8t5f

From Proteopedia

(Difference between revisions)

Revision as of 10:27, 10 January 2024

De novo design of high-affinity protein binders to bioactive helical peptides

Structural highlights

8t5f is a 3 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 1.99Å
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Disease

PTHY_HUMAN Defects in PTH are a cause of familial isolated hypoparathyroidism (FIH) [MIM:146200; also called autosomal dominant hypoparathyroidism or autosomal dominant hypocalcemia. FIH is characterized by hypocalcemia and hyperphosphatemia due to inadequate secretion of parathyroid hormone. Symptoms are seizures, tetany and cramps. FIH exist both as autosomal dominant and recessive forms of hypoparathyroidism.^[1] ^[2] ^[3]

Function

PTHY_HUMAN PTH elevates calcium level by dissolving the salts in bone and preventing their renal excretion. Stimulates [1-14C]-2-deoxy-D-glucose (2DG) transport and glycogen synthesis in osteoblastic cells.^[4]

Publication Abstract from PubMed

Many peptide hormones form an alpha-helix upon binding their receptors(1-4), and sensitive detection methods for them could contribute to better clinical management of disease(5). De novo protein design can now generate binders with high affinity and specificity to structured proteins(6,7). However, the design of interactions between proteins and short peptides with helical propensity is an unmet challenge. Here, we describe parametric generation and deep learning-based methods for designing proteins to address this challenge. We show that by extending RFdiffusion(8) to enable binder design to flexible targets, and to refining input structure models by successive noising and denoising (partial diffusion), picomolar affinity binders can be generated to helical peptide targets both by refining designs generated with other methods, or completely de novo starting from random noise distributions. To our knowledge these are the highest affinity designed binding proteins against any protein or small molecule target generated directly by computation without any experimental optimisation. The RFdiffusion designs enable the enrichment and subsequent detection of parathyroid hormone and glucagon by mass spectrometry, and the construction of bioluminescence-based protein biosensors. The ability to design binders to conformationally variable targets, and to optimise by partial diffusion both natural and designed proteins, should be broadly useful.

De novo design of high-affinity binders of bioactive helical peptides.,Torres SV, Leung PJY, Venkatesh P, Lutz ID, Hink F, Huynh HH, Becker J, Yeh AH, Juergens D, Bennett NR, Hoofnagle AN, Huang E, MacCoss MJ, Exposit M, Lee GR, Bera AK, Kang A, De La Cruz J, Levine PM, Li X, Lamb M, Gerben SR, Murray A, Heine P, Korkmaz EN, Nivala J, Stewart L, Watson JL, Rogers JM, Baker D Nature. 2023 Dec 18. doi: 10.1038/s41586-023-06953-1. PMID:38109936^[5]

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

References

↑ Arnold A, Horst SA, Gardella TJ, Baba H, Levine MA, Kronenberg HM. Mutation of the signal peptide-encoding region of the preproparathyroid hormone gene in familial isolated hypoparathyroidism. J Clin Invest. 1990 Oct;86(4):1084-7. PMID:2212001 doi:http://dx.doi.org/10.1172/JCI114811
↑ Sunthornthepvarakul T, Churesigaew S, Ngowngarmratana S. A novel mutation of the signal peptide of the preproparathyroid hormone gene associated with autosomal recessive familial isolated hypoparathyroidism. J Clin Endocrinol Metab. 1999 Oct;84(10):3792-6. PMID:10523031
↑ Datta R, Waheed A, Shah GN, Sly WS. Signal sequence mutation in autosomal dominant form of hypoparathyroidism induces apoptosis that is corrected by a chemical chaperone. Proc Natl Acad Sci U S A. 2007 Dec 11;104(50):19989-94. Epub 2007 Dec 3. PMID:18056632 doi:10.1073/pnas.0708725104
↑ Zoidis E, Ghirlanda-Keller C, Schmid C. Stimulation of glucose transport in osteoblastic cells by parathyroid hormone and insulin-like growth factor I. Mol Cell Biochem. 2011 Feb;348(1-2):33-42. doi: 10.1007/s11010-010-0634-z. Epub, 2010 Nov 13. PMID:21076856 doi:10.1007/s11010-010-0634-z
↑ Torres SV, Leung PJY, Venkatesh P, Lutz ID, Hink F, Huynh HH, Becker J, Yeh AH, Juergens D, Bennett NR, Hoofnagle AN, Huang E, MacCoss MJ, Expòsit M, Lee GR, Bera AK, Kang A, De La Cruz J, Levine PM, Li X, Lamb M, Gerben SR, Murray A, Heine P, Korkmaz EN, Nivala J, Stewart L, Watson JL, Rogers JM, Baker D. De novo design of high-affinity binders of bioactive helical peptides. Nature. 2023 Dec 18. PMID:38109936 doi:10.1038/s41586-023-06953-1

