance. And that was demonstrated in our study.”

“Population and molecular inventory” of the gut microbiome

The meticulous and unprecedented work started with a complete survey of the bacteria present in the capybara’s intestine, in addition to the expressed genes and metabolites produced from plant fibers. To understand the processes of depolymerization of lignocellulosic fibers and the efficient transformation of sugars into energy, a vast combination of techniques, methodologies and resources, including synchrotron light at the MX2 and SAXS1 beamlines of the Brazilian Synchrotron Light Laboratory (LNLS), was required, from the population scale of microorganisms to the atomic and molecular level of enzymes.

Read more the the LNLS website

Advances in understanding superconducting material

Advances in understanding superconducting material

Superconductivity has the potential to revolutionize technology, whether in lossless power transmission, more efficient electric motors and other applications. Recently these investigations have gained a new ally: Sirius

Imagine a future with batteries that don’t need charging, electric cars at more affordable prices, highly efficient electric motors and cheaper electricity due to ease in their transmission and storage. Gaining a deeper knowledge of the phenomenon of superconductivity is the key to this true technological revolution, which would have a potential impact on all types of electrical equipment.  

This is because superconductivity is the property that allows certain materials to conduct electrical current without resistance and therefore without loss of energy. In Brazil, about 7.5% of electricity is lost in transmission and distribution, since the materials of these systems dissipate part of the energy, for example, in the form of heat. Also electric cars, even though they are much more efficient than ordinary combustion-powered cars, still lose up to 15% of the energy when charging batteries.  

In view of the importance of this field, the National Center for Research in Energy and Materials (CNPEM), an organization supervised by the Ministry of Science, Technology of Innovations (MCTI), has been actively working to advance the understanding of the phenomenon of superconductivity. One of the research fronts in this area seeks to develop new tools for the experimental study of the physical phenomenon of superconductivity with the aid of superpotent X-rays generated by Sirius. 

Read more on the Sirius website

Image: The Ema light line is one of the most advanced scientific tools for experiments seeking solutions for technologies involving superconductivity

Civil engineer plays key role in construction of Brazil’s light source

Civil engineer plays key role in construction of Brazil’s light source

Sirius is the only light source in Latin America and is located at the Brazilian Center for Research in Energy and Materials. Mayara Adorno is a civil engineer and her role has been to oversee the technology control of the structures that house the synchrotron machine.

In her #LightSource Selfie, Mayara explains how she was attracted by the opportunity to work on a large project, taking it from paper plans through to completion. As with all large scale science facility construction projects, there were daily challenges for Mayara and her engineering colleagues. She says, “I’ve learned a lot from the project and this was very important for my professional and personal growth. I would advise any young engineer not to give up on your dreams and, this way, become a person who always wants to be open to learn and teach.” “It makes me really proud to know that Sirius has turned into the great science infrastructure from the efforts and dedications of many professionals from different areas, including myself.”

Mayara Adorno, Civil Engineer, at Sirius