Towards genome-scale structure prediction for transmembrane proteins

Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
Naama HurwitzD T Jones

Abstract

In this paper we briefly review some of the recent progress made by ourselves and others in developing methods for predicting the structures of transmembrane proteins from amino acid sequence. Transmembrane proteins are an important class of proteins involved in many diverse biological functions, many of which have great impact in terms of disease mechanism and drug discovery. Despite their biological importance, it has proven very difficult to solve the structures of these proteins by experimental techniques, and so there is a great deal of pressure to develop effective methods for predicting their structure. The methods we discuss range from methods for transmembrane topology prediction to new methods for low resolution folding simulations in a knowledge-based force field. This potential is designed to reproduce the properties of the lipid bilayer. Our eventual aim is to apply these methods in tandem so that useful three-dimensional models can be built for a large fraction of the transmembrane protein domains in whole proteomes.

References

May 1, 1990·Biochemistry·J L Popot, D M Engelman
Jan 1, 1990·Annual Review of Cell Biology·S J Singer
Aug 4, 1989·Science·D C ReesD Eisenberg
Jan 1, 1984·Proceedings of the National Academy of Sciences of the United States of America·D EisenbergT C Terwilliger
May 5, 1982·Journal of Molecular Biology·J Kyte, R F Doolittle
Mar 1, 1995·Protein Science : a Publication of the Protein Society·B RostC Sander
Apr 1, 1993·Health Economics·D J TorgersonI T Russell
Jan 1, 1993·Protein Engineering·P CronetG Vriend
Jan 1, 1993·Protein Science : a Publication of the Protein Society·D DonnellyT L Blundell
Jan 1, 1996·Nucleic Acids Research·A Bairoch, R Apweiler
Aug 1, 1996·Protein Science : a Publication of the Protein Society·B RostR Casadio
Jan 1, 1996·Progress in Biophysics and Molecular Biology·G von Heijne
Aug 15, 1997·Structure·C A OrengoJ M Thornton
Feb 12, 1998·Proceedings of the National Academy of Sciences of the United States of America·N N Dewji, S J Singer
Mar 27, 1998·FEBS Letters·D T Jones
May 6, 1998·Protein Science : a Publication of the Protein Society·E Wallin, G von Heijne
Oct 7, 1998·Protein Science : a Publication of the Protein Society·K SeshadriA Elofsson
Jun 18, 1999·Proteins·T J Stevens, I T Arkin
Jul 20, 1999·Annual Review of Biophysics and Biomolecular Structure·S H White, W C Wimley
Dec 11, 1999·Nucleic Acids Research·H M BermanP E Bourne
Mar 8, 2000·Microbiology and Molecular Biology Reviews : MMBR·M van Geest, J S Lolkema
Aug 31, 2000·Annual Review of Biochemistry·J L Popot, D M Engelman
Feb 24, 2001·Quarterly Reviews of Biophysics·G von Heijne
Jul 4, 2001·The Journal of Biological Chemistry·S H WhiteK Hristova
Sep 12, 2001·Current Opinion in Biotechnology·P AmstutzA Plückthun
May 30, 2002·Genome Génome / Conseil National De Recherches Canada·Paola LabombardaSergio Arcioni
Nov 21, 2002·Protein Science : a Publication of the Protein Society·Johan NilssonGunnar Von Heijne
Mar 1, 2003·Biophysical Journal·C-M Chen, C-C Chen
Mar 14, 2003·Journal of Molecular Biology·Karin MelénGunnar von Heijne
Jun 26, 2003·Nucleic Acids Research·Andrew Kernytsky, Burkhard Rost
Dec 21, 2004·Nucleic Acids Research·Nicola J MulderCathy H Wu
Jan 14, 2005·Nucleic Acids Research·Bin TianCarol S Lutz

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Citations

May 31, 2012·Proceedings of the National Academy of Sciences of the United States of America·Timothy Nugent, David T Jones
Mar 10, 2006·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·David T JonesJanet M Thornton
Sep 21, 2013·BMC Bioinformatics·Timothy Nugent, David T Jones
Mar 20, 2008·BMC Bioinformatics·Madhavi GanapathirajuJudith Klein-Seetharaman
Jul 8, 2011·Biology Direct·Jimin PeiNick V Grishin
Mar 26, 2013·Briefings in Bioinformatics·M Michael Gromiha, Yu-Yen Ou
Dec 5, 2006·FEBS Letters·Yanhong LiLing Yang
Oct 1, 2006·Expert Opinion on Drug Discovery·Adriano Martinelli, Tiziano Tuccinardi
Apr 5, 2007·Proteins·Cen Gao, Harry A Stern
Jan 16, 2007·Biophysical Journal·Martin B UlmschneiderAlfredo Di Nola
Sep 29, 2006·Journal of Molecular Biology·Sarel J FleishmanNir Ben-Tal
Jul 11, 2006·Current Opinion in Structural Biology·Sarel J Fleishman, Nir Ben-Tal
Apr 11, 2008·Structure·Kathryn A ScottMark S P Sansom
Nov 6, 2007·The Journal of Biological Chemistry·Meytal LandauNir Ben-Tal

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