Fiona Whelan
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freewhelan.bsky.social
Fiona Whelan
@freewhelan.bsky.social
970 followers 1.3K following 460 posts
Biochemistry, cryo-EM, crystallography, dabbling in microED, biophysics, modelling; always up for coffee! Uni of Adelaide for the moment.
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#AusBiotech kicked off with an enlightening session on curating #Bioprecincts and the essentiality of a good coffee shop! Today marks the official start of this inspiring global meeting. Finding out where #AdelaideBioMedCity research & workforce training fit into our national #biomedtech capability.
October 22, 2025 at 12:20 AM
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With a delegation visiting IIT Roorkee- Great to meet Pravindra Kumar and Saugata Hazra and tour the amazing facilities here. The student talks were excellent 👏👏 Thanks for having us Roorkee!
August 30, 2025 at 3:36 AM
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Great to be involved in this research on the Ghrelin receptor, out now in Molecular Cell - with potential for translation to improve quality of life for Parkinson's disease patients!
Download now for free via this link:

authors.elsevier.com/c/1lARg3vVUP...

www.uq.edu.au/news/article...
May 29, 2025 at 6:05 AM
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Happy to report our enzyme found a home! rdcu.be/eaGXG New kid on the block P450 O-demethylase SyoA-the specificity of a monooxygenase with the simplicity of catalysis driven by peroxide. Retrofit your P450 with this active site chemistry today! #lignin #syringol Out today in Nature Communications.
February 21, 2025 at 12:17 AM
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#LorneProteins2025 Sparrow Session Charlie Bond: PPR proteins (35 aa). Modular repeats. Bind nucleic acid, shuffle nucleic acid binding sequ by shuffling specific repeats. Form a helical hairpin. 100s in plants.. siRNAs turn on or off messages for variegation.
Charlie Bond behind a lectern in a T-shirt from 1997 Lorne with his protein structure printed on it! Focus on passive binding to RNA. PPR binds to prevent nuclease digestion. Base recognition mechanism? What features of target transcript affect binding? Length? Fold? How PPR proteins recognise RNA - 5th and last AA dictates RNA sequence specificity. Apo structure and bound structure. High resolution but crystallographically complex infinite lattice. SAXS - same conformational change. Brady J made a FRET sensor for binding. 2 positions 8 repeats apart. Two dyes. Plate based FRET assay, binding affinities. UoW collaboration single molecule FRET - characterisation of PPR protein conformational change in real time. Biotinylated it, immobilised, TIRF Microscopy, measure fluorescence. Donor vs acceptor. Measure hundreds of events. Histogram in presence of target RNA. Sequ mismatches? Mutations at 3' end - still bind well. Mutations in middle, no RNA binding. No mismatches a week off rate! Single mismatch - down to a minute. Truncating? At least 11 bases for tight binding. Mutants - correlation between number of consecutive repeats binding to RNA. Mismatches to create dynamic binding. Longer RNAs? Non cognate sequ flanking. 3' vs 5' - decreases binding; but forms structures that interfere with binding. Longer RNA takes longer to bind. Are they scanning? Labelled RNA - Compaction occurs at same time as cognate RNA is bound. PPRs restricted to organelles to speed their binding to cognate RNA sequences?
February 10, 2025 at 1:55 AM
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#LorneProteins2025 Alisa Glukhova-Sparrow Session: PORCN as regulator of Wnt signalling. Does it oligomerise? No. Thermostability enhanced with C59. Amenable to cryoEM? 34 mG/mL!! 2.4 Å resolution. Active site still occupied in the apo purified protein. Extremely rigid. Rotation of a Trp +/- inhib.
Alisa Glukhova in a check jacket presenting a talk on Wnt signalling regulator Porcupine and a cautionary tale on frizzled receptor cryoEM blob interpretability! FZD engage G protein uniquely. G protein binding mediated by a lipid molecule? There's density there where it engages the g protein. Phospholipid or detergent? In nanodiscs POPC/POPG nanodisc with DDM. Dissimilar to LMNG; Density still there. Metabolomics- abundance of PG. Actual ligand? Everything in the lab had LMNG contamination. Density is probably LMNG. Different mode of engagement; mutations led to enhanced binding of G protein by TRUPATH assay.
