Abstract 2421 A molecular model of the MATα_HMG/MCM1/DNA ternary complex

Background: The sex-determining genes of fungi reside at one or two specialized regions of the chromosome and are known as the mating-type loci. Structural similarities between the yeast α-domain of MATα1 and the some experimentally determined HMG-box domain (such as LEF-1) have been demonstrated. [1,2] A ternary complex that involves the yeast homeodomain of MATα2 complexed with a general transcription factor MCM1 bound to DNA has been solved by X-ray crystallography. [3] Our previous studies have established a model of MATα_HMG as having a classical HMG-box motif of three alpha-helical regions with a non-homologous C-terminal extended tail region. Objective: To provide a synthetic in-silico model of the MATα_HMG/MCM1/DNA ternary complex found in the upstream activating sequences of alpha-specific genes in yeast. Methods: Models of MATα_HMG were created using MODELLER [4] and compared similar models of yeast MATα_HMG using the AlphaFold database. The x-ray crystal structure of the MATα2/MCM1/DNA and LEF-1/DNA [5] were used in Yasara [6] to create an in-silico model of MATα_HMG/MCM1/DNA. Results: All 10 modelled yeast used (Zygosaccharomyces pseudoballil, Kazachstania saulgensis, Kluyveromyces delphensis, Kluyveromyces marxianus, Kluyveromyces waltii, Komagataelis phaffil, Ogataea minuta, Pichia agusta, Saccharomyces cerevisiae, Zygosaccharomyces rousii) all converged onto a similar fold which can be called the α-domain. This α-domain will have: (1) an HMG interaction helix; (2) a long (20 aa) unstructured loop; (3) an HMG-box core motif with three α-helices; (4) a C-terminal extension. Structural variability is only found in the long unstructured loop and the C-terminal extension. Overall RMSD of all 10 structures is 2.29 angstroms. This model was used to create an in-silico synthetic model of the MATα_HMG/MCM1/DNA ternary complex. We believe that our in-silico model will help guide future attempts to characterize this complex completely by x-ray crystallography or cryo-electron microscopy. References [1] Benkhali J., et. al., (2013) "A network of HMG-box transcription factors regulates the sexual cycle in the Fungus Podospora anserine," PLoS Genetics, vol 9(7), p1-20; [2] Jackson D., Lawson T., Villafane R., Gary L., (2013) "Modeling the structure of yeast MATα1: an HMG-box motif with a C-terminal helical extension," Open Journal of Biophysics, vol 1a, p1-13 [3] Tan S., Richmond T.J. (1998) "Crystal structure of the MATalpha2/MCM1/DNA ternary complex," Nature, 391(6668), p660-666 [4] Šali A., Blundell T.L., (1993) "Comparative protein modelling by satisfaction of spatial restraints," J. Mol. Biol. 234, 779-815, 1993. [5] Love J.J., et. al., (1995)"Structural basis for DNA bending by the architectural transcription factor LEF-1," Nature, 376, p791-95 [6] Krieger E., Vriend G., (2015)"New ways to boost molecular dynamics simulations" J. Comput. Chem., 36(13), p996-1007. National Science Foundation Huntingdon College.