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sbgridconsortium · 2 months

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Using flies to study neurodegeneration

This publication highlight is part of the SBGrid/Meharry Medical College Communities Project, focused on science education and demonstrating how structural biology and preclinical science connect to medicine.

In the body, proteins carry out vital tasks to keep us alive. In order to do the wide variety of tasks needed to keep a living system going, proteins can form unique structures in order to carry out each unique function. These structures are encoded into the protein by its amino acid sequences, which are in turn determined by an mRNA sequence that is encoded by a DNA sequence. Information flows from DNA to RNA to protein structure in the cell and if any problems occur in this information pipeline, detrimental consequences follow. One example of a problem in the pipeline is a mutation in the DNA causing proteins to fold into the wrong shape and not be able to carry out their function. This is the case for Huntington’s Disease. In this neurodegenerative disease, the DNA that makes up the Huntington gene is mutated, almost resembling a skipping record, repeating the same nucleotide phrase, cytosine–adenine–guanine (CAG), over and over again. This repetition causes the resulting protein to have long regions unfolded or misfolded because of repeats of the glutamine amino acid (Gln, Q) and is referred to as a polyQ disease. Proteins with polyQ tracts are enriched in genes with neuronal function and typically aggregate together and cause the tragic symptoms that are hallmarks of the disease. In a recent publication in a IUCr Journal, SBGrid member Dr. Dierk Niessing, publishes a new protein structure that could help limit the aggregation of Huntington gene proteins.

Pictured above is the determined structure of TRMT2A in Drosophila melanogaster. PDB:7PV5. CC BY SBGRID

Recent studies have shown that the inhibition of a protein called TRMT2A can lessen the aggregation of Huntington proteins, which means that TRMT2A could be a potential target for therapeutic molecules. If a drug can inhibit TRMT2A activity, it has the potential to help with Huntington’s disease. In order to determine how well this hypothesis works, we need a model organism that allows for ethical experimentation. Luckily, Dr. Dierk Niessing found a homolog of TRMT2A in the common fruit fly. He used protein crystallography and x-ray diffraction to observe the structure of this homologous protein. Upon examination, this fruit fly homolog had a different sequence than the human TRMT2A protein but a very similar structure. All the catalytic residues, the functionally relevant amino acids in the human protein, were also conserved in the fruit fly protein. This paper builds a case using structural biology that this fruit fly protein is a very similar homolog to the human TRMT2A protein. The implications of these findings mean that fruit flies could be an effective model to study how well drugs that target this protein are able to lessen Huntington symptoms. Read more about this fruit fly homolog in the Acta Crystallographica Section F.

-Vida Storm Robertson, Fisk University

Vida Storm Robertson is a Masters Student in Chemistry at Fisk University working in both solid-state and solution based structural determination techniques. He plans on starting a PhD program in biophysics in the fall of 2024.

#sbgrid #science #structural biology

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sbgridconsortium · 2 months

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Metals as nutrients for bacteria to thrive

Copper is a micronutrient that helps regulate many important functions needed for bacteria to survive. However, high amounts of copper can be toxic to bacteria so it’s important for bacteria to be able to maintain homeostasis. Copper’s main role is to act as a cofactor. A cofactor is a non-protein molecule that is crucial for a protein to carry out its function. Many proteins use copper as a molecular helper; because of this, copper is essential for all living things, yet, it is still unclear how bacteria get and maintain their copper levels. The work titled Stabilization of a Cu-binding site by a highly conserved tryptophan residue by SBGrid member Oriana Fisher looks into how the Gram-positive bacterium Bacillus subtilis regulates copper levels.

Structure of copper(II) (tan spheres) bound to the mutant YcnIW137F. CC BY SBGRID.

