Tag: biochemistry

Scientists develop strategy to engineer artificial allosteric sites in protein complexes

Scientists develop strategy to engineer artificial allosteric sites in protein complexes

According to a recently published research paper by a team of scientists, a groundbreaking approach has been developed to create artificial allosteric sites (where by binding an effector molecule, activity at the distal active site is regulated) in protein complexes. This breakthrough research holds significant promise for a wide range of applications in industrial, biological, medical, and agricultural fields.

The team’s work is published in Nature Chemistry on 06 July 2023 at 16:00 (London time).


Protein complexes, such as hemoglobin and molecular motors, exert concerted functions through cooperative work between the subunits (constituent proteins in the protein complex). This orchestration is enabled by the allosteric mechanism. The allosteric effect, regulation of function at an active site in a subunit by the binding of an effector molecule to an allosteric site in another subunit, was originally proposed in the 1960s and since then it has remained one of the most important topics in the biochemistry field. The research team developed a strategy for designing artificial allosteric sites into protein complexes to regulate a concerted function of a protein complex. “The creation of artificial allosteric sites into protein complexes has the potential to reveal fundamental principles for allostery and serve as tools for synthetic biology,” said Nobuyasu Koga, a professor at the Osaka University.


The research team hypothesized that allosteric sites in protein complexes can be created by restoring lost functions of the pseudo-active sites which are predicted to have been lost during evolution. Various protein complexes include subunits that have pseudo-active sites. It has been
reported that pseudo-active sites have an allosteric connection with active sites in other subunits. For example, a pseudo-active site in a subunit, which has lost ATPase activity but still exhibits ATP-binding ability, activates another subunit’s active site upon binding to ATP. (At the cellular
level, ATP is the source of energy. ATPase describes the enzyme’s ability to decompose ATP.) Such studies support the idea that distinct allosteric sites can be created into protein complexes by engineering pseudo-active sites.

Read more on the Photon Factory website

Image: Fig. 1 Design of allosteric sites into a rotary molecular motor

Picking up good vibrations – of proteins – at CHESS

Picking up good vibrations – of proteins – at CHESS

A new method for analyzing protein crystals – developed by Cornell researchers and given a funky two-part name – could open up applications for new drug discovery and other areas of biotechnology and biochemistry.

The development, outlined in a paper published March 3 in Nature Communications, provides researchers with the tools to interpret the once-discarded data from X-ray crystallography experiments – an essential method used to study the structures of proteins. This work, which builds on a study released in 2020, could lead to a better understanding of a protein’s movement, structure and overall function.

Protein crystallography produces bright spots, known as Bragg peaks, from the crystals, providing high-resolution information about the shape and structure of a protein. This process also captures blurry images – patterns and clouds related to the movement and vibrations of the proteins – hidden in the background of the Bragg peaks.

These background images are typically discarded, with priority given to the bright Bragg peak imagery that is more easily analyzed.

“We know that this pattern is related to the motion of the atoms of the protein, but we haven’t been able to use that information,” said lead author Steve Meisburger, Ph.D. ’14, a former postdoctoral researcher in the lab of Nozomi Ando, M.S. ’04, Ph.D. ’09, associate professor of chemistry and chemical biology in the College of Arts and Sciences. “The information is there, but we didn’t know how to use it.  Now we do.”

Meisburger worked closely with Ando to develop the robust workflow to decode the weak background signals from crystallography experiments called diffuse scattering. This allows researchers to analyze the total scattering from crystals, which depends on both the protein’s structure and the subtle blur of its movements.

Their two-part method – which the team dubbed GOODVIBES and DISCOBALL – simultaneously provides a high-resolution structure of the protein and information on its correlated atomic movements.

GOODVIBES analyzes the X-ray data by separating the movements – subtle vibrations – of the protein from other proteins that might be moving around it. DISCOBALL independently validates these movements for certain proteins directly from the data, allowing researchers to trust the results from GOODVIBES and understand what the protein might be doing.

Read more on CHESS website

Image: Meisburger, Case, & Ando (2020) Nat Commun 11, 1271

Tiny proteins found across the animal kingdom play a key role in cancer spread

Tiny proteins found across the animal kingdom play a key role in cancer spread

Researchers from McGill University have made an exciting discovery about specific proteins involved in the spread of certain cancers.

Dr. Kalle Gehring, professor of biochemistry and founding director of the McGill Centre for Structural Biology, and his team have focused on unravelling the mystery around phosphatases of regenerating liver (PRLs). These proteins are found in all kinds of animals and insects — from humans to fruit flies – and play a unique role in the growth of cancerous tumours and the spread of cancer throughout the body.

“It’s important for us to study PRLs because they are so important in cancer,” said Gehring, “In some cancers, like metastatic colorectal cancer, the proteins are overexpressed up to 300-fold.”

This overexpression of PRLs makes cancer cells more metastatic and drives the spread to other organs.

In his most recent paper, published in the Journal of Biological Chemistry, Gehring and his colleagues confirmed that PRLs exist in all kinds of single- and multi-cell animals. Data collected at the Canadian Light Source (CLS) at the University of Saskatchewan confirmed the role of PRLs in binding magnesium transporters, helping to further the understanding of how these proteins influence human disease.

