Tag Archives: #proteins

Researchers Solve A Puzzle To Design Larger Proteins (Chemistry)

A team from Japan and the United States has identified the design principles for creating large “ideal” proteins from scratch, paving the way for the design of proteins with new biochemical functions.

Their results appear June 24, 2021, in Nature Communications.

The team had previously developed principles to design small versions of what they call “ideal proteins,” which are structures without internal energetic frustration.

Such proteins are typically designed with a molecular feature called beta strands, which serve a key structural role for the molecules. In previous designs, the researchers successfully designed alpha-beta proteins with four beta strands.

“The ideal proteins we have created so far are much more stable and more soluble than proteins commonly found in nature. We think these proteins will become useful starting points for designing new biochemical functions of interest,” said co-first author Rie Koga, researcher in Exploratory Research Center of Life and Living Systems of Japan’s National Institutes of Natural Sciences (NINS).

The team found that while the designed proteins were structurally ideal, they are too small to harbor functional sites.

“We set out to test the generality of the design principles we developed previously by applying them to the design of larger alpha-beta proteins with five and six beta strands,” said co-first author Nobuyasu Koga, associate professor in the Institute for Molecular Science of NINS.

The results were puzzling. They found that their experimental structures differed from their computer models, resulting in proteins that folded differently by swapping the internal locations of their beta strands. The team struggled with the strand swapping puzzle, but by iterating between computational design and laboratory experiments, they reached a conclusion.

“We emphasize that experimental structure determination is important for iterative improvement of computational protein design,” said co-first author Gaohua Liu, chief scientific officer of Nexomics Biosciences.

“Sometimes we learn the most from these ideal proteins when their experimental structures differ, rather than match, their intended design, since this can lead to a deeper understanding of the underlying principles”, added Gaetano Montelione, co-author and professor of chemistry and chemical biology at Rensselaer Polytechnic Institute.

The reason for the strand swapping, they determined, was due to the strain of the whole system on the foundational backbone structure. According to Nobuyasu Koga, the strain is global, instead of connection to connection. Proteins can adjust the length and register of strands across the system to alleviate this backbone strain.

Next, the researchers plan to continue studying the trade-off between more functional proteins with what could be considered less-than-ideal qualities.

“We would like to design proteins with more complex functional sites by incorporating non-ideal features such as longer loops, which are important not only for function but also for relieving global backbone strain,” said David Baker, co-author and professor of biochemistry at the University of Washington.

Featured image: (left) The strand order swapping in de novo design of larger alpha-beta proteins has been a long-standing problem for the research team. (right) Backbone ensembles generated from folding simulations identified that backbone strain caused the strand swapping. © NINS/IMS

Reference: Koga, N., Koga, R., Liu, G. et al. Role of backbone strain in de novo design of complex α/β protein structures. Nat Commun 12, 3921 (2021). https://doi.org/10.1038/s41467-021-24050-7

Provided by NINS

Study Clarifies Why Some Proteins “Flock Together” in the Nucleus (Biology)

The nucleus is much more than a storage compartment for chromosomes: It also contains the complex machinery that produces transcripts of the genes that are currently needed and releases them into the cell body. Some of the proteins involved herein are not evenly distributed in the nucleus, but cluster at specific sites. A study by the universities of Würzburg, Heidelberg and Bonn with the help of Evotec SE at the Martinsried site now shows how these “flash mobs” are regulated. In the long term, the results could also yield new therapeutic approaches for spinal muscular atrophy. They are published in the journal Cell Reports.

Almost all cells in our body contain a nucleus: a somewhat spherical structure that is separated from the rest of the cell by a membrane. Each nucleus contains all the genetic information of the human being. So it serves as a kind of library – but one with strict requirements: If the cell needs the building instructions for a protein, it won’t simply borrow the original information. Instead, a transcript of it is made in the nucleus.

The machinery required for this is very complex, not least because the transcripts are not simple copies. In addition to essential information, genes also contain numerous passages of meaningless “garbage”. They are removed when the transcript is made. Biologists call this editorial revision “splicing”.

“An important role in splicing is played by the SMN complex, a ‘molecular machine’ consisting of nine different proteins,” explains Prof. Dr. Oliver Gruss from the Institute of Genetics at the University of Bonn, who is also a member of the university’s transdisciplinary research area “Life and Health”. “Interestingly, these machines are not evenly distributed in the nucleus. Instead, they accumulate at specific sites called Cajal bodies.” However, there are no transport mechanisms in the cell nucleus that bring the SMN complexes to Cajal bodies. Instead, the SMN proteins themselves have certain properties that are responsible for their aggregation. Which ones these are, was unclear until now.