The authors looked at the ycnKJI operon that contains three copper-using proteins. An operon is a group of genes that are all controlled by the same promoter, or the place where genes are turned “on”. They found that a member of the ycnKJI operon, YcnI, a copper-binding protein whose function is still unknown, prefers to bind the oxidized version of copper. This oxidized version is known as Copper(II) oxide or Cu(II). By creating a mutated version of Ycnl where they swapped out a conserved tryptophan for phenylalanine, they found that even though tryptophan, an amino acid and binding site of Cu(II), is found in about 98% of this family of copper-binding proteins, it is not essential for Cu(II) binding. The conserved tryptophan, however, is necessary for maintaining the stability of Cu(II) binding to the protein.

Read more in the Journal of Inorganic Biochemistry.

- KeAndreya Morrison, Meharry Medical College

#sbgrid #science #bacteria

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sbgridconsortium · 3 months

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A small molecule that clogs up ribosome machinery

Ribosomes are essential molecular machines in the cell. They create proteins through the translation of RNA into an amino acid sequence. This process of translation is an important topic of study for molecular and structural biologists because of its vital role in maintaining life and the proteome. The production of the full proteome is essential for life and any variance or interference in the process could lead to drastic consequences. Because of this, the study of how small molecules and drugs interact and influence the ribosome is an ever-present question for structural biologists and medicinal chemists. In Nature Chemical Biology, SBGrid member Dr. Susan Shao from Harvard University, shows the unique effect that a small molecule, SRI-41315, has on the ribosome.

Ribosomes are made of many different protein and RNA units. The process of creating amino acid chains from an RNA transcript is highly dynamic and requires the timely introduction and removal of a library of participating molecules in the translation symphony. One of these molecular players in translation is eukaryotic translation termination factor 1, eRF1. This protein binds to the ribosome subunits and aids in the termination or conclusion of the translation process. eRF1 helps the ribosome read the translation instruction, the mRNA, and helps the ribosome know when to stop and remove the finished amino acid chain. The small molecule SRI-41315 has been known to degrade eRF1, but the mechanism for this degradation was unknown until Dr. Susan Shao and colleagues proposed the following using cryo-EM and molecular assays:

Pictured above is small molecule SRI-41315 (gray) interaction with eRF1 (green) and RNA (orange) in the ribosomal complex. PDB:8SCB. CC BY SBGRID

Using electron microscopy at cryogenic temperatures, a technique known as cryo-EM, Dr. Shao was able to create a model of eRF1 in complex with a ribosome with SRI-41315 bound. In this model, SRI-41315 was shown to act as a glue in the machine. This small molecule locked eRF1 into a specific configuration, limiting the dynamic process of translation. By gumming up the ribosomal machine, SRI-41315 increased eRF1 degradation and affected the machine's ability to accurately produce functional proteins. The ability of this small molecule to indirectly slow down and effect the efficiency of translation is a very compelling observation and provides evidence for the wide array of functions small molecules can have in living systems.

To learn more about the clog in the ribosomal machine, continue reading at Nature Chemical Biology.

Vida Storm Robertson, Fisk University

#sbgrid #structural biology #cryo em #member publication

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sbgridconsortium · 3 months

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An inside look into the Powerhouse of the Cell

Mitochondria are the powerhouses of the cell. We’ve all heard this phrase at some point in our lives, but what does it mean on a molecular level? A mitochondrion is an organelle in cells like animals, plants and humans that functions to provide the cell with energy in the form of a molecule called adenosine triphosphate, or ATP. A sufficient stock of ATP is produced in mitochondria when cells in our body convert food into energy, or what is known as cellular respiration. More specifically, cellular respiration is when our cells take in glucose and oxygen through many steps and then release carbon dioxide, water, and energy. An important step is to store this energy into a form that can be used in different parts of the cell when needed. This is done by moving electrons (really small particles that are a part of atoms) by a group of biomolecules called proteins. These proteins come together to form an electron transport chain. As the name suggests, the electron transport chain is a series of processes where electrons are transported from one molecule (donor) to another molecule (acceptor) resulting in the formation of ATP. For the electron transport chain to work, it relies on electron donor molecules produced from the Krebs cycle, also known as the citric acid cycle.