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/8t5f"

@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 8t5f is ON HOLD  until Paper Publication
+==De novo design of high-affinity protein binders to bioactive helical peptides==
+<StructureSection load='8t5f' size='340' side='right'caption='[[8t5f]], [[Resolution|resolution]] 1.99&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[8t5f]] is a 3 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=8T5F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8T5F 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]] 1.99&#8491;</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=8t5f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8t5f OCA], [https://pdbe.org/8t5f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8t5f RCSB], [https://www.ebi.ac.uk/pdbsum/8t5f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8t5f ProSAT]</span></td></tr>
+</table>
+== Disease ==
+[https://www.uniprot.org/uniprot/PTHY_HUMAN PTHY_HUMAN] Defects in PTH are a cause of familial isolated hypoparathyroidism (FIH) [MIM:[https://omim.org/entry/146200 146200]; also called autosomal dominant hypoparathyroidism or autosomal dominant hypocalcemia. FIH is characterized by hypocalcemia and hyperphosphatemia due to inadequate secretion of parathyroid hormone. Symptoms are seizures, tetany and cramps. FIH exist both as autosomal dominant and recessive forms of hypoparathyroidism.<ref>PMID:2212001</ref> <ref>PMID:10523031</ref> <ref>PMID:18056632</ref>
+== Function ==
+[https://www.uniprot.org/uniprot/PTHY_HUMAN PTHY_HUMAN] PTH elevates calcium level by dissolving the salts in bone and preventing their renal excretion. Stimulates [1-14C]-2-deoxy-D-glucose (2DG) transport and glycogen synthesis in osteoblastic cells.<ref>PMID:21076856</ref>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Many peptide hormones form an alpha-helix upon binding their receptors(1-4), and sensitive detection methods for them could contribute to better clinical management of disease(5). De novo protein design can now generate binders with high affinity and specificity to structured proteins(6,7). However, the design of interactions between proteins and short peptides with helical propensity is an unmet challenge. Here, we describe parametric generation and deep learning-based methods for designing proteins to address this challenge. We show that by extending RFdiffusion(8) to enable binder design to flexible targets, and to refining input structure models by successive noising and denoising (partial diffusion), picomolar affinity binders can be generated to helical peptide targets both by refining designs generated with other methods, or completely de novo starting from random noise distributions. To our knowledge these are the highest affinity designed binding proteins against any protein or small molecule target generated directly by computation without any experimental optimisation. The RFdiffusion designs enable the enrichment and subsequent detection of parathyroid hormone and glucagon by mass spectrometry, and the construction of bioluminescence-based protein biosensors. The ability to design binders to conformationally variable targets, and to optimise by partial diffusion both natural and designed proteins, should be broadly useful.
-Authors:
+De novo design of high-affinity binders of bioactive helical peptides.,Torres SV, Leung PJY, Venkatesh P, Lutz ID, Hink F, Huynh HH, Becker J, Yeh AH, Juergens D, Bennett NR, Hoofnagle AN, Huang E, MacCoss MJ, Exposit M, Lee GR, Bera AK, Kang A, De La Cruz J, Levine PM, Li X, Lamb M, Gerben SR, Murray A, Heine P, Korkmaz EN, Nivala J, Stewart L, Watson JL, Rogers JM, Baker D Nature. 2023 Dec 18. doi: 10.1038/s41586-023-06953-1. PMID:38109936<ref>PMID:38109936</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 8t5f" style="background-color:#fffaf0;"></div>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Homo sapiens]]
+[[Category: Large Structures]]
+[[Category: Baker D]]
+[[Category: Bera AK]]
+[[Category: Kang A]]
+[[Category: Leung PJY]]
+[[Category: Torres SV]]

8t5f

From Proteopedia

Revision as of 10:27, 10 January 2024

De novo design of high-affinity protein binders to bioactive helical peptides

Structural highlights

Disease

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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