Read more on the Canadian Light Source website

Unravelling the molecular structure, self-assembly, and properties of a cephalopod protein variant

Unravelling the molecular structure, self-assembly, and properties of a cephalopod protein variant

Cephalopods, such as the loliginid in Figure 1A, are known for their remarkable ability to rapidly change the color and appearance of their skin. These capabilities are enabled in part by unique structural proteins called reflectins, which play essential roles in optical behavior of cephalopod skin cells. Moreover, reflectins have demonstrated exciting potential as functional materials within the context of biophotonic and bioelectronic systems. Given reflectins’ demonstrated significance from both fundamental biology and applications perspectives, some research effort has been devoted to resolving their three-dimensional (3D) structures. However, the peculiar sequence composition of reflectins has made them extremely sensitive to subtle changes in environmental conditions and prone to aggregation, thus significantly complicating the study of their structure-function relationships and precluding their definitive molecular-level structural characterization. In this work, we have elucidated the structure of a reflectin variant at the molecular level, demonstrated a robust methodology for controlling its assembly and optical properties.


We began our studies by rationally selecting a prototypical reflectin variant (RfA1TV) by using a bioinformatics-guided approach (Figure 1B). Next, we not only produced the variant in high yield and purity but also optimized conditions for maintaining this protein in a monomeric state (Figure 1C). We then probed the protein with small angle X-ray scattering (SAXS) using the Austrian SAXS beamline at the Elettra Synchrotron Laboratory in Trieste, Italy. For this purpose, a well-dispersed solution of RfA1TV was prepared in a low-pH buffer and transferred into a glass capillary, which was positioned in the path of an incident X-ray beam. The X-rays scattered by the solution-borne RfA1TV molecules formed a 2-D pattern on a Pilatus3 1M detector (Figure 1D). Subsequently, radial averaging and image calibration of the two-dimensional data furnished corresponding one-dimensional curves, which were further processed, analyzed, and correlated with other experiments to obtain insight into the protein’s geometry (Figure 1E).

Read more on the Elettra website

Image: (A) A camera image of a Doryteuthis pealeii squid. (B) An illustration of the selection of the prototypical truncated reflectin variant (RfA1TV) from full-length Doryteuthis pealeii reflectin A1. (C) A digital camera image of a solution of primarily monomeric RfA1TV (Upper) and a corresponding cartoon of RfA1TV monomers (Lower Inset). (D) An illustration of the SAXS analysis of the reflectin variant, wherein incident X-rays are scattered by the solution-borne proteins to furnish a corresponding scattering pattern. (E)The 3D structure of RfA1TV (random coils – gray, helices – orange, β-strands – purple). 

Credit: This figure has been adapted from M. J. Umerani*, P. Pratakshya* et al.Proc. Natl. Acad. Sci. U.S.A 117, 32891-32901 (2020).

Inorganic nanoparticles activity as artificial pro-enzymes

Inorganic nanoparticles activity as artificial pro-enzymes

Research opens perspective for treatment of several diseases tailored to the needs of each patient

From the biochemical point of view, we are a complex set of interconnected chemical reactions. The molecules that make up our bodies are in constant transformation, and this is what makes it possible for us to get energy from food, to regenerate damage to our tissues, and to synthesize the compounds necessary for life.
These modifications usually occur with the aid of other molecules called enzymes, which promote and accelerate chemical reactions without being consumed during the process.

For the proper functioning of this complex system, the enzymes must act only at the necessary place and time. Hence, nature has developed an ingenious strategy for this to happen: inactive forms of enzymes, known as proenzymes, are continuously produced, but are activated only by specific stimuli.
The occurrence of a problem in the production of these enzymes can result in highly debilitating diseases. However, the treatment of patients by means of enzymatic replacement from natural sources is not always an adequate solution.
Therefore, researchers have been investigating synthetic systems to mimic the action of natural enzymes for biomedical applications and one of the most promising alternatives is the use of nanoparticles.

>Read more on the Brazilian Synchrotron Light Laboratory website

Image: Schematic figure of the action of the ultrafine cerium(III) hydroxide and cerium oxide CeO (2-x) nanoparticles . Back cover image from the Journal of Materials Chemistry B [1].

Probing tumour interiors

Probing tumour interiors

X-ray fluorescence mapping to measure tumour penetration by a novel anticancer agent.

A new anticancer agent developed by the University of Warwick has been studied using microfocus synchrotron X-ray fluorescence (SXRF) at I18 at Diamond Light Source. As described in The Journal of Inorganic Biochemistry, researchers saw that the drug penetrated ovarian cancer cell spheroids and the distribution of zinc and calcium was perturbed.  

Platinum-based chemotherapy agents are used to treat many cancer patients, but some can develop resistance to them. To address this issue, scientists from the University of Warwick sought to employ alternative precious metals. They developed an osmium-based agent, known as FY26, which exhibits high potency against a range of cancer cell lines. To unlock the potential of this novel agent and to test its efficacy and safety in clinical trials, the team need to fully understand its mechanism of action.