The Krebs cycle is a metabolic pathway in the mitochondria that allows our bodies to break down carbohydrates to be used for energy. This process starts with pyruvate entering the system and, after several steps, ends with the production of several molecules such as, ATP, NADH, and FADH2. These important molecules enter the electron transport chain acting as electron donors to make more ATP. CO2 is also produced from the Krebs cycle and enters other metabolic pathways. All of the steps in the Krebs cycle are carried out by different enzymes. One of the enzymes is succinate dehydrogenase (SDH). As a member of the electron transport chain in mitochondria, SDH or complex II, catalyzes the formation of fumarate from succinate- releasing FADH2 as a byproduct. SDH produces a fraction of the total ATP, but is important for a wide range of cellular activities, such as suppressing tumor growth and neurological development. Although the importance of SDH has been widely established, what is unknown are the details of how the regulation of SDH assembly factors (SDHAF) and SDH assemble into a functional unit.

Left: structure of SDHA-SDHAF2-SDHAF4 assembly intermediate (PDB: 8DYD). Green: SDH, purple: SDHAF4, orange: SDHAF2. Right: structure of SDHA-SDHAF4 assembly intermediate (PDB: 8DYE). Green: SDH, orange: SDHAF4. CC BY SBGRID.

To address this question, SBGrid member Tina Iverson investigated the intermediate complexes formed by the SDHAF subunits and cofactors. Through the use of cellular studies and biochemical experiments, along with X-ray crystallography and NMR for structural studies, the authors were able to map out the different intermediate complexes that lead to the formation of the fully matured SDH. Interestingly, the authors found that regions of the assembly proteins can transition from ordered (a protein with a secondary structure) to disordered (a protein with no secondary structure) and that this change is important for the transfer between intermediate complexes. These results shed light on the previously unknown steps of the formation of a mature and functional complex II of the electron transport chain.

Read more in PLOS One

- KeAndreya Morrison, Meharry Medical College

#sbgrid #science #structural biology

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sbgridconsortium · 7 months

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A personal history of the great Crystallography pioneer Dr. Wayne Hendrickson

SBGrid member Dr. Janet L. Smith writes a beautiful history of crystallography legend and pioneering physicist Wayne Hendrickson in the International Union of Crystallography Journal. In this commentary, Dr. Smith gives a wonderful history of Dr. Hendrickson’s academic work as he developed into the world class researcher we all know today. Hendricks recently won the Ewald Prize from the International Union of Crystallography and published a magnum opus of sorts accumulating his lifelong work on solving the phase problem titled “Facing the phase problem”. This article describes how Dr. Hendrickson and his colleagues, including Dr. Smith, approached the phase problem, created solutions for it, and applied those solutions to modern technologies that now solve this problem with general ease. Dr. Smith then provides vital personal chronologies to the discussions in her follow up article in which she describes how Hendrickson, over the course of his career, systematically attacked this problem and developed the methodologies for which he is now famous. This biographical retelling of his work helps to humanize this great scientist and visualize his impact on the field of structural biology. The combination of Dr. Hendrickson’s scientific anthology and Dr. Smith's historical retelling reads together as a great biographical story of how great scientists are born and evolve into the giants we know today. Dr. Hendrickson's monograph and Dr. Smith's commentary can both be found in the International Union of Crystallography Journal.

Pictured below is PDB entry 1HR3, the first structure Dr. Janet L. Smith and Dr. Wayne Hendrickson published together in 1983 at the Naval Research Laboratory.

- Vida Storm Robertson, Fisk University

Vida Storm Robertson is a Masters Student in Chemistry at Fisk University working in both solid state and solution based structural determination techniques. He plans on starting a PhD program in biophysics next fall.

#structural biology #sbgrid #science #research

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sbgridconsortium · 7 months

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Radical Reactions - Yvain Nicolet - Institut de Biologie Structurale

Sharing some of our #SBGrid member tales from the last year. This one from January 2023.

The periodic table may be an icon of chemistry, but a cluster of elements at its center gives biology some essential pop and sparkle. Yvain Nicolet at the Institut de Biologie Structurale (IBS) in Grenoble, France, wants to learn exactly how those transition metals in the middle of the table put more pizzazz in proteins.

