Solution Structure of a Soluble Fragment Derived from a Membrane Protein by Shotgun Proteolysis

Overview

Journal Protein Eng Des Sel

Publisher Oxford University Press

Specialties Biochemistry
Biotechnology

Date 2015 Apr 17

PMID 25877662

Citations 2

Authors

Mark D Allen

Mary Christie

Peter Jones

Benjamin T Porebski

Brendan Roome

Stefan M V Freund

Ashley M Buckle

Mark Bycroft

Daniel Christ

Affiliations

Soon will be listed here.

Abstract

We have previously reported a phage display method for the identification of protein domains on a genome-wide scale (shotgun proteolysis). Here we present the solution structure of a fragment of the Escherichia coli membrane protein yrfF, as identified by shotgun proteolysis, and determined by NMR spectroscopy. Despite the absence of computational predictions, the fragment formed a well-defined beta-barrel structure, distantly falling within the OB-fold classification. Our results highlight the potential of high-throughput experimental approaches for the identification of protein domains for structural studies.

Citing Articles

RcsF-independent mechanisms of signaling within the Rcs phosphorelay.

Petchiappan A, Majdalani N, Wall E, Gottesman S PLoS Genet. 2024; 20(12):e1011408.

PMID: 39724052 PMC: 11709261. DOI: 10.1371/journal.pgen.1011408.

Evolutionary analysis and structure modelling of the Rcs-repressor IgaA unveil a functional role of two cytoplasmic small β-barrel (SBB) domains.

Rodriguez L, Penalver M, Casino P, Garcia-Del Portillo F Heliyon. 2023; 9(6):e16661.

PMID: 37303533 PMC: 10248123. DOI: 10.1016/j.heliyon.2023.e16661.

Distinct domains of Escherichia coli IgaA connect envelope stress sensing and down-regulation of the Rcs phosphorelay across subcellular compartments.

Hussein N, Cho S, Laloux G, Siam R, Collet J PLoS Genet. 2018; 14(5):e1007398.

PMID: 29852010 PMC: 5978795. DOI: 10.1371/journal.pgen.1007398.

References

Porter R . The hydrolysis of rabbit y-globulin and antibodies with crystalline papain. Biochem J. 1959; 73:119-26. PMC: 1197021. DOI: 10.1042/bj0730119. View

Kelley L, MacCallum R, STERNBERG M . Enhanced genome annotation using structural profiles in the program 3D-PSSM. J Mol Biol. 2000; 299(2):499-520. DOI: 10.1006/jmbi.2000.3741. View

Cornilescu G, Delaglio F, Bax A . Protein backbone angle restraints from searching a database for chemical shift and sequence homology. J Biomol NMR. 1999; 13(3):289-302. DOI: 10.1023/a:1008392405740. View

Dodd R, Allen M, Brown S, Sanderson C, Duncan L, Lehner P . Solution structure of the Kaposi's sarcoma-associated herpesvirus K3 N-terminal domain reveals a Novel E2-binding C4HC3-type RING domain. J Biol Chem. 2004; 279(51):53840-7. DOI: 10.1074/jbc.M409662200. View

Cabantous S, Waldo G . In vivo and in vitro protein solubility assays using split GFP. Nat Methods. 2006; 3(10):845-54. DOI: 10.1038/nmeth932. View

Finn R, Clements J, Eddy S . HMMER web server: interactive sequence similarity searching. Nucleic Acids Res. 2011; 39(Web Server issue):W29-37. PMC: 3125773. DOI: 10.1093/nar/gkr367. View

Dyson M, Perera R, Shadbolt S, Biderman L, Bromek K, Murzina N . Identification of soluble protein fragments by gene fragmentation and genetic selection. Nucleic Acids Res. 2008; 36(9):e51. PMC: 2396403. DOI: 10.1093/nar/gkn151. View

Bachmann B . Pedigrees of some mutant strains of Escherichia coli K-12. Bacteriol Rev. 1972; 36(4):525-57. PMC: 408331. DOI: 10.1128/br.36.4.525-557.1972. View

Christ D, Winter G . Identification of protein domains by shotgun proteolysis. J Mol Biol. 2006; 358(2):364-71. DOI: 10.1016/j.jmb.2006.01.057. View

10.

Englander S, Wand A . Main-chain-directed strategy for the assignment of 1H NMR spectra of proteins. Biochemistry. 1987; 26(19):5953-8. DOI: 10.1021/bi00393a001. View

11.

Madera M, Vogel C, Kummerfeld S, Chothia C, Gough J . The SUPERFAMILY database in 2004: additions and improvements. Nucleic Acids Res. 2003; 32(Database issue):D235-9. PMC: 308851. DOI: 10.1093/nar/gkh117. View

12.

DAngelo S, Velappan N, Mignone F, Santoro C, Sblattero D, Kiss C . Filtering "genic" open reading frames from genomic DNA samples for advanced annotation. BMC Genomics. 2011; 12 Suppl 1:S5. PMC: 3223728. DOI: 10.1186/1471-2164-12-S1-S5. View

13.

Cho S, Szewczyk J, Pesavento C, Zietek M, Banzhaf M, Roszczenko P . Detecting envelope stress by monitoring β-barrel assembly. Cell. 2014; 159(7):1652-64. DOI: 10.1016/j.cell.2014.11.045. View

14.

Bernstein F, Koetzle T, Williams G, Meyer Jr E, Brice M, Rodgers J . The Protein Data Bank: a computer-based archival file for macromolecular structures. Arch Biochem Biophys. 1978; 185(2):584-91. DOI: 10.1016/0003-9861(78)90204-7. View

15.

Guindon S, Dufayard J, Lefort V, Anisimova M, Hordijk W, Gascuel O . New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol. 2010; 59(3):307-21. DOI: 10.1093/sysbio/syq010. View

16.

Brunger A . Version 1.2 of the Crystallography and NMR system. Nat Protoc. 2007; 2(11):2728-33. DOI: 10.1038/nprot.2007.406. View

17.

Letunic I, Doerks T, Bork P . SMART 7: recent updates to the protein domain annotation resource. Nucleic Acids Res. 2011; 40(Database issue):D302-5. PMC: 3245027. DOI: 10.1093/nar/gkr931. View

18.

Jones D . Protein secondary structure prediction based on position-specific scoring matrices. J Mol Biol. 1999; 292(2):195-202. DOI: 10.1006/jmbi.1999.3091. View

19.

Pedelacq J, Nguyen H, Cabantous S, Mark B, Listwan P, Bell C . Experimental mapping of soluble protein domains using a hierarchical approach. Nucleic Acids Res. 2011; 39(18):e125. PMC: 3185438. DOI: 10.1093/nar/gkr548. View

20.

Shi J, Blundell T, Mizuguchi K . FUGUE: sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties. J Mol Biol. 2001; 310(1):243-57. DOI: 10.1006/jmbi.2001.4762. View