enzyme – Lightsources.org

Undermining the foundations of bacterial resistance

2023/05/102023/05/12

Scientists from the University of Guelph have used the Canadian Light Source (CLS) at the University of Saskatchewan to better understand how several infectious bacteria, including E. coli., build a protective sugar-based barrier that helps cloak their cells.

Published in the Journal of Biological Chemistry, the Guelph research provides the very early steps toward new treatments for E. coli and a whole range of bacteria. Their particular focus is on strains of E. coli that cause urinary tract and bloodstream infections, particularly those that are antibiotic resistant.

The research is looking to understand the enzyme that many infectious bacteria use to build the foundations of their protective capsule. The capsule helps shield the bacterium from attack by the human immune system and exists in many clinically distinct variants.

Making vaccines or drugs that targets the capsule itself directly is impractical as such treatments would target only a few bacteria. Instead, the Guelph team is focused on a key enzyme that builds the capsule foundation. This foundation could serve as a common point of attack, allowing a single treatment for several key pathogens infecting humans and livestock.

“We are interested in the machinery that builds the bacterium’s protective layer,” said Dr. Chris Whitfield, Professor Emeritus in the Department of Molecular and Cellular Biology. “By understanding and targeting the machinery, we can render the pathogen unable to survive in the host”.

Read more on the Canadian Light Source website

Image : Matthew Kimber, Chris Whitfield, and enzyme

Natural substances show promise against coronavirus

2022/08/182022/08/18

X-ray screening identifies compounds blocking a major corona enzyme

Three natural compounds present in foods like green tea, olive oil and red wine are promising candidates for the development of drugs against the coronavirus. In a comprehensive screening of a large library of natural substances at DESY’s X-ray source PETRA III the compounds bound to a central enzyme vital for the replication of the coronavirus. All three compounds are already used as active substances in existing drugs, as the team headed by Christian Betzel from the University of Hamburg and Alke Meents from DESY reports in the journal Communications Biology. However, if and when a corona drug can be developed on the basis of these compounds remains to be investigated.

“We tested 500 substances from the Karachi Library of Natural Compounds if they bind to the papain-like protease of the novel coronavirus, which is one of the main targets for an antiviral drug,” explains the study’s main author Vasundara Srinivasan from the University of Hamburg. “A compound that binds to the enzyme at the right place can stop it from working.”

The papain-like protease (PL^pro) is a vital enzyme for virus replication: When a cell is hijacked by the coronavirus, it is forced to produce building blocks for new virus particles. These proteins are manufactured as a long string. PL^pro then acts like a molecular pair of scissors, cutting the proteins from the string. If this process is blocked, the proteins cannot assemble new virus particles.

Read more on the DESY website

Image: The paper’s main author Vasundara Srinivasan at an X-ray set-up to test protein crystals in the lab.

Credit: University of Hamburg, Susanna Gevorgyan

How a soil microbe could rev up artificial photosynthesis

2022/04/292022/05/05

Researchers discover that a spot of molecular glue and a timely twist help a bacterial enzyme convert carbon dioxide into carbon compounds 20 times faster than plant enzymes do during photosynthesis. The results stand to accelerate progress toward converting carbon dioxide into a variety of products.

Plants rely on a process called carbon fixation – turning carbon dioxide from the air into carbon-rich biomolecules – for their very existence. That’s the whole point of photosynthesis, and a cornerstone of the vast interlocking system that cycles carbon through plants, animals, microbes and the atmosphere to sustain life on Earth.

But the carbon fixing champs are not plants, but soil bacteria. Some bacterial enzymes carry out a key step in carbon fixation 20 times faster than plant enzymes do, and figuring out how they do this could help scientists develop forms of artificial photosynthesis to convert the greenhouse gas into fuels, fertilizers, antibiotics and other products.

Now a team of researchers from the Department of Energy’s SLAC National Accelerator Laboratory, Stanford University, Max Planck Institute for Terrestrial Microbiology in Germany, DOE’s Joint Genome Institute (JGI) and the University of Concepción in Chile has discovered how a bacterial enzyme – a molecular machine that facilitates chemical reactions – revs up to perform this feat.

Rather than grabbing carbon dioxide molecules and attaching them to biomolecules one at a time, they found, this enzyme consists of pairs of molecules that work in sync, like the hands of a juggler who simultaneously tosses and catches balls, to get the job done faster. One member of each enzyme pair opens wide to catch a set of reaction ingredients while the other closes over its captured ingredients and carries out the carbon-fixing reaction; then, they switch roles in a continual cycle.

Read more on the SLAC website

Capybara gut holds valuable enzymes for biotechnology

2022/04/132022/06/23

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

Developing pain medication with fewer side effects

2021/11/302021/12/01

Opiates like morphine and codeine provide many patients with relief: from the ache felt after mild surgery to chronic pain experienced by cancer patients. However, this type of medication can cause multiple side effects and can lead to physical dependency with long-term use. Improving pain medication would help millions of people to have a better quality of life.