February 10, 2025 at 1:23 AM
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#LorneProteins2025 APS session Sheena D'Arcy. PKL; Homotetramer 3 domains TIM barrel/dimer interface active site cap/allosteric activator. HDX to determine allosteric H bonding networks with allosteric regulators bound. Elegant allosteric expts for rational drug design. ✨️
RBC form PKR, liver cells PKL, PKM in muscle, ALT Splicing of PKM1 and PKM2 22 aa different. PKM1 stable tetramer, not allosterically regulated. Single conformation. PKM2 ligand regulated to promote dimer to tetramer shift. R-state to T-state. PKL therapeutics? NA fatty liver disease. Cardiovascular disease, obesity, cirrhosis, liver cancer. Prevent lipid build up in the liver? Understanding allosteric regulation. Activators and inhibitors identified which bind in the same pocket as mitapivat. Tetrameric R state defined structurally. ATP products as allosteric regulators? 6 nM PKL with saturating ligand - tetrameric with and without. CryoEM B-domain not modelled. 6 structures. 2.9-3.4 Å. B domain disordered in solution? Unliganded PKL. First example as xtals need ligand to xtallise. A to C domains for a rigid body core, variability comes from T to R state transition? Yes, like PKM. 2nd structure nope - R-like state. Angle of rotation... T and R state is 13 degrees. PKL 8.1 deg. Perhaps as unliganded? FBPR2 - most activated structure. Mitapivat 50:50 split of rotation/activated state. Greatest angle of activated state 10 deg. HD exchange coupled to MS o monitor allosteric changes. Bottom up - protein vs + ligand. Deuterium label, monitor over time. Quench and denature and proteolyse. FBP binding and allosteric motions detected. B domain still flexible. FBP and mitapivit both induce similar allosteric changes but have distinct binding sites. Slightly different, mitapivit D uptake slightly higher than FBP bound. + ATP? 55% saturation ATP has minimal allosteric effects. FBP mimics ATP. Rational design of activators and inhibitors. HDX to define activator/inhibitor state. Beautiful! Allosteric motions of domains correlate with PKL activity.
February 9, 2025 at 11:27 PM
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#LorneProteins2025 APS session: #glycotime with Mark Larance O-fucosylation; human fucosyltransferases. Domain specific EGF-like & thrombospondin fucosylation. Platelet proteome..whither FUT11? EMI domain FUT AF3 model. Foldseek to identify novel substrates with similar fold/divergent sequence! 👀
Mark Larance in a white shirt behind a podium. Presenting a talk on identification of new fucosyltransferases. POFUT - Fucosylation in the ER supporting protein secretion. EMI domains, correlated with 95% modification. Foldseek for similar structures? Yes! But no primary sequ similarity. EMI domain containing human proteome. Iterative fold seek to find EMI domain like folds. Matrix binding domains. Bind to the POFUTs. Are fucosylated. They're everywhere bound to firbrillin-1. Important for signalling in the ECM. Critical in your eye for focusing! FUT specificity for these EMI like folds. Ko mice - drop in secretion of 50%. Foldseek to identify novel substrate proteins. Why not secreted without that modification?
February 9, 2025 at 10:54 PM
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#LorneProteins2025 AMPS session: Christian Makhoul on HD CAG repeat expansion. Protein painting in human stem cell based HD model to identify HTT interactions/networks via CYS reactivity. Auto regulation of repeat expansion? Amazing insights and international collaborative networks 👏🌎
Christian Makhoul stands behind a lectern in a blue shirt. Minimal rhetorical whirls. What is protein painting? Aa selective reagents to measure reactivity or accessibility. E.g. CYS. Protein complex formation. Tpe-MI labelling. Wt vs disease models. HD neurons 13 proteins with sig altered reactivity. Not enough for functional enrichment. 2 shown to interact with HTT. Neurogenesis and DNA repair functions. Many in PCNA network. PCNA mismatch repair recruitment. Novel HTT binding protein? NanoBiT assay, LuTHy binary interaction reporter - in cell BRET and luciferase readout after affinity immunocapture. Driving it's own repeat expansion?
