User:Eric Martz/Sandbox 3
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| - | == | + | ==Notes on mini- and microproteins== |
| - | + | ===Micro=== | |
| - | + | *2018: Microproteins are "translated from protein-coding small open reading frames (smORFs, less than 100–150 codons in length)." "to reduce false positives... most genome annotation pipelines required ORFs to be at least 300 nucleotides long (i.e. 100 amino acids) resulting in most smORFs being missed." <ref>PMID: 30415582</ref> | |
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| - | + | *2015: "MicroProteins (miPs) are short, usually single-domain proteins that, in analogy to miRNAs, heterodimerize with their targets and exert a dominant-negative effect." They "disrupt the formation of homodimeric, heterodimeric, or multimeric complexes". "The term ‘microProtein’ was coined due to their small size and negative regulatory similarity to miRNAs" <ref>PMID: 26115780</ref> | |
| - | Below are non-interactive mockups just to suggest the look for a user interface. | ||
| - | *Links do not work. | ||
| - | *The color key image should be centered (I could not get it centered in the mockup). | ||
| - | *[✓] represents a checkbox. When checked, it will color the chain by conservation, and spacefill it. When unchecked, that chain will become a gray backbone trace. | ||
| - | *The link to ''Explanation'' would go to a Proteopedia page of explanation. It might be a revised version of [[Conservation, Evolutionary]]. | ||
| + | *2011 review <ref>PMID: 21151039</ref> | ||
| - | + | ===Mini=== | |
| - | + | *2017: Miniproteins are "polypeptide chains <40 amino acids in length that adopt defined and stable 3D structures". They are often designed, or screened from designed libraries. <ref>PMID: 28832117</ref> | |
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| - | < | + | *2017: De novo designed: <ref>PMID: 28953867</ref> |
| - | < | + | *2015: Viruses have hydrophobic, membrane-spanning miniproteins. <ref>PMID: 26057606</ref> <ref>PMID: 24742054</ref> |
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| - | < | + | *2011: Cysteine knot miniproteins are a subset of miniproteins that can be natural or engineered. <ref>PMID: 22204431</ref> |
| - | + | ==In Proteopedia== | |
| - | + | *There are about 60 entries found with a search for "miniprotein" (but no such category). | |
| - | + | *[[:Category:Microprotein]] has 3 entries, and [[:Category:Hybrid microprotein]] has 1. | |
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| - | <tr><td style="background-color:#bac9f7;color:#040d44;vertical-align:top;text-align:left;" | ||
| - | > <b>Show Conservation for Chain(s):</b> | ||
| - | </td><td align="left" style="background-color:#ace3ac;border-top:2px solid #dddddd; border-right:2px solid #dddddd" width="230"> Rows = identical sequences:<br> | ||
| - | [✓]A [✓]B<br> [✓]C [✓]D | ||
| - | </td></tr> | ||
| - | + | ==References== | |
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Current revision
Contents |
Notes on mini- and microproteins
Micro
- 2018: Microproteins are "translated from protein-coding small open reading frames (smORFs, less than 100–150 codons in length)." "to reduce false positives... most genome annotation pipelines required ORFs to be at least 300 nucleotides long (i.e. 100 amino acids) resulting in most smORFs being missed." [1]
- 2015: "MicroProteins (miPs) are short, usually single-domain proteins that, in analogy to miRNAs, heterodimerize with their targets and exert a dominant-negative effect." They "disrupt the formation of homodimeric, heterodimeric, or multimeric complexes". "The term ‘microProtein’ was coined due to their small size and negative regulatory similarity to miRNAs" [2]
- 2011 review [3]
Mini
- 2017: Miniproteins are "polypeptide chains <40 amino acids in length that adopt defined and stable 3D structures". They are often designed, or screened from designed libraries. [4]
- 2017: De novo designed: [5]
- 2011: Cysteine knot miniproteins are a subset of miniproteins that can be natural or engineered. [8]
In Proteopedia
- There are about 60 entries found with a search for "miniprotein" (but no such category).
- Category:Microprotein has 3 entries, and Category:Hybrid microprotein has 1.
References
- ↑ Rathore A, Martinez TF, Chu Q, Saghatelian A. Small, but mighty? Searching for human microproteins and their potential for understanding health and disease. Expert Rev Proteomics. 2018 Dec;15(12):963-965. doi:, 10.1080/14789450.2018.1547194. Epub 2018 Nov 15. PMID:30415582 doi:http://dx.doi.org/10.1080/14789450.2018.1547194
- ↑ Eguen T, Straub D, Graeff M, Wenkel S. MicroProteins: small size-big impact. Trends Plant Sci. 2015 Aug;20(8):477-82. doi: 10.1016/j.tplants.2015.05.011. Epub, 2015 Jun 23. PMID:26115780 doi:http://dx.doi.org/10.1016/j.tplants.2015.05.011
- ↑ Staudt AC, Wenkel S. Regulation of protein function by 'microProteins'. EMBO Rep. 2011 Jan;12(1):35-42. doi: 10.1038/embor.2010.196. Epub 2010 Dec 10. PMID:21151039 doi:http://dx.doi.org/10.1038/embor.2010.196
- ↑ Baker EG, Bartlett GJ, Porter Goff KL, Woolfson DN. Miniprotein Design: Past, Present, and Prospects. Acc Chem Res. 2017 Sep 19;50(9):2085-2092. doi: 10.1021/acs.accounts.7b00186., Epub 2017 Aug 23. PMID:28832117 doi:http://dx.doi.org/10.1021/acs.accounts.7b00186
- ↑ Chevalier A, Silva DA, Rocklin GJ, Hicks DR, Vergara R, Murapa P, Bernard SM, Zhang L, Lam KH, Yao G, Bahl CD, Miyashita SI, Goreshnik I, Fuller JT, Koday MT, Jenkins CM, Colvin T, Carter L, Bohn A, Bryan CM, Fernandez-Velasco DA, Stewart L, Dong M, Huang X, Jin R, Wilson IA, Fuller DH, Baker D. Massively parallel de novo protein design for targeted therapeutics. Nature. 2017 Oct 5;550(7674):74-79. doi: 10.1038/nature23912. Epub 2017 Sep 27. PMID:28953867 doi:http://dx.doi.org/10.1038/nature23912
- ↑ Opella SJ. Relating structure and function of viral membrane-spanning miniproteins. Curr Opin Virol. 2015 Jun;12:121-5. doi: 10.1016/j.coviro.2015.05.006. Epub 2015 , Jun 6. PMID:26057606 doi:http://dx.doi.org/10.1016/j.coviro.2015.05.006
- ↑ DiMaio D. Viral miniproteins. Annu Rev Microbiol. 2014;68:21-43. doi: 10.1146/annurev-micro-091313-103727. Epub, 2014 Apr 10. PMID:24742054 doi:http://dx.doi.org/10.1146/annurev-micro-091313-103727
- ↑ Kolmar H. Natural and engineered cystine knot miniproteins for diagnostic and therapeutic applications. Curr Pharm Des. 2011 Dec;17(38):4329-36. PMID:22204431
