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J. E. Masse, B. Wong, Y. -M. Yen, F. H.-T. Allain, R. C. Johnson and J. Feigon, “The S. cerevisiae Architectural HMGB Protein NHP6A Complexed with DNA: DNA and Protein Conformational Changes upon Binding,” Journal of Molecular Biology, Vol. 323, No. 2, 2002, pp. 263-284. doi:10.1016/S0022-2836(02)00938-5

has been cited by the following article:

• 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.