title: Uses of phage display in agriculture: sequence analysis and comparative modeling of late embryogenesis abundant client proteins suggest protein-nucleic acid binding functionality.
abstract: A group of intrinsically disordered, hydrophilic proteins-Late Embryogenesis Abundant (LEA) proteins-has been linked to survival in plants and animals in periods of stress, putatively through safeguarding enzymatic function and prevention of aggregation in times of dehydration/heat. Yet despite decades of effort, the molecular-level mechanisms defining this protective function remain unknown. A recent effort to understand LEA functionality began with the unique application of phage display, wherein phage display and biopanning over recombinant Seed Maturation Protein homologs from Arabidopsis thaliana and Glycine max were used to retrieve client proteins at two different temperatures, with one intended to represent heat stress. From this previous study, we identified 21 client proteins for which clones were recovered, sometimes repeatedly. Here, we use sequence analysis and homology modeling of the client proteins to ascertain common sequence and structural properties that may contribute to binding affinity with the protective LEA protein. Our methods uncover what appears to be a predilection for protein-nucleic acid interactions among LEA client proteins, which is suggestive of subcellular residence. The results from this initial computational study will guide future efforts to uncover the protein protective mechanisms during heat stress, potentially leading to phage-display-directed evolution of synthetic LEA molecules.
authors: Agricultural Science Center, Department of Horticulture, University of Kentucky, Lexington, KY 40546, USA.
authors: Rekha
authors: R
authors: Kushwaha
authors: A Bruce
authors: AB
authors: Downie
authors: Christina M
authors: CM
authors: Payne
mesh_terms: D000383:Agriculture; D000595:Amino Acid Sequence; D029681:Arabidopsis Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D003198:Computer Simulation; D018869:Heat-Shock Response; D064267:Intrinsically Disordered Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009696:Nucleic Acids / Q000378:metabolism; D019151:Peptide Library; D010940:Plant Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D011485:Protein Binding; D011487:Protein Conformation
chemical_list: D029681:Arabidopsis Proteins; D064267:Intrinsically Disordered Proteins; D009696:Nucleic Acids; D019151:Peptide Library; D010940:Plant Proteins; C066246:late embryogenesis abundant protein, plant
references: FEBS Lett. 1985 Jul 1;186(1):1-7
references: 2989003
references: Proteins. 2010 May 15;78(7):1798-802
references: 20196080
references: Structure. 2008 Apr;16(4):535-48
references: 18400176
references: Trends Genet. 2000 Jun;16(6):276-7
references: 10827456
references: Proc Natl Acad Sci U S A. 2010 Nov 16;107(46):19754-9
references: 20974910
references: Plant Physiol. 2003 Mar;131(3):963-75
references: 12644649
references: Bioinformatics. 2006 Jan 15;22(2):195-201
references: 16301204
references: Plant Cell. 2007 May;19(5):1580-9
references: 17526751
references: Trends Biochem Sci. 1991 Jul;16(7):246-50
references: 1926332
references: Nucleic Acids Res. 2007 Jul;35(Web Server issue):W585-7
references: 17517783
references: Comp Biochem Physiol B Biochem Mol Biol. 2001 Apr;128(4):613-24
references: 11290443
references: Science. 2011 Dec 16;334(6062):1524-9
references: 22096102
references: Biochem J. 2005 May 15;388(Pt 1):151-7
references: 15631617
references: Bioinformatics. 2005 Apr 1;21(7):951-60
references: 15531603
references: Biochim Biophys Acta. 2001 Jan 12;1544(1-2):196-206
references: 11341929
references: Nucleic Acids Res. 2010 Jan;38(Database issue):D211-22
references: 19920124
references: EMBO J. 1982;1(8):945-51
references: 6329717
references: Protein Sci. 2005 Oct;14(10):2601-9
references: 16155204
references: Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W335-9
references: 16845021
references: BMC Bioinformatics. 2008 Jul 17;9:312
references: 18637174
references: Plant Physiol. 1999 May;120(1):237-44
references: 10318701
references: J Mol Biol. 1998 May 29;279(1):257-70
references: 9636715
references: Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W244-8
references: 15980461
references: Biochemistry. 1981 Jul 7;20(14):4162-8
references: 7284317
references: J Mol Biol. 2004 Jun 25;340(1):141-77
references: 15184028
references: Trends Biochem Sci. 1990 Nov;15(11):430-4
references: 2126155
references: Nucleic Acids Res. 2000 Jan 1;28(1):235-42
references: 10592235
references: Science. 2011 Nov 18;334(6058):941-8
references: 22052974
references: Proc Natl Acad Sci U S A. 1981 Jun;78(6):3824-8
references: 6167991
references: Bioinformatics. 1999 Apr;15(4):305-8
references: 10320398
references: J Mol Biol. 1982 May 5;157(1):105-32
references: 7108955
references: Int J Mol Sci. 2012;13(6):6582-6603
references: 22837651
references: Proc Natl Acad Sci U S A. 1986 Feb;83(4):907-11
references: 2869483
references: Plant Physiol. 2006 Jun;141(2):638-50
references: 16565295
references: Annu Rev Physiol. 1998;60:73-103
references: 9558455
references: Proteins. 2009 May 1;75(2):518-23
references: 19137618
references: Nucleic Acids Res. 2009 Jan;37(Database issue):D387-92
references: 18931379
references: Cryobiology. 2004 Jun;48(3):215-28
references: 15157771
references: Structure. 2006 Jan;14(1):43-50
references: 16407064
references: Protein Sci. 1995 Aug;4(8):1587-95
references: 8520485
references: Annu Rev Physiol. 2011;73:115-34
references: 21034219
references: Proc Natl Acad Sci U S A. 2012 Oct 2;109(40):16149-54
references: 22991464
references: Proc Natl Acad Sci U S A. 2000 Feb 29;97(5):2385-90
references: 10681458
references: Plant Cell Environ. 2010 Mar;33(3):418-30
references: 20002332
references: Biopolymers. 2007 Apr 5-15;85(5-6):456-70
references: 17219397
references: Biol Chem. 1996 Sep;377(9):555-61
references: 9067253
references: Enzyme Microb Technol. 1994 Jun;16(6):450-6
references: 7764886
references: J Cell Biol. 1988 Sep;107(3):897-905
references: 2901422
references: Proc Natl Acad Sci U S A. 1987 Apr;84(7):1814-8
references: 3104905
references: Nat Methods. 2011 Dec 25;9(2):173-5
references: 22198341
references: Plant Physiol. 2010 Sep;154(1):373-90
references: 20668063
references: Biochim Biophys Acta. 2010 Jul;1804(7):1432-42
references: 20215054
references: J Mol Biol. 1993 Feb 20;229(4):1165-74
references: 8445645
references: Science. 2006 Sep 29;313(5795):1968-72
references: 16931718
references: Mol Med Today. 1995 Sep;1(6):270-7
references: 9415161
references: Nat Protoc. 2009;4(1):1-13
references: 19131951
references: Trends Cell Biol. 2009 May;19(5):228-35
references: 19342240
references: Plant Physiol. 2000 Feb;122(2):597-608
references: 10677452
references: Plant Physiol. 2002 Mar;128(3):822-32
references: 11891239
references: Bioinformatics. 2011 Feb 1;27(3):343-50
references: 21134891
references: J Biol Chem. 2010 Nov 26;285(48):37281-92
references: 20870712