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Computational approaches for structure-based functional annotation of an uncharacterized protein (Q182S9) of Clostridium difficile
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1  Department of Biochemistry and Molecular Biology, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj 8100, Bangladesh
Academic Editor: Omar Cauli

Published: 04 September 2025 by MDPI in The 1st International Online Conference on Diseases session Infectious Diseases
Abstract:

C. difficile is a bacterium that causes severe diarrhea and may result in colon cancer. C. difficile are anaerobic, motile bacteria that are found practically everywhere, but particularly in soil. C. difficile produces up to three distinct toxins and lacks catalase and superoxide dismutase. Stressful conditions cause bacteria to release spores, which are resistant to harsh environments and cannot be destroyed by active bacteria. This study aims to investigate the C. difficile protein sequence, learn about its physicochemical properties, conduct structure-based functional analysis, anticipate domains for specific functional predictions, and investigate secondary and tertiary structures. According to its physicochemical qualities, the protein's sequence contains more negatively charged residues than positively charged residues. The aliphatic index suggests that this protein has adequate thermostability. Documentation also validates the protein's hydrophilic nature. This protein includes an uncharacterized stationary-phase protein (YicC). This protein aids in the 3' to 5' exoRNase PNPase's degradation of the sRNA RhyB and appears to produce a 5'-phosphate and a 3'-OH group. This protein has a domain named the sugar transport 2 domain, which is an IMP, and it is believed that this protein might play a role in the transfer of glucose. The secondary structural analysis revealed that the alpha helix was the most prominent structural element, followed by random coils and extended strands. Furthermore, two separate programs, AlphaFold and SWISS-MODEL, predicted the protein's tertiary structure. After examining various structures, the structural assessment study determined that the SWISS-MODEL program's prediction was the best, taking into account the values for the most wanted and extra-allowed areas in the plot statistics. Potential therapies and immunizations can target this protein in order to prevent microbial infection and prevent the protein from infecting cells.

Keywords: Clostridium difficile; Stationary-phase protein; YicC; Sugar transport 2 domain

 
 
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