Computational Biology-Assisted and Experimentally Validated of Various Protease Cleavage Activities on Surface Proteins Using the Murine Retinal Tissue

Ayudha Bahana Ilham Perdamaian; Titi Marsifah; Nina Sakina Lessy; Dewi Kartikawati Paramita; Bjorn Voss; Muhammad Bayu Sasongko; Supanji Supanji

doi:10.2991/978-94-6239-762-0_15

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Computational Biology-Assisted and Experimentally Validated of Various Protease Cleavage Activities on Surface Proteins Using the Murine Retinal Tissue

Authors

Ayudha Bahana Ilham Perdamaian¹^{, 2}, Titi Marsifah³, Nina Sakina Lessy³, Dewi Kartikawati Paramita⁴^{, 5}^{, 6}, Bjorn Voss⁷, Muhammad Bayu Sasongko², Supanji Supanji²^{, *}

¹Doctorate Program of Medicine and Health Science, Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia

²Department of Ophthalmology, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia

³Master Program of Biomedical Science, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia

⁴Department of Histology and Molecular Biology, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia

⁵Study Center for Biotechnology, Universitas Gadjah Mada, Yogyakarta, Indonesia

⁶Integrated Research Laboratory, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia

⁷RNA-Biology and Bioinformatics, Institute of Biomedical Genetics, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany

^*Corresponding author. Email: supanji@ugm.ac.id

Corresponding Author

Supanji Supanji

Available Online 4 September 2026.

DOI: 10.2991/978-94-6239-762-0_15 How to use a DOI?
Keywords: FACS; Machine Learning; In Silico; Cell Dissociation; Specific Protease
Abstract: Efficient dissociation of retinal cells requires careful selection of proteases to preserve surface epitopes critical for downstream analyses. This study aimed to identify the most suitable protease for murine retina dissociation without compromising key surface markers. Retinas were harvested from normal C57BL/6 mice and treated with various proteases, including papain, trypsin, Liberase (consisting of collagenase and thermolysin), elastase, and proteinase K. In silico analyses using Expasy Peptide Cutter, Rapid Peptide Generator, and HADDOCK docking. This in silico analysis was followed by experimental validation through retinal tissue dissociation and assessment of cell viability. Results showed that trypsin produced the highest cell yield, followed by Liberase, while papain and trypsin minimally cleaved surface epitopes. Immunofluorescence confirmed that Liberase preserved the SSEA-1, CD73, and CD147 epitopes best, followed by papain. These findings underscore the significance of protease selection for retinal cell dissociation and provide a framework for optimizing procedures to preserve functional surface proteins in downstream applications.
Open Access: Open Access This chapter is licensed under the terms of the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License (http://creativecommons.org/licenses/by-nc-nd/4.0/), which permits any noncommercial use, sharing, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license and indicate if you modified the licensed material. You do not have permission under this license to share adapted material derived from this chapter or parts of it.

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Volume Title: Proceedings of the 6th International Conference on Bioinformatics, Biotechnology, and Biomedical Engineering (BIOMIC 2025)
Series: Advances in Health Sciences Research
Publication Date: 4 September 2026
ISBN: 978-94-6239-762-0
ISSN: 2468-5739
DOI: 10.2991/978-94-6239-762-0_15 How to use a DOI?
Open Access: Open Access This chapter is licensed under the terms of the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License (http://creativecommons.org/licenses/by-nc-nd/4.0/), which permits any noncommercial use, sharing, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license and indicate if you modified the licensed material. You do not have permission under this license to share adapted material derived from this chapter or parts of it.

Cite this article

ris enw bib

TY  - CONF
AU  - Ayudha Bahana Ilham Perdamaian
AU  - Titi Marsifah
AU  - Nina Sakina Lessy
AU  - Dewi Kartikawati Paramita
AU  - Bjorn Voss
AU  - Muhammad Bayu Sasongko
AU  - Supanji Supanji
PY  - 2026
DA  - 2026/09/04
TI  - Computational Biology-Assisted and Experimentally Validated of Various Protease Cleavage Activities on Surface Proteins Using the Murine Retinal Tissue
BT  - Proceedings of the 6th International Conference on Bioinformatics, Biotechnology, and Biomedical Engineering (BIOMIC 2025)
PB  - Atlantis Press
SP  - 238
EP  - 250
SN  - 2468-5739
UR  - https://doi.org/10.2991/978-94-6239-762-0_15
DO  - 10.2991/978-94-6239-762-0_15
ID  - Perdamaian2026
ER  -

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