SMN complexes carry an unusually large number of phosphate groups

SMN complexes have a prominent feature: They carry an unusually large number of phosphate groups, which are small molecular residues with a phosphorus atom in the center. “We suspected that this phosphorylation promotes their mass clustering into Cajal bodies,” explains Dr. Maximilian Schilling from the research group around Oliver Gruss.

Prof. Dr. Oliver Gruß
Prof. Dr. Oliver Gruss – from the Institute of Genetics at the University of Bonn.© Barbara Frommann/Uni Bonn

Phosphate groups are not part of the actual blueprint of a protein – they are added later and can also be removed again. This is often how the cell regulates the activity of the respective protein. The phosphate group is attached in this process by certain enzymes, the kinases. “We have now inhibited each of the hundreds of human kinases individually and looked at how that affects the formation of Cajal bodies,” Schilling says.

In this way, they encountered a network of kinases, which, when inhibited, caused the Cajal bodies to largely disappear. Further analyses showed that in the absence of these kinases, phosphorylation of SMN complexes at specific sites decreased sharply. This then causes the flash mobs in the nucleus to cease – the Cajal bodies disintegrate. The finding is particularly interesting because the kinases identified not only regulate splicing, but also the translation of the gene transcripts edited in this way into proteins. These are therefore enzymes that are crucial for various steps in this vital process.

Mutation causes severe disease

The SMN complex is known to human geneticists not only for its role in splicing: Individual mutations in its blueprint result in a serious disease, spinal muscular atrophy, in those affected. One in about 6,000 newborns is born with this genetic defect. Treatment is extremely expensive; the cost per patient runs into millions. “Some of the gene defects that cause spinal muscular atrophy are near the phosphorylation sites of the SMN complex,” explains Gruss. “Affected individuals may therefore have impaired attachment of phosphate groups to these sites, and consequently also impaired formation of Cajal bodies. We suspect that this causes splicing to be impaired, which subsequently results in the disease symptoms.”

The kinases identified may therefore also be suitable as a starting point for new therapies. Preliminary results from mouse model cells for human spinal muscular atrophy show that agents that increase kinase activity also improve Cajal body formation. “It is completely unclear whether these agents also ameliorate pathological changes in a complex organism,” cautions Gruss against inflated expectations. “That new treatment options will eventually emerge from this is therefore still speculation at this stage.”

Participating institutions and funding:
The universities of Bonn, Würzburg and Heidelberg were involved in the study. It was funded by the German Research Foundation (DFG) and the US-American CURE SMA Foundation.

Publication: Maximilian Schilling, Archana B. Prusty, Björn Boysen, Felix S. Oppermann, Yannick L. Riedel, Alma Husedzinovic, Homa Rasouli, Angelika König, Pradhipa Ramanathan, Jürgen Reymann, Holger Erfle, Henrik Daub, Utz Fischer and Oliver J. Gruss: TOR signaling regulates liquid phase separation of the SMN complex governing snRNP biogenesis; Cell Reports; DOI: 10.1016/j.celrep.2021.109277 Link to the study: https://www.cell.com/cell-reports/fulltext/S2211-1247(21)00644-6

Featured image: SMN is concentrated – in the Cajal bodies (left, red) in the nucleus of human cells (blue). If phosphorylation of SMN is inhibited, the concentration ceases and Cajal bodies disappear.© AG Gruss / University of Bonn

Provided by University of Bonn

How DNA Opens While Wrapped Around Proteins? (Biology)

Researchers from the Hubrecht Institute in Utrecht (The Netherlands) and the Max Planck Institute for Molecular Biomedicine in Münster (Germany) used computer simulations to reveal in atomic detail how a short piece of DNA opens while it is tightly wrapped around the proteins that package our genome. These simulations provide unprecedented insights into the mechanisms that regulate gene expression. The results were published in PLoS Computational Biology on the 3rd of June.

Every cell in the body contains two meters of DNA. In order to fit all the DNA in the cell’s small nucleus, the DNA is tightly packed in a structure known as chromatin. Chromatin is an array of identical smaller structures named nucleosomes. In a single nucleosome, DNA is wrapped around 8 proteins called histones. Chromatin is not uniformly compact across the genome. The tightness of the packaging is important in regulating which genes are expressed and therefore which proteins are produced by a cell.

Transitions from tightly to loosely packed DNA – from closed to open chromatin – are essential for cells to convert to another cell type. These cell conversions are hallmarks of development and disease, but are also often used in regenerative therapies. Understanding how such transitions occur may contribute to understanding diseases and optimizing therapeutical cell type conversions.

