Drug discovery; chemistry; Biophysics; Membrane proteins; #cryoEM; crystallography; #MicroED; Opinions my own. 👋👋👋
Los Angeles, CA
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#cryoEM with energy filter & electron counting significantly increased resolution even for a full size protein like proteinase K. Sub-atomic resolution #MicroED rivals best reported Xray of Proteinase K but by using crystals a billionth the size. A section of the map is shown
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#cryoEM #MicroED with electron counting. Protein structure at 0.8A resolution. Ab initio phasing for two proteins facilitated by electron counting on a falcon 4 direct electron detector. A section of the map is shown below
biorxiv.org/content/10.1101/…
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Sometimes you meet PIs who seem friendly but their students tell a completely different story. Talk to the students and postdocs. If the PI doesnt want you to - something is off so run to the hills. Always ask lab members about lab culture and environment. Best advice I ever got
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"Determined" and "solved" are words reserved for experiments, not to predictions. They predicted structures. But predictions shouldn't be taken as facts. Too many fields of science suffered and still do by wrong predictions and computer simulations science.org/content/article/…
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Reviewers of our paper asked for experiments that exist in the literature. So we referred to 4(!) pubs with said experiments. Rejected. Reviewer 1 says they dont believe the published literature. What happened science? When did it turn to a belief rather than data driven system?
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Did you ever present a seminar to non scientists? You typically lose 80% of the audience by using the word "protein"
Good luck
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Nanocrystals of femtogram amounts of organic materials, one billionth the size of crystals used for X-ray, led to atomic-resolution structures by MicroED. "Powder to structure" could be the next big thing in chemical synthesis. dx.doi.org/10.26434/chemrxiv… #microed #CryoEM #UCLA #HHMI
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Reviewers - please refrain from asking for extensive additional experiments. Its hard to get anything done now so asking for more experiments = giving the kiss of death. Instead consider contacting the authors to discuss results as colleagues to reach an accord & accept the ms
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👋👋 Home run week for graduate student Cody Gillman. The structure of the neurotoxin palytoxin determined by #MicroED. long awaited for, over 30 years of effort with no luck by xray. #MicroED structure identified binding mode to the Na+/K+ ATPase. biorxiv.org/content/10.1101/…
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Scientific journals should stay out of politics. Stop assuming everyone is the same. You are just alienating people which is exactly what you preach not to do.
I am a scientist with a research paper scheduled for publication in Nature this week. I have no disappointment, much less alarm, at the vote. Nature's news desk should interview a broader set of scientists. Or better yet, Nature's news desk should focus on science, not politics.
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Excited to share the latest #MicroED #CryoEM study - collaboration w @francesarnold lab to determine the novel structure of a directed evolution enzyme. @EmmaDanelius started the reaction on the crystals and captured the metal carbene reactive intermediate biorxiv.org/content/10.1101/…
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Structure of a novel enzyme used everyday In laboratories around the world. It doesnt express well so structure by Xray was not possible. However, tiny amounts of material gave nanocrystals and #MicroED delivered a structure using a single nanocrystal
biorxiv.org/content/10.1101/…
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Ive been working with membrane proteins for more then 20 years and I can state the following without blinking an eye:
Membrane proteins are egocentric with a complex narcissistic personality.
I challange anyone to disagree - but please provide evidence.
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Everyone boasting structure in 2 days; structure in 30min (which we are guilty of also). But, people, whats the rush? Stop and smell the roses. Enjoy the process. Learn cryoem. Learn crystallography. Dont just learn to press a button. Theres too much to miss by rushing. Have fun.
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We dont have enough structures of membrane proteins. The majority remain unknown and AI often fails when it comes to these samples. They are truly tough and challenging to work with
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The most significant result is the ability to determine high resolution structures of important membrane proteins with an almost complete membrane bilayer around the protein. #MicroED Human Adenosine A2a receptor with lipids in yellow. Cholesterol purple. biorxiv.org/content/10.1101/…
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If you want to join someones lab just ask. Send an email. Whats the worst thing that can happen?
