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@paulschanda.bsky.social

Passionate for integrated structural biology, including NMR and many more. Particularly interested in protein dynamics, and therefore chaperones, enzymes and mitochondrial protein import. Fortunate to lead a great research team at IST Austria.

999 Followers  |  135 Following  |  79 Posts  |  Joined: 07.11.2024  |  1.9525

Latest posts by paulschanda.bsky.social on Bluesky

I encourage you to at least comment on pubpeer.com. These comments will be seen by the community. (I have a plugin on my browser that shows me pubpeer comments, as soon as I am on a web page of a paper that has comments on pubpeer). If they are really bad, best contact the journal.

08.08.2025 04:47 β€” πŸ‘ 0    πŸ” 0    πŸ’¬ 0    πŸ“Œ 0

Do you mean that the stats in the SI are not real? How can they be better than the PDB stats?

07.08.2025 18:05 β€” πŸ‘ 0    πŸ” 0    πŸ’¬ 1    πŸ“Œ 0

I'm deeply saddened by the situation in Gaza.

Over the last 15 years I have frequently worked as reviewer for Israeli research institutions and funding agencies (for free; common in academia).

In light of the situation I refuse to do that work in the future, until very strong changes happen.

06.08.2025 14:40 β€” πŸ‘ 0    πŸ” 0    πŸ’¬ 0    πŸ“Œ 0

What was the artefact we overcame? Artefactual decay (eg. of 15N) coherence due to dipolar couplings to 1H spins. Even in deuterated sparsely protonated samples.
The solution? 1H decoupling, carefully choosing its amplitude.
Bonus we get a "local 1H spectrum" at each 15N site - from 15N relaxation!

06.08.2025 11:01 β€” πŸ‘ 1    πŸ” 0    πŸ’¬ 0    πŸ“Œ 0

We identify and overcome an overlooked artefact in such measurements that hampered proper quantitative analysis.
Moreover, we show that sample deuteration - which so far was believed to be essential for such experiments - is not needed. Even for protonated samples one gets clean information
2/n

06.08.2025 10:57 β€” πŸ‘ 1    πŸ” 0    πŸ’¬ 0    πŸ“Œ 0
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Bumps on the Road: The Way to Clean Relaxation Dispersion Magic-Angle Spinning NMR Microsecond-to-millisecond motions are instrumental for many biomolecular functions, including enzymatic activity and ligand binding. Bloch-McConnell Relaxation Dispersion (BMRD) Nuclear Magnetic Resonance (NMR) spectroscopy is a key technique for studying these dynamic processes. While BMRD experiments are routinely used to probe protein motions in solution, the experiment is more demanding in the solid state, where dipolar couplings complicate the spin dynamics. It is believed that high deuteration levels are required and sufficient to obtain accurate and quantitative data. Here we show that even under fast magic-angle spinning and high levels of deuteration artifactual β€œbumps” in 15N R1ρ BMRD profiles are common. The origin of these artifacts is identified as a second-order three-spin Mixed Rotational and Rotary Resonance (MIRROR) recoupling condition. These artifacts are found to be a significant confounding factor for the accurate quantification of microsecond protein dynamics using BMRD in the solid state. We show that the application of low-power continuous wave (CW) decoupling simultaneously with the 15N spin-lock leads to the suppression of these conditions and enables quantitative measurements of microsecond exchange in the solid state. Remarkably, the application of decoupling allows the measurement of accurate BMRD even in fully protonated proteins at 100 kHz MAS, thus extending the scope of ΞΌs dynamics measurements in MAS NMR.

Our latest publication in @jacs.acspublications.org is out: pubs.acs.org/doi/10.1021/...
We show clean ways to probe dynamics on microsecond time scales by relaxation-dispersion MAS #NMR. Microsecond motions are often essential for function e.g. in enzymes.
1/n

06.08.2025 10:53 β€” πŸ‘ 10    πŸ” 3    πŸ’¬ 2    πŸ“Œ 0

In the open review process at @group-ampere.bsky.social 's Magnetic Resonance journal, the Discussion about an analysis of the carbon footprint of NMR conferences is still open for a few days.
mr.copernicus.org/preprints/mr...
Feel free to leave a comment there!

20.07.2025 10:02 β€” πŸ‘ 3    πŸ” 5    πŸ’¬ 0    πŸ“Œ 0
Arginine Dynamics Probed by Magic-Angle Spinning Nmr with a Specific Isotope-Labeling Scheme The specific introduction of 1H-13C or 1H-15N moieties into otherwise deuterated proteins holds great potential for high-resolution solution and magic-angle spi

πŸ“’New preprint
We developed an isotope-labeling scheme which allows probing arginine side chain motion in proteins w solution/MAS #NMR. The method is readily applicable to large proteins (here: a 130 kDa enzyme). @istaresearch.bsky.social & Lichtenecker @univie.ac.at
papers.ssrn.com/sol3/papers....