Computational nanoscope

One step in the opening of chromatin is the motion of DNA while wrapped in nucleosomes. Like all molecular structures in our cells, nucleosomes are dynamic. They move, twist, breathe, unwrap and wrap again. Visualizing these motions using experimental methods is often very challenging. One alternative is to use the so-called “computational nanoscope”

Researchers use the term computational nanoscope to refer to a set of computer simulation methods. These methods enable them to visualize the movements of molecules over time. Over the past years, the methods have become so accurate that researchers started referring to them as a computational nanoscope; observing the molecules moving on the computer is similar to observing them under a very high resolution nanoscope.

Nucleosomes breathing

Jan Huertas and Vlad Cojocaru, supported by Hans Schöler from the Max Planck Institute for Molecular Biomedicine (Münster, Germany), generated multiple real-time movies of the movements of nucleosomes, each covering one microsecond from the nucleosome lifetime. Using these movies, they monitored how the nucleosomes open and close in a motion known as nucleosome breathing.

In their new paper, published in PLoS Computational Biology, Huertas and Cojocaru describe what causes nucleosome breathing. First, they found that the order in which the building blocks of DNA are arranged – the DNA sequence – is important for nucleosome breathing.  Second, the dynamics of histone tails are essential for this process. These histone tails are flexible regions in the histones that play a role in the regulation of gene expression. While the role of histone tails has been studied intensively, little is known about how they influence the motions of single nucleosomes. With their simulations, Huertas and Cojocaru described the relationship between histone tails and nucleosome breathing in atomic detail.

Histone modifications

“Being able to observe the breathing of nucleosomes in computer simulations is very challenging. The fact that we have now been able to visualize this represents a major step towards simulating the complete spectrum of nucleosome dynamics, from breathing to unwrapping. It also allows us to study how these motions are affected by modifications of the histones, which occur in different cells and regions of our DNA. Our simulations revealed that two histone tails are responsible for keeping the nucleosome closed. Only when these flexible tails moved away from particular regions of DNA, the nucleosome was able to open,” says research leader Cojocaru.

Huertas, first author in the publication and recent PhD-graduate, adds: “Active (open) and inactive (closed) chromatin contain different modifications of histone tails. The next step is to perform simulations with such modifications. The atomic resolution of the simulations would allow us to pinpoint how each modification affects nucleosomes and chromatin dynamics.”

Towards understanding epigenetics

All three researchers are excited about the future of the use of atomistic computer simulations in understanding gene expression mechanisms in development and disease. “With the further increase of computational power available in the world, we will soon be able to simulate milliseconds of a nucleosome lifetime with all its atoms included. Furthermore, we will be able to routinely simulate multiple nucleosomes to study the effect of different modifications of histones on gene expression. This will give unprecedented insights into the mechanisms that regulate gene expression,” Cojocaru concludes.

Featured image: This image shows three microseconds from the life time of a nucleosome. Snapshots in time were taken every 4 nanoseconds and were superimposed on the core region of the histones (white). The positions of the DNA (yellow) and the flexible histone tails (blue, green, red, orange, cyan) in all snapshots are shown. The ample motion of the DNA arms is known as nucleosome breathing motion. Remarkably, in this nucleosome, the lower arm moves more than the upper one due to the DNA sequence. Credit: Jan Huertas and Vlad Cojocaru, ©MPI for Molecular Biomedicine, ©Hubrecht Institute.


Huertas J, Schöler HR, Cojocaru V (2021) Histone tails cooperate to control the breathing of genomic nucleosomes. PLoS Comput Biol 17(6): e1009013. doi:10.1371/journal.pcbi.1009013

Provided by Hubrecht Institute

New Insight Into Protein Production in Brain Could Help Tackle Dementia (Neuroscience)

A pioneering new study led by UCL scientists has revealed, for the first time, a layer of genetic material involved in controlling the production of tau; a protein which plays a critical role in serious degenerative conditions, such as Parkinson’s and Alzheimer’s disease.

The international research, conducted in mice and cells, also revealed this material is part of a larger family of non-coding genes* which control and regulate other similar brain proteins, such as beta amyloid associated with Alzheimer’s and alpha-synuclein implicated in Parkinson’s disease and Lewy body dementia.

Researchers say the breakthrough findings, published in Nature, shed an important new light on how proteins linked to neurological conditions are produced and controlled, and could pave the way for new treatments for a wide range of dementia related diseases.