February 9, 2025 at 10:36 PM
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Albert Heck: Joint APS session #LorneProteins2025 Novel insights from MS. Antibodies in human blood. Purify all Igs. Proteases to cleave the hinge region:Fabs are released. L chain and part of H: all of CDRs. Lc-ms intact mass. 10^9 masses.. Really? IgG clonal repertoire is personalised!
Albert Heck behind a lectern in a fancy white jacket. Speaking about mass spectrometry over a 25 year history in his lab. Longitudinal IgG1 profiling with vaccination. What's happening to the antibody profile? Doesn't change at all! Individual can be identified from their repertoire! Proteins in blood-the human plasma proteome. Mostly analysing albumin. IgG1, IgM, IgA... deplete or focus? What we know: IgA monomer, pentameter, hexameters? Fc, Fabs, hypervariable CDRs for antigen recognition. Glycosylations and disulphide bonds different for each Ig. IgAs and IgMs as therapeutics? Repertoire size 10^18 theoretically. 10^9 circulating peripheral naive mature B-cells. Recombination of small genes. NGS is the current standard to map IgG repertoires. Let's look directly with MS! Purify IgG1/all IgGs... bacterial proteases to selectively cleave the hinge region Fabs are released. Light chain and part of heavy chain: all of CDRs. About 50 kDa. Lc-ms intact mass. 10^9 masses? Really? Can we look only at antibodies of interest? Purify with antigen. Lots of antibodies made, many not cross reactive to different spike variants. Applying this to detecting citrullinated antigens - in RA. Pathogens vs autoantigens. Redefining the structure of IgM. Pentameter + joining chain. CryoEM often don't explain which IgM... serum proteomics looking at abundance of IgM. Covariant concentration? CD5L fully assoc with IgM in serum. No free CD5L. IgM and J chain associated. 1 CD5L per J chain. Single molecule MS. 2D mass spectra. Coexpressed with J chain; resolves an intact pentamer of IgM. Disulphide bonded to IgM. Serum only. Not milk or saliva.
February 9, 2025 at 10:09 PM
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Our inspirational Leach Lecturer Frances Separovic. A champion of women in STEM. "A reluctant chemist". Croatia to Broken Hill. A peace lover. First in family to finish primary school. And one cool Professor 😎. #LorneProteins2025
February 9, 2025 at 8:57 AM
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Leach Lecture time! Celebrating the fine tradition of our favourite informal protein conference #LorneProteins2025. Remembering Syd Leach with his daughter Deb.
February 9, 2025 at 8:46 AM
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Hannah Shafaat-metalloenzymes. Pulse EPR, Raman spec. 2ndary coordination sphere mutants-NMR Most active mutants shifts peak position & line width. Psychrophilic activity tied to higher dynamics. Predict increased catalysis by engineering ⬆️ dynamics. #LorneProteins2025
Woman behind a podium smiling through the AV trauma prior to presenting a talk on metalloenzymes. Prot:solvent interface to tune reactivity and dynamics. NiFe active site, H bonded, channels for H and substrates, tertiary structure supported by quaternary protein fold. Electrochemistry, direct probe of activity. Electrocatalytic H production.. NiRD and FeRD. Turnover frequency vs pH - no dependence. Eyring analysis - intramolecular proton transfer as rate determining step. Quant electrochemical simulations. CYS movement pointing outwards to inwards is the largest energy barrier. Single CYS mutants to His at each site in the NiRD. XANES 1S orbital of Ni.. mutants have different electrochemical impacts. Shifts from tetrahedral to square planar geometry - catalysis only in tetrahedral geometry.
