Structural characterization of N-terminus of XIAP associated factor 1

Abstract

The main focus of this thesis is to study the physical characteristics of the N-terminus of human XAF1 protein, a 17kD protein named NTA1, by biophysical methods. Structural studies of the N-terminus of XAF1 serves as a base for the studies of the structure and function relationship of the N-terminus, and the same maybe true for the full length XAF1.

Bioinformatics analysis shows that NTA1 shares high sequence identity with the TRAF-type zinc finger domain-containing protein 1 (TRAFD1) and FLN29. Protein structure prediction has been performed on NTA1 by the I-TASSER web server. The prediction result suggests that NTA1 is a structure that consists of α-helices which are joined by flexible linkers. The loose structure shown by I-TASSER is expected to have high solvent accessibility. This coincides with the deuterium exchange data. In addition, by the CD approach, NTA1 was estimated to contain high α-helix content. This result is consistent with the bioinformatics prediction and the secondary structure obtained from the chemical shift index method as well. The physical characterizations of NTA1 showed that NTA1 is a loosely packed protein; and the five zinc ions are bound in the protein structure. Based on the chemical shifts of β-carbons, the Cysteine residues Cys8, Cys11, Cys34, Cys37, Cys50, Cys59, Cys62, Cys86, Cys89 and Cys115 showed a significantly downfield shift, they are probably involved in the zinc ions coordination. The dynamic property of NTA1 was investigated by NMR techniques. Backbone dynamics of NTA1 reveal that NTA1 does not have a typical spherical structure, it is anisotropic. Residues corresponding to the zinc finger regions in the predicted structure show large R2/R1 and S2 values, while regions shown to be flexible linkers in the 3D structure prediction show small R2/R1 and S2 values. Thus, the protein structure homology modeling data are supported by the backbone dynamics data.