Lead author, Dr Roberto Simone (UCL Queen Square Institute of Neurology), said: “Tau plays a vital role inside our brain cells: It helps to stabilise and maintain the cytoskeletal structures that allow different materials to be transported to where they need to be. We know that too much tau is detrimental – the excess unused tau converts into toxic species that may be responsible for damaging cells and driving the spread and progression of degenerative disease. However, despite the fact that tau has been studied for more than three decades, until now we did not know how tau protein production is controlled.”

For the laboratory-based study, researchers identified a section of genetic material known as ‘antisense long non-coding RNA’ (lncRNA). They discovered this material does not make tau directly but helps to regulate, fine-tune and repress the production of the protein inside brain cells. This precision provided by antisense lncRNA in tau regulation could be crucial for smooth functioning of the brain’s nerve cells.

Research group leader, Professor Rohan de Silva (UCL Queen Square Institute of Neurology) said: “Excitingly, we found that the lncRNA that controls tau is not unique. Other key proteins we know to be involved in neurological conditions, including alpha-synuclein in Parkinson’s disease and beta-amyloid in Alzheimer’s disease, are controlled by very similar lncRNAs. This means we may have found the key to regulating the production of a whole range of proteins involved in brain function and the development of these devastating conditions.

“It’s early days but we hope that these exciting new insights will lead to the development of drugs that can keep tau and other proteins under control, and that these therapies could be life-changing for degenerative brain conditions that as yet, have no treatments to halt, let alone slow their progression.”

Other neurological conditions associated with the tau protein include corticobasal degeneration and progressive supranuclear palsy.

Targeting tau to create new treatments

Professor de Silva said: “Genetic studies have previously shown that people who have a particular form of the tau gene – called H1 – are more likely to get Parkinson’s disease, corticobasal degeneration and progressive supranuclear palsy. We know that people with the H1 form of the gene produce more tau. We also know the lncRNA we’ve identified helps to limit tau production, and that studies using post-mortem brain tissue show this lncRNA may be reduced in people with Parkinson’s disease.

“So, if we can find a way to boost the levels of this lncRNA, we might be able to reduce the production of tau protein which could help to slow or stop the damage to cells inside the brain.”

He added: “That’s exactly what we are working on now. Specifically, we are developing a gene therapy to deliver this lncRNA to brain cells and we’re currently testing whether this approach can reduce tau levels in mice and other animal models. If it’s successful, we hope to take this approach forward to be developed as a new therapy that can one day be tested in people.”

Professor David Dexter, Associate Director of Research at Parkinson’s UK, said: “This important research provides fantastic new insights into how tau production is controlled inside brain cells, and presents an exciting new opportunity for developing therapies that target this. It’s especially exciting to see that similar mechanisms may be involved in controlling the production of many other key proteins implicated in other neurological conditions, as it suggests strategies targeting these mechanisms could be effective across many conditions.”

This research has involved collaborations within UCL and with research groups at the Francis Crick Institute, UK Dementia Research Institute, St George’s University of London, Karolinska Institute, Sweden and the University of Trento, Italy.

Funding for this study came from Reta Lila Weston Trust, Wellcome Trust, Medical Research Council (MRC), Parkinson’s UK, CBD Solutions, PSP Association and CurePSP.

* Non-coding DNA: Our genome contains coding genes, the parts of our DNA that contain instructions for making proteins, the building blocks of our bodies. However, these coding genes make up only a small part of our genome – a mere 3% of the 3 billion letters (the nucleotides) of our genetic material. Until recently, the remainder of the genome (non-coding) was regarded as junk DNA, without known function. However, it is now clear that the DNA that lies in-between the coding genes is emerging as crucially important not only in human evolution but also in regulating function of cells and influencing the way coding genes produce proteins.


Featured Image

  • Beta-Amyloid Plaques (seen in brown) and Tau (seen in blue) in the Brain. Credit: National Institute on Aging, NIH, on Flickr

Provided by University College London

Force-sensing PIEZO Proteins Are at Work in Plants, Too (Botany)

Proteins that enable the sense of touch in humans have an evolutionary cousin that helps plants grow their root systems.

A family of proteins that sense mechanical force—enabling our sense of touch and many other important bodily functions—also are essential for proper root growth in some plants, according to a study led by scientists at Scripps Research and Howard Hughes Medical Institute (HHMI).

The discovery, published in the Proceedings of the National Academy of Sciences, points to an ancient evolutionary origin for the PIEZO proteins, which until now had mainly been characterized in animals. This advance in basic biology may also lead to new strategies for improving crop yields, the researchers say.

