Structural characterization of DNA-binding domain of essential mammalian protein TTF 1

• Published in: Bioscience reports 2024-08, Vol.44 (8)
• Main Authors: Singh, Gajender, Bhopale, Abhinetra Jagdish, Khatri, Saloni, Prakash, Prashant, Kumar, Rajnish, Singh, Sukh Mahendra, Singh, Samarendra Kumar
• Format: Article
• Language: English
• Subjects: Amino Acid Sequence; Amino acids; Atomic structure; Binding; Binding Sites; Bioinformatics; Biotechnology; Cellular structure; Chromatin remodeling; Computational Biology; Deoxyribonucleic acid; DNA; DNA - metabolism; DNA biosynthesis; DNA damage; DNA repair; DNA-Binding Proteins - chemistry; DNA-Binding Proteins - genetics; DNA-Binding Proteins - metabolism; Gene expression; Homogeneity; Homology; Humans; Mammals; Molecular Dynamics Simulation; Protein Binding; Protein Domains; Protein Engineering; Protein Stability; Protein structure; Proteins; Replication initiation; RNA polymerase; RNA processing; rRNA; Structural analysis; Structural Biology; Transcription Factors - chemistry; Transcription Factors - genetics; Transcription Factors - metabolism; Transcription termination; Transcription termination factor 1; Yeast
• ISSN: 0144-8463; 1573-4935; 1573-4935
• DOI: 10.1042/BSR20240800

Transcription Termination Factor 1 (TTF1) is a multifunctional mammalian protein with vital roles in various cellular processes, including Pol I-mediated transcription initiation and termination, pre-rRNA processing, chromatin remodelling, DNA damage repair, and polar replication fork arrest. It comprises two distinct functional regions; the N-terminal regulatory region (1-445 aa), and the C-terminal catalytic region (445-859 aa). The Myb domain located at the C-terminal region is a conserved DNA binding domain spanning from 550 to 732 aa (183 residues). Despite its critical role in various cellular processes, the physical structure of TTF1 remains unsolved. Attempts to purify the functional TTF1 protein have been unsuccessful till date. Therefore, we focused on characterizing the Myb domain of this essential protein. We started with predicting a 3-D model of the Myb domain using homology modelling, and ab-initio method. We then determined its stability through MD simulation in an explicit solvent. The model predicted is highly stable, which stabilizes at 200ns. To experimentally validate the computational model, we cloned and expressed the codon optimized Myb domain into a bacterial expression vector and purified the protein to homogeneity. Further, characterization of the protein shows that, Myb domain is predominantly helical (65%) and is alone sufficient to bind the Sal Box DNA. This is the first-ever study to report a complete in silico model of the Myb domain, which is physically characterized. The above study will pave the way towards solving the atomic structure of this essential mammalian protein.