The Construction of a Molecular Model for the Ternary Protein Complex of Intrinsic Coagulation Pathway Factors Provides Novel Insights for the Pathogenesis of Cross-Reactive Material Positive Coagulation Factor Mutations.

Publisher: MDPI Country of Publication: Switzerland NLM ID: 101092791 Publication Model: Electronic Cited Medium: Internet ISSN: 1422-0067 (Electronic) Linking ISSN: 14220067 NLM ISO Abbreviation: Int J Mol Sci Subsets: MEDLINE

Original Publication: Basel, Switzerland : MDPI, [2000-

Mutation* ; Factor VIIIa*/chemistry ; Factor VIIIa*/genetics ; Factor VIIIa*/metabolism ; Factor IXa*/chemistry ; Factor IXa*/genetics ; Factor IXa*/metabolism ; Blood Coagulation Factors*/genetics ; Blood Coagulation Factors*/chemistry ; Blood Coagulation Factors*/metabolism; Humans ; Molecular Dynamics Simulation ; Blood Coagulation ; Protein Binding ; Factor X/chemistry ; Factor X/genetics ; Factor X/metabolism ; Models, Molecular

The human coagulation pathway orchestrates a complex series of events vital for maintaining vascular integrity, in which the intrinsic pathway plays a pivotal role in amplifying and propagating the coagulation response. Dysregulation of this pathway can lead to various bleeding disorders and thrombotic complications, posing significant health risks. In this pathway, the activation of Factor (F) X zymogen is catalyzed by the FVIIIa-FIXa binary complex, but knowledge about this is still incomplete. Understanding the structural and functional intricacies of the FVIIIa-FIXa-FX (zymogen) complex is imperative for unraveling the molecular mechanisms underlying coagulation regulation and guiding the development of targeted therapeutic interventions. In this study, utilizing Alphafold-Multimer and molecular dynamics (MD) simulations, we provide insights into factor interactions within the ternary complex and propose novel functional mechanisms contributing to the functional defects inflicted by their cross-reactive material (CRM) positive mutations. The amino acid residue replacement impairs the coagulation function by interfering with structure elements, including the following: (1) a knot-like structure between Arg-562 of FVIIIa's 558-Loop (residue 555-571) and the 333-Loop of FIXa (residue 333-346) contributes to FVIIIa-FIXa binding; (2) the a2 region of FVIIIa (residue 716-740) opens the lid of active site (FIXa's 266-Loop, residue 256-270) and facilitates substrate binding; (3) the activation peptide (AP) of FX zymogen (residue 143-194) not only assists in the activation of itself but also adheres the interface of the three factors like a double-sided tape. Our work provides novel insights for the pathogenesis of a number of reported clinical CRM-positive mutations and may lay the groundwork for the structure-based development of therapeutic interventions.

