Team:UST Beijing/Modeling
Functions are determined by structures. It is helpful for us to grasp the protein structure, and we could know the function of proteins better. So, we use supercomputer to predict the protein structure, since it is much less expensive, faster, and able to a large scale generate protein structures than classical methods.
Protein Structure Models
Due to the fact that the real structure of Lanosterol Synthase is known, so we begin from protein data bank in Europe. We firstly obtained Canonical number: P48449(pdb|1w6k|), and then the amino acid sequence of Lanosterol was found in Uniprot, shown as following:
>pdb|1w6k|A
MTEGTCLRRRGGPYKTEPATDLGRWRLNCERGRQTWTYLQDERAGREQTGLEAY
ALGLDTKNYFKDLPKAHTAFEGALNGMTFYVGLQAEDGHWTGDYGGPLFLLPGL
LITCHVARIPLPAGYREEIVRYLRSVQLPDGGWGLHIEDKSTVFGTALNYVSLRI
LGVGPDDPDLVRARNILHKKGGAVAIPSWGKFWLAVLNVYSWEGLNTLFPEMWLF
PDWAPAHPSTLWCHCRVDGPASTAFQEHVSRIPDYLWMGLDGMKMQGTNGSQIWD
TAFAIQALLEAGGHHRPEFSSCLQKAHEFLRLSQVPDNPPDYQKYYRQMRKGGFS
FSTLDCGWIVSDCTAEALKAVLLLQEKCPHVTEHIPRERLCDAVAVLLNMRNPDG
GFATYETKRGGHLLELLNPSEVFGDIMIDYTYVECTSAVMQALKYFHKRFPEHRA
AEIRETLTQGLEFCRRQQRADGSWEGSWGVCFTYGTWFGLEAFACMGQTYRDGTA
CAEVSRACDFLLSRQMADGGWGEDFESCEERRYVQSAQSQIHNTCWAMMGLMAVR
HPDIEAQERGVRCLLEKQLPNGDWPQENIAGVFNKSCAISYTSYRNIFPIWALGR
FSQLYPERALAGHP
And the starting about 90 amino acids are membrane bound sequences. We make a chimera sequence using the Lanosterol Synthase homologue, Dammarenediol Synthase. It’s Pangu sequence. Then, we use the online servers, Swiss-Model, to generate high quality predictions of 3D structure of protein molecules from amino sequences. shown as following:
>pdb||A
MTEGTCLRRRGGPYKTEPATDLGRWRLNCERGRQTWTYLQDERAGREQTGLEAYALG
LDTKNYFKDLPKAHTAFEGALNGMTFYVGLQAEDGHYDAVTTAVKKALRLNRAIQAHDG
HWPAENAGSLLYTPPLIIALYISGTIDTILTKQHKKELIRFVYNHQNEDGGWGSYIEGHS
TMIGSVLSYVMLRLLGEGLAESDDGNGAVERGRKWILDHGGAAGIPSWGKTYLAVLGVYE
WEGCNPLPPEFWLFPSSFPFHPAKMWIYCRCTYMPMSYLYGKRYHGPITDLVLSLRQEIY
NIPYEQIKWNQQRHNCCKEDLYYPHTLVQDLVWDGLHYFSEPFLKRWPFNKLRKRG
LKRVVELMRYGATETRFITTGNGEKALQIMSWWAEDPNGDEFKHHLARIPDFLWIAEDGM
TVQSFGSQLWDCILATQAIIATNMVEEYGDSLKKAHFFIKESQIKENPRGDFLKMC
RQFTKGAWTFSDQDHGCVVSDCTAEALKCLLLLSQMPQDIVGEKPEVERLYEAVNVLLYL
QSRVSGGFAVWEPPVPKPYLEMLNPSEIFADIVVEREHIECTASVIKGLMAFKCLH
PGHRQKEIEDSVAKAIRYLERNQMPDGSWYGFWGICFLYGTFFTLSGFASAGRTYDNSEA
VRKGVKFFLSTQNEEGGWGESLESCPSEKFTPLKGNRTNLVQTSWAMLGLMFGGQA
ERDPTPLHRAAKLLINAQMDNGDFPQQEITGVYCKNSMLHYAEYRNIFPLWALGEYRKRVW
Swiss Model is an automated system for modelling the 3D structure of a protein from its amino acid sequence using homology modelling techniques. We use OSC as the template to predict 3D model of Pangu. The model is named Pangu-Swiss Model.
After docking simulation, make the qualitative analysis of the results of the docking and evaluate model quality on Pangu.
Reference
Marco Biasini; Stefan Bienert; Andrew Waterhouse; Konstantin Arnold; Gabriel Studer; Tobias Schmidt; Florian Kiefer; Tiziano Gallo Cassarino; Martino Bertoni; Lorenza Bordoli; Torsten Schwede. (2014). SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information. Nucleic Acids Research (1 July 2014) 42 (W1): W252-W258; doi: 10.1093/nar/gku340.
Arnold, K., Bordoli, L., Kopp, J. and Schwede, T. (2006) The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling. Bioinformatics, 22, 195-201. Benkert, P., Biasini, M. and Schwede, T. (2011) Toward the estimation of the absolute quality of individual protein structure models. Bioinformatics, 27, 343-350
