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A protein folding mystery solved: Study explains core packing fractions

phys.org

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Re: A protein folding mystery solved: Study explains core packing fractions

#11

Post by timewizard »

ChuckMcM wrote: post #2

This is the kind of cool stuff I'm going to miss during the coming dark ages. When ever I read this in a paper: "The authors acknowledge support from NIH Training Grant No. T32GM145452 (A.T.G., C.S.O., and Z.L.), NIH Training Grant No. T15LM007056-37 (J.A.L.), and the High Performance Computing facilities operated by Yale's Center for Research Computing." All of these things (the NIH and Yale's Center for Research Co…

> relied so heavily

One grant started in 1987 and has extensions running into 2027 for dozens of different sub-projects. Total award so far has been $13.1m. The other grant is for up to $800k over 5 years for 5 student positions ostensibly worth $32k per year. The YCRC seems to be funded directly by Yale.

https://www.highergov.com/grant/T32GM145452/

https://www.highergov.com/grant/T15LM007056/

> sing ideologically pure songs for dear Leader.

Hot take; however, perhaps the energy put into this ideological signalling could be better spent on working to solve what is a relatively small problem.

Re: A protein folding mystery solved: Study explains core packing fractions

#12

Post by thaumasiotes »

therein wrote: post #8
refactor_master wrote: post #5

Earlier quoted context omitted.

No sources cited?

It comes across borderline comical when a man gets asked for his sources while he is clearly stating his formed opinion based on his impressions. It is hard to think of an example without sounding like I am exaggerating. Imagine if you shared on a thread that Rust has a great ecosystem but it is a little bit too overhyped and someone so cleverly asked for you to cite sources. Do you really rely on academic studies to…

There was a thread on HN semi-recently where I observed that if you think about classifying complexities ("big-O of n squared") by polynomial degree (so we think of O(n^2) as "2"), the logarithm function gives you a literally infinitesimal value.

I was then asked about sources for what amounts to an easy homework problem.

Re: A protein folding mystery solved: Study explains core packing fractions

#13

Post by hengheng »

try_the_bass wrote: post #7
ChuckMcM wrote: post #2

This is the kind of cool stuff I'm going to miss during the coming dark ages. When ever I read this in a paper: "The authors acknowledge support from NIH Training Grant No. T32GM145452 (A.T.G., C.S.O., and Z.L.), NIH Training Grant No. T15LM007056-37 (J.A.L.), and the High Performance Computing facilities operated by Yale's Center for Research Computing." All of these things (the NIH and Yale's Center for Research Co…

> This is the kind of cool stuff I'm going to miss during the coming dark ages. I really don't get this level of hyperbole. There's so much hand-wringing about funding getting cut, but it turns out it's like a 15% reduction[0]. That's not an insignificant amount, but it's not the end of the world. Taken naively, that's 15% less research that gets done. One can hope that, being a pillar of academia, the intelligent fo…

In any other industry, a 15% cut would be Bad News, and people would be talking about ripple effects, they would call it a "shock" and talk about the long-term consequences.

Re: A protein folding mystery solved: Study explains core packing fractions

#14

Post by jibal »

timr wrote: post #9
ChuckMcM wrote: post #2

This is the kind of cool stuff I'm going to miss during the coming dark ages. When ever I read this in a paper: "The authors acknowledge support from NIH Training Grant No. T32GM145452 (A.T.G., C.S.O., and Z.L.), NIH Training Grant No. T15LM007056-37 (J.A.L.), and the High Performance Computing facilities operated by Yale's Center for Research Computing." All of these things (the NIH and Yale's Center for Research Co…

> "The authors acknowledge support from NIH Training Grant No. T32GM145452 (A.T.G., C.S.O., and Z.L.), NIH Training Grant No. T15LM007056-37 (J.A.L.), and the High Performance Computing facilities operated by Yale's Center for Research Computing." Well, NIH training grants aren't going anywhere, so far as I know, and the high-performance computing facilities may or may not be affected by a cut in indirects. If they a…

Lots of things are possible while clearly not true, and that's one of them.

