Digital construction and comparison of hypotetical three dimensional protein models of human tumour necrosis factor (TNF) receptor-associated factor (TRAF) genes

Toh, Wooi Sheng. (2010) Digital construction and comparison of hypotetical three dimensional protein models of human tumour necrosis factor (TNF) receptor-associated factor (TRAF) genes. [Final Year Project Report] (Unpublished)

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Abstract

TRAFs are the cytoplasmic adapter proteins that interact with the Tumour Necrosis Factor Receptor (TNFR) family. In human and mammals, there are seven members (TRAF1 - 7) in the TRAFs family. These members share a common TRAF domain at the Carboxyl terminus (C-terminus) and zinc fingers at the amino terminus (N- terminus) with the exception of TRAFI that does not share the ring and zinc fingers, and TRAF7 that does not share the TRAF domain. Previous studies showed that TRAFs regulate the signaling or pathways which were closely related to the apoptosis process. Thus, these processes promote the survival of cancer cell and are linked to cancer development. In order to understand the function of TRAFs in cancer development and between TRAFs family member, three dimensional proteins (3D) models were constructed and used to simulate the interaction of TRAFs protein with other adapter protein in the pathway. The construction of TRAFs models were based on homology modeling, threading modeling and ah initio modeling methods using ModWeb, SWISS-MODEL and I-TASSER severs. There were total 77 models constructed for 7 TRAFs member from the 3 server; 18 from ModWeb, 24 from SWISS- MODFL. and 35 from I-TASSER. These models were then evaluated with ProSa-web, PROVE and PROCI-IECK tools. The full length models were used to perform docking simulation with ASK-1 and TRADD proteins.

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