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Journal:Proteins:3

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<Structure load=''' size='200' frame='true' align='right' caption='Never Born 1856 AF2' scene='96/964832/Morph_backbone/3' />

Revision as of 09:09, 4 May 2023

Contents

Do Newly Born orphan proteins resemble Never Born proteins? A study using three deep learning algorithms

Newly Born proteins, or orphan proteins, have no sequence homology to other proteins and occur in single species or within a taxonomically restricted gene family

Never Born proteins are random polypeptides with amino acid content similar to that of native proteins.

Can recently developed AI/Deep Learning tools for predicting 3D protein structures like:

  • AlphaFold2 (AF2)
  • RoseTTAFold (RTF)
  • Evolutionary Scale Modeling (ESM-2)

be useful to see if Newly Born proteins are similar to Never Born proteins?

Sequences of Never Born proteins by Tretyachenko et al.[1] showed experimentally that some folded into compact structures [Fig. 1], while others belong to the category of intrinsically disordered proteins (IDPs)[2] [Fig. 2].


Never Born 1856 AF2

Drag the structure with the mouse to rotate








extra stuff: < and > signs. You may include any references to papers as in: the use of JSmol in Proteopedia [3] or to the article describing Jmol [4] to the rescue.

Function

Disease

Relevance

Structural highlights

sample

This is a sample scene created with SAT to by Group, and another to make of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.

References

  1. ↑ Tretyachenko V, Vymětal J, Bednárová L, Kopecký V Jr, Hofbauerová K, Jindrová H, Hubálek M, Souček R, Konvalinka J, Vondrášek J, Hlouchová K. Random protein sequences can form defined secondary structures and are well-tolerated in vivo. Sci Rep. 2017 Nov 13;7(1):15449. PMID:29133927 doi:10.1038/s41598-017-15635-8
  2. ↑ Dunker AK, Silman I, Uversky VN, Sussman JL. Function and structure of inherently disordered proteins. Curr Opin Struct Biol. 2008 Dec;18(6):756-64. Epub 2008 Nov 17. PMID:18952168 doi:10.1016/j.sbi.2008.10.002
  3. ↑ Hanson, R. M., Prilusky, J., Renjian, Z., Nakane, T. and Sussman, J. L. (2013), JSmol and the Next-Generation Web-Based Representation of 3D Molecular Structure as Applied to Proteopedia. Isr. J. Chem., 53:207-216. doi:http://dx.doi.org/10.1002/ijch.201300024
  4. ↑ Herraez A. Biomolecules in the computer: Jmol to the rescue. Biochem Mol Biol Educ. 2006 Jul;34(4):255-61. doi: 10.1002/bmb.2006.494034042644. PMID:21638687 doi:10.1002/bmb.2006.494034042644

Proteopedia Page Contributors and Editors (what is this?)

Joel L. Sussman, Jaime Prilusky

This page complements a publication in scientific journals and is one of the Proteopedia's Interactive 3D Complement pages. For aditional details please see I3DC.
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