protein – Page 2 – Lightsources.org

Researchers use CHESS to map protein motion

2020/03/092020/04/02

Cornell structural biologists took a new approach to using a classic method of X-ray analysis to capture something the conventional method had never accounted for: the collective motion of proteins.

And they did so by creating software to painstakingly stitch together the scraps of data that are usually disregarded in the process.
Cornell structural biologists took a new approach to using a classic method of X-ray analysis to capture something the conventional method had never accounted for: the collective motion of proteins. And they did so by creating software to painstakingly stitch together the scraps of data that are usually disregarded in the process.
Their paper, “Diffuse X-ray Scattering from Correlated Motions in a Protein Crystal,”published March 9 in Nature Communications.
As a structural biologist, Nozomi Ando, M.S. ’04, Ph.D. ’08, assistant professor of chemistry and chemical biology, is interested in charting the motion of proteins, and their internal parts, to better understand protein function. This type of movement is well known but has been difficult to document because the standard technique for imaging proteins is X-ray crystallography, which produces essentially static snapshots.

Image: This slice through the three-dimensional diffuse map shows intense peaks resulting from lattice vibration, as well as cloudy features caused by internal protein motions.

ALS reveals vulnerability in cancer-causing protein

2020/02/172020/02/20

A promising anticancer drug, AMG 510, was developed by Amgen with the help of novel structural insights gained from protein structures solved at the Advanced Light Source (ALS).

Mutations in a signaling protein, KRAS, are known to drive many human cancers. One specific KRAS mutation, KRAS(G12C), accounts for approximately 13% of non-small cell lung cancers, 3% to 5% of colorectal cancers, and 1% to 2% of numerous other solid tumors. Approximately 30,000 patients are diagnosed each year in the United States with KRAS(G12C)-driven cancers.

Despite their cancer-triggering significance, KRAS proteins have for decades resisted attempts to target their activity, leading many to regard these proteins as “undruggable.” Recently, however, a team led by researchers from Amgen identified a small molecule capable of inhibiting the activity of KRAS(G12C) and driving anti-tumor immunity. Protein crystallography studies at the ALS provided crucial information about the structural interactions between the potential drug molecule and KRAS(G12C).

Image: A structural map of KRAS(G12C), showing the AMG 510 molecule in the binding pocket. The yellow region depicts where AMG 510 covalently attaches to the KRAS protein.
Credit: Amgen

Discovering a whole new family of copper-binding proteins

2020/01/162020/01/23

While studying a class of copper-containing enzymes, a team of researchers discovered and characterised a new family of fungal proteins.

Their study has now been published on Nature Chemical Biology, including analysis performed at BioMAX. The article is published together with a parallel study that sheds light on one of the potential biological roles of the proteins in this new family.

In contrast with a certain romanticised idea of research, scientific discoveries seldom come with a shouted “eureka!” as to mark the end of a linear intellectual endeavour. Much more frequently, new scientific findings emerge from observations where a scientist’s first reaction might sound like “that’s odd…”. Perhaps that was how the authors of this study reacted when they realised what they were looking at wasn’t what they were looking for.

In an article published this week on Nature Chemical Biology, a team of scientists from INRA, University of Copenhagen, Marseille Université, and University of York characterised a new family of proteins, named X325, found in various fungal lineages. The article is published together with a parallel study in which one protein of this new family, Bim1, is described as involved in fungal meningitis.

The authors were initially searching for new lytic polysaccharide monooxygenases (LPMOs), copper-dependent enzymes specialised in the degradation of polysaccharides and widely used in the production of biofuels. The proteins of this new family seemed promising candidates since they share many structural features and a probable common ancestor with LPMOs. However, the researchers proved that the members of this LPMO-like protein family are not involved in polysaccharides degradation, but they more likely play a role in the regulation of copper ion content in the organisms where they are expressed.

>Read more on the MAX IV website

Image: Copper binding site of two different proteins. Left: LaX325 protein belonging to the newly identified LPMO-like protein family X325. Right: cellulose cleaving LPMO enzyme TaAA9.
Image developed by Tobias Tandrup, University of Copenhagen.

Using European XFEL to shed light on photosynthesis

2019/11/082019/11/14

First membrane protein studied at European XFEL

In a paper now published in Nature Communications an international group of scientists show that the fast X-ray pulse rate produced by the European XFEL can be used to study the structure of membrane proteins such as those involved in the process of photosynthesis. These results open up eagerly awaited experimental opportunities for scientists studying these types of proteins.

Large proteins and protein complexes are difficult to study with traditional structural biology approaches. Large protein complexes, such as those that sit across cell membranes and regulate traffic in and out of cells, are difficult to crystalize and generally only produce small crystals that are hard to analyse. The extremely fast X-ray pulses generated by European XFEL now enable scientists to collect large amounts of data from a stream of small crystals to develop detailed models of the 3D structure of these proteins.