About one-third of proteins contain transition metals, such as cobalt, copper, molybdenum, or iron. The Nicolet lab mainly studies metalloproteins that contain iron-sulfur clusters but also scrutinizes enzymes that make these clusters. "Transition metals are often key components of the proteins in terms of function," Nicolet says. "They are only few atoms in a structure and sit in specific sites, but they enable specific activities, notably in enzymes, but not only in enzymes." Metals give proteins some superpowers in the form of new chemical properties and functions not otherwise possible with combinations of the 22 amino acids.

"They enhance the reactivity of the proteins by making many strange active sites that are very interesting," he says. These reactions can be blazingly fast with complex chemistry. And they are technically challenging to study.

The lab investigates enzymes that use metals, as well as proteins that build the metal cofactors and insert them into the enzymes. "We try to trigger the reaction in a crystal and to trap the different intermediates during the reaction to characterize by structural biology," Nicolet says.

Many metalloproteins evolved in a time before oxygen and can only make their razzle-dazzle moves in an anaerobic space. To prevent oxygen from destroying their molecules, experiments in the Nicolet lab take place in a series of six large anaerobic chambers filled with nitrogen.

The researchers reach in through gloves built into the airtight boxes to work with samples and equipment. There, cells are grown and broken up. The cell extracts are cleared and proteins separated by chromatography. Crystallization robots in one glove box screen for optimum conditions that researchers can manually reproduce in another box and freeze in liquid nitrogen. From there, the synchrotron is only 500 meters away.

"We determine 3D structures at moderate to high resolution," Nicolet says. "At first, we aim at determining where the metals are in a given protein, and how they interact with their environment (the protein matrix). We also aim at determining the structure of the metallocofactors or metal binding sites in terms of ligands and geometry.

"Then in a second step, we aim at understanding how these metals confer a specific activity to the protein," he continues. "For instance, in an enzyme, we would get intermediate states with the metal in a different coordinate and/or redox state to better understand what is going on during the reaction."

One milestone of the lab's work arose from successfully trapping an unexpected radical intermediate of NosL, a radical S-adenosyl-L-methionine (SAM) enzyme, in the process of generating a peptide with potent activity against gram-positive bacterial pathogens (Science, 2016).

Crystallography provided the position of the atoms, and for this paper they also used a spectroscopy technique called electron paramagnetic resonance (EPR), which gives the position of unpaired electrons near atoms.

Two months later, the group reported results from a study in which they carried out radical based chemistry catalyzed by the radical SAM enzyme HydE from beginning to end in a crystal (Nature Chemistry, 2016).

The image shows substrate processing and product transfer within HydE cavity during the FeFe-hydrogenase active site assembly process. Credit: Y.Nicolet

More recently, Nicolet's team characterized intermediates in the assembly of the nitrogenase, a key player in the global nitrogen cycle. The enzymatic complex nitrogenase catalyzes the reduction of nitrogen gas N2 to ammonia NH3, transforming nitrogen and returning it to plants. Specifically, the paper reported the X-ray structure of NifB protein from a nitrogen-fixing bacteria, one of a dozen proteins required to assemble the nitrogenase active site (Journal of the American Chemical Society, May 2020).

"For nitrogenase, there is a dedicated machinery with very, very challenging chemistry involved, and this is what we are attacking over the few next years," he says.

Nicolet was born and raised in Grenoble, France, where he now lives and works. Growing up in the city, he became an accomplished cello player with ambitions of becoming a professional musician. He started college in Grenoble. When a music school in Paris turned down his application, he chose to pursue science at what is now the University of Strasbourg. In Strasbourg, all the science classes emphasized the three-dimensional structures of molecules, whether it was enzymology, DNA replication, or proteins. He completed his undergraduate degree and stayed for graduate training in chemistry, biology, crystallography and nuclear magnetic resonance (NMR).