Re: A protein folding mystery solved: Study explains core packing fractions

#15

Post by [deleted] »

ChuckMcM wrote: post #2

This is the kind of cool stuff I'm going to miss during the coming dark ages. When ever I read this in a paper: "The authors acknowledge support from NIH Training Grant No. T32GM145452 (A.T.G., C.S.O., and Z.L.), NIH Training Grant No. T15LM007056-37 (J.A.L.), and the High Performance Computing facilities operated by Yale's Center for Research Computing." All of these things (the NIH and Yale's Center for Research Co…

[deleted]

Re: A protein folding mystery solved: Study explains core packing fractions

#16

Post by gilleain »

The 'explanation' in the article is a little thin:

Why is the packing fraction 55% maximum (in globular proteins)? "The answer seems to be that the packing fraction stops increasing when the protein cores jam or rigidify." Ok, so ...

> "That is, the individual amino acids that make up the protein core couldn't compress any further when the protein folded"

So they can't pack any further because they 'jam'? Ohhh, from the abstract of the paper:

> "... However, important developments in the physics of jamming in particulate systems can shed light on the packing of protein cores. ... Then, we develop an all-atom model for proteins and find that, above ∼0.55, protein cores undergo a jamming-like transition"

Possibly this is related to the need for protein cores to remain relatively 'liquid', as enzymes (for example) need to be somewhat flexible when binding/releasing substrates. A fully 'jammed'/packed core would lead to an inflexible structure with lower ability to ... er... move, bind stuff (I'm handwaving here :) )

Re: A protein folding mystery solved: Study explains core packing fractions

#17

Post by agoose77 »

try_the_bass wrote: post #7
ChuckMcM wrote: post #2

This is the kind of cool stuff I'm going to miss during the coming dark ages. When ever I read this in a paper: "The authors acknowledge support from NIH Training Grant No. T32GM145452 (A.T.G., C.S.O., and Z.L.), NIH Training Grant No. T15LM007056-37 (J.A.L.), and the High Performance Computing facilities operated by Yale's Center for Research Computing." All of these things (the NIH and Yale's Center for Research Co…

> This is the kind of cool stuff I'm going to miss during the coming dark ages. I really don't get this level of hyperbole. There's so much hand-wringing about funding getting cut, but it turns out it's like a 15% reduction[0]. That's not an insignificant amount, but it's not the end of the world. Taken naively, that's 15% less research that gets done. One can hope that, being a pillar of academia, the intelligent fo…

I want to be careful about what I write given the context of what's going on, and the personal ramifications that can have.

Suffice to say, it's worth considering whether the cost of a decision can be interpreted solely as how much money there is vs the wider ecosystem level consequences of said decision.

Re: A protein folding mystery solved: Study explains core packing fractions

#18

Post by dbspin »

try_the_bass wrote: post #7
ChuckMcM wrote: post #2

This is the kind of cool stuff I'm going to miss during the coming dark ages. When ever I read this in a paper: "The authors acknowledge support from NIH Training Grant No. T32GM145452 (A.T.G., C.S.O., and Z.L.), NIH Training Grant No. T15LM007056-37 (J.A.L.), and the High Performance Computing facilities operated by Yale's Center for Research Computing." All of these things (the NIH and Yale's Center for Research Co…

> This is the kind of cool stuff I'm going to miss during the coming dark ages. I really don't get this level of hyperbole. There's so much hand-wringing about funding getting cut, but it turns out it's like a 15% reduction[0]. That's not an insignificant amount, but it's not the end of the world. Taken naively, that's 15% less research that gets done. One can hope that, being a pillar of academia, the intelligent fo…

The fraud issues you mention are real and pressing... They're also completely disconnected from blanket cuts to NIH funding. There seems to be some kind of grasping for a positive in heavy cuts to essential research here. Put another way, there is zero selective pressure for 'less fraudulent' research to be cut. If anything, this applies selective pressure on publish or perish, false positive, press release style research. Harsh cuts in funding always penalise blue sky research, controversial work and anything that isn't guaranteed to bring press to the funding institution.

> Run a few plagiarism/LLM checks, fire/expel the worst offenders, and you've already saved a significant fraction of the newfound deficit!

This is absurdly reductive, and doesn't connect with the genuine issues at play incentivising good research and detecting fraud.

Re: A protein folding mystery solved: Study explains core packing fractions

#20

Post by pfdietz »

"In living organisms, every protein—a type of biological polymer consisting of hundreds of amino acids—carries out specific functions, such as catalysis, molecule transport, or DNA repair. To perform these functions, they must fold up into specific shapes."

This is not true. There are some proteins that are intrinsically disordered, not folding into any preferred way, but they still perform biological functions.

https://en.wikipedia.org/wiki/Intrinsically_disordered_prote...

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