>Read more on the European XFEL website

Image (extract, full illustration in the article): Graphic shows the basic design of a serial femtosecond crystallography experiment at European XFEL. X-ray bursts strike crystallized samples resulting in diffraction patterns that can be reassembled into detailed images.
Credit: Shireen Dooling for the Biodesign Institute at ASU

Structure and functional binding epitopes of VISTA

2019/09/302019/10/10

V-domain Ig Suppressor of T-cell Activation (VISTA) is an immune checkpoint protein involved in the regulation of T cell activity. Checkpoint proteins are overexpressed by cancer cells or surrounding immune cells and prevent anti-tumor activity by co-opting natural regulation mechanisms to escape immune clearance. Compared to healthy tissues, VISTA is upregulated on tumor infiltrating leukocytes, including high expression on myeloid-derived suppressor cells (MDSCs). Through VISTA signaling, these inhibitory immune cells prevent effective antigen presentation and indirectly promote tumor growth. VISTA is implicated in a number of human cancers including skin (melanoma), prostate, colon, pancreatic, ovarian, endometrial, and non-small cell lung. VISTA is a known member of the B7 protein family but the mechanism of action is still unclear as VISTA has been shown to function as both a ligand^1,2 and a receptor³. In the model of VISTA as a receptor, the proposed ligand of interaction is V-set and immunoglobulin domain containing 3 (VSIG3)^4,5.

>Read more on the SSRL website

Image: Structure of human VISTA with extended C-C’ loop (blue), mapped VSTB/VSIG3 binding epitope (red), and disulfide bonds (yellow).

Discoveries map out CRISPR-Cas defence systems in bacteria

2019/09/252019/09/27

For the first time, researchers at the University of Copenhagen have mapped how bacterial cells trigger their defence against outside attacks. This could affect how diseases are fought in the future.

With the aid of highly advanced microscopes and synchrotron sources, researchers from the University of Copenhagen have gained critical insight into how bacteria function as defence mechanisms against attacks from other bacteria and viruses. The study, which has just been published in the renowned journal, Nature Communications, also describes how the defence systems can be activated on cue. This discovery can turn out to be an important cornerstone in fighting diseases in the future.

The researchers have shown how a cell attacked by a virus activates a molecule called COA (Cyclic Oligoadenylate), which in turn activates a so-called protein complex called CSX1 to eradicate the attacker.

>Read more on the MAX IV website

Image: Model of the CSX1 protein complex.

A citizen-science computer game for protein design

2019/09/172019/09/26

Using the computer game, “Foldit,” nonexpert citizen scientists designed new proteins whose structures, verified at the Advanced Light Source (ALS), were equivalent in quality to and more structurally diverse than computer-generated designs.

Proteins constitute the biomachinery—the cellular gears and levers—that make our bodies work. When this machinery is running smoothly, nutrients get absorbed, cells regenerate, and so on. When the machinery breaks down, the tools needed to fix the problem (i.e. drug molecules) are often proteins themselves.

Until recently, the pool of proteins available for such therapeutic purposes was limited to those found in nature. But natural proteins represent a small subset of all the possible ways to link 20 amino acids—the basic building blocks of all proteins—into chains hundreds, even thousands, of units long. On top of this, there are countless ways in which any given protein chain can fold—a key aspect of functionality.

In the last 20 years, “de novo” protein design (from scratch as opposed to starting with a known protein) has taken off, promising cheap and effective drugs with fewer side effects. But given the huge number of possibilities available, scientists are limited in their ability to fully explore this vast “protein space.”

Image: The user interface of Foldit, a free online computer game developed to crowdsource problems in protein modeling. (a) The Foldit score: better models yield higher scores. (b) The design palette allows players to change the amino acids in the protein chain. (c) The “pull” tool allows players to manipulate the 3D structure of the model. (d) The “undo” graph tracks the score as a model is developed and allows players to backtrack. (e) Additional tool selections.

Preventing heart attacks

2019/08/082019/08/13

Scientists have taken an important step towards finding a potential cure for the disease that causes strokes and heart attacks in seniors and increases the mortality rate of diabetic and chronic kidney disease patients.
Researchers from the University of McGill and SickKids Toronto in collaboration with Universite de Montreal developed a simplified laboratory model that mimics the formation of mineral deposits that harden arteries and leads to these devastating conditions.
They used the Canadian Light Source (CLS) at the University of Saskatchewan to understand the type of minerals that formed and how they develop on the arteries.
“The goal in developing our lab model is that it would help us understand the mineralization process. We can then mimic what happens, and use it to test hypotheses on why the minerals are forming and also test some drugs to find something that can stop it,” said lead researcher Dr. Marta Cerruti.
Her six-member team is focused on the poorly understood process of how minerals form and grow on elastin, a protein on artery walls that provides the elasticity needed for blood flow to the heart, said Cerruti, an associate professor in Materials Engineering at McGill.
The hypothesis is that calcium phosphate-containing minerals form inside the walls of arteries and then calcify into a bone-like substance that narrows arteries and causes them to lose elasticity crucial for blood flow.

