Network pattern of residue packing in helical membrane proteins and its application in membrane protein structure prediction

Protein Engineering, Design & Selection : PEDS
Vagmita Pabuwal, Zhijun Li

Abstract

De novo protein structure prediction plays an important role in studies of helical membrane proteins as well as structure-based drug design efforts. Developing an accurate scoring function for protein structure discrimination and validation remains a current challenge. Network approaches based on overall network patterns of residue packing have proven useful in soluble protein structure discrimination. It is thus of interest to apply similar approaches to the studies of residue packing in membrane proteins. In this work, we first carried out such analysis on a set of diverse, non-redundant and high-resolution membrane protein structures. Next, we applied the same approach to three test sets. The first set includes nine structures of membrane proteins with the resolution worse than 2.5 A; the other two sets include a total of 101 G-protein coupled receptor models, constructed using either de novo or homology modeling techniques. Results of analyses indicate the two criteria derived from studying high-resolution membrane protein structures are good indicators of a high-quality native fold and the approach is very effective for discriminating native membrane protein folds from less-native ones. These findings should be of help for...Continue Reading

References

May 1, 1990·Biochemistry·J L Popot, D M Engelman
Jan 1, 1986·Annual Review of Biophysics and Biophysical Chemistry·D M EngelmanA Goldman
Oct 25, 1996·Journal of Medicinal Chemistry·M KontoyianniT P Lybrand
Jun 13, 1997·Journal of Molecular Biology·T ShiehS O Smith
Sep 1, 1997·Nucleic Acids Research·S F AltschulD J Lipman
Feb 21, 1998·Nucleic Acids Research·F HornG Vriend
May 6, 1998·Protein Science : a Publication of the Protein Society·E Wallin, G von Heijne
Nov 1, 1996·Nature Biotechnology·J Drews
Sep 24, 1999·Journal of Molecular Biology·N Kannan, S Vishveshwara
Jan 13, 2000·Protein Science : a Publication of the Protein Society·J U Bowie
Feb 19, 2000·Current Opinion in Biotechnology·K G Fleming
May 24, 2000·Proceedings of the National Academy of Sciences of the United States of America·M EilersP J Fleming
Aug 10, 2000·Nature·R AlbertA L Barabasi
Mar 10, 2001·Nature·E J Nestler, D Landsman
Jun 8, 2001·Proteins·D J JacobsM F Thorpe
Jul 21, 2001·Biophysical Journal·J Liang, K A Dill
Aug 24, 2001·Journal of Molecular Biology·L Adamian, J Liang
Oct 23, 2001·Methods in Enzymology·Irache VisiersHarel Weinstein
Apr 20, 2002·Biophysical Journal·Markus EilersSteven O Smith
Jun 27, 2002·Proceedings of the National Academy of Sciences of the United States of America·Nikolay V DokholyanEugene I Shakhnovich
Aug 22, 2002·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·M VendruscoloM Karplus
Oct 4, 2002·Chembiochem : a European Journal of Chemical Biology·Thomas Klabunde, Gerhard Hessler
Jan 10, 2003·Nucleic Acids Research·Brigitte BoeckmannMichel Schneider
Feb 13, 2003·Journal of Molecular Biology·Pramod P WangikarSunita Sarawagi
Oct 29, 2003·Trends in Endocrinology and Metabolism : TEM·Sadashiva S KarnikTakanobu Takezako
Nov 26, 2003·Journal of Molecular Biology·Lesley H Greene, Victoria A Higman
Dec 26, 2003·Biophysical Journal·Ali Rana AtilganCanan Baysal
Apr 28, 2004·FEBS Letters·L OliveiraG Vriend
Jun 25, 2004·Protein Science : a Publication of the Protein Society·Stephen H White
Sep 2, 2004·Biophysical Journal·Aaron K Chamberlain, James U Bowie
Sep 2, 2004·Protein Science : a Publication of the Protein Society·Ken SaleMalin M Young
Oct 7, 2004·Biophysical Journal·Marina GimpelevBarry Honig
Nov 17, 2004·Journal of Molecular Biology·Gil AmitaiShmuel Pietrokovski
Dec 21, 2004·Nucleic Acids Research·Gábor E TusnádyIstván Simon
Jul 1, 2005·Protein Science : a Publication of the Protein Society·Andreas Bernsel, Gunnar Von Heijne
Sep 15, 2005·Chemical Reviews·Francesca Fanelli, Pier G De Benedetti
Sep 17, 2005·Science·Philip BradleyDavid Baker
Sep 24, 2005·Nature·Michael SocolichRama Ranganathan
Mar 28, 2006·Protein Engineering, Design & Selection : PEDS·Usha K Muppirala, Zhijun Li

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Citations

Mar 8, 2012·Journal of Computer-aided Molecular Design·Andrew J Heim, Zhijun Li
Dec 5, 2008·Protein Engineering, Design & Selection : PEDS·Vagmita Pabuwal, Zhijun Li
Nov 11, 2017·Scientific Reports·Jayaraman ThangappanSun-Gu Lee
Apr 24, 2009·Journal of Biomolecular Structure & Dynamics·Anupam Nath Jha, Saraswathi Vishveshwara

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