“Our finding that PIEZO proteins work as transducers of mechanical forces in plants, as well as animals, suggests the broad importance of these proteins for living organisms on Earth,” says lead author Seyed Ali Reza Mousavi, PhD, a postdoctoral research associate in the Scripps Research laboratory of Ardem Patapoutian, PhD.

“It’s remarkable that evolution has utilized the same type of molecule for us to sense touch and for plant roots to sense the hardness of soil,” says Patapoutian, professor and Presidential Endowed Chair in Neurobiology at Scripps Research and an investigator at HHMI.

Patapoutian, the senior author of the study, is credited with the discovery of PIEZO proteins about a decade ago—an accomplishment that earned him the 2020 Kavli Prize in Neuroscience and many other awards. The discovery led to a host of additional findings that have shed light on how to a range of medical conditions, from heart failure to chronic pain.

Sensing physical force

PIEZO proteins have little resemblance to any other family of biological proteins. In mammals—the only large class of animals in which they have been studied much—they form striking, propeller-like structures in the outer membranes of cells.

When stretched or pressed beyond a threshold, these structures allow charged molecules, called ions, to flow into or out of their host cells.

The two PIEZO proteins in mammals, PIEZO1 and PIEZO2, underlie a wide variety of functions that require this conversion of mechanical force to cellular signals—functions including the sense of touch, the sense of body and limb positions that enables balance, the sense of bladder fullness and the regulation of blood pressure.

Patapoutian’s lab and others have found PIEZO-type proteins, with apparent mechanical sensor functions, in other animals including Drosophila fruit flies.

An important role in the plant kingdom

When in the long history of life on Earth did these unique, versatile proteins evolve? To help address that question, Mousavi and other members of Patapoutian’s team examined Arabidopsis thaliana, a weedy relative of the mustard plant that’s a standard lab model for plant biology research. Arabidopsis’s genome includes a gene encoding a PIEZO-type protein, hinting that these proteins work as mechanosensors in the plant kingdom, too.

The scientists first examined the locations in the plant where the protein, PZO1, is made, and found it concentrated in the root tips. Deleting the PZO1 gene, they observed that the Arabidopsis plants grew shorter roots. In a lengthy set of further experiments, they found that PZO1 in root tip cells responds to mechanical stimuli with ion flows—which establishes it as a mechanosensor like its mammalian counterparts.

Exactly how PZO1’s mechanosensing abilities help roots grow remains a mystery. But Mousavi, Patapoutian and colleagues suspect that it helps root tip cells sense and adjust themselves to the potentially strong mechanical forces they encounter as the root tries to penetrate soils—especially drier, harder soils.

“If the activity of PZO1 increases, it might help plants expand their root systems in dry conditions and get better access to water,” Mousavi says. If that proves to be the case, boosting PZO1 activity could be a way of increasing crop yields in difficult soil conditions, he says.

Mousavi is now trying to clarify PZO1’s precise function in Arabidopsis with experiments in real-world conditions. He also hopes to study the role of PIEZO-type proteins in food crops including maize and rice.

The study, “PIEZO ion channel is required for root mechanotransduction in Arabidopsis thaliana” was authored by Seyed Mousavi, Adrienne Dubin, Wei-Zheng Zeng, Adam Coombs, Khai Do, Darian Ghadiri, William Keenan, Chennan Ge, Yunde Zhao and Ardem Patapoutian.

Support for the research was provided by the Swiss National Science Foundation (P300PA_164695, P2LAP3_151727), the National Institutes of Health (GM114660, R01HL143297), HHMI, and the China Scholarship Council (to UCSD).

Featured image: Arabidopsis thaliana, a plant commonly known as thale cress, is often used as a laboratory model to study the molecular underpinning of plant biology. Scripps Research scientists have shown that the plant’s roots use a “mechanosensor” protein that is present in all animals to sense its surroundings as it grows. (Image courtesy of Seyed Ali Reza Mousavi, PhD)

Provided by Scripps

Fundamental Regulation Mechanism of Proteins Discovered (Biology)

A research team led by Göttingen University find novel switch in proteins with wide-ranging implications for medical treatments

Proteins perform a vast array of functions in the cell of every living organism with critical roles in almost every biological process. Not only do they run our metabolism, manage cellular signaling and are in charge of energy production, as antibodies they are also the frontline workers of our immune system fighting human pathogens like the coronavirus. In view of these important duties, it is not surprising that the activity of proteins is tightly controlled. There are numerous chemical switches that control the structure and, therefore, the function of proteins in response to changing environmental conditions and stress. The biochemical structures and modes of operation of these switches were thought to be well understood. So a team of researchers at the University of Göttingen were surprised to discover a completely novel, but until now overlooked, on/off switch that seems to be a ubiquitous regulatory element in proteins in all domains of life. The results were published in Nature.