Image: Marta Cerruti (left) and Ophelie Gourgas in a laboratory using a Raman machine.

Mutated protein could become a non-hormonal contraceptive target

2019/07/222019/07/31

An international team of scientists from the Karolinska Institutet in Sweden and Nagoya University has explained how mutations in egg coat protein ZP1 cause infertility in women. The study suggests that ZP1 could be a promising candidate for future non-hormonal contraceptive efforts.
ZP1 is a glycoprotein involved in the fertilization of eggs by cross-linking egg coat filaments. Because studies in mice showed that lack of ZP1 reduces but does not abolish fertility, scientists believed that this molecule was also not crucial for fertility in humans. This new study, however, suggests that ZP1 may have a much more important role in human reproduction than previously thought. “The results were a big surprise because they suggested that mutations that truncate the human ZP1 protein cause female sterility by hindering its cross-linking function, rather than interfering with other egg coat proteins”, explains Luca Jovine, professor at the Karolinska Institutet and leader of the study.

>Read more on the ESRF website

Image: The mutation W83R of human ZP1 does not hinder its secretion but reduces its cross-linking (panel b), likely due to the fact that – as suggested by the structure of chicken ZP1 (panel a) – W83 (W72 in chicken ZP1) stacks between a sugar attached to ZP1 and the loop that makes the cross-link (“cd loop”). The part of the sugar chain that stacks against W83, which is a fucose residue, was only resolved in the structure of the fully glycosylated protein (violet) whose data came from ESRF ID23-1.

Potassium hunting on protein factories

2019/06/072019/06/17

Amazing insights into the location of elusive potassium ions on bacterial ribosomes

Groundbreaking research at the new long-wavelength macromolecular crystallography beamline (I23) at Diamond Light Source has for the first time demonstrated the location of potassium ions in bacterial ribosomes. Ribosomes are the protein factories of cells and although they are vital for life, little was known of the sites of metal ions that are crucial for their structure and function. The work recently published in Nature Communications showcases the fantastic applications of the I23 beamline and sheds light on the important role of potassium ions.

Image: (extract, full image here) 70S ribosome elongation complex (potassium atoms rendered as green spheres).

The interaction between two proteins involved in skin mechanical strength

2019/05/172019/05/28

A research team from the Centro de Investigación del Cáncer of the Universidad de Salamanca has obtained a detailed 3D image of the union between two hemidesmosomal proteins.

The structure of this complex has been unveiled using XALOC beamline techniques, at the ALBA Synchrotron. The results, published in “Structure”, provide insights to understand how these epithelial adhesion structures are formed. Researchers from Centro de Investigación del Cáncer – Instituto de Biología Molecular y Celular del Cáncer of Salamanca, from Centro Universitario de la Defensa in Zaragoza, and from the Netherlands Cancer Institute in Amsterdam have described how two essential proteins interact to each other in order to join epidermis and dermis together. This study reveals at atomic scale how the binding between two hemidesmosomal proteins called integrin α6β4 and BP230 takes place.
Epithelial tissues, such as epidermis, settle on fibrous sheets called basement membrane, formed by extracellular matrix proteins. The junction between epithelia and basement membrane happens through hemidesmosomes, multi-protein complexes located at the membrane of epithelial cells. Integrin α6β4 is an essential protein of the hemidesmosomes, which adheres to proteins of the basement membrane. Inside the cell cytoplasm, plectin and BP230 proteins bind to α6β4 and connect it to the intermediate filaments of the cytoskeleton. Genetic or autoimmune alterations that affect the hemidesmosomal proteins reduce skin resistance and cause diseases such as bullous pemphigoid and various types of epidermolysis bullosa.

>Read more on the ALBA website

Image: Structure of β4(WT)-BP230 complex.

Capturing protein motion at FemtoMAX

2019/04/052019/04/09

Your body contains a large variety of different proteins. They are big, complex molecules with diverse functions, from transporting oxygen in your blood to making your muscles contract.