In a dinner discussion, a friend noted his interest in inorganic chemistry and suggested a structural biology lab in Grenoble working on metalloproteins. He moved back to complete his PhD at what is now the Université Grenoble Alpes. Nicolet worked on the structure of the [FeFe]-hydrogenase (an enzyme that makes or use molecular hydrogen), basic science with a potential application in producing alternative fuel.

From there, he joined the Drennan Lab at the Massachusetts Institute of Technology. In Cambridge, he discovered radical-based chemistry working on this newfound Radical SAM Proteins superfamily, now known for their ability to synthesize many vitamins, cofactors, or antibiotics.

He moved back to Grenoble for a one-year postdoctoral fellowship with the European Synchrotron Radiation Facility. In 2004, he joined IBS as a scientist and became a group leader there in 2016.

The Nicolet lab often dives into the molecular mechanisms of phenomenon discovered by other groups. "In my lab, we are not at the beginning of the discovery, and we are probably not at the end of the process," he says. "We focus on the molecular mechanisms inside the enzymes."

In a new challenge, the lab has set up a system to use cryo-electron microscopy to examine the assembly dynamics and reactions at room temperature without oxygen. Nicolet is interested in the basic science of radical chemistry, but he also hopes to be able to harness a radical enzyme and modify its catalytic activity to produce a molecule through directed evolution, such as a better antibiotic.

Nicolet also enjoys taking a bigger picture view of the nitrogen cycle, thanks to his garden. He came late to the activity and confesses that he is not good at growing vegetables. "You can observe the nature or the interaction between the different organisms that live together from bacteria to insects and plants," he says. "For me, it's the best way to contemplate what Darwin described as natural selection. And evolution. I'm not very good at producing vegetables, but I really enjoy seeing how all these organisms compete together or help each other as well.

-Carol Cruzan Morton

#sbgrid #structural biology #member tale #metalloproteins

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sbgridconsortium · 8 months

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Second Takes - Andrea Thorn - University of Hamburg

Sharing some of our #SBGrid developer tales from the last year. This one from February 2023.

Andrea Thorn had been a junior group leader for a less than a year when, in early January 2020, researchers in China identified the cause of a mysterious contagious illness with pneumonia-like symptoms. Less than a week later, they released its genetic code, which revealed the novel virus to be a close cousin to the SARS coronavirus (SARS-CoV-1) that caused an outbreak in 2002-2003.

The rapid scientific response gave Thorn an idea for a talk she was due to give over coffee and cake to colleagues in her building at the Julius Maximilian University of Würzburg in Germany. She ran the only lab there focused on new computational methods for experimental structural biology. Most scientists in the building were infectious disease specialists.

"I needed to explain to them how my work was relevant," she says. Thorn works on ways to better model the atomic structures of RNA and proteins to make them useful for structure-based drug discovery, something that quickly would become more important as researchers rushed to respond to COVID-19.

Molecular models are a foundation of modern drug and vaccine development. They enable scientists to identify how to break the cycle of infection by targeting the right spot in the right protein. But even the most carefully determined structures reported in the most prestigious journals are imperfect interpretations of experimental data, Thorn says. Small errors can have large consequences in the search for a drug with the right fit.

When Thorn was preparing for her talk, no structures from the SARS-CoV-2 virus had been published yet. But more than 100 structures from SARS-CoV-1 were available in the worldwide Protein Data Bank (wwPDB). The structures ranged from a key protease in viral replication to the spike protein needed to attach and enter host cells.

From a random sample of five, Thorn found three SARS structures to illustrate the point of her research: Most protein structures can be improved with additional analysis.

Her talk was well received, germinating the seed of another idea that first seemed outlandishly bold and then became increasingly urgent as COVID-19 spread and the death toll soared. Thorn floated the idea over dinner with her mentor, Arwen Pearson in Hamburg: Analyze and correct all SARS structures. Pearson encouraged her, as did another senior colleague, Elspeth Garman of Oxford University.

In March 2020, as the first SARS-CoV-2 structures were being reported, Thorn first got her own small group on board and within a week pulled together a team of like-minded and mostly junior structural biology developers from all over the globe as the “Coronavirus Structural Task Force”. Many of them were international specialists in their respective fields, she notes.

