Intrinsically Disordered Proteins

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7 What about the stability of Intrinsically Disordered Proteins (IDP)?
By Francesco Secundo · National Research Council

Jeffrey Brender · University of Michigan

I interpreted the question as asking if IDPs remain active in extreme conditions. This is a different question then if it can recover its structure af... [more]

I interpreted the question as asking if IDPs remain active in extreme conditions. This is a different question then if it can recover its structure after denaturing conditions. I think this is an interesting question but it is difficult to measure experimentally as the binding partner of the IDP will generally not be stable in most extreme cases. For denaturants such as urea this is almost certainly the case. But for organic solvents and IDP binding partners who have very stable alpha helical structures it may not be. Has anyone ever took an IDP that binds to a stable alpha-helical partner, put it in 30 % trifluoroethanol (or equivalent), and: 1. Shown that IDP binding is either retained or lost when the IDP becomes folded 2. Showed that unlike the IDP itself, the IDP binding partner retains a similar conformation under these conditions?

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25 A reflection on intrinsically disordered proteins
By Giovanni Colonna · Second University of Naples

Artem Badasyan · University of Nova Gorica

To Richard: I meant, that physics normally answers to the question "why", and explains the grounds, while pure biology gives the answer to "how" and s... [more]

To Richard: I meant, that physics normally answers to the question "why", and explains the grounds, while pure biology gives the answer to "how" and shows what happens with nice figures and snapshots, that illustrate how do the things happen, without explaining. To some scientists such an opinion may sound rude :-) The most of papers I have read on disordered proteins (for instance, Tompa P et al paper) were describing such proteins in terms of their biological function, evolutionary mechanisms that made such proteins important, etc, not attempting to explain or at least to formulate the problem in polymer physics way. It is interesting and informative, but doesn't anyhow answer "why". Richard said: "I think that many here (including myself) would agree with you and have been saying just that - the globular/disordered distinction is useful in some situations, not in others." --- My suggestion is to check if there is any difference in basic polymeric characteristics between what is called "globular" and "disordered" protein, before going further. Do (quasi)phase diagrams differ, for example? And I do not argue against anyone's opinion, presented above, I am trying to complement the opinions by my own, personal view on state-of-the-art in the field. I appreciate your comments, Thank you!

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Open Proximal radial distribution functions
Have you ever applied proximal radial distribution functions on intrinsically disordered proteins?

Have you ever applied proximal radial distribution functions on intrinsically disordered proteins?

By Orkid Coskuner · University of Texas at San Antonio

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7 Large-size disordered protein molecular dynamics simulations without parallel tempering
By Orkid Coskuner · University of Texas at San Antonio

Orkid Coskuner · University of Texas at San Antonio

It is quite unrealistic to be certain about reaching equilibrium structures when it comes to disordered large-size proteins that do not have a stable ... [more]

It is quite unrealistic to be certain about reaching equilibrium structures when it comes to disordered large-size proteins that do not have a stable structure. I agree with Francesco and I also agree with Anurag, who apparently experienced this issue in practice. Most recently, we developed a new method with Olivia that determines the secondary structure conversion free energy changes at the atomic level with dynamics. We are looking for structural variables that relate with free energy and I think clustering methods fail currently regarding large size IDPs. Also, potential energy is not related and then again it would matter how you calculate the free energy in general, i.e., harmonic or quasi-harmonic etc. We are working on this problem and we will share our outcomes here with you all. Thank you for your time and the nice discussion we have had here.

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15 Reliable intrinsic disordered protein databases?
By Ankush Sharma · Second University of Naples

Tomas Di Domenico · University of Padua

Hi David! Thanks for the positive comments. Your suggestion is actually very interesting. We have some updates in the works that have to do with expe... [more]

Hi David! Thanks for the positive comments. Your suggestion is actually very interesting. We have some updates in the works that have to do with experimental conditions for both the reference sequences and also for the annotating sequences, in our path to try to understand the true nature of different disorder phenomena. I've looked at your paper: it's indeed quite interesting. I'll give it a good read and then maybe we can discuss it further. Cheers!

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About Intrinsically Disordered Proteins

Intrinsically unstructured proteins, often referred to as naturally unfolded proteins or disordered proteins, are proteins characterized by lack of stable tertiary structure when the protein exists as an isolated polypeptide chain (a subunit) under physiological conditions in vitro.

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Yanhui Xu

Fudan University
Alexei S Soares

Brookhaven National Laboratory
Arnaud Ducruix

Université René Descartes - Paris 5
Luca Federici

Università degli Studi G. d'Annunzio Chieti e Pescara
Agnes Toth-Petroczy

Weizmann Institute of Science
Zimei Bu

City College of New York
Andrew Pati

University of California, Los Angeles
Min Woo Sung

Texas A&M University
Fritz karl Winkler

Paul Scherrer Institut
Bjørn Dalhus

University of Oslo

Intrinsically Disordered Proteins

About Intrinsically Disordered Proteins

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