Amir Bitran

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

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

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

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.

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

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

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

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

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.

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....

Hi, this link is broken fyi

congrats Julia!!

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)

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

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

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

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

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

At the Stand up for science march, San Francisco

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...

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.

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 🧪

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.