8bwf

From Proteopedia

(Difference between revisions)

Current revision

PTBP1 RRM1 bound to an allosteric inhibitor

Structural highlights

8bwf is a 32 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.9Å
Ligands:	, , , , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

PTBP1_HUMAN Plays a role in pre-mRNA splicing and in the regulation of alternative splicing events. Activates exon skipping of its own pre-mRNA during muscle cell differentiation. Binds to the polypyrimidine tract of introns. May promote RNA looping when bound to two separate polypyrimidine tracts in the same pre-mRNA. May promote the binding of U2 snRNP to pre-mRNA. Cooperates with RAVER1 to modulate switching between mutually exclusive exons during maturation of the TPM1 pre-mRNA. Represses the splicing of MAPT/Tau exon 10.^[1] ^[2] ^[3] ^[4] ^[5]

Publication Abstract from PubMed

The diverse role of the splicing factor PTBP1 in human cells has been widely studied and was found to be a driver for several diseases. PTBP1 binds RNA through its RNA-recognition motifs which lack obvious pockets for inhibition. A unique transient helix has been described to be part of its first RNA-recognition motif and to be important for RNA binding. In this study, we further confirmed the role of this helix and envisioned its dynamic nature as a unique opportunity to develop stapled peptide inhibitors of PTBP1. The peptides were found to be able to inhibit RNA binding via fluorescence polarization assays and directly occupy the helix binding site as observed by protein crystallography. These cell-permeable inhibitors were validated in cellulo to alter the regulation of alternative splicing events regulated by PTBP1. Our study demonstrates transient secondary structures of a protein can be mimicked by stapled peptides to inhibit allosteric mechanisms.

Rationally designed stapled peptides allosterically inhibit PTBP1-RNA-binding.,Schmeing S, Amrahova G, Bigler K, Chang JY, Openy J, Pal S, Posada L, Gasper R, 't Hart P Chem Sci. 2023 Jul 13;14(31):8269-8278. doi: 10.1039/d3sc00985h. eCollection 2023 , Aug 9. PMID:37564416^[6]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Markovtsov V, Nikolic JM, Goldman JA, Turck CW, Chou MY, Black DL. Cooperative assembly of an hnRNP complex induced by a tissue-specific homolog of polypyrimidine tract binding protein. Mol Cell Biol. 2000 Oct;20(20):7463-79. PMID:11003644
↑ Wang J, Gao QS, Wang Y, Lafyatis R, Stamm S, Andreadis A. Tau exon 10, whose missplicing causes frontotemporal dementia, is regulated by an intricate interplay of cis elements and trans factors. J Neurochem. 2004 Mar;88(5):1078-90. PMID:15009664
↑ Lin JC, Tarn WY. Exon selection in alpha-tropomyosin mRNA is regulated by the antagonistic action of RBM4 and PTB. Mol Cell Biol. 2005 Nov;25(22):10111-21. PMID:16260624 doi:http://dx.doi.org/10.1128/MCB.25.22.10111-10121.2005
↑ Lin JC, Tarn WY. RBM4 down-regulates PTB and antagonizes its activity in muscle cell-specific alternative splicing. J Cell Biol. 2011 May 2;193(3):509-20. doi: 10.1083/jcb.201007131. Epub 2011 Apr , 25. PMID:21518792 doi:http://dx.doi.org/10.1083/jcb.201007131
↑ Oberstrass FC, Auweter SD, Erat M, Hargous Y, Henning A, Wenter P, Reymond L, Amir-Ahmady B, Pitsch S, Black DL, Allain FH. Structure of PTB bound to RNA: specific binding and implications for splicing regulation. Science. 2005 Sep 23;309(5743):2054-7. PMID:16179478 doi:http://dx.doi.org/309/5743/2054
↑ Schmeing S, Amrahova G, Bigler K, Chang JY, Openy J, Pal S, Posada L, Gasper R, 't Hart P. Rationally designed stapled peptides allosterically inhibit PTBP1-RNA-binding. Chem Sci. 2023 Jul 13;14(31):8269-8278. PMID:37564416 doi:10.1039/d3sc00985h

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/8bwf"

@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 8bwf is ON HOLD  until Paper Publication
+==PTBP1 RRM1 bound to an allosteric inhibitor==
+<StructureSection load='8bwf' size='340' side='right'caption='[[8bwf]], [[Resolution|resolution]] 2.90&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[8bwf]] is a 32 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8BWF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8BWF FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.9&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2JN:2-METHYL-D-NORLEUCINE'>2JN</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MK8:2-METHYL-L-NORLEUCINE'>MK8</scene>, <scene name='pdbligand=NH2:AMINO+GROUP'>NH2</scene>, <scene name='pdbligand=S9X:2-azanyl-2-butyl-hexanal'>S9X</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=8bwf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8bwf OCA], [https://pdbe.org/8bwf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8bwf RCSB], [https://www.ebi.ac.uk/pdbsum/8bwf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8bwf ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/PTBP1_HUMAN PTBP1_HUMAN] Plays a role in pre-mRNA splicing and in the regulation of alternative splicing events. Activates exon skipping of its own pre-mRNA during muscle cell differentiation. Binds to the polypyrimidine tract of introns. May promote RNA looping when bound to two separate polypyrimidine tracts in the same pre-mRNA. May promote the binding of U2 snRNP to pre-mRNA. Cooperates with RAVER1 to modulate switching between mutually exclusive exons during maturation of the TPM1 pre-mRNA. Represses the splicing of MAPT/Tau exon 10.<ref>PMID:11003644</ref> <ref>PMID:15009664</ref> <ref>PMID:16260624</ref> <ref>PMID:21518792</ref> <ref>PMID:16179478</ref>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The diverse role of the splicing factor PTBP1 in human cells has been widely studied and was found to be a driver for several diseases. PTBP1 binds RNA through its RNA-recognition motifs which lack obvious pockets for inhibition. A unique transient helix has been described to be part of its first RNA-recognition motif and to be important for RNA binding. In this study, we further confirmed the role of this helix and envisioned its dynamic nature as a unique opportunity to develop stapled peptide inhibitors of PTBP1. The peptides were found to be able to inhibit RNA binding via fluorescence polarization assays and directly occupy the helix binding site as observed by protein crystallography. These cell-permeable inhibitors were validated in cellulo to alter the regulation of alternative splicing events regulated by PTBP1. Our study demonstrates transient secondary structures of a protein can be mimicked by stapled peptides to inhibit allosteric mechanisms.
-Authors:
+Rationally designed stapled peptides allosterically inhibit PTBP1-RNA-binding.,Schmeing S, Amrahova G, Bigler K, Chang JY, Openy J, Pal S, Posada L, Gasper R, 't Hart P Chem Sci. 2023 Jul 13;14(31):8269-8278. doi: 10.1039/d3sc00985h. eCollection 2023 , Aug 9. PMID:37564416<ref>PMID:37564416</ref>
-Description:
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
+<div class="pdbe-citations 8bwf" style="background-color:#fffaf0;"></div>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Homo sapiens]]
+[[Category: Large Structures]]
+[[Category: Gasper R]]
+[[Category: Schmeing S]]
+[[Category: Vetter I]]
+[[Category: T Hart P]]

8bwf

From Proteopedia

Current revision

PTBP1 RRM1 bound to an allosteric inhibitor

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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