Dr. Ken Ng, a professor at the University of Windsor and adjunct professor at the University of Calgary (UCalgary), and Sam Carr, a PhD student from UCalgary, have been working with Dr. Peter Facchini’s group at UCalgary to better understand how natural opiates are produced. The team has narrowed their focus on one enzyme in the last stage of opiate assembly, a process that occurs naturally in the poppy plant.

“Imagine this sort of like an assembly line,” Carr said. “There are a lot of different steps in this specific pathway, and each enzyme contributes a different step from the starting product to the finished drug.”

Read more on the Canadian Light Source (CLS) website

Image: Structure of the enzyme studied, a molecule of codeine, and a seed capsule from an opium poppy.

Credit: Sam Carr.

Surprising behavior of a fatty acid enzyme with potential biofuel applications

2021/04/222021/04/27

Derived from microscopic algae, the rare, light-driven enzyme converts fatty acids into starting ingredients for solvents and fuels.

Although many organisms capture and respond to sunlight, it’s rare to find enzymes – proteins that promote chemical reactions in living things – that are driven by light. Scientists have identified only three so far. The newest one, discovered in 2017, is called fatty acid photodecarboxylase (FAP). Derived from microscopic algae, FAP uses blue light to convert fatty acids into hydrocarbons that are similar to those found in crude oil.

“A growing number of researchers envision using FAPs for green chemistry applications because they can efficiently produce important components of solvents and fuels, including gasoline and jet fuels.” says Martin Weik, the leader of a research group at the Institut de Biologie Structurale at the Université Grenoble Alpes.

Weik is one of the primary investigators in a new study that has captured the complex sequence of structural changes, or photocycle, that FAP undergoes in response to light, which drives this fatty acid transformation. Researchers had proposed a possible FAP photocycle, but the fundamental mechanism was not understood, partly because the process is so fast that it’s very difficult to measure. Specifically, scientists didn’t know how long it took FAP to split a fatty acid and release a hydrocarbon molecule.

Experiments at the Linac Coherent Light Source (LCLS) at the Department of Energy’s SLAC National Accelerator Laboratory helped answer many of these outstanding questions. The researchers described their results in Science.

Read more on the SLAC website

Image: A study using SLAC’s LCLS X-ray laser captured how light drives a series of complex structural changes in an enzyme called FAP, which catalyzes the transformation of fatty acids into starting ingredients for solvents and fuels. This drawing captures the starting state of the catalytic reaction. The dark green background represents the protein’s molecular structure. The enzyme’s light-sensing part, called the FAD cofactor, is shown at center right with its three rings absorbing a photon coming from bottom left. A fatty acid at upper left awaits transformation. The amino acid shown at middle left plays an important role in the catalytic cycle, and the red dot near the center is a water molecule.

Credit: Damien Sorigué/Université Aix-Marseille

A new enzyme cocktail can digest plastic waste six times faster

2020/09/292020/10/06

Research undertaken at Diamond has allowed scientists to create a super-enzyme that degrades plastic bottles six times faster than before.

The super-enzyme, derived from bacteria that lives on a diet of plastic, enables the full recycling of plastic bottles.

Plastic pollution is a global threat as plastics are rarely biodegradable and they can remain in the environment for centuries. One of the most abundant plastics that contributes hugely to this dire situation is poly(ethylene terephthalate) (PET).

PET is used largely in textiles, where it is commonly referred to as polyester, but it is also used as packaging for liquids and foodstuffs. PET’s excellent water-repellent properties led to it being the plastic of choice for soft drink bottles. However, the water resistance of PET means that they are highly resistant to natural biodegradation and can take hundreds of years to break down in the environment.

In 2018, researchers discovered that a unique bacterium (Ideonella sakaiensis 201-F6) was found feeding on waste from an industrial PET recycling facility. The bacterium had the amazing ability to degrade PET and use it to provide carbon for energy. Central to this ability was the production of a PET-digesting enzyme, known as PETase.

How cellular proteins control cancer spread

2020/08/112020/08/11

New finding may help focus the search for anti-cancer drugs

A new insight into cell signals that control cancer growth and migration could help in the search for effective anti-cancer drugs. A team of researchers has revealed key biochemical processes that advance our understanding of colorectal cancer, the third most common cancer among Canadians.

Using the CMCF beamline at the Canadian Light Source (CLS) at the University of Saskatchewan, scientists from McGill University and Osaka University in Japan were able to unlock the behavior of an enzyme involved in the spread of cancer cells. The team found that there is a delicate interaction between the enzyme, PRL3, and another protein that moves magnesium in and out of cells. This interaction is crucial to colorectal cancer growth.