Hematol Oncol Clin North Am. 2021 Dec;35(6):1131-1142. (PMID: 34535289)
J Mol Biol. 2022 Sep 15;434(17):167626. (PMID: 35595166)
Nature. 2021 Aug;596(7873):583-589. (PMID: 34265844)
J Chem Theory Comput. 2012 May 8;8(5):1542-1555. (PMID: 22582031)
J Biol Chem. 1994 Aug 12;269(32):20522-7. (PMID: 8051150)
J Biol Chem. 1996 Jan 26;271(4):1935-40. (PMID: 8567641)
J Biol Chem. 1999 Oct 15;274(42):29826-30. (PMID: 10514461)
Haematologica. 2005 May;90(5):707-10. (PMID: 15921397)
Virology. 2022 Aug;573:96-110. (PMID: 35738174)
Protein Sci. 2018 Jan;27(1):293-315. (PMID: 29067766)
Blood Res. 2014 Jun;49(2):85-94. (PMID: 25025009)
Nucleic Acids Res. 2019 Jan 8;47(D1):D520-D528. (PMID: 30357364)
Antibodies (Basel). 2024 May 02;13(2):. (PMID: 38804304)
J Biol Chem. 2009 Feb 6;284(6):3379-88. (PMID: 19047063)
Nat Struct Biol. 2003 Dec;10(12):980. (PMID: 14634627)
J Med Chem. 2015 Aug 13;58(15):6225-36. (PMID: 26151189)
J Comput Chem. 2005 Dec;26(16):1668-88. (PMID: 16200636)
J Clin Med. 2020 Aug 01;9(8):. (PMID: 32752154)
Biochim Biophys Acta Gen Subj. 2023 Aug;1867(8):130381. (PMID: 37207906)
Front Med (Lausanne). 2018 Oct 02;5:281. (PMID: 30333979)
J Thromb Haemost. 2010 Feb;8(2):286-93. (PMID: 19874476)
J Thromb Haemost. 2023 May;21(5):1164-1176. (PMID: 36787808)
Blood. 2021 Oct 7;138(14):1258-1268. (PMID: 34077951)
Blood. 2020 Dec 3;136(23):2703-2714. (PMID: 32678887)
J Chem Phys. 2004 May 22;120(20):9665-78. (PMID: 15267980)
J Thromb Haemost. 2003 Apr;1(4):773-81. (PMID: 12871415)
Curr Opin Struct Biol. 2023 Dec;83:102709. (PMID: 37778185)
N Engl J Med. 2009 Oct 22;361(17):1671-5. (PMID: 19846852)
Thromb Haemost. 2011 Nov;106(5):893-900. (PMID: 21947241)
J Biol Chem. 1998 Jul 24;273(30):19049-54. (PMID: 9668086)
J Chem Theory Comput. 2015 Aug 11;11(8):3696-713. (PMID: 26574453)
Biochem Biophys Res Commun. 2014 Sep 26;452(3):408-14. (PMID: 25157807)
Biophys J. 2002 Mar;82(3):1190-206. (PMID: 11867437)
Zhonghua Xue Ye Xue Za Zhi. 1997 Sep;18(9):464-7. (PMID: 15625837)
Int J Mol Sci. 2023 Jun 30;24(13):. (PMID: 37446083)
Bioorg Med Chem Lett. 2015 Nov 1;25(21):4945-4949. (PMID: 25978966)
Haematologica. 2020 Feb 20;106(1):264-268. (PMID: 32079698)
J Med Chem. 2023 Apr 27;66(8):5332-5363. (PMID: 37037122)
Acta Biochim Pol. 2016;63(1):11-16. (PMID: 26824291)
Blood. 2008 Feb 1;111(3):1240-7. (PMID: 17965321)
Chem Sci. 2023 Jan 10;14(6):1443-1452. (PMID: 36794205)
Nat Rev Cardiol. 2019 Mar;16(3):166-179. (PMID: 30429532)
Thromb Haemost. 2013 Jul;110(1):53-61. (PMID: 23677006)
Hematol Oncol Clin North Am. 2022 Aug;36(4):797-812. (PMID: 35773055)
Nature. 2024 Jun;630(8016):493-500. (PMID: 38718835)
J Chem Theory Comput. 2013 Jul 9;9(7):3084-95. (PMID: 26583988)
J Biol Chem. 2001 May 11;276(19):16302-9. (PMID: 11278963)
Mol Genet Genomic Med. 2013 Nov;1(4):238-45. (PMID: 24498619)
J Biol Chem. 1998 May 15;273(20):12089-94. (PMID: 9575152)
Bioorg Med Chem Lett. 2015 Apr 1;25(7):1635-42. (PMID: 25728130)
J Biol Chem. 2020 Nov 6;295(45):15198-15207. (PMID: 32859749)
J Med Chem. 2022 Aug 11;65(15):10419-10440. (PMID: 35862732)
Blood Adv. 2021 Mar 9;5(5):1324-1332. (PMID: 33656538)
J Biol Chem. 1981 Apr 10;256(7):3433-42. (PMID: 6782101)
J Biol Chem. 1997 Jan 24;272(4):2082-8. (PMID: 8999906)
Blood Adv. 2022 Jun 14;6(11):3240-3254. (PMID: 35255502)
Hematol Oncol Clin North Am. 2021 Dec;35(6):1143-1155. (PMID: 34607716)
N Engl J Med. 2016 May 26;374(21):2044-53. (PMID: 27223146)
Chemistry. 2012 Jan 2;18(1):213-22. (PMID: 22162109)
J Biol Chem. 2013 May 24;288(21):15057-64. (PMID: 23580639)
FEBS Lett. 2022 Jun;596(12):1567-1575. (PMID: 35181908)
Hematol Oncol Clin North Am. 2021 Dec;35(6):1117-1129. (PMID: 34389199)
Nucleic Acids Res. 2007 Jan;35(Database issue):D301-3. (PMID: 17142228)
Blood. 2014 Jan 2;123(1):113-20. (PMID: 24227818)
Blood Rev. 2018 Nov;32(6):433-448. (PMID: 30075986)
FEBS Open Bio. 2019 Aug;9(8):1370-1378. (PMID: 31077577)
J Biol Chem. 2009 Nov 20;284(47):32248-55. (PMID: 19801661)
Molecules. 2017 Sep 22;22(10):. (PMID: 28937618)
Proc Natl Acad Sci U S A. 2010 Nov 30;107(48):20732-7. (PMID: 21068371)
J Thromb Haemost. 2013 Jul;11(7):1329-40. (PMID: 23617593)
J Mol Biol. 2015 Jan 30;427(2):248-58. (PMID: 25234087)
Structure. 2009 Dec 9;17(12):1669-1678. (PMID: 20004170)
Thromb Haemost. 2010 Sep;104(3):432-9. (PMID: 20539911)
Semin Intervent Radiol. 2018 Jun;35(2):99-104. (PMID: 29872244)
J Med Chem. 2003 Oct 9;46(21):4405-18. (PMID: 14521405)

31770772 National Natural Science Foundation of China; YG2024QNA07 the Fundamental Research Funds for the Central Universities

Keywords: FVIIIa-FIXa-FX (zymogen) ternary complex; intrinsic coagulation pathway; molecular dynamics simulations; molecular modeling; protein interactions

72175-66-7 (Factor VIIIa)
EC 3.4.21.22 (Factor IXa)
9001-29-0 (Factor X)
0 (Blood Coagulation Factors)

Date Created: 20250613 Date Completed: 20250613 Latest Revision: 20250615

20250617

PMC12155561

10.3390/ijms26115191

40508000