iiinova — where your digital self keeps evolving

Amir Bitran @amirbitran.bsky.social · 5h

is there a mistake for the San Francisco/Oakland numbers? It seems strange to me that average rainfall there is less than San Jose

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Amir Bitran @amirbitran.bsky.social · 16/09/2026

Congrats Andrew, very excited for you and looking forward to more great science out of your lab!

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Reposted by Amir Bitran

Stirling Churchman @stirlingchurchman.bsky.social · 28/07/2026

RNA-seq tells us how much RNA is present in the cell. But to understand gene regulation, we need to easily measure the synthesis and decay rates driving this abundance. We introduce AIR-seq: analog intrinsic recoding sequencing. (1/6) www.biorxiv.org/content/10.6...

biorxiv.org

Analog intrinsic recoding measures RNA dynamics without chemical conversion

Steady-state RNA abundance measurements mask the synthesis and decay rates that shape gene expression. Analog intrinsic recoding sequencing (AIR-seq) repurposes the base-pairing properties of N4-hydro...

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Amir Bitran @amirbitran.bsky.social · 05/07/2026

So incredibly grateful to my mentors Susan Marqusee and Carlos Bustamante, my generous funding (shout out to @jcchildsfund.bsky.social), talented undergrads I mentored, the supportive protein folding community, and everybody in my labs for their incredible feedback! Hope to get your thoughts! (12/n)

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Amir Bitran @amirbitran.bsky.social · 05/07/2026

In summary, the ribosome uses diverse strategies to regulate protein folding, dependent not just on folding thermodynamics, but also kinetics + coupling to elongation. In the future, can extend this to study how co-translational folding links to evolutionary fitness and misfolding disease. (11/n)

Nascent chain folding depends on kinetic competition between translation and folding rates.
For details, see discussion in attached manuscript

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Amir Bitran @amirbitran.bsky.social · 05/07/2026

So the non-equilibrium nature of translation elongation is critical to help HaloTag avoid this problematic intermediate and achieve a high folding yield. This points to the need to develop more biophysical approaches that probe folding during active elongation. (10/n)

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Amir Bitran @amirbitran.bsky.social · 05/07/2026

Notably, this minimal co-translational folding isn’t because HaloTag CAN’T fold on the ribosome, but rather it doesn’t have time to! When we artificially stall translation and give the nascent chain time to reach equilibrium, it actually populates an intermediate similar to that in refolding! (9/n)

$Fitted fractional populations associated with natively protected mode for indicated peptides from each RNC construct (opaque markers), and intermediate mode for peptide 37-66 (empty markers) (F) Native protected fraction vs time for the same peptides as in E but now as a function of time during active translation elongation$

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Amir Bitran @amirbitran.bsky.social · 05/07/2026

This is really important since the refolding intermediate upon denaturant dilution is known to aggregate. The ribosome thus introduces a “memory” of sorts that biases the protein to avoid this intermediate and the problematic aggregation. (8/n).

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Amir Bitran @amirbitran.bsky.social · 05/07/2026

But something wildly different happens for HaloTag, which attains higher folding yield when translated vs refolded from denaturant. Turns out HT hardly folds on the ribosome, showing only weak HDX protection But once released, it folds through a different intermediate than when refolded! (7/n)

$(F) Schematic of HaloTag co-and-post translational folding with solid colors highlighting structures spanned by at least one peptide showing at least 50% natively protected fraction at the indicated times, striped colors indicating significant burst phase protection, white indicating no protection, and gray indicating no peptide coverage. (G) Same as (F) now depicting Halo Tag refolding from 7.5M urea.$

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Amir Bitran @amirbitran.bsky.social · 05/07/2026

We see something similar in a TIM barrel, aTS, where an N-terminal region roughly corresponding to a half barrel folds on the ribosome. Co-translational folding of TIM barrels has long been predicted, and we can now see it! Turns out this specific protein also folds similarly off the ribosome (6/n)

Schematic of aTS folding. Solid colors refer to peptides with >10% natively protected population.

