Structure of the adenovirus E4 Orf6 protein predicted by fold recognition and comparative protein modeling

To facilitate investigation of the molecular and biochemical functions of t he adenovirus E4 Orf6 protein, we sought to derive three-dimensional struct ural information using computational methods, particularly threading and co mparative protein modeling. The amino acid sequence of the protein was used for secondary structure and hidden Markov model (HMM) analyses, and for fo ld recognition by the ProCeryon program. Six alternative models were genera ted from the top-scoring folds identified by threading. These models were e xamined by 3D-1D analysis and evaluated in the light of available experimen tal evidence, The final model of the E4 protein derived from these and addi tional threading calculations was a chimera, with the tertiary structure of its C-terminal 226 residues derived from a TIM barrel template and a mainl y alpha -nonbundle topology for its poorly conserved N-terminal 68 residues . To assess the accuracy of this model, additional threading calculations w ere performed with E4 Orf6 sequences altered as in previous experimental st udies. The proposed structural model is consistent with the reported second ary structure of a functionally important C-terminal sequence and can accou nt for the properties of proteins carrying alterations in functionally impo rtant sequences or of those that disrupt an unusual nine-coordination motif . (C) 2001 Wiley-Liss, Inc.