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All Journal Indonesian Journal of Chemistry Genbinesia Journal of Biology
Wicaksono, Adhityo
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Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Chemical Engineering, Chemistry & Bioengineering Chemistry Health Professions Immunology & microbiology

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Computational Study of Photosynthetic Pigments: Toward Synthetic Photosynthesis Engineering Wicaksono, Adhityo; Prakoso, Muhammad Ja'far; Ridarto, Afif Maulana Yusuf; Parikesit, Arli Aditya
Indonesian Journal of Chemistry Vol 25, No 4 (2025)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/ijc.105059

Abstract

Chlorophyll is a widely known photosynthetic pigment in plants, algae, and cyanobacteria, along with bacteriochlorophyll in some photosynthetic bacteria. The pigments consist of tetrapyrrole structures that carry a single magnesium atom at the center. They play important parts in the light-harvesting process in photosynthesis. This study aimed to characterize and compare the electronic profiles of chlorophyll and bacteriochlorophyll pigments by using in silico computational approaches, such as density functional theory (DFT), electronic transfer property analysis, and protein-pigment interaction studies via molecular docking. The results showed that chlorophylls a, b, and c have the highest energy gaps at the ground state DFT. For bacteriochlorophylls, bacteriochlorophylls g and b have the highest energy gaps. The time-dependent DFT and the follow-up calculations, including extinction coefficient, tunneling rate, and coherence time, indicated bacteriochlorophyll g as a highly promising and efficient pigment. Additionally, chlorophyll c and bacteriochlorophylls c and d showed the strongest binding affinities with the chlorophyll-binding protein of plant photosystem II. This study provides a comprehensive and replicable computational pipeline for pigment profiling, advancing future synthetic photosynthesis designs through combined quantum and synthetic biology insights.
Viroinformatics study: polytope mapping of envelope glycoprotein to tackle HIV-2 infection and develop vaccine candidate Kharisma, Viol Dhea; Widyananda, Muhammad Hermawan; Probojati, Rasyadan Taufiq; Ansori, Arif Nur Muhammad; Murtadlo, Ahmad Affan Ali; Tamam, Muhammad Badrut; Wicaksono, Adhityo; Turista, Dora Dayu Rahma
Genbinesia Journal of Biology Vol. 1 No. 1 (2021): November 2021
Publisher : Generasi Biologi Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.55655/genbinesia.v1i1.6

Abstract

Human Immunodeficiency Virus type 2 (HIV-2) has been identified to exhibit an ability to resist antiretroviral administration and many scientists has predicted increases in the pathogenicity of HIV-2. The development of a vaccine against the type 1 virus (HIV-1) infection has reached the phase 3 clinical trial stage, but currently there is no information on the development of a vaccine against HIV-2. Vaccine development to trigger an increase in the coverage of the expansion of protection can be done through B cell polytope. This study aims to provide an important preliminary for the construction of vaccine candidates by identifying the peptides that make up the B cell polytope in the HIV-2 envelope glycoprotein region. The HIV-2 sequence was obtained from the database. The study followed by 3D modelling, prediction of linear B-cell epitope mapping, antigenicity, allergenicity, peptide properties, and immune simulation was carried out via a webserver. The 3D structure of the peptide was displayed through molecular visualization software. The results showed that the 23-mer peptides E1 'HPRYTGVKNIRDITLTEPGRGSD', F1 'NFIENRKGTQHN' 12-mer, M1 'YLKDQARLNS' 10-mer, N1 'PWVNDSIQPNWNNMTWQQWELQVRD' 25-mer, and O1 'KLQNSWNMGVQTO' can be used as a candidate polytope HIV-2 vaccine because it is recognized by B cells is an antigenic peptide with stable molecule, non-allergenic. The peptides trigger proliferation and activation of B cells to produces a humoral response and work as functionally protective antibody for neutralization of HIV-2. Key words: Acquired Immune Deficiency Syndrome, B-cell, Bioinformatics, Human Immunodeficiency Virus, Retrovirus
Co-Authors Adi Sofyan Ansori, Muhammad Arli Aditya Parikesit Kharisma, Viol Dhea Murtadlo, Ahmad Affan Ali Prakoso, Muhammad Ja'far Rasyadan Taufiq Probojati Ridarto, Afif Maulana Yusuf Tamam, Muhammad Badrut Turista, Dora Dayu Rahma Widyananda, Muhammad Hermawan