Sandbox Reserved 1849

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Line 44: Line 44:
===Function===
===Function===
-
The effect of the minibinders’ higher affinity to the spike protein RBD is that ACE2’s binding site is now sterically blocked, meaning that it can’t bind to the spike protein and initiate the infection pathway. This effectively hinders the effects of the virus, which was the goal of creating these minibinders.
+
The effect of the minibinders’ higher affinity to the spike protein RBD is that ACE2’s binding site is now sterically blocked, meaning that it can’t bind to the spike protein and initiate the infection pathway. This effectively hinders the effects of the virus, which was the goal of creating these minibinders<ref name="Longxing">PMID:32907861</ref>.
==Design==
==Design==

Revision as of 05:29, 15 April 2025

This Sandbox is Reserved from March 18 through September 1, 2025 for use in the course CH462 Biochemistry II taught by R. Jeremy Johnson and Mark Macbeth at the Butler University, Indianapolis, USA. This reservation includes Sandbox Reserved 1828 through Sandbox Reserved 1846.
To get started:
  • Click the edit this page tab at the top. Save the page after each step, then edit it again.
  • show the Scene authoring tools, create a molecular scene, and save it. Copy the green link into the page.
  • Add a description of your scene. Use the buttons above the wikitext box for bold, italics, links, headlines, etc.

More help: Help:Editing

SARS-COV2 Minibinders

LCB1 (PDB:7JZU) | An example of a novel minibinder, LCB1 (Blue), bound to the spike RBD of SARS-COV-2 (Off-White)

Drag the structure with the mouse to rotate

Color Key

-> ACE2

-> Spike RBD

-> AHB2

-> LCB1

-> LCB3

References

[1] [2] [3] [4] [6] [5] [7] [8] [9]

  1. 1.00 1.01 1.02 1.03 1.04 1.05 1.06 1.07 1.08 1.09 1.10 1.11 1.12 1.13 1.14 1.15 1.16 1.17 1.18 1.19 1.20 1.21 Cao L, Goreshnik I, Coventry B, Case JB, Miller L, Kozodoy L, Chen RE, Carter L, Walls AC, Park YJ, Strauch EM, Stewart L, Diamond MS, Veesler D, Baker D. De novo design of picomolar SARS-CoV-2 miniprotein inhibitors. Science. 2020 Oct 23;370(6515):426-431. PMID:32907861 doi:10.1126/science.abd9909
  2. 2.0 2.1 2.2 2.3 2.4 Case JB, Chen RE, Cao L, Ying B, Winkler ES, Johnson M, Goreshnik I, Pham MN, Shrihari S, Kafai NM, Bailey AL, Xie X, Shi PY, Ravichandran R, Carter L, Stewart L, Baker D, Diamond MS. Ultrapotent miniproteins targeting the SARS-CoV-2 receptor-binding domain protect against infection and disease. Cell Host Microbe. 2021 Jul 14;29(7):1151-1161.e5. PMID:34192518 doi:10.1016/j.chom.2021.06.008
  3. 3.0 3.1 Sang P, Chen YQ, Liu MT, Wang YT, Yue T, Li Y, Yin YR, Yang LQ. Electrostatic Interactions Are the Primary Determinant of the Binding Affinity of SARS-CoV-2 Spike RBD to ACE2: A Computational Case Study of Omicron Variants. Int J Mol Sci. 2022 Nov 26;23(23):14796. PMID:36499120 doi:10.3390/ijms232314796
  4. 4.00 4.01 4.02 4.03 4.04 4.05 4.06 4.07 4.08 4.09 4.10 4.11 4.12 Huang Y, Yang C, Xu XF, Xu W, Liu SW. Structural and functional properties of SARS-CoV-2 spike protein: potential antivirus drug development for COVID-19. Acta Pharmacol Sin. 2020 Sep;41(9):1141-1149. doi: 10.1038/s41401-020-0485-4., Epub 2020 Aug 3. PMID:32747721 doi:http://dx.doi.org/10.1038/s41401-020-0485-4
  5. 5.0 5.1 5.2 5.3 Zhang J, Xiao T, Cai Y, Chen B. Structure of SARS-CoV-2 spike protein. Curr Opin Virol. 2021 Oct;50:173-182. PMID:34534731 doi:10.1016/j.coviro.2021.08.010
  6. 6.0 6.1 6.2 Yuan Y, Cao D, Zhang Y, Ma J, Qi J, Wang Q, Lu G, Wu Y, Yan J, Shi Y, Zhang X, Gao GF. Cryo-EM structures of MERS-CoV and SARS-CoV spike glycoproteins reveal the dynamic receptor binding domains. Nat Commun. 2017 Apr 10;8:15092. doi: 10.1038/ncomms15092. PMID:28393837 doi:http://dx.doi.org/10.1038/ncomms15092
  7. 7.0 7.1 7.2 Kuba K, Yamaguchi T, Penninger JM. Angiotensin-Converting Enzyme 2 (ACE2) in the Pathogenesis of ARDS in COVID-19. Front Immunol. 2021 Dec 22;12:732690. PMID:35003058 doi:10.3389/fimmu.2021.732690
  8. 8.0 8.1 Kuba K, Imai Y, Rao S, Gao H, Guo F, Guan B, Huan Y, Yang P, Zhang Y, Deng W, Bao L, Zhang B, Liu G, Wang Z, Chappell M, Liu Y, Zheng D, Leibbrandt A, Wada T, Slutsky AS, Liu D, Qin C, Jiang C, Penninger JM. A crucial role of angiotensin converting enzyme 2 (ACE2) in SARS coronavirus-induced lung injury. Nat Med. 2005 Aug;11(8):875-9. PMID:16007097 doi:10.1038/nm1267
  9. 9.0 9.1 Valetti F, Gilardi G. Improvement of biocatalysts for industrial and environmental purposes by saturation mutagenesis. Biomolecules. 2013 Oct 8;3(4):778-811. PMID:24970191 doi:10.3390/biom3040778
Personal tools