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Amir Bitran @amirbitran.bsky.social · 05/07/2026

We can watch nascent proteins fold piece-by-piece! Here is some data for E. coli CMPK. Each line in panel C reflects folded fraction vs time for a specific stretch of residues during + after synthesis. We see a specific subdomain folds during synthesis, while the protein core folds after (5/n).

$(A) Structure of E. coli CMPK (PDB ID 2CMK) with colored HDX-MS reporter peptides, three of which are labeled.(C) Fractional population associated with natively protected mode vs. elongation time for indicated peptides. (D) Schematic of CMPK co-translational folding. Structures spanned by peptides showing >40% natively protected population at the indicated times are colored solid, provided the native mode is ≤60% deuterated, while peptides showing ≥60% fractional population in a partially protected mode (<80% of maximal deuteration, see Materials and Methods) are shown in dashed colors. Peptides satisfying neither condition are shown in white, and gray denotes structures lacking peptide coverage.$

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Amir Bitran @amirbitran.bsky.social · 05/07/2026

To solve this, I developed an approach based on hydrogen deuterium exchange mass spectrometry (HDX-MS) to detect the high-resolution, time-resolved folding of nascent proteins in a synchronized in vitro translation reaction! This entails enriching the “needle” out of the haystack as shown: (4/n)

Summary of experimental design from Fig. 2B. Synchronized translation is achieved by pre-initiating ribosomes on mRNA (step 1) followed by addition of complete amino acid mix and pre-charged tRNA to begin elongation (step 2) coupled to nascent chain biotinylation. At various elongation times, an aliquot is simultaneously pulsed with deuterium to label exposed amides and bound to streptavidin beads (step 3). The HDX reaction is quenched via acidification, which also dissociates ribosomes while nascent chains (NCs) remain bound to beads. (step 4). NCs are digested into peptides via addition of pepsin to the beads (step 5), then analyzed for deuteration via liquid-chromatography mass spectrometry (step 6).

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Amir Bitran @amirbitran.bsky.social · 05/07/2026

But studying this process poses a giant “needle in the haystack” problem since we need to read out the dynamic conformation of a nascent protein amidst a sea of other proteins involved in translation. The kinetic coupling between folding and translation also creates a crazy complex signal. (3/n)

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Amir Bitran @amirbitran.bsky.social · 05/07/2026

Tools like AlphaFold are great for predicting protein structure, but we still hardly understand *HOW* proteins fold so reliably. For many proteins, it’s crucial to begin folding piece-by-piece on the ribosome, which facilitates the structural search and helps avoid misfolding + aggregation. (2/n)

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Amir Bitran @amirbitran.bsky.social · 05/07/2026

I am delighted to share that my newest manuscript and the first of my postdoc in the Marqusee and Bustamante labs, “A detailed molecular picture of protein folding during active translation”, is now on the BioRXiv! (1/n) www.biorxiv.org/content/10.6...

biorxiv.org

A detailed molecular picture of protein folding during active translation

All proteins can begin to fold on the ribosome, and many proteins critically rely on co-translational folding to attain their native conformation. The molecular details underlying this crucial process...

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Amir Bitran @amirbitran.bsky.social · 23/02/2026

Would love to see you at my talk and/or poster at BPS this week!

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Amir Bitran @amirbitran.bsky.social · 09/01/2026

Had a blast at the protein folding GRC, my absolute favorite meeting. It feels like a family reunion, and always rejuvenates my passion for science. Can't wait for 2028!

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Reposted by Amir Bitran

Marqusee Lab @marquseelab.bsky.social · 04/01/2026

The Marqusee lab is at the 2026 protein folding Gordon Research seminar + conference! Amir will be giving a 10 min talk at the GRS today, while Eva will give a 10 min talk at the GRC on Tuesday! Susan will serve as a panelist on today's career panel at the GRS!

