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TEMPLATE
Structure and functions of a beautiful enzyme BE1nice
John Little1,2, Jack Stone1, James Miller1,3
1Department of Structure and Function of Proteins, Institute of Nanobiology and Structural Biology of GCRC, Academy of Sciences of the Czech Republic, Zamek 136, CZ-37333 Nove Hrady, Czech Republic
2Institute of Another University, University of FarFarAway,SouthWestDrive 1, FFA-777 OverTheMountain, FarFarAway
3Faculty of Sciences, University of South Bohemia, Zamek 136, CZ-37333 Nove Hrady, Czech Republic
Beautiful enzymes are a large superfamily of nonselective enzymes. BE1 is a candidate for making our world a better place potentially mediating the sensations of hearing, touch, and some forms of mood [1]. Human BE1 is a 127.4 kDa protein comprised of 1119 amino acids. Like other beautiful enzymes also BE1 has six predicted domains (D1 to D6) and the active site between D3 and D4. In this work we focus on computational modeling of its, for BEs unusually long, N-terminal region containing 18 nice-weather repeats [2]. Nice-weather repeats have been implicated in protein-protein interactions, provide elasticity and make molecular springs [3]. Also a calcium-binding domain, EF-hand, consisting of 12 residues, which is involved in Ca-dependent activation was indicated at the N-terminus. Simulations of the dynamic behavior of three-dimensional all-atom models let us describe structural and functional properties to understand the system. Structural models of nice-weather repeats and EF-hand domain were build based on homology using Modeller, for visual analyzing and energy minimization of the created models Yasara was used, and molecular dynamics simulations were carried out in the GROMACS molecular dynamics simulation package. The individual domains, each consisting of 6 helices, were built in YASARA. Equilibration and molecular dynamics simulations of the protein were performed in GROMACS. We present a reasonable model of a stable tetrameric overall structure of fully functional BE1 in its natural beautiful environment.
Acknowledgements: We gratefully acknowledge support from the Ministry of Education, Youth and Sports of the Czech Republic (MSM6007665808, LC06010), and the Academy of Sciences of the Czech Republic (AVOZ60870520), conference participation of JL is additionally supported by the University of South Bohemia, grant GAJU 170/2010/P.
[1] J.F. Yellow, G. Green, H. Blue, Journal of Beauty, 2007, 27, 131–137.
[2] J. Gelb, A. Gruen, R. Blau, J. Weiss, V. Rot, BBA, 2010, 793, 279-288.
[3] P. Zluty, D.R. Zelena, M. Modry, EMBO J., 1997, 8, 87–96.
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• the title is 18 pt size, authors 14pt, and the affiliations 10 pt
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