Protein-protein interaction and coarse grained simulation study of glioblastoma multiforme reveals novel pathways of Gpr17

• Autorzy: Gnanavel M. , Yli-Harja O. , Kandhavelu M.
• Języki publikacji: EN

Abstrakty

EN

Studies of receptor mediated signaling networks in neuronal cells pro vide a unique opportunity to uncover the basis of many diseases. Receptor signaling c ascades proceed from the cell surface, where extra cellular factors interact with their specific receptors e.g. G-Protein Coupled Receptors ( GPR ). Recent studies have shown that the activation or suppression of GPR 17 in diseased neuronal cells has potential impact in altering the tumor con ditions. We identified many hundred times expressions of GPR 17 in Glioblastoma Multiforme ( GBM ) from the RNA -Seq data. We also observed many other genes having similar expression patt erns with GPR 17, indicating possible connections of this receptor with diverse gen e products. We performed a coarse-grained simulation of ∼ 500 proteins inside a cytoplasm like a box with solvent water molecules. The summarized protein interaction networks r esulted from a coarsegrained simulation and large scale protein-protein docking reveals nov el molecular connections and pathways.

Słowa kluczowe

EN

signaling network; RNA-Seq; coarse-grain; Glioblastoma Multiforme; pathways

PL

sieci sygnalizacyjne; RNA Seq; glejak wielopostaciowy

• Wydawca: Politechnika Gdańska
• Czasopismo: TASK Quarterly : scientific bulletin of Academic Computer Centre in Gdansk
• Rocznik: 2014
• Tom: Vol. 18, No 4
• Strony: 321--325
• Opis fizyczny: Bibliogr. 15 poz., rys., wykr., tab.

Twórcy

autor

Gnanavel M.

• Molecular Signaling Lab, Computational Systems Biology Signal Processing Department, Tampere University of Technology 33101 Tampere, Finland

autor

Yli-Harja O.

• Molecular Signaling Lab, Computational Systems Biology Signal Processing Department, Tampere University of Technology 33101 Tampere, Finland
• Institute for Systems Biology 1441N 34th St, Seattle, WA 98103–8904, USA

autor

Kandhavelu M.

• Molecular Signaling Lab, Computational Systems Biology Signal Processing Department, Tampere University of Technology 33101 Tampere, Finland

Bibliografia

• [1] Hennen S, Wang H, Peters L, Merten N, Simon K, Spinrath A, Bl ̈attermann S, Akkari R, Schrage R, Schr ̈oder R, Schulz D, Vermeiren C, Zimmermann K, Kehraus S, Drewke C, Pfeifer A, K ̈onig G M, Mohr K, Gillard M, M ̈uller C E, Lu Q R, Gomeza J and Kostenis E 2013 Sci. Signal. 6 , ra93
• [2] Lecca D, Trincavelli M L, Gelosa P, Sironi L, Ciana P, Fumagalli M, Villa G , Verderio C, Grumelli C, Guerrini U, Tremoli E, Rosa P, Cuboni S, Martini C, Buffo A, Cimino M and Abbracchio M P 2008 PloS One 3 (10) , e3579
• [3] Benned-Jensen T and Rosenkilde M M 2010 Br. J. Pharmacol. 159 (5) 1092
• [4] Marucci G, Lammi C, Buccioni M, Dal Ben D, Lambertucci C, Amantini C, Santoni G, Kandhavelu M, Abbracchio M P, Lecca D, Volpini R and Cristalli G 2011 Anal. Biochem. 414 300
• [5] Boda E, Vigan`o F, Rosa P, Fumagalli M, Labat-Gest V, Tempia F, Abbracchio M P, Dimou L and Buffo A 2011 Glia 59 ( 12 ) 1958
• [6] Apweiler R, Bairoch A, Wu C H, Barker W C, Boeckmann B, Ferro S, Gasteiger E, Huang H, Lopez R, Magrane M, Martin M J, Natale D A, O’Donovan C, Redaschi N and Yeh L-S L 2004 Nucleic Acids Res. 32 , D115
• [7] Berman H M, Westbrook J, Feng Z, Gilliland G, Bhat T N, Weissig H, Shindy alov I N and Bourne P E 2000 The Protein Data Bank, Nucleic Acids Res. 28 235
• [8] Sali A and Blundell T L 1993 Comparative protein modelling by satisfaction of spatial restraints, J. Mol. Biol. 234 779
• [9] Phillips J C, Braun R, Wang W, Gumbart J, Tajkhorshid E, Villa E, Chipot C, Skeel R D, Kal ́e L and Schulten K 2005 Scalable molecular dynamics with NAMD 26
• [10] Collins F S 2007 The Cancer Genome Atlas (TCGA)
• [11] Anders S and Huber W 2010 Genome Biol 11 , R106
• [12] McGuffee S R and Elcock A H 2010 PLoS Comput. Biol. 6
• [13] Marrink S J, Risselada H J, Yefimov S, Tieleman D P and De Vries A H 2007 J. Phys. Chem. B 111 7812
• [14] Pronk S, P ́all S, Schulz R, Larsson P, Bjelkmar P, Apostolov R, Shirts M R, Smith J C, Kasson P M, Van Der Spoel D, Hess B and Lindahl E 2013 Bioinformatics 29 845
• [15] Shannon P, Markiel A, Ozier O, Baliga N S, Wang J T, Ramage D, Amin N, Schwikowski B and Ideker T 2003 Genome Res. 13 2498