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Amir Bitran @amirbitran.bsky.social · 28/12/2025

Thrilled to be giving a talk at the University of Chile tomorrow on my research (in spanish/spanglish)! Feel free to scan the QR code below, or contact me for a link if you're interested in joining!

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Amir Bitran @amirbitran.bsky.social · 26/11/2025

Really excited to be giving a seminar next week at @purduechemistry.bsky.social

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Amir Bitran @amirbitran.bsky.social · 11/11/2025

Thrilled to be part of the Everyday Scientist project run by the awesome JCC fellowship--a community I'm honored to be a part of. Check out this short video on my research and spread the word about how awesome science can be!

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Amir Bitran @amirbitran.bsky.social · 06/09/2025

Many thanks to my wonderful Ph.D. advisor Eugene Shakhnovich for supporting me through this work, to Marina Rodnina and her lab for an inspiring collaboration from which I learned so much, and to my co-first author Siyu Wang for her dedicated and brilliant work on the experiments presented here

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Amir Bitran @amirbitran.bsky.social · 06/09/2025

This study, combining simulation and experiment, generates a unique atomistically-resolved picture of co-translational folding and the pipeline represents a technical advance that may inform future mechanistic folding studies on complex proteins, including those implicated in misfolding disease

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Amir Bitran @amirbitran.bsky.social · 06/09/2025

The co-translational chaperone trigger factor is found to also destabilize this intermediate, consistent with previous findings suggesting this chaperone may prevent premature nasent chain collapse and favor post-translatioanl folding in certain proteins

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Amir Bitran @amirbitran.bsky.social · 06/09/2025

In contrast, mutations to other residues were predicted minimally affect the intermediate while strongly impacting the final native state stability, pointing to a hierarchy of interactions in both states. Remarkably, experiments by the Rodnina lab using PET and FRET validated this exact hierarchy.

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Amir Bitran @amirbitran.bsky.social · 06/09/2025

Interestingly, our simulations predict this non-native intermediate is stabilized by interactions between hydrophobic residues that are solvent exposed in the native state. Thus, our simulations predicted that by mutating these specific residues, the co-trans intermediate would be disrupted

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Amir Bitran @amirbitran.bsky.social · 06/09/2025

To address this, we ran atomistic simulations of small HemK terminal domain, previously shown by the Rodnina lab to adopt a non-native co-translational intermediate. Using DBFOLD, a technique I developed in my PhD, we could predict detailed atomistic structures of this intermediate

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Amir Bitran @amirbitran.bsky.social · 06/09/2025

Many proteins are known to start folding as they are being translated on the ribosome, and this non-eqilibirum process may be critical for ensuring correct folding. Yet it is extremely challenging to gain a detailed atomistic picture of translational folding with any single existing technique

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Amir Bitran @amirbitran.bsky.social · 06/09/2025

Although deep learning tools like AlphaFold have transformed our ability to predict protein structures, we still do not fully understand how these native states are mechanistically attained in vivo, a question with key implications in misfolding disease and improving protein design

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Amir Bitran @amirbitran.bsky.social · 06/09/2025

Really thrilled to share my latest co-first author publication in Science Advances, the culmination of a project from my PhD with Eugene Shakhnovich and a wonderful collaboration with the lab of Marina Rodnina www.science.org/doi/full/10....

science.org

Cotranslational protein folding through non-native structural intermediates

Early folding intermediates form via non-native contacts and are reshaped by chaperones during protein synthesis on the ribosome.