Read more on the Canadian Light Source website

Image: Members of the Gehring research laboratory discussing the results of a protein purification.

Research could lead to better herbicides and infection treatments

2020/07/302020/08/19

Researchers from the University of Queensland (UQ) have used the Australian Synchrotron and cryo-electron microscopy in China to determine the three-dimensional structure of a complex enzyme found in plants microbes that could be used to develop advanced herbicides and treatments for infection.

A large international team led by Prof Luke Guddat of UQ published the structure of the enzyme acetohydroxyacid synthase (AHAS) in the journal Nature and also explained the first step in how the enzyme regulates the biosynthesis of three essential amino acids, leucine, valine and isoleucine.

“The way that the complex regulates this pathway had been unknown until now. We were finally able to explain it by understanding how the entire structure was assembled,” said Prof Guddat, who has been researching this enzyme for twenty years.

Read more on the Australian Synchrotron website

Image: The 3D structure resembles a ‘Maltese Cross’.

New substance library to accelerate the search for active compounds

2020/07/132020/07/23

In order to accelerate the systematic development of drugs, the MX team at the Helmholtz-Zentrum Berlin (HZB) and the Drug Design Group at the University of Marburg have established a new substance library. It consists of 1103 organic molecules that could be used as building blocks for new drugs. The MX team has now validated this library in collaboration with the FragMAX group at MAX IV. The substance library of the HZB is available for research worldwide and also plays a role in the search for substances active against SARS-CoV-2.

For drugs to be effective, they usually have to dock to proteins in the organism. Like a key in a lock, part of the drug molecule must fit into recesses or cavities of the target protein. For several years now, the team of the Macromolecular Crystallography Department (MX) at HZB headed by Dr. Manfred Weiss together with the Drug Design Group headed by Prof. Gerhard Klebe (University of Marburg) has therefore been working on building up what are known as fragment libraries. These consist of small organic molecules (fragments) with which the functionally important cavities on the surface of proteins can be probed and mapped. Protein crystals are saturated with the fragments and then analysed using powerful X-ray light. This allows three-dimensional structural information to be obtained at levels of atomic resolution. Among other things, it is possible to find out how well a specific molecule fragment docks to the target protein. The development of these substance libraries took place as part of the joint Frag4Lead research project and was funded by the German Federal Ministry of Education and Research (BMBF).

Read more on the BESSY II website

Image : For the study, the enzyme endothiapepsin (grey) was combined with molecules from the fragment library. The analysis shows that numerous substances are able to dock to the enzyme (blue and orange molecules). Every substance found is a potential starting point for the development of larger molecules.

Credit: Wollenhaupt/HZB

Helping our immune systems bypass antibiotic resistance

2020/07/012020/07/01

Over 700,000 people die each year due to drug-resistant diseases and this figure could increase to 10 million per year by 2050, according to a 2019 report.

As the search continues for new antibiotics to treat drug-resistant infections, a group of researchers used the Canadian Light Source (CLS) at the University of Saskatchewan to address the problem from a different direction, by trying to weaken the ability of bacteria to develop resistance in the first place.

“The goal is to knock the bacterial cells down in terms of their resistance,” said Dr. Anthony Clarke, Professor and Dean of Science at Wilfrid Laurier University and adjunct professor at the University of Guelph. “We haven’t been successful over the last 30 years in finding new classes of antibiotics so, in the short term, we’re trying to weaken the cells so our own immune system can take over to fight infection.”

The target for his team’s work is peptidoglycan, which gives bacterial cell walls their rigidity. “Think of it as building a brick wall around the bacteria’s cells,” said Clarke. Since peptidoglycan can be broken down by lysozyme, an enzyme that exists in human immune systems, bacteria have developed strategies that block these enzymes by modifying their peptidoglycan, thereby “cementing the bricks in place,” and resisting our defences.

Read more on the Canadian Light Source website

Image: Dr. Clarke inspecting flasks of bacterial cultures in a student laboratory.

Preventing hospital-acquired pneumonia

2020/05/072020/05/11

Researchers used the Canadian Light Source (CLS) at the University of Saskatchewan to identify a previously unrecognized family of enzymes that put us at risk for deadly diseases.

Klebsiella pneumoniae is responsible for a variety of hospital-acquired infections such as pneumonia and sepsis. The bacterium has become increasingly resistant to antibiotics, making it a focus of interest for health care professionals and researchers.

>Read more on the Canadian Light Source website

Image: Chris Whitfield has been working on polysaccharides like LPS throughout his career.

The future of fighting infections

2019/08/212019/08/22

Scientists analyze 3D model of proteins from disease-causing bacteria at the CLS.

