Comparison of PGH2 binding site in prostaglandin synthases.

BMC Bioinformatics
Padmapriya Paragi-Vedanthi, Mukesh Doble

Abstract

Prostaglandin H2 (PGH2) is a common precursor for the synthesis of five different Prostanoids via specific Prostanoid Synthases. The binding of this substrate with these Synthases is not properly understood. Moreover, currently no crystal structure of complexes bound with PGH2 has been reported. Hence, understanding the interactions of PGH2 and characterizing its binding sites in these synthases is crucial for developing novel therapeutics based on these proteins as targets. Shape and physico-chemical properties of the PGH2 binding sites of the four prostanoid synthases were analyzed and compared in order to understand the molecular basis of the specificity. This study provides models with predicted pockets for the binding of PGH2 with PGD, PGE, PGF and PGI Synthases. The results closely match with available experimental data. The comparison showed seven physico-chemical features that are common to the four PGH2 binding sites. However this common pattern is not statistically unique and is not specific enough to distinguish between proteins that can or cannot bind PGH2. A large scale search in ASTRAL data bank, a non redundant Protein Data Bank, for a similar pattern showed the uniqueness of each of the PGH2 binding site in thes...Continue Reading

References

Aug 1, 1992·The American Journal of Physiology·W L Smith
Jan 18, 1969·Nature·C S WrightJ Kraut
Dec 29, 1998·The Journal of Biological Chemistry·T SuzukiK Watanabe
Dec 11, 1999·Nucleic Acids Research·M Kanehisa, S Goto
Dec 11, 1999·Nucleic Acids Research·H M BermanP E Bourne
Dec 11, 1999·Nucleic Acids Research·S E BrennerM Levitt
Nov 16, 2002·Prostaglandins & Other Lipid Mediators·Makoto MurakamiIchiro Kudo
Nov 16, 2002·Prostaglandins & Other Lipid Mediators·Kikuko Watanabe
Nov 16, 2002·Prostaglandins & Other Lipid Mediators·Lee-Ho Wang, Richard J Kulmacz
Mar 11, 2003·Nature Structural Biology·Tsuyoshi InoueYoshihiro Urade
Jun 5, 2003·Proteins·Dina Schneidman-DuhovnyHaim J Wolfson
Jun 14, 2003·Biochemical and Biophysical Research Communications·Kikuko WatanabeYoshihiro Ohmiya
Aug 5, 2003·Prostaglandins, Leukotrienes, and Essential Fatty Acids·Yoshihide Kanaoka, Yoshihiro Urade
Nov 7, 2003·European Journal of Vascular and Endovascular Surgery : the Official Journal of the European Society for Vascular Surgery·J Vane, R E Corin
Dec 19, 2003·Nucleic Acids Research·John-Marc ChandoniaSteven E Brenner
Dec 20, 2003·Prostaglandins, Leukotrienes, and Essential Fatty Acids·Rachel J A HelliwellMurray D Mitchell
Feb 3, 2004·The Journal of Biological Chemistry·Tali GidalevitzYair Argon
Feb 26, 2004·Biochemistry·Junichi KomotoFusao Takusagawa
Apr 29, 2004·Journal of Biochemistry·Tsuyoshi InoueYoshihiro Urade
Apr 28, 2005·Journal of Molecular Biology·Taro YamadaFusao Takusagawa
Jun 28, 2005·Nucleic Acids Research·Dina Schneidman-DuhovnyHaim J Wolfson
Jun 28, 2005·Proteins·Yuval InbarHaim J Wolfson
Mar 17, 2006·Clinical Immunology : the Official Journal of the Clinical Immunology Society·Jean Y ParkSteven B Abramson
Apr 7, 2006·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Maxim ShatskyHaim J Wolfson
Jul 4, 2006·Trends in Pharmacological Sciences·Klaus Scholich, Gerd Geisslinger
Oct 6, 2006·Journal of Molecular Biology·Chia-Wang ChiangNei-Li Chan

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