09.07.2025 14:42 β€” πŸ‘ 8    πŸ” 3    πŸ’¬ 0    πŸ“Œ 0
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Academics say flying to meetings harms the climate β€” but they carry on A survey at one of the biggest UK research universities finds that staff often end up flying to meetings despite a preference to avoid air travel.

www.nature.com/articles/d41...

07.07.2025 04:11 β€” πŸ‘ 1    πŸ” 0    πŸ’¬ 0    πŸ“Œ 0
Preview
Quantifying the carbon footprint of conference travel: the case of NMR meetings Abstract. Conference travel contributes to the climate footprint of academic research. Here, we provide a quantitative estimate of the carbon emissions associated with conference attendance by analyzi...

I'm glad we got our preprint about conference-travel CO2 emissions out in @group-ampere.bsky.social‬ ’s journal before #EUROMAR2025 started. Maybe it sparks interesting in-person discussions about future conference modi/places? Feel free to contribute your thoughts: mr.copernicus.org/preprints/mr...

07.07.2025 03:45 β€” πŸ‘ 9    πŸ” 4    πŸ’¬ 1    πŸ“Œ 0

Congrats to all prize recipients. Much deserved!

07.07.2025 03:36 β€” πŸ‘ 3    πŸ” 0    πŸ’¬ 0    πŸ“Œ 0

ENC at the East Coast would have saved CO2, too.

ISMRM had a more broad distribution.
But I guess a more central location (eg Germany, France) would avoid a few thousand tons of CO2. Honolulu isn't the center of mass. Nor is Cape Town.
Future generations may find our conference tourism weird.

03.07.2025 12:35 β€” πŸ‘ 2    πŸ” 0    πŸ’¬ 0    πŸ“Œ 0

I am happy to share python code that calls carbontracer and returns CO2 estimates, so you can test various scenarios.

Not sure this rough estimate helps, but: ENC (close to San Francisco, 31% Europeans, 61% NAmerican, 7% Asian, 1% NZ+AU) had an average footprint of 2.7 tons (~2x less than ISMRM).

03.07.2025 12:32 β€” πŸ‘ 2    πŸ” 0    πŸ’¬ 1    πŸ“Œ 0
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Interesting talk at ISMRM 2025 Hawaii about sustainable MRI equipment?

Some thoughts about the choice of location: people traveled 100 million km to get there, emitting 28000 tons of CO2.
Worth considering for a future conference (that may again include a sustainability talk) @ismrm.bsky.social

03.07.2025 10:20 β€” πŸ‘ 2    πŸ” 0    πŸ’¬ 0    πŸ“Œ 0
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I have estimated the carbon emissions of the ISMRM conference 2024 in Honolulu.

Attending the conference emits about 4.9 tons/person on average. The location is far from the center-of-mass of the participants. Is this location really a good idea? Is it worth the damage?

@ismrm.bsky.social

03.07.2025 10:11 β€” πŸ‘ 4    πŸ” 1    πŸ’¬ 2    πŸ“Œ 0

Sorry, and yes, I've seen that.

02.07.2025 21:30 β€” πŸ‘ 1    πŸ” 0    πŸ’¬ 0    πŸ“Œ 0

Interesting. I had found that paper -- which claimed that the conformation was codon-dependent -- intriguing and counter-intuitive. Thought-provoking, one may say. Seems like you have clarified this question.

02.07.2025 20:54 β€” πŸ‘ 1    πŸ” 0    πŸ’¬ 1    πŸ“Œ 0

By any chance, do you have a list of cities of affiliation? That's generally the most tedious part to do.

02.07.2025 20:35 β€” πŸ‘ 1    πŸ” 0    πŸ’¬ 2    πŸ“Œ 0

Great idea ;-)
If you have a participant list, I can calculate the carbon footprint of the Honolulu MRI meeting. Probably it would set a new record in our list, probably >4 tons/person on average. (The round-trip from Europe is ~6 tons.)

It is quite absurd to bring the entire community there.

02.07.2025 04:35 β€” πŸ‘ 2    πŸ” 0    πŸ’¬ 1    πŸ“Œ 0
Preview
Quantifying the carbon footprint of conference travel: the case of NMR meetings Abstract. Conference travel contributes to the climate footprint of academic research. Here, we provide a quantitative estimate of the carbon emissions associated with conference attendance by analyzi...

I really like the open community reviewing process at MR, the journal of @group-ampere.bsky.social
Having community comments and reviews online and open for discussion is a nice way of doing open constructive reviews
Our latest one, on a broad topic awaits comments
mr.copernicus.org/preprints/mr...