Millions of people are affected by the Streptococcus pneumoniae bacterium, which can cause sinus infections, middle ear infections and more serious life-threatening diseases, like pneumonia, bacteremia, and meningitis. Up to forty percent of the population are carriers of this bacterium.
Researchers from the University of Victoria (UVic) used the Canadian Light Source (CLS) at the University of Saskatchewan to study proteins that the pathogen uses to break down sugar chains (glycans) present in human tissue during infections. These proteins are key tools the bacterium uses to cause disease.

They used the Canadian Macromolecular Crystallography Facility (CMCF) at the CLS to determine the three-dimensional structure of a specific protein, an enzyme, that the bacterium produces to figure out how it interacts with and breaks down glycans.

Image: The 3D structure of an enzyme from the disease-causing bacterium Streptococcus pneumoniae.

Scienstists make breakthrough in creating universal blood type

2019/06/102019/06/13

Enzymes in the human gut can convert A blood type into O.

Half of all Canadians will either need blood or know someone who needs it in their lifetime. Researchers from the University of British Columbia have made a breakthrough in their technique for converting A and B type blood into universal O, the type that is most needed by blood services and hospitals because anyone can receive it.
In a paper published in Nature Microbiology, Stephen Withers and a multidisciplinary team of researchers from the University of British Columbia show how they successfully converted a whole unit of A type blood to O type using their system. They were able to remove the sugars from the surface of the red blood cells with help from a pair of enzymes that were isolated from the gut microbiome of an AB+ donor.
The Canadian Light Source (CLS) at the University of Saskatchewan (UofS) played a critical role in understanding the structure of a previously unknown enzyme that was part of this pair. The researchers were unable to identify what this unique enzyme looked like from the gene sequence they had. Crystallography, done at the CLS, was crucial for the researchers to understand how this enzyme works and why it had a particular affinity for the A type blood.

“Molecular scissors” for plastic waste

2019/04/122019/04/12

A research team from the University of Greifswald and Helmholtz-Zentrum-Berlin (HZB) has solved the molecular structure of the important enzyme MHETase at BESSY II.

MHETase was discovered in bacteria and together with a second enzyme – PETase – is able to break down the widely used plastic PET into its basic building blocks. This 3D structure already allowed the researchers to produce a MHETase variant with optimized activity in order to use it, together with PETase, for a sustainable recycling of PET. The results have been published in the research journal Nature Communications.

Plastics are excellent materials: extremely versatile and almost eternally durable. But this is also exactly the problem, because after only about 100 years of producing plastics, plastic particles are now found everywhere – in groundwater, in the oceans, in the air, and in the food chain. Around 50 million tonnes of the industrially important polymer PET are produced every year. Just a tiny fraction of plastics is currently recycled at all by expensive and energy-consuming processes which yield either downgraded products or depend in turn on adding ‘fresh’ crude oil.

Image: At the MX-Beamlines at BESSY II, Gottfried Palm, Gert Weber and Manfred Weiss could solve the 3D structure of MHETase.
Credit: F. K./HZB

Enzyme structure of bacteria that causes tuberculosis

2019/02/072019/02/14

Results on its interaction with antibiotics may lead to the development of new forms of treatment for this disease.

Tuberculosis is a chronic infection usually caused by a bacterium called Mycobacterium tuberculosis. This bacterium infects cells of the immune system called alveolar macrophages, which are responsible for removing pollutants and microorganisms from the surface of the alveoli, where the exchange of gases occurs during respiration.
It is estimated that approximately two billion people worldwide are infected with M. tuberculosis without symptoms. However, the clinical manifestations of the disease may appear at any time in life, especially when the immune system is weakened, such as due to malnutrition or diseases such as cancer and AIDS.
Tuberculosis is considered a curable disease when the patient is diagnosed and treated promptly with antibiotics. Nevertheless, the chronicity of this infection makes it difficult to eradicate bacteria altogether. Generally, patients must take the medication for several months, making it harder for them to persist in the treatment and favoring the emergence of antibiotic-resistant bacteria. In recent years, the emergence of new bacteria, resistant to routine treatments, has been a worldwide concern and it is imperative to seek new therapeutic strategies against this disease.

Image: (extract, full image here) Elements of the secondary structure of L,D-transpeptidase-3 from Mycobacterium tuberculosis acylated by an acetyl fragment derived from faropenem. Beta sheets in red, α-helices in yellow and the loops are shown in green. The figure shows, at the amino terminus (N-ter), the bacterial domain similar to immunoglobulin (BIg) and in the carboxy terminus the catalytic domain (CD). B-loop is a unique structure of this enzyme when compared to the other M. tuberculosis L,D-transpeptidases. In blue is shown an acetyl fragment covalently attached to cysteine 246 at the active site of the enzyme. Figure taken with Pymol.