February 9, 2025 at 6:24 AM
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#LorneProteins2025 Michael Parker with a chance for Lorne anecdotes! Temp records 45.7 deg C! To 8 deg C 😆 That's Lorne 🤷‍♀️ Conference diversity initiative dating back over a decade. Now entrenched in the program 👏
February 9, 2025 at 5:48 AM
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#LorneProteins2025 Chris Greening - enzymatically driven ATP and electricity generation from air. Organisms that can live on air. Passive diffusion. Trace gas oxidation widespread strategy. Soil bacteria - Important for atmosphere, biodiversity and ecosystems! Amazing work supported by a great team
Man behind podium in a red Hawaiian shirt performing a rhetorical whirl gesture while giving a presentation. Describing mycobacterium smegmatis - take up trace gases to generate protons for energy generation. Oxidises atmospheric CO during carbon starvation express CODH. Ashleigh and David purified them 👏. Huc hydrogenase catalytically efficient; CO dehydrogenase catalytically perfect. Rhys and Hari - cryoEM - Huc selects H2 over O2. HucM membrane associated but not embedded. Menaquinone/menaquinol membrane gradient. Transferred through a hydrophobic tube. Huc evolved from low affinity oxygen sensitive enzymes. Hannah Shafast interpreting the chemistry. Huc-mediated ATP synthesis from air without any by-products. Expanding feed stocks of fuel cells. Stable at 60 deg C! Poison insensitive. Robust power generation on waste feedstocks.
February 9, 2025 at 5:38 AM
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Kicking off #LorneProteins2025 with Olga Boudker putting AV through their paces! Glu transporters 30 Å elevator transport - Bidirectional, dependent on sodium gradient direction. Ancestral gene prediction. Fresh water ancestor Na binding sites lost. Uncoupled transporters connected to aa metabolism.
Picture of a woman in an orange shirt smiling behind a podium.
February 9, 2025 at 5:12 AM
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That's a wrap! With this awesome crew of go getters 🤩 We pulled off such a smooth huge conference! Thanks to all the #bmh2024 speakers, attendees and the never say die organisers. A privilege to work with you all! Let's never attempt this again 🫡
A group of Australian academics standing shoulder to shoulder, celebrating organising the successful Biomolecular Horizons Congress 2024, Melbourne, Victoria.
November 17, 2024 at 9:56 AM
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#bmh2024 Joan of Arc and a metric ton of Bingsu. Landmarks and life lessons. #toomuchbingsu #bingsuOD #BIGbingsu
November 20, 2024 at 3:04 PM
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Happy days international women in STEM. Hope you have a riveting kind of day 🤓💜
November 20, 2024 at 3:04 PM
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Mutationsn- alphafold- doesn't work well yet. Predicting structure from MSA - evolutionary history is key to AF prediction. So mutations aren't freed from this stronger correlation. Average out sequence variation. Protein language models... ESMFold
November 20, 2024 at 3:26 PM
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#lorneproteins Howlett Session last but not least... Mohammed AlQuraishi - OpenFold - can be trained. Fold exclusion experiments: trained on subsets of the pdb? Better performance on a smaller training set relative to AlphaFold.
November 20, 2024 at 3:16 PM
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Simple is deceptive... T maritime pentamer. Pore lining loops. Robust to sequence variation... and on to unpublished data 🤐🫶👏👏
November 20, 2024 at 3:26 PM
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Min proteins force gradient formation, not just organise the ring. Can Mins act on DNA? Added biotin, DNA origami... unrelated factors - Mins can push other stuff on the membrane through "diffusiophoresis" 🤩.
November 20, 2024 at 4:09 PM
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November 20, 2024 at 3:57 PM
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Next... Ruska and TEM. Dubochet and cryoTEM. Blobology. Better detectors, motion correction... atomic structures. Mitochondrial ribosomes? The resolution revolution!
November 20, 2024 at 4:39 PM