Ab initio modelling of an essential mammalian protein: Transcription Termination Factor 1 (TTF1)

Abstract

Transcription Termination Factor 1 (TTF1) is an essential mammalian protein that regulates cellular transcription, replication fork arrest, DNA damage repair, chromatin remodelling etc. TTF1 interacts with numerous cellular proteins to regulate various cellular phenomena, and plays a crucial role in maintaining normal cellular physiology, dysregulation of which has been reported towards cancerous transformation of the cells. However, despite its key role in cellular physiology, the complete structure of human TTF1 has not been elucidated to date, either experimentally or computationally. Hence, understanding the structure of human TTF1 becomes highly important for studying its functions and interactions with other cellular factors. Therefore, the aim of this study was to construct the complete structure of human TTF1 protein, using molecular modelling approaches. Owing to the lack of suitable homologues in the PDB, the complete structure of human TTF1 was constructed using ab initio modelling. The structural stability was determined using molecular dynamics (MD) simulations in explicit solvent, and trajectory analyses. The representative structure of human TTF1 was obtained by trajectory clustering, and the central residues were determined by centrality analyses of the residue interaction network of TTF1. Two residue clusters, in the oligomerisation domain and C-terminal domain, were determined to be central to the structural stability of human TTF1. To the best of our knowledge, this study is the first to report the complete structure of human TTF1, and the results obtained herein will provide structural insights for future research in cancer biology and related studies.Author SummaryThe transcription termination factor 1 (TTF1) is an essential multifunctional mammalian protein which plays important role in regulating important cellular process like transcription, replication, DNA damage repair, chromatin remodelling etc. and its dysregulation leads to various cancers. Despite its being such an important factor, the complete structure of human TTF1 has not been determined to date, either using experimental techniques or computationally. Therefore, the aim of this study was to construct the complete structure of human TTF1 using computational modelling. In this study the complete structure of human TTF1 was constructed by ab initio modelling using iTasser. The stability of this model was determined by 200 ns molecular dynamics (MD) simulations. The representative conformation of human TTF1 was further determined by clustering the simulation trajectory and the residues that are central to the stability of this structure were identified. The results demonstrate the presence of two residue clusters in human TTF1, one in the oligomerisation domain and other in the C-terminal domain, which were found to be crucial for the structural stability of this protein. Hence, the results of this study will aid future studies in this field towards engineering this important protein for further biochemistry and cell biology research.

Biophysical Characterization of an Essential Mammalian Protein; Transcription Termination Factor I (TTF1)

“…Deconvolution of spectra collected from CD and Raman spectroscopy shows that TTF1 is a helical protein and this finding justifies its DNA binding activity. The above finding is in agreement with our computational model for full length TTF1 as well 16 . Previous literatures reporting protein DNA atomic structures have shown that the DNA is stabilized between the helices of those proteins 2,31 .…”

“…The secondary structure estimation after spectra deconvolution (as mentioned in material and methods) gave estimated percentage of α-helices (53.1%), β-sheets (6.4%) and random coils (40.4%) (Table 3), confirming predominantly the helical nature of the protein 28 . The above finding is in very much agreement with our computational abinitio study and simulation data of human TTF1 protein 16 . Raman spectroscopy is an important tool to study secondary structure of proteins and peptides.…”

“…Even though TTF1 being an essential multifunctional protein, almost nothing is known about its biophysical character or structure. The only study revealing its structural model (computationally) is reported from our lab 16 . Hence, it's important to understand the biophysical characters of this protein in order to engineer this protein for structural and mechanistic studies.…”

“…However, to date, no research on its structural characterisation; neither computational nor physical has been reported yet. The very first article which reports ab-initio modelling of this essential protein has been communicated from our lab 16 . Considering the multifunctional and essential nature of TTF1, it becomes important to elucidate the structural knowledge in order to understand the mechanisms of action and use the same towards its therapeutic applications.…”