Professor Kai Tittmann © Kamala Elisa Tittmann

The researchers investigated a protein from the human pathogen Neisseria gonorrhoeae that causes gonorrhea, a bacterial infection with over 100 million cases worldwide. This disease is typically treated with antibiotics but increasing rates of antibiotic resistance pose a serious threat. In order to identify new treatments, they studied the structure and mechanism of a protein that is a key player in carbon metabolism of the pathogen. Surprisingly, the protein can be switched on and off by oxidation and reduction (known as a “redox switch). The scientists suspected this was caused by a common and well-established “disulfide switch” formed between two cysteine amino acids. When they deciphered the X-ray structures of the protein in the “on” and “off” state at the DESY particle accelerator in Hamburg, Germany, they were hit by an even bigger surprise. The chemical nature of the switch was completely unknown: it is formed between a lysine and a cysteine amino acid with a bridging oxygen atom.

“I couldn’t believe my eyes,” says Professor Kai Tittmann, who led the study, when he remembers seeing the structure of the novel switch for the first time. “We thought initially that this must have formed artificially as a by-product of the experimental process as this chemical entity was unknown.” However, numerous repetitions of the experiments always gave the same result and an analysis of the protein structure database further disclosed that there are many other proteins that very likely possess this switch, which apparently escaped earlier detection as the resolution of the protein structure analysis was insufficient to detect it for certain. The researchers admit that good fortune was on their side because the crystals they measured allowed the protein structure to be determined at extremely high resolution, meaning the novel switch couldn’t be missed. “The extensive screening for high-quality protein crystals has really paid off, I couldn’t be happier,” says Marie Wensien, first author of the paper.

The researchers believe the discovery of the novel protein switch will impact the life sciences in numerous ways, for instance in the field of protein design. It will also open new avenues in medical applications and drug design. Many human proteins with established roles in severe diseases are known to be redox-controlled and the newly discovered switch is likely to play a central role in regulating their biological function as well.

Researchers from the Göttingen Center for Molecular Biosciences (GZMB), the Faculty of Chemistry of the University of Göttingen, the Max Planck Institute for Biophysical Chemistry and the Hannover Medical School contributed to the study.

Featured image: Protein structure with the newly identified switch between a cysteine and lysine residue showing its structure and electron density. This discovery has wide-reaching implications for understanding and treating diseases. © K. Tittmann

Original publication: Marie Wensien et al. A lysine-cysteine redox switch with an NOS bridge regulates enzyme function. Nature 2021. DoI: 10.1038/s41586-021-03513-3

Provided by University of Göttingen

HKU Scientists Develop a New Chemical Tool That Sheds Light on How Proteins Recognise & Interact with Each Other (Chemistry)

A research group led by Professor Xiang David LI from the Research Division for Chemistry and the Department of Chemistry, The University of Hong Kong, has developed a novel chemical tool for elucidating protein interaction networks in cells. This tool not only facilitates the identification of a protein’s interacting partners in the complex cellular context, but also simultaneously allows the ‘visualisation’ of these protein-protein interactions. The findings were recently published in the prestigious scientific journal Molecular Cell.

In the human body, proteins interact with each other to cooperatively regulate essentially every biological process ranging from gene expression and signal transduction, to immune response.  As a result, dysregulated protein interactions often lead to human diseases, such as cancer and Alzheimer’s disease. In modern biology, it is important to comprehensively understand protein interaction networks, which has implications in disease diagnosis and can facilitate the development of treatments.

To dissect complex protein networks, two questions need to be answered: the ‘who’ and ‘how’ of protein binding. The ‘who’ refers to the identification of a protein’s interacting partners, whereas the ‘how’ refers to the specific ‘binding regions’ that mediate these interactions. Answering these questions is challenging, as protein interactions are often too unstable and too transient to detect. To tackle this issue, Professor Li’s group has previously developed a series of tools to ‘trap’ the protein-to-protein interactions with a chemical bond. This is possible because these tools are equipped with a special light-activated ‘camera’ – diazirine group that capture every binding partner of a protein when exposed to UV light. The interactions can then be examined and interpreted. Unfortunately, the ‘resolution’ of this ‘camera’ was relatively low, meaning key information about how proteins interact with each other was lost. To this end, Professor Li’s group has now devised a new tool (called ADdis-Cys) that has an upgraded ‘camera’ to improve the ‘resolution’. An alkyne handle installed next to the diazirine makes it possible to ‘zoom in’ to clearly see the binding regions of the proteins. Coupled with state-of-the-art mass spectrometry , ADdis-Cys is the first tool that can simultaneously identify a protein’s interacting partners and pinpoint their binding regions.