01.07.2025 17:41 β€” πŸ‘ 2    πŸ” 2    πŸ’¬ 0    πŸ“Œ 1
Distribution of participants' location. The vast majority of participants comes from Germany, UK, France and Switzerland (i.e. rather far from Oulu). But there are also a >60 participants from Finland, so having the conference there is certainly great for the location NMR community.

Distribution of participants' location. The vast majority of participants comes from Germany, UK, France and Switzerland (i.e. rather far from Oulu). But there are also a >60 participants from Finland, so having the conference there is certainly great for the location NMR community.

Estimated emissions for travel to NMR conferences (out-and-back). Note that they are likely underestimated because we assumed direct flights from the participant's home affiliation to the conference. Adding a stop-over would add ca. 100 kg CO2.

Estimated emissions for travel to NMR conferences (out-and-back). Note that they are likely underestimated because we assumed direct flights from the participant's home affiliation to the conference. Adding a stop-over would add ca. 100 kg CO2.

Follow-up on our number-crunching of the CO2 footprint of #nmr conferences. The EUROMAR 2025, happening in lovely Northern Finland (Oulu) emits ~1.8 tons CO2 per person, ~2-fold higher than previous EUROMARs (around 1 ton). The choice of location matters.
It will surely be a great meeting. Enjoy.

29.06.2025 19:06 β€” πŸ‘ 1    πŸ” 1    πŸ’¬ 0    πŸ“Œ 0

This study has been part of a course that I had the chance to teach, together with two colleagues, and a great group of students. @istaresearch.bsky.social
Topic: Understanding the connection of energy and climate change. Great to work with this team!

(I got inspired by theshiftproject.org)

28.06.2025 11:22 β€” πŸ‘ 1    πŸ” 0    πŸ’¬ 0    πŸ“Œ 0
MR - Home

The journal at which our preprint is posted (Magnetic Resonance - www.magnetic-resonance-ampere.net), has a nice interactive open review system. Comment our analysis (and many other #nmr papers). www.magnetic-resonance-ampere.net/peer_review/...

27.06.2025 19:08 β€” πŸ‘ 1    πŸ” 0    πŸ’¬ 0    πŸ“Œ 0
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How much CO2 is emitted, on average, when travelling to a conference? Here are the numbers, using the attendee lists of major #nmr conferences over the last ten years.

27.06.2025 19:05 β€” πŸ‘ 0    πŸ” 0    πŸ’¬ 0    πŸ“Œ 0
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What if we reduced the carbon footprint of conferences by hundreds of tons of CO2 -- simply by choosing the locations more smartly? Here are our estimates/predictions for EUROMAR (#nmr) conferences.

27.06.2025 19:02 β€” πŸ‘ 2    πŸ” 0    πŸ’¬ 0    πŸ“Œ 0
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Is train travel really emitting less CO2? After all, doesn't the construction and maintenance of the train infrastructure require a lot of energy & hence produce a lot of emissions? Here are our estimates -- including infrastructure emissions. Clearly: prefer trains over flights. (Details -> paper)

27.06.2025 18:59 β€” πŸ‘ 0    πŸ” 0    πŸ’¬ 0    πŸ“Œ 0
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How much is the CO2 footprint of conference travel as compared to other research activities? This graph shows our estimates (single conference visit on the left, year-long research activity on the right (details in the paper).

27.06.2025 18:56 β€” πŸ‘ 1    πŸ” 1    πŸ’¬ 0    πŸ“Œ 0
Preview
Quantifying the carbon footprint of conference travel: the case of NMR meetings Abstract. Conference travel contributes to the climate footprint of academic research. Here, we provide a quantitative estimate of the carbon emissions associated with conference attendance by analyzi...

Train travel can drastically cut carbon emissions. Our results highlight concrete ways institutions and individuals can reduce their footprintβ€”without giving up collaboration.

Want the numbers? Details? Caveats? Read and comment on our preprint here:
πŸ‘‰ mr.copernicus.org/preprints/mr...
7/n

27.06.2025 18:04 β€” πŸ‘ 3    πŸ” 0    πŸ’¬ 0    πŸ“Œ 1

We examined strategies to reduce this impact:
– more thoughtful venue selection
– decentralized meetings
– switching from planes to trains (in doing so, we explicitly considered infrastructure emissions too, to get reliable numbers)
6/n

27.06.2025 18:03 β€” πŸ‘ 0    πŸ” 0    πŸ’¬ 0    πŸ“Œ 0

We also compared conference travel to other research activities. At our institute, business travel makes up ~20% of the total research footprint. It's far from negligible. 5/n

27.06.2025 18:02 β€” πŸ‘ 0    πŸ” 0    πŸ’¬ 0    πŸ“Œ 0

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