This applies for any level - undergrad, grad, post, specialist, tech - just reach out and see what happens.
Good things take effort and some initiative
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I am excited to share with you this new #MicroED study which will undoubtedly change the way GPCR structures are determined. Many congratulations to @ScienceMick and our collaborators Vadim Cherezov & @NannengaLab
biorxiv.org/content/10.1101/…
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Happy to report that this study is now published #openaccess
nature.com/articles/s41592-0…
#cryoEM #MicroED with electron counting. Protein structure at 0.8A resolution. Ab initio phasing for two proteins facilitated by electron counting on a falcon 4 direct electron detector. A section of the map is shown below
biorxiv.org/content/10.1101/…
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Comparing cryoem with xray crystallography is a waste of time. The information content is different. One delivers information on dynamics and charge while the other delivers an electron density. Both have an important place in structural biology
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Happy to report close to 400 distinct hydrogen atoms in sub atomic MicroED structure of lysozyme.
Study by @maxclabbers @ScienceMick and twitterless Johan Hattne
biorxiv.org/content/10.1101/…
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I worry that we will only have virtual conferences in the future. So much is lost in a virtual meeting. Some of the most important contacts, ideas, scientific discussions are made over a beer or at dinner and not at the session per se. this is completely lost in a virtual format
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For 40 billion dollars he could have bought at least two titan krioses and why is no one talking about that??
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Happy to share this study which is finally published. Links to original Biorxiv and the final paper below. Work that started years ago while at Janelia looking at how lipids flip. Lipids traverse and rotate easily but flipping usually require ATP. But not with this transporter..
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It is my pleasure to present a project that started 3 decades ago; my PhD project which is only now complete, and only required a brand new field to be invented, a group of heroes and some incredible biochemistry to crack this Diva:
biorxiv.org/content/10.1101/…
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Biorxiv preprints have a doi. It is a public record and should thus be referenced if relevant. As long as you dont - you send the message that only peer review, as toxic as it is, behind closed doors, is acceptable and referenceable. Not good enough. You need to change!
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Biochemistry in a nutshell:
1. n=CV=m/M
2. +/- 10% will still work
3. Life is unpredictable - dont approach it with complicated physics and mathematical explanations
4. Equipment to master will range from 2c plastic to multi-million dollar machines
5. Enjoy your time
6. Publish
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I am honored and humbled to recieve the inaugural #MicroED innovation award. It is incredible to see how this method gained and continues to gain momentum and the field is growing in big part thanks to the amazing lab members and our collaborators
At #acamtg2023, we presented the first ever @thermofisher #MicroED Innovation Award to Dr. Tamir Gonen - @gonenlab.
This award recognizes outstanding contributions in this impactful field, which broadens the reach of #cryoEM.
Congrats, Dr. Gonen!
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electron microscopes do not give an electron density map. its a charge density or simply density. Either way "electron density" is simply wrong.
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Skyler: "Walt, what should we do with all of this money?"
Walter: "How much is there? Is it enough to cover microscope time?"
#cryoem
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Things we used to do in #CryoEM that are now considered novelty or outrageous.
I decided to jot down some not-so-distant memories of routine things in cryoEM. Feel free to add as I cant remember everything. Many details are missing. If you know - you know
A thread/list
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It always surprises me how many structural biologists and biochemists do not know the names, symbols and chemical structures and properties for all amino acids 😳
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MicroED Imaging Center
We are delighted to announce that the National Institutes of Health is helping us establish a Biotechnology Development Research Center focused on MicroED at UCLA School of Medicine, named MicroED Imaging Center (MEDIC).
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Protein folding and structure prediction are very different. Its kinda like a road trip: The latter describes the destination while the former describes the route to the destination.
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Very excited to share with you the 0.5A resolution structure if hexagonal ice lh determined by #MicroED. Hydrogens identified as well as polar bonds and proton wires. An atomic reason for differences in snowflakes is discussed. doi.org/10.26434/chemrxiv.82….