In the published paper, Professor Li’s lab was able to comprehensively identify many protein interactions — some known and some newly discovered — that are important for the regulation of essential cellular processes such as DNA replication, gene transcription and DNA damage repair.  Most importantly, Professor Li’s lab was able to use ADdis-Cys to reveal the binding regions mediating these protein interactions. This tool could lead to the development of chemical modulators that regulate protein interactions for treating human diseases. As a research tool, ADdis-Cys will find far-reaching applications in many areas of study, particularly in disease diagnosis and therapy.

For more information about the paper “A tri-functional amino acid enables mapping of binding sites for posttranslational modification-mediated protein-protein interactions” published in Molecular Cell, please visit: https://www.cell.com/molecular-cell/fulltext/S1097-2765(21)00268-9

Featured image: The ADdis-Cys ‘camera’ can simultaneously identify a protein’s interacting partners and pinpoint their binding regions. © HKU

Provided by HKU

Researchers Identify the Proteins That Cause Intestinal Disease (Biology)

How do bacteria take over intestinal cells? Now we know

Researchers from Tel Aviv University have created an artificial intelligence platform that can identify the specific proteins that allow bacteria to infect the intestines – a method that paves the way for the creation of smart drugs that will neutralize the proteins and prevent disease, without the use of antibiotics. Participating in the study, which was published in the prestigious journal Science, were Ph.D. student Naama Wagner and Prof. Tal Pupko, head of the Shmunis School of Biomedicine and Cancer Research at the Faculty of Life Sciences and the new Center for Artificial Intelligence & Data Science at Tel Aviv University. The international partners in the study included researchers from Imperial College (led by Prof. Gad Frankel) and the Institute for Cancer Research in London, as well as from the Technical University and the National Center for Biotechnology in Madrid.

Intestinal diseases are caused by pathogenic bacteria that attach to our intestinal cells. Once attached, the bacteria use a kind of molecular syringe to inject intestinal cells with proteins called “effectors.” These effectors work together to take over healthy cells, like hackers that take over computer servers using a combination of lines of code. However, until now scientists have not known what protein combination it is that cracks the cell’s defense mechanisms. Now, the Tel Aviv University researchers’ artificial intelligence platform has identified novel effectors in the bacteria, which have been experimentally tested and validated. Subsequently, laboratory experiments conducted in London successfully predicted the protein combinations that lead to the pathogenic bacteria taking over the intestines.

“In this study, we focused on a bacterium that causes intestinal disease in mice, a relative of the E. coli bacteria that cause intestinal disease in humans, so as not to work directly with the human pathogen”, explains Ph.D. student Naama Wagner. “The artificial intelligence we created knows how to predict effectors in a variety of pathogenic bacteria, including bacteria that attack plants of economic importance. Our calculations were made possible by advanced machine-learning tools that use the genomic information of a large number of bacteria. Our partners in England proved experimentally that the learning was extremely accurate and that the effectors we identified are indeed the weapons used by the bacteria.”

“Pathogenic bacteria are treated with antibiotics,” says Prof. Tal Pupko. “But antibiotics kill a large number of species of bacteria, in the hope that the pathogenic bacteria will also be destroyed. So antibiotics are not a rifle but a cannon. Moreover, the overuse of antibiotics leads to the development of antibiotic-resistant bacteria, a worldwide problem that is getting worse. Understanding the molecular foundation of the disease is a necessary step in the development of drugs that are smarter than antibiotics, which will not harm the bacterial population in the intestines at all. This time we discovered the effectors of gut bacteria that attack rodents, but this is just the beginning. We are already working on detecting effectors in other bacteria in an attempt to better understand how they carry out their mission in the target cells they are attacking.”