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Reposted by Amir Bitran

Emily J @emexastris.bsky.social · 07/07/2025

Are you from one of these states? Then we need your help to save American science! The Senate Appropriations Committee will be marking up the President's Budget Request for science on Wednesday. People have been saying the proposed cuts "decimated" US science, but that's wrong: they are apocalyptic

A map of the US with the states the republican senators are from marked in red and states the democratic senators are from marked in blue:
Senator Susan Collins (Republican - Maine)
Senator Mitch McConnell(Republican - Kentucky)
Senator Lisa Murkowski(Republican - Alaska)
Senator Lindsey Graham(Republican - South Carolina)
Senator Jerry Moran(Republican - Kansas)
Senator John Hoeven(Republican - North Dakota)
Senator John Boozman(Republican - Arkansas)
Senator Shelley Moore Capito(Republican - West Virginia)
Senator John Kennedy(Republican - Louisiana)
Senator Cindy Hyde-Smith(Republican - Mississippi)
Senator Bill Hagerty(Republican - Tennessee)
Senator Katie Britt(Republican - Alabama)
Senator Markwayne Mullin(Republican - Oklahoma)
Senator Deb Fischer(Republican - Nebraska)
Senator Mike Rounds(Republican - South Dakota)
Patty Murray(Democrat - Washington)
Richard Durbin(Democrat - Illinois)
Jack Reed(Democrat - Rhode Island)
Jeanne Shaheen(Democrat - New Hampshire)
Jeff Merkley(Democrat - Oregon)
Christopher Coons(Democrat - Delaware)
Brian Schatz(Democrat - Hawaii)
Tammy Baldwin(Democrat - Wisconsin)
Chris Murphy(Democrat - Connecticut)
Chris Van Hollen(Democrat - Maryland)
Martin Heinrich(Democrat - New Mexico)
Gary Peters(Democrat - Michigan)
Kirsten Gillibrand(Democrat - New York)
Jon Ossoff(Democrat - Georgia)

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Amir Bitran @amirbitran.bsky.social · 09/06/2025

heard it as a rumble more than I felt it in Berkeley

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Reposted by Amir Bitran

Sam Berry @sberry.bsky.social · 13/05/2025

Lovely article from our colleague Kseniia Petrova, who has been wrongfully imprisoned for months: www.nytimes.com/2025/05/13/o...

nytimes.com

Opinion | The Science I Would Be Doing if I Weren’t in ICE Detention

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Amir Bitran @amirbitran.bsky.social · 08/05/2025

Such an honor to give a talk at the annual @jcchildsfund.bsky.social retreat as a third year (!!) fellow. Thank you to the JCC for the fantastic support and lifelong community

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Amir Bitran @amirbitran.bsky.social · 08/03/2025

At the Stand up for science march, San Francisco

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Reposted by Amir Bitran

Chaya Czernowin @chaya-czernowin.bsky.social · 12/02/2025

Dear all , Here is a call of more than 80 Israeli musicians re the situation in Israel and Palestine. We will be grateful for sharing over social media widley. www.facebook.com/permalink.ph...

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Reposted by Amir Bitran

Mark Peifer (He, him) @peiferlabunc.bsky.social · 08/02/2025

Here's a very important update from the AAMC (Association of American Medical Colleges) on the proposed cuts to NIH Indirect costs: "Every year since 2017, the annual spending bill that funds NIH has included language prohibiting the Administration from making changes to F&A cost rates" 1/2 🧪

Section 224 of Public Law (PL) 118–47 as carried forward by PL 118-158:

SEC. 224. In making Federal financial assistance, the provisions relating to indirect costs in part 75 of title 45, Code of Federal Regulations, including with respect to the approval of deviations from negotiated rates, shall continue to apply to the National Institutes of Health to the same extent and in the same manner as such provisions were applied in the third quarter of fiscal year 2017. None of the funds appropriated in this or prior Acts or otherwise made available to the Department of Health and Human Services or to any department or agency may be used to develop or implement a modified approach to such provisions, or to intentionally or substantially expand the fiscal effect of the approval of such deviations from negotiated rates beyond the proportional effect of such approvals in such quarter.

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Reposted by Amir Bitran

Cooper Battle @chbattle.com · 05/02/2025

Extremely disappointed to see HHMI decide to kill their Inclusive Excellence program, including terminating the current IE3 awards to over a hundred institutions effective this year in the middle of a 6-year grant. I was hoping HHMI (and other private funders) would continue to lead the way.

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