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S. Raman, R. Vernon, J. Thompson, M. Tyka, R. Sadreyev, J. Pei, D. Kim, E. Kellogg, F. DiMaio, O. Lange, L. Kinch, W. Sheffler, B. Kim, R. Das, N. V. Grishin and D. Baker, “Structure Prediction for CASP8 with All-Atom Refinement Using Rosetta,” Proteins: Structure, Function and Bioinformatics, Vol. 77, No. S9, 2009, pp. 89-99. doi:10.1002/prot.22540

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• TITLE: Modeling the Structure of Yeast MATα1: An HMG-Box Motif with a C-Terminal Helical Extension

  AUTHORS: Doba Jackson, Tarnisha Lawson, Robert Villafane, Lisa Gary

  KEYWORDS: MATα1; MATα2; Gene Regulation; Mating-Type; Yeast; α-Domain; Combinatorial Control of Transcription

  JOURNAL NAME: Open Journal of Biophysics, Vol.3 No.1, January 30, 2013

  ABSTRACT: The yeast MATα1 is required for the activation of α-specific genes in Saccharomyces cerevisiae and thus confers the α-cell identity of the yeast. MATα1 contains a domain called the α-domain which has significant sequence identity to the HMG-box family of proteins. A multiple sequence alignment of several α-domains and various structurally determined HMG-box domains has revealed that both domains possess very similar structural and functional residues. We found that the basic amino acids of the N-terminal loop, the intercalating hydrophobic residues of the first helix, and the hydrophobic residues required for interactions within the core of the protein are remarkably conserved in α-domains and HMG-box proteins. Our generated molecular models suggest that the first and third helix will be shorter and that the HMG-box core is not an isolated domain. The region beyond the conserved HMG-box motif contains an extended helical region for about 20 - 30 amino acids. Structural models generated by comparative modeling and ab initio modeling reveal that this region will add two or more additional α-helices and will make significant contacts to helix III, II and I of the HMG-box core. We were able to illustrate how the extended α-domain would bind to DNA by merging of the α-domain and the LEF-1/DNA complex. The models we are reporting will be helpful in understanding how MATα1 binds to DNA with its partner MCM1 and activates transcription of α-specific genes. These models will also aid in future biophysical studies of MATα1 including the crystallization and structure determination.