Featured image: Prof. Tal Pupko © Tel-Aviv University

Reference: David Ruano-Gallego, Julia Sanchez-Garrido, Zuzanna Kozik, Elena Núñez-Berrueco, Massiel Cepeda-Molero, Caroline Mullineaux-Sanders, Jasmine Naemi-Baghshomali Clark, Sabrina L. Slater, Naama Wagner, Izabela Glegola-Madejska, Theodoros I. Roumeliotis, Tal Pupko, Luis Ángel Fernández, Alfonso Rodríguez-Patón, Jyoti S. Choudhary, Gad Frankel, “Type III secretion system effectors form robust and flexible intracellular virulence networks”, Science  12 Mar 2021: Vol. 371, Issue 6534, eabc9531 DOI: 10.1126/science.abc9531

Provided by Tel-Aviv University

New Brain Proteins Suspected of Causing Depression (Neuroscience)

Can they play a pivotal role in treating the illness, as well?

Using an innovative protein-based approach, researchers at the Atlanta VA Medical Center and nearby Emory University have found genes and corresponding proteins that could point the way to new depression treatments.

“We are very excited to continue to work on these promising targets in our lab but caution that the road leading to new drugs is long and difficult.”

Using a proteome-wide association study (PWAS) that integrated genome-wide association study (GWAS) data with human brain proteomic and genetic data, researchers have identified 19 genes that may lead to depression by altering brain protein levels. They also pinpointed 25 such proteins that offer promise as potential targets for new depression treatments.

The researchers detail their approach and findings in April 2021 in the journal Nature Neuroscience.

Identifying brain proteins that cause depression

Depression is a common condition, but current treatments are ineffective for many people with the mental illness. This research sets the stage for finding new drugs to treat the illness by identifying important gene-protein pairs that likely contribute to the cause of depression and could serve as promising targets for future studies, according to lead researcher Dr. Aliza Wingo, a psychiatrist at the Atlanta VA. She’s also an associate professor at Emory University.

Wingo works with Dr. Thomas Wingo, the first author of the study, at their joint laboratory at the Atlanta VA and Emory. The lab focuses on understanding the genetic basis of brain illnesses. They collaborated on the study with investigators at Emory’s Center of Neurodegenerative Disease.

In seeking new therapies, the research team, with support from VA and the National Institutes of Health, aimed to identify brain proteins that likely cause depression. The team hypothesized that genetic variants influence depression by altering levels of certain brain proteins.

Genome-wide association studies played a key role in the research but were not sufficient by themselves, explained Thomas Wingo. GWAS is an important tool for its ability to spot variations associated with medical conditions, including depression, but the genome scans do not shed light on how genetic variations translate into increased disease risk. So the study design combined GWAS and human brain proteomic data toward answering the question, how can variations in brain protein levels explain some of the inherited risk for depression?

By examining proteins—which are the final products of gene expression and the main functional components of cells—PWAS can help elucidate the biological mechanisms underlying depression. The approach can importantly supplement information from GWAS by finding changes in the way a protein is being expressed in a normal gene versus a variant. Despite proteins’ promise as biological informants, and in spite of the fact that proteins make up the bulk of drug targets and biomarkers, this study was conspicuous among depression studies for its direct look at proteins.

Biomarkers for depressive symptoms

It was this rare scientific method—using  the “largest and deepest reference human brain proteomes and summary statistics from the latest GWAS of depression,” according to the authors—that allowed the researchers to identify the total of 25 proteins of interest, 20 of which prior GWAS studies did not peg as implicated in depression.

As for the 19 genes they homed in on, the researchers determined they “contribute to depression pathogenesis through modulating their brain protein abundance.” The brain protein fluctuations detected by uniting GWAS and human brain proteomic data are likely among the earlier biological changes in depression and may predispose a person to the illness, said Aliza Wingo, making the findings particularly compelling in terms of therapeutic potential.

Follow-up research, including tests in model systems, is crucial to further examine the identified genes’ possible roles in depression and to seek additional implicated genes and proteins, the study authors said. The provocative suggestion that the implicated proteins appear to contribute to the inherited risk of depression has spurred ongoing work at the Wingos’ lab.

“We are very excited to continue to work on these promising targets in our lab but caution that the road leading to new drugs is long and difficult,” said Thomas Wingo, noting another clinical hope based on this area of study: “We take heart that these findings could also prove useful as biomarkers for depressive symptoms. An effective biomarker—like hemoglobin A1C for diabetes—could help with diagnosis and management of depression.”

Featured image: In their lab at the Atlanta VA and Emory University, Dr. Thomas Wingo and Dr. Aliza Wingo (foreground) have found genes and corresponding proteins that could open doors for new depression treatments. (This photo by Lisa Pessin was taken before the current pandemic.)

Reference: Thomas Wingo et al., “Brain proteome-wide association study implicates novel proteins in depression pathogenesis, Nature Neuroscience (2021). DOI: 10.1038/s41593-021-00832-6

Provided by US Department of Veteran Affairs