They met online every weekday and posted daily updates to GitHub for anyone to access. Every Wednesday, when new wwPDB structures were released, their automated pipeline identified new coronavirus structures and assessed the quality of a representative sample of models and experimental data. When they improved a structure, they sent it back to the original authors to update the wwPDB entry, no strings attached.

For their web site (https://insidecorona.net), the group wrote blog posts to share with colleagues the larger story emerging from aggregated data of multiple structures. They wrote explanatory pieces for the public. They posted a 3D printable model of SARS-CoV-2.

Coronavirus Structural Task Force website: https://insidecorona.net. Image credit: Thomas Splettstößer

A year into the pandemic, structural biologists had released a total of 1,146 SARS structures covering 18 proteins from both SARS-CoV-1 and SARS-CoV-2. Most were derived by X-ray crystallography (73%) and single particle cryo-electron microscopy (cryo-EM) (24%) (Nature Structural & Molecular Biology, January 2021).

The task force's analytical pipeline deployed software programs from contributors inside and outside the Task Force. Among them were two tools previously developed by Thorn—AUSPEX, used for experimental X-ray data to detect sample measurement and processing problems (Acta Crystallographica, 2017) and, for experimental cryo-EM data, HARUSPEX, a neural network tool to automatically distinguish between nucleic acids and protein and to assign secondary protein structure elements (Angewandte Chemie, International Edition, 2020).

"We didn't do any peer reviewed publication until 2021," Thorn says about the task force. "We just wanted to fight the pandemic. The whole thing was fast. We pushed and pushed and pushed against corona so that drug developers and vaccine developers would have the right data. You know, it's been fantastic. It was born out of spontaneous willingness. I wish science would always be like this."

The task force published a description of its work (Nature Structural & Molecular Biology, May 2021). In 2023, Thorn says a dozen articles are in progress for peer-reviewed journals to summarize the combined information and results of their work, as well as to note questions yet to be answered about SARS-CoV-2. The task force will wind down in summer 2023. Thorn is strategizing on the next steps for a tenured academic position.

Thorn grew up in Germany in an intellectual family. Her father is a chemist, her mother an artist and entrepreneur. She is the third-born child with three brothers.

She calls her path to structural biology straightforward. One of her early science-related memories goes back to age 3, when her father explained surface tension to her with the gravity-defying demonstration of floating a needle on water. "My dad showed that to me with his always huge confidence that I would understand everything," Thorn says.

The family moved four times when Thorn was in elementary school. She supplemented the patchwork early education with natural curiosity. She read voraciously from the family library, made observations with a home microscope, and conducted chemistry experiments on the sly. In her mother's atelier, she also painted on large blank canvases.

In her teens, she and her friends were early adopters of live action role-playing games that have subsequently become popular in Germany. Participants assume the roles of characters and act out scenarios in a collaborative storytelling experience. To prepare for her roles, she researched scenarios ranging from futuristic military campaigns in Libya to glial cell retrieval from patients. "I read up to 600 pages a day when I was a teenager," she says.

In school, Thorn's studies became concentrated in chemistry and art. She continued first to a bachelor's degree and a master's degree, a prerequisite for her PhD.

She excelled in the lab and in computational chemistry, but her breakthrough lessons came after she failed quantum chemistry. She sought a tutor in the solid-state physics department, where her academic track record was unknown. A professor she consulted for a referral, Helmuth Zimmermann, volunteered to oversee weekly tutoring for Thorn and other classmates who needed help.

"Arguably those tutoring sessions did more for my education than everything else that semester," she says. "I'd never used maths before to describe things in nature in that way and fell in love with that."

One day, in response to Thorn's curiosity, the professor explained his research, which was measuring crystals to determine the structure of molecules. "I was hooked, because that meant the maths that I just learned could be applied far beyond class," she says. "It meant you could use them to find out the structure of crystal lattices and, with the structure of crystal lattices, the structure of molecules."