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I dont understand why people feel they need to justify why they stay or leave academia. Who cares? Do whats best for you and let the rest do what is best for them. Why always feel you need to explain or justify and expect academics to get annoyed? Its your life and your decision
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#MicroED used to determine the absolute configuration of a natural product. We are very excited about this paper and the implications for natural product chemistry. Great collaboration @gonenlab and van der Donk lab. science.sciencemag.org/conte…
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the keystone symposia in cryoem which is virtual is charging a registration fee of $275. This is uncalled for, too high and disgusting. I would not pay a single dollar for a virtual conference and I am sorry that colleagues in #cryoem are going along with it and did not protest
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For the #cryoem folks that like to think crystallography is dead, here is a quote from Pawel Penczek "we (in @joachimfrank lab) realized many years ago that the best samples were coming from crystallographers"
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If you cant resolve individual atoms you dont have an atomic structure 🙄 why is that so difficult to grasp? So many people just say atomic this atomic that then proceed to discuss a 4A map ... not cool
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"I'm pleased to inform you that your manuscript has been accepted for publication without change."
Im speechless 🥹
That like never happens....
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If you are a PI and require your lab personnel to continue with experiments and to continue coming to the lab - in my opinion - you should not be in science because you are acting irresponsibly and arrogantly. Shame on you for ever.
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I want to turn into one of those folks that sleep through an entire talk then wake up to ask the most potent thoughtful deep question 🧐
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Suspended drop crystallization. No support film eliminates preferential orientation on grids and no handling of sample prior to #MicroED
biorxiv.org/content/10.1101/…
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On left: 0.1" screws. Electronic store 10c each
On right: #cryoem accessory screws. Specialist seller $10,000 each back ordered 4 months.
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We should define "affordable" better. A burger is affordable. A $1M microscope is not. Unless we have a cryoTEM for less than 500k it is still difficult to fund
The people want a cryoTEM with FEG and a DED camera for <500k.
☝️ that - would be impactful
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Happy to report the #MicroED structure of meclizine. First generation anti histamine used to treat vertigo and motion sickness (marketed as Bonine) been used for over 70 years without a known structure nor mechanism of action or how it binds to the histamine H1 receptor
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It is great to see the #MicroED field growing and gaining momentum. I am aware of 5 new PIs that were hired this year. I am proud to say that 4 of those talented individuals were postdocs from our lab & they are now off to start their own groups. So proud of their achievements 😁
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Folks,
1. Distance yourself from toxic negative people. Cut them out of your life.
2. Surround yourself with people that want the best for you. That add positively to your life and career.
3. Trust your gut
4. Only you know whats best for you. Know who are your friends.
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We are excited to share our latest breakthrough in #MicroED: the first example of Experimental phasing of MicroED data using a combination of heavy metal and radiation damage biorxiv.org/content/10.1101/…
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Please RT:
MicroED Course for 2020 registration is now open. Virtual and free
Sample preparation methodologies
Data collection EPU-D
Cameras
FIB-milling procedures for MicroED
Data analysis
registration site:
cryoem.ucla.edu/course-2020
#cryoEM #crystallography #MicroED
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I cant stand supplementary material. Why cant everything be together as one paper especially now that everything is virtual and no one should be constrained by printed page numbers
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Folks please remember, when looking for a lab to join, always talk with current *and* past trainees. Joining a lab that nurtures and supports trainees is more important than where they publish.
I cant stress that enough. Join a lab that will help guide you in your career
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It took all morning but today I decided to make nutella stuffed yeast raised hannuka donuts because why not
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This preprint demonstrates the use of a low end electron microscope and a cheap CCD for #MicroED. Structures of Several small molecules determined at atomic resolution. #Cryoem #crystallography #CHEMISTRY. Every chemistry department should do #MicroED. TG biorxiv.org/content/10.1101/…
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The impact of your work matters. Not the impact factor of the journal you publish in. Please note the difference
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Isn't it funny how we now just expect atomic resolution each time we begin a project? Just a few years ago we were happy to just purify our proteins and have a nice looking gel
Science expectations are now overinflated
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