Many proteins change their shape and move as they perform their task. A research team from the University of Gothenburg recently visited the beamline FemtoMAX to develop a method for studying moving proteins. They use electric fields to stimulate motion of the proteins in a sample while imaging them with the X-ray beam.
To study how proteins move, we need something to nudge them and then image them after they have changed position. Certain proteins are activated by light and in that case, the researchers can hit them with a laser pulse to provoke the motion. However, that is far from always the case. In the method being developed by the Gothenburg team, the proteins are instead subjected to an electric field that make them move.
The field is synchronized to the short, femtosecond scale (10^-15 s) X-ray pulses delivered at beamline FemtoMAX. Each X-ray pulse hitting the sample is like taking a photograph using extremely short shutter speed, just like trying to get sharp images of players on a football field. The X-ray pulses at FemtoMAX are short enough to let the researchers capture the instantaneous position of the protein. By varying the time between the electric field and the X-ray pulse they can see different stages of the movement and even put the frames together as a movie of the protein motion.

A new molecule could help put the STING on cancer

2019/03/132019/03/18

The protein STING (stimulator of interferon genes) is a component of the innate immune system. It plays a major role in the immune response to cancer, and abnormal STING signaling has been shown to be associated with certain cancers. Immunomodulatory approaches using agonists to target STING signaling are therefore being investigated as anticancer treatments. However, the compounds in clinical trials typically are injected intratumorally in patients with solid cancers. In this study, researchers discovered a novel STING agonist, known as an amidobenzimidazole (ABZI), which can be given by intravenous injection and could therefore potentially open up its evaluation as a treatment for hard-to-reach cancers. Using x-ray diffraction data collected at the U.S. Department of Energy’s Advanced Photon Source (APS), researchers from GlaxoSmithKline (GSK) investigated ABZI compounds and STING. Their results, published in the journal Nature, may have important implications for anticancer immunotherapy.

STING is a protein that mediates innate immunity, and one function of the STING signaling pathway is in mobilizing an immune response against tumors. STING proteins can be activated by cyclic dinucleotides, small molecules that are made by the cytosolic DNA sensor, cGAS, upon sensing of DNA leaking out of the nucleus as a result of DNA damage, including that which might be associated with cancer development.

Figure: X-ray crystal structure of the STING protein bound to one of the new molecules.

Clear view of “Robo” neuronal receptor opens door for new cancer drugs

2019/03/072019/03/12

During brain development, billions of neuron nerve cells must find accurate pathways in the brain in order to form trillions of neuronal circuits enabling us to enjoy cognitive, sensory and emotional wellbeing.

To achieve this remarkable precision, migrating neurons use special protein receptors that sense the environment around them and guide the way so these neurons stay on the right path. In a new study published in Cell, researchers from Bar-Ilan University and Tel Aviv University in Israel, EMBL Grenoble in France and University of Exeter in the UK report on their discovery of the intricate molecular mechanism that allows a key guidance receptor, “Robo”, to react to signals in its environment.

One of the most important protein signaling systems that guide neurons consists of the cell surface receptor “Robo” and its external guidance cue, “Slit”. “Slit and Robo can be identified in virtually all animals with a nervous system, from a 1 mm-long nematode all the way to humans,” explains researcher Yarden Opatowsky, associate professor and head of the Laboratory of Structural Biology at Bar-Ilan University and who led the research.

Image: A surface representation of the crystal structure of the extracellular portion of human Robo2. The yellow region represents the domain where dimerisation takes place. Here, we see it blocked by the other domains, meaning dimerisation cannot take place and that Robo2 is inactivated.
Credit: Y. Opatowsky.

Encapsulation of drugs for new cancer treatments

2019/02/192019/02/27

Research develops hydrogel from silk protein with potential application in photodynamic therapy

Cancer is a set of diseases characterized by uncontrolled multiplication of cells. One of the main methods for treating this disease is chemotherapy, which uses drugs to block the growth of those cells or to destroy them. In this way, most drugs used interfere with mitosis, the cellular mechanism by which new cells are produced. Therefore, both cancerous and healthy cells are affected, leading to several side effects.
Worldwide, considerable effort has been directed at developing new methods that act directly on the target of treatment. This is the case of so-called photodynamic therapy (PDT), a minimally invasive therapeutic procedure that selectively acts on malignant cells.
The procedure involves the administration of a light-sensitive substance, called a photosensitizing agent. When irradiated at specific wavelengths, the photosensitizer releases oxygen in reactive chemical forms that promote the death of malignant cells, infectious agents and the removal of burns.

A timely solution for the photosynthetic oxygen evolving clock

2019/01/252019/01/31

XFEL Hub collaboration reveals the intermediates of the photosynthetic water oxidation clock

A large international collaborative effort aided by the XFEL Hub at Diamond Light Source has generated the most detailed time-resolved studies to date of a key protein involved in photosynthesis. The pioneering work, recently published in Nature, shows how photosystem II harnesses light energy to produce oxygen – insights that could direct a next generation of photovoltaic cells.
>Read more on the Diamond Light Source website

Image: this figure is issued from a video you can watch here.