She skipped her prescribed medicinal chemistry classes in favor of crystallography lectures, which were not in her curriculum plan. One day, her crystallography lecturer refused to answer her question about SHELX, a crystal structure refinement program, saying she wasn't smart enough to understand.

"I was so angry, I printed out the SHELX manual, which is 100 pages, and I read the whole fricking thing." She came to the next class armed with new and more detailed questions. "It turned out he didn't know so much about crystallography," she says.

When it came time to choose a PhD group, Thorn had a list. The list included George Sheldrick at University of Göttingen, who developed SHELX. On the way to a holiday live role-play destination, she stopped by his lab to scout it out informally. Unexpectedly, she had a long conversation with him that ended with an immediate offer of doing her PhD thesis in his group.

She thrived in the high-performing lab and found fellow role-play enthusiasts. When she was teaching her first classes as a PhD student, a friend came to collect her for lunch. He noted her stance in front of the students (who were much older than her) looked like the last weekend's live role play when she had played a commanding leader with feet planted and shoulders squared as she led her warriors into battle.

In 2011, Thorn graduated with her doctorate and four new first-author publications from her thesis. The morning after her defense, she married her childhood sweetheart, a chemist. Within a year, she had secured a prestigious three-year Marie Curie fellowship for independent research at the MRC Laboratory of Molecular Biology in Cambridge, followed by a brief but productive stint at University of Oxford.

Homesick for Germany and their parents, she returned with high expectations of becoming an assistant professor, something that remains a goal. She secured outside funding and became a group leader at University of Würzburg in 2019 and moved to Universität Hamburg in 2020.

The task force may be winding down, but its value lingers in Thorn's mind as an unmet need in science. She has been thinking about the volume of data being generated by the structural biology community and how to combine the data for more meaningful interpretation and usefulness. She also takes it as an example of what is possible when experts across the globe start to collaborate on an important problem.

"We are generating data like crazy," she says, “beyond the capacity of individuals to assimilate and make sense of details from different techniques across labs. "In Germany, we have this beautiful word, Datennachnutzung. It means you are using experimental data for a second time to find new insights. And that's something we absolutely need to do."

-Carol Cruzan Morton

#sbgrid #structural biology #developer tale #software #covid 19

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sbgridconsortium · 8 months

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How one amino acid can affect light absorption of bacteria

Plants and bacteria use light for energy and to carry out many essential functions, but scientists are still trying to understand how they are able to harness light from the sun. Proteins can form unique shapes and arrangements that allow them to somehow transform light into energy and signals, but the mechanism for such actions is not clearly understood. One such protein is found in cyanobacteria and is used to help these bacteria make decisions about movement and aggregation based on the quantity of light they receive. The protein responsible is named cyanobacteriochrome Slr1393 and in a study published in the Journal of Molecular Biology, SBGrid member Katrina Forest and colleagues investigate the interesting ability of this protein to convert from absorbing red light to absorbing green light.

Pictured above is Cyanobacteriochrome Slr1393 (teal). Tryptophan 496 is shown in purple overlapping with PCB chromophore (green). PDB:5DFX. CC BY SBGRID

Using a large toolkit of different spectroscopies, including UV-vis, IR and UV-RR, this team of researchers showed that the switching abilities of this protein appear to be caused by the alignment of a singular tryptophan residue. In the red absorbance confirmation it appears that the tryptophan residue is stacking with other cyclic and conjugated molecules. Spectroscopy results suggest that this double bond stacking helps this protein absorb light in the red wavelengths. When the tryptophan residue is moved out of a stacking arrangement, spectra results suggest that the protein is more adept at absorbing light in the green wavelengths. This theory was supported with mutant proteins that replace this key tryptophan with a less optically active residue, valine. Spectra showed that this valine mutated protein absorption did not have much meaningful change when converting between red and green absorbing conformation. These results suggest that the absorption properties of light sensitive proteins can be very sensitive and reliant on the precise 3D structure of these molecules.

Read more in the Journal of Molecular Biology.

-Vida Storm Robertson, Fisk University

#sbgrid #science #structural biology #spectroscopy #research

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