To explore how FY26 behaves in tumours, the team grew ovarian cancer spheroids and used SXRF at I18 to probe the depth of penetration of the drug. They noted that FY26 could enter the cores of the spheroids, which is critical for its activity and very encouraging for the future of the drug. SXRF also enabled them to probe other metals within the cells, which showed that the distribution of zinc and calcium was altered, providing new insights into the mechanism of FY26-induced cell death.

>Read more on the Diamond Light Source website

Figure: (extract) A) Structure of FY26and related complexes, [(ŋ6-p-cym)Os(Azpy-NMe2)X]+. B) Bright field images and SXRF elemental maps of Os, Ca and Zn in A2780 human ovarian carcinoma spheroid sections (500 nm thick) treated with 0.7 µM FY26(½ IC50) for 0 or 48 h. Raster scan: 2×2 µm2 step size, 1 s dwell time. Scale bar 100 µm. Calibration bar in ng mm-2. Yellow squares in bright field images indicate areas of the spheroid studied using SXRF. Red areas in SXRF elemental maps indicate the limits of the spheroids. C) Average Os content (in ng mm-2) as a function of distance from A2780 3D spheroid surface, after treatment for 16 h (green), 24 h (blue) or 48 h (red) with 0.7 µM FY26. 
Canadian researchers unlock how seaweed is digested

Canadian researchers unlock how seaweed is digested

Cattle on the Prairies are hundreds of kilometres from the coast and yet it’s possible that seaweed could make its way into their diet as an additive.

“Seaweed is an incredible opportunity. It is a sustainable feedstock. It grows rapidly, it doesn’t require arable land or fresh water to grow,” said Wade Abbott, research scientist at Agriculture and Agi-Food Canada’s Lethbridge Research and Development Centre.

It may seem like a leap to go from the human gut to that of cattle, but Abbott explained that by understanding the human gut microbiome, or microorganisms, and the microbiome’s ability to use the sugars found in seaweed in its symbiotic relationship with the host, he sees potential to expand what is now a limited use of algae products.

>Read more on the Canadian Light Source website

Image: Culturing gut bacteria in the lab (shown in these test tubes) allows researchers ‎to determine which genes in the genomes of bacteria are activated and discover new enzymes that digest rare substrates like agarose.
Credit: Wade Abbott

Metallic drivers of Alzheimer’s disease

Metallic drivers of Alzheimer’s disease

The detection of iron and calcium compounds in amyloid plaque cores

X-ray spectromicroscopy at the Scanning X-ray Microscopy beamline (I08), here at Diamond, has been utilised to pinpoint chemically reduced iron and calcium compounds within protein plaques derived from brains of Alzheimer’s disease patients. The study, published in Nanoscale, has shed light on the way in which metallic species contribute to the pathogenesis of Alzheimer’s disease and could help direct future therapies.

Alzheimer’s disease is a neurodegenerative disease that is associated with dementia and shortened life expectancy. The disease is characterised by the formation of protein plaques and tangles in the brain that impair function. As well as protein plaques, perturbed metal ion homeostasis is also linked with pathogenesis, and iron levels in particular are elevated in certain regions of the brain.

A team of scientists with a long history in exploring biomineralisation in Alzheimer’s brains set out to characterise the iron species that are associated with the amyloid protein plaques. They extracted samples from the brains of two deceased patients who had Alzheimer’s and applied synchrotron X-ray spectromicroscopy to differentiate the iron oxide phases in the samples.

They noted evidence that the chemical reduction of iron, and indeed the formation of a magnetic iron oxide called magnetite, which is not commonly found in the human brain, had occurred during amyloid plaque formation, a finding that could help inform the outcomes of future Alzheimer’s therapies.

>Read more on the Diamond Light Source website

Image: Synchrotron soft X-ray nano-imaging and spectromicroscopy reveals iron and calcium biomineralisation in Alzheimer’s disease amyloid plaques.

Scientists map important immune system enzyme for the first time

Scientists map important immune system enzyme for the first time

Biochemists from McGill University are getting a good look at just how a specific enzyme that is part of the human immune system interacts with a certain group of bacteria that are described as gram-negative.

Researchers around the world “have been studying the enzyme, known as AOAH, for more than 30 years. This is the first time anyone has been able to see exactly what it looks like,” according to Bhushan Nagar, an associate professor of biochemistry at McGill University in Montreal.

More than that, the 3D images captured a moment in time which shows just how AOAH inactivates a toxic molecule that is commonly part of various gram-negative bacteria. The research was conducted at the Canadian Light Source.

Numerous types of gram-negative bacteria exist throughout the environment. While some are harmless, many cause a variety of human illnesses, says Nagar. For example, several species such as E. coli and Salmonella, cause food borne illness. Others cause infections such as pneumonia, meningitis, bloodstream infections or gonorrhea.

>Read more on the Canadian Light Source

Image: Bhushan Nagar (principal investigator), Alexei Gorelik (first author of paper) and Katalin Illes (research assistant at Nagar lab) at their McGill University lab.
Credit: Bhushan Nagar.