Structural and Functional Elucidation of IF-3 Protein of Chloroflexus aurantiacus Involved in Protein Biosynthesis: An In Silico Approach

Abstract

Chloroflexus aurantiacus is a thermophilic bacterium that produces a multitude of proteins within its genome. Bioinformatics strategies can facilitate comprehending this organism through functional and structural interpretation assessments. This study is aimed at allocating the structure and function through an in silico approach required for bacterial protein biosynthesis. This in silico viewpoint provides copious properties, including the physicochemical properties, subcellular location, three-dimensional structure, protein-protein interactions, and functional elucidation of the protein (WP_012256288.1). The STRING program is utilized for the explication of protein-protein interactions. The in silico investigation documented the protein’s hydrophilic nature with predominantly alpha (α) helices in its secondary structure. The tertiary-structure model of the protein has been shown to exhibit reasonably high consistency based on various quality assessment methods. The functional interpretation suggested that the protein can act as a translation initiation factor, a protein required for translation and protein biosynthesis. Protein-protein interactions also demonstrated high credence that the protein interconnected with 30S ribosomal subunit involved in protein synthesis. This study bioinformatically examined that the protein (WP_012256288.1) is affiliated in protein biosynthesis as a translation initiation factor IF-3 of C. aurantiacus.

A Bioinformatic Approach for Molecular Characterization and Functional Annotation of an Uncharacterized Protein from Vibrio cholerae

“…The protein's subcellular location was documented using the PSORTb v.3.0.3, SOSUI assessment tool, PSLpred server, HMMTOP v.2.0, and TMHMM server v.2.0 [11][12][13].…”

“…The ProtParam program on the ExPASy server was used to determine the physicochemical characteristics of the protein (EET91795.1). The protein consists of 161 amino acids, where Val (17) represented the amino acid of the greatest quantity, followed by Ala (14), Arg (7), Asn (9), Asp (3), Cys (3), Gln (6), Glu (10), Gly (10), His (7), Ile (12), Leu (13), Lys (5), Met (5), Phe (4), Pro (6), Ser (13), Thr (12), Trp (2), and Tyr (3). The time it takes for the radiolabeled target protein concentration to decrease by 50% from the level at the beginning of the chase is known as the protein half-life.…”

Computational Approaches for Structure-Based Functional Annotation of an Uncharacterized Conserved Protein of Acinetobacter baumannii

“…The ScanProsite tool of the ExPASy software [15] was also utilized to identify protein motifs. The evolutionary relationships of the protein SSI32830.1 were detected by the SuperFamily program [16].…”

In-Silico Approaches for Molecular Characterization and Structure-Based Functional Annotation of the Matrix Protein from Nipah henipavirus

“…pfam00661). Viral matrix proteins are structural proteins that connect the viral envelope and the virus core [46,47]. The matrix protein plays an important role in virus assembly and in linking the viral envelope with the virus core.…”

“…pfam00661). A protein superfamily is a group of proteins made up of one or more protein families [46,53,54]. The set of all superfamilies must be a partitioning of the set of all protein sequences or subsequences defined by the protein families' relationship, and each superfamily must be closed under transitivity [54].…”