3D profile-based approach to proteome-wide discovery of novel human chemokines.

PloS One
Aurelie TomczakM Teresa Pisabarro

Abstract

Chemokines are small secreted proteins with important roles in immune responses. They consist of a conserved three-dimensional (3D) structure, so-called IL8-like chemokine fold, which is supported by disulfide bridges characteristic of this protein family. Sequence- and profile-based computational methods have been proficient in discovering novel chemokines by making use of their sequence-conserved cysteine patterns. However, it has been recently shown that some chemokines escaped annotation by these methods due to low sequence similarity to known chemokines and to different arrangement of cysteines in sequence and in 3D. Innovative methods overcoming the limitations of current techniques may allow the discovery of new remote homologs in the still functionally uncharacterized fraction of the human genome. We report a novel computational approach for proteome-wide identification of remote homologs of the chemokine family that uses fold recognition techniques in combination with a scaffold-based automatic mapping of disulfide bonds to define a 3D profile of the chemokine protein family. By applying our methodology to all currently uncharacterized human protein sequences, we have discovered two novel proteins that, without having ...Continue Reading

References

Feb 1, 1996·European Journal of Immunology·A A MaghazachiT J Schall
Feb 1, 1996·Journal of Molecular Graphics·W HumphreyK Schulten
Sep 1, 1997·Nucleic Acids Research·S F AltschulD J Lipman
May 30, 1998·Proceedings of the National Academy of Sciences of the United States of America·J SchultzC P Ponting
Apr 6, 1999·Journal of Neurovirology·J Hesselgesser, R Horuk
Apr 9, 1999·Protein Engineering·B Rost
May 8, 1999·Gene·J E Tabaska, M Q Zhang
Jul 1, 1999·Journal of Interferon & Cytokine Research : the Official Journal of the International Society for Interferon and Cytokine Research·K A Roebuck
May 9, 2000·The Journal of Immunology : Official Journal of the American Association of Immunologists·P GéninJ Hiscott
Jul 6, 2000·Cytokine·T P ShanleyA Denenberg
Aug 15, 2000·Annual Review of Biophysics and Biomolecular Structure·M A Martí-RenomA Sali
Feb 24, 2001·Bratislavské lekárske listy·M Buc, M Bucova
Feb 9, 2002·Proteins·M J SipplM Wiederstein
Sep 17, 2002·Briefings in Bioinformatics·Christian J A SigristPhilipp Bucher
Mar 26, 2003·Cytokine & Growth Factor Reviews·Xuri Li, Ulf Eriksson
Apr 30, 2003·Expert Opinion on Biological Therapy·Robert J B Nibbs, Gerard J Graham
Jun 26, 2003·Nucleic Acids Research·Pål PuntervollToby J Gibson
Oct 28, 2003·Proteins·Lisa N KinchNick V Grishin
Dec 19, 2003·Nucleic Acids Research·Alex BatemanSean R Eddy
Jan 28, 2004·Comptes rendus biologies·Orit ShmueliDoron Lancet
Apr 30, 2004·Protein Engineering, Design & Selection : PEDS·Jannick Dyrløv BendtsenSøren Brunak
May 21, 2004·Protein Science : a Publication of the Protein Society·Guoli Wang, Roland L Dunbrack
Jun 25, 2004·Nucleic Acids Research·Karsten HillerDieter Jahn
Aug 6, 2004·The European Respiratory Journal·A GerberF Bühling
Sep 2, 2004·Protein Science : a Publication of the Protein Society·Zemin Zhang, William J Henzel
Oct 23, 2004·Proceedings of the National Academy of Sciences of the United States of America·Dafang WanJianren Gu
Jul 12, 2005·Biochemical and Biophysical Research Communications·Giovanni MagistrelliNicolas Fischer
Sep 28, 2005·Proteins·Guoli WangRoland L Dunbrack
Oct 8, 2005·Journal of Computational Chemistry·David Van Der SpoelHerman J C Berendsen
Dec 31, 2005·Nucleic Acids Research·Cathy H WuBaris Suzek
Jan 13, 2006·British Journal of Pharmacology·James E Pease, Timothy J Williams

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Citations

Sep 17, 2013·Protein Science : a Publication of the Protein Society·Mark R BellJames E Strickler
Feb 5, 2021·ACS Nano·Marcelo D T TorresCesar de la Fuente-Nunez

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Methods Mentioned

BETA
glycosylation
X-ray
transfection
Circular Dichroism
PCR
transgenic
electrophoresis
chips
infrared

Software Mentioned

XtractAll
GROMOS96
Peakfit
VMD
Discovery Studio
ProHit Professional
Ensembl genebuild
ELM
Memsat
MOE

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