همایش ملی بیوانفورماتیک ایران

صفحه اصلی / 4th international edition and 13th Iranian Conference on Bioinformatics

Structural and Biochemical Insights into Single-Stranded DNA-Binding Protein Complexes: A Comparative Study of DnaT, DnaBC, and Pab-RPA

نویسندگان :

Arshia Jahangiri¹ Maryam Azimzadeh Irani² Aida Arezoumandchafi³

1- Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran 2- Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran 3- Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran

کلمات کلیدی :

single-stranded DNA-binding proteins،protein-DNA interactions،hydrophobicity analysis،active site architecture

چکیده :

Single-stranded DNA binding protein complexes play an important role in maintaining genome stability during essential processes such as replication and repair (Madru et al., 2023). These complexes stabilize ssDNA against degradation and facilitate interactions vital for DNA metabolism (Madru et al., 2023). This study investigates three representative ssDNA-binding complexes—DnaT84-153-dT10 (Liu et al., 2014), DnaB-DnaC (Arias-Palomo et al., 2019), and Pyrococcus abyssi Replication Protein A (Madru et al., 2023)—focusing on their structural and functional characteristics. A comparison of the compositions and active site properties will be particularly addressed. Understanding the unique features of these complexes provides valuable information on genome maintenance and evolutionary adaptations. Structural data for DnaT84-153 (PDB ID 4OU6(Liu et al., 2014)), DnaBC (PDB ID 6QEM(Arias-Palomo et al., 2019)), and Pab-RPA (PDB ID 8AAS(Madru et al., 2023)) were retrieved from the Protein Data Bank (Burley et al., 2023). PyMOL was used to study active site residues and visualization of the structural composition comprising helix, sheet, and loop compositions (Schrödinger, LLC, 2023). Physical and chemical parameters, including hydrophobicity, charge, and stability indices, were calculated using ProtParam (Gasteiger et al., 2005). Hydrophobicity analysis and further details on amino acid interactions were confirmed using Biovia Discovery Studio (BIOVIA, Dassault Systèmes, 2023). The analysis unraveled unique structural and biochemical features at the active sites of the studied complexes. Pab-RPA, the active site of RPA2 consists of one helix, eight sheets, and nine loops, while RPA1 contains three helices, seven sheets, and nine loops, which indicate ssDNA stabilization. The DnaBC complex's active site has nine helices, six sheets, and fourteen loops per subunit, consistent with its helicase-loading function for bacterial replication. Each of the five subunits comprising the active site of DnaT contains three helices, two sheets, and four loops per subunit, stabilizing replication intermediates. Additionally, RPA1 is characterized by a lack of polar residues in conjunction with two non-polar residues, whereas RPA2 contains one polar and one non-polar residue. DnaBC contains four polar residues and zero non-polar residues, while DnaT contains neither polar nor non-polar residues. Hydrophobicity analysis revealed predominantly hydrophobic active sites, with GRAVY values of -0.354 (RPA1), -0.379 (RPA2), -0.286 (DnaBC), and -0.150 (DnaT). Charge calculations demonstrated diverse ssDNA interaction mechanisms: RPA1 and RPA2 carried negative charges (-14 and -1, respectively), DnaT was neutral, and DnaBC carried a positive charge of +3. Stability indices indicated that DnaT (38.6) and RPA2 (1.37) were more stable compared to DnaBC and RPA1, both of which had instability indices exceeding 40. The findings underscore the structural and biochemical variability of ssDNA-binding complexes, elucidating the presence of unique hydrophobic binding pockets. Such information affords a significant understanding of the strategic targeting of these complexes across diverse applications, encompassing therapeutic interventions and mechanistic investigations.