In silico investigation of GAPOR-ferredoxin interaction in Methanococcus Maripaludis S2

Thumbnail Image

Files

Aaltonen_Andrei_2025.pdf (15.3 MB)

URL

Journal Title

Journal ISSN

Volume Title

Sähkötekniikan korkeakoulu | Bachelor's thesis
Unless otherwise stated, all rights belong to the author. You may download, display and print this publication for Your own personal use. Commercial use is prohibited.

Authors

Date

2025-05-29

Department

Major/Subject

Bioinformaatioteknologia

Mcode

ELEC3016

Degree programme

Sähkötekniikan kandidaattiohjelma

Language

en

Pages

27+8

Series

Abstract

Methanococcus maripaludis S2 is a model organism for methanogens that utilize the hydrogenotrophic pathway, where carbon dioxide and hydrogen gas is converted into methane and possibly in the future other higher-value products. The metabolic engineering of M. maripaludis enables the pursuit of novel technologies into, for example, carbon capture to combat climate change. However, before the metabolism of M. maripaludis can be engineered, it must be understood. An important metabolic pathway is glycolysis, in which Glyceraldehyde-3-phosphate ferredoxin oxidoreductase (GAPOR) plays an important role. Despite it being known that GAPOR uses ferredoxin as a substrate, it remains unknown which specific ferredoxin it interacts with, and what the characteristics of this interaction are. This study sought to elucidate these unknowns. It was hypothesized that electrostatic interactions play a crucial role in facilitating the protein protein interaction. The objectives of the study were achieved in silico by first filtering for 8 candidate ferredoxins. The active residues for the 8 ferredoxins and GAPOR were computed using CASTpFold, which were then used for HADDOCK docking, resulting in 8 GAPOR-ferredoxin complexes. These complexes were finally evaluated using PRODIGY. Additionally, electrostatic surface maps were calculated with APBS. The study found some evidence to suggest that GAPOR may prefer to complex with Q6LXV0 and Q6LXV2. Firstly, they were scored highest by PRODIGY, with scores of −11.0 ± 0.766 kcal/mol and −11.8 ± 0.492 kcal/mol respectively. Secondly, when excluding Q6LX46 and Q6LXS5; Q6LXV0 and Q6LXV2 remained as the ferredoxins with highest HADDOCK score −101 ± 3.27 kcal/mol and −107 ± 8.68 kcal/mol respectively. Additionally, the electrostatic surface potentials close to the PPI site were shown to be relatively negatively charged, which may serve to stabilize the complex. Furthermore, the predicted PPI site on GAPOR was shown to be relatively positively charged. However, these results were not robustly significant, so they must be considered critically and do not serve as definitive indication of anything. The intended way to engage with these results is to consider them as foundation for future better studies into the GAPOR-ferredoxin complex and perhaps into similar in silico studies.

Description

Supervisor

Turunen, Markus

Thesis advisor

de Dios Mateos, Enrique

Keywords

ferredoxin, GAPOR, PPI, in silico

Other note

Citation

Permanent link to this item

https://urn.fi/URN:NBN:fi:aalto-202506104404

Collections

[kand] Sähkötekniikan korkeakoulu / ELEC