Invertebrate Primitive Antibody Anti-HRP-HRP Complex. Modelisations by Alpha Fold 3: Parameters

Immunology of Invertebrates, Orléans University, France

*Corresponding author: Michel Leclerc, Immunology of Invertebrates, Orléans University, France, Tel: 0238410209, Email: [email protected]

Received Date: July 30, 2025

Published Date: September 03, 2025

Citation: Leclerc M. (2025). Invertebrate Primitive Antibody Anti-HRP-HRP Complex. Modelisations by Alpha Fold 3: Parameters. Mathews J Immunol Allergy. 9(1):36.

Copyrights: Leclerc M. © (2025).

ABSTRACT

Recently, we have shown a modelisation of the Invertebrate sea star Asterias rubens HRP-anti HRP complex. Now, by the use of Alpha Fold 3 model, we present some parameters which characterise the interaction of the sea star Ab-Ag complex when compared to Vertebrates.

Keywords: Alpha Fold 3 Modelisations, IPA, Parameters.

INTRODUCTION

Introducing Alpha Fold 3 a new Al model developed by Google and Deep Mind and Isomorphic Labs. By accurately predicting the structure of proteins, DNA, RNA, ligands and more, and how they interact [1].

In 2009, the used HRP (Horse-Radish Peroydase) as antigen in sea star Asterias rubens (Goteborg University, Sweden) was not clearly identified. We have been obliged, 16 years later to modelise this HRP antigen, according 3 Protein sequences, separately, and, which are repertoried in Uniprot. In these conditione we hoped to find the appropriate one. But other sequences can be used for our work next.

As for the sea star antibody, we have performed the better sequence, in view to obtain a pTM superior to 0.8, as it is asked for Vertebrate antibodies.

RESULTS

The first Protein Alpha Fold 3 analysis of the sea star Ab sequence shows that it contains a N-ter part that Alpha Fold 3 doesn’t know how to model

Thus, the sequence for modelisation will be:

>>SSA

IYTFREQPSDTSALQGSTVVLHCSVEQYINTTAIVWWSRDSVISHNKDLKLSSLNTDQLQRYSISGDASRGEFNLKIVNFTATDAASYRCQM

Effectively, it is of better quality, with a pTM of 0.88, when compared to Vertebrates.The 3D modelisation of the corresponding sequence is given below (Figure 1) :

Figure 1. Modelisation of sea star anti-HRP antibody with CDR regions in red.

As for the antigens, we have tested, first (1) protein sequence of HRP neutral, secondly (2) HRP C1A one, thirdly (3) HRP C1A variant one

1)       La HRP-Neutral: https://www.uniprot.org/uniprotkb/Q42517/entry

>HRP-N (327 AA, incorporated peptid below in red)

MKTQTKVMGGHVLLTVFTLCMLCSAVRAQLSPDIYAKSCPNLLQIVRDQVKIALKAEIRMAASLIRLHFHDCFVNGCDASVLLDGTNSEKLAIPNVNSVRGFEVIDTIKAAVENACPGVVSCADILTLAARDSVYLSGGPQWRVALGRKDGLVANQSSANNLPSPFEPLDAIIAKFAAVGLNVTDVVALSGAHTFGQAKCDLFSNRLFNFTGAGTPDSTLETTLLSDLQTVCPIGGNGNKTAPLDRNSTDAFDNNYFKNLLEGKGLLSSDQILFSSDLAVNTTKRLVEAYSRSQYLFFRDFTCSMIRMGSLVNGASGEVRTNCRVIN

2)       La HRP-C1A: https://www.uniprot.org/uniprotkb/P00433/entry

>HRP-C1A (353 AA, incorporated peptid; below in red)

MHFSSSSTLFTCITLIPLVCLILHASLSDAQLTPTFYDNSCPNVSNIVRDTIVNELRSDPRIAASILRLHFHDCFVNGCDASILLDNTTSFRTEKDAFGNANSARGFPVIDRMKAAVESACPRTVSCADLLTIAAQQSVTLAGGPSWRVPLGRRDSLQAFLDLANANLPAPFFTLPQLKDSFRNVGLNRSSDLVALSGGHTFGKNQCRFIMDRLYNFSNTGLPDPTLNTTYLQTLRGLCPLNGNLSALVDFDLRTPTIFDNKYYVNLEEQKGLIQSDQELFSSPNATDTIPLVRSFANSTQTFFNAFVEAMDRMGNITPLTGTQGQIRLNCRVVNSNSLLHDMVEVVDFVSSM

3)       La HRP-A2: https://www.uniprot.org/uniprotkb/P80679/entry

>HRP-A2 (305 AA, no peptid)

QLNATFYSGTCPNASAIVRSTIQQAFQSDTRIGASLIRLHFHDCFVDGCDASILLDDSGSIQSEKNAGPNANSARGFNVVDNIKTALENTCPGVVSCSDILALASEASVSLTGGPSWTVLLGRRDSLTANLAGANSAIPSPFEGLSNITSKFSAVGLNTNDLVALSGAHTFGRARCGVFNNRLFNFSGTNGPDPTLNSTLLSSLQQLCPQNGSASTITNLDLSTPDAFDNNYFANLQSNNGLLQSDQELFSTLGSATIAVVTSFASNQTLFFQAFAQSMINMGNISPLTGSNGEIRLDCKKVDGS

We have found, that neutral HRP fixed our antibody in a better way than the 2 other HRP, at 0.77 pTM. For information the Ab-Ag complex, in Alpha Fold 3 is given below, in these conditions:

SEA STAR ANTI-HRP -HRP COMPLEX, AT 0.77 PTM (ALPHA FOLD 3)

CONCLUSION

We retain mainly that the interaction between the IPA (Invertebrate Primitive Antibody) or sea star anti-HRP antibody- HRP antigen, (neutral HRP) culminates at 077 pTM., which is slightly inferiror to0.8, when compared to Vertebrate Ab-Ag complex. But, it is a preliminary data for these first results. We have, in the future to compose with other parameters such as new HRP protein sequences to test and a new Alpha Fold model. As new HRP sequences we ‘ll try that of HRP Armoracia rusticana: Uniprot K B and PRXC1C HRP one.

Whatever our IPA resembles in many points to Vertebrate ones [2-4].

REFERENCES

1. Jumper J, Evans R, Pritzel A, Green T, Figurnov M, Ronneberger O, et al. (2021). Highly accurate protein structure prediction with AlphaFold. Nature. 596(7873):583-589.
2. Leclerc M. (2023). The Sea Star Anti-HRP Protein (IPA: Production in a CHO Protocol, Its Specificity in ELISA. Presence of CDR1 and CDR2 Regions. Aspects of Invertebrate Primitive Antibody. Mathews J Immunol Allergy. 8(1):26.
3. Leclerc M. (2024). Determination of the CDR (CDR1, CDR2) Complementary-Determining Region Invertebrate Primitive Antibody from Sea Star. Mathews J Immunol Allergy. 8(1):25.
4. Leclerc M. (2023). Modelizations in 3D of the Anti-HRP Sea Star (or Starfish) Primitive Antibody (IPA): Their Relations with Mus Musculus Fab and In A General Way Mammal Antibodies. Mathews J Immunol Allergy. 8(1):27