Small peptide binding stiffens the ubiquitin-like protein SUMO1

Biophysical Journal

Volumn 108, Issue 2, 2015, Pages 360-367

  Kotamarthi, Hema Chandra ^a   Yadav, Anju ^a   Ainavarapu, Sri Rama Koti ^a  

^a TATA INSTITUTE OF FUNDAMENTAL RESEARCH   (India)

Author keywords

[No Author keywords available]

Indexed keywords

EUKARYOTA;

PEPTIDE FRAGMENT; PROTEIN BINDING; SUMO 1 PROTEIN; SUMO1 PROTEIN, HUMAN;

AMINO ACID SEQUENCE; CHEMISTRY; HUMAN; METABOLISM; MOLECULAR DYNAMICS; MOLECULAR GENETICS; PROTEIN FOLDING; PROTEIN TERTIARY STRUCTURE;

AMINO ACID SEQUENCE; HUMANS; MOLECULAR DYNAMICS SIMULATION; MOLECULAR SEQUENCE DATA; PEPTIDE FRAGMENTS; PROTEIN BINDING; PROTEIN FOLDING; PROTEIN STRUCTURE, TERTIARY; SUMO-1 PROTEIN;

EID: 84921453925     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1016/j.bpj.2014.11.3474     Document Type: Article

References (34)

1. J.M. Sanchez-Ruiz Ligand effects on protein thermodynamic stability Biophys. Chem. 126 2007 43 49
2. X. Hu, and H. Li Force spectroscopy studies on protein-ligand interactions: a single protein mechanics perspective FEBS Lett. 588 2014 3613 3620
3. 2+ binding enhanced mechanical stability of an archaeal crystallin PLoS ONE 9 2014 e94513
4. H.C. Kotamarthi, and R. Sharma S.R. Ainavarapu Multiple unfolding pathways of leucine binding protein (LBP) probed by single-molecule force spectroscopy (SMFS) J. Am. Chem. Soc. 135 2013 14768 14774
5. S.R. Ainavarapu, and L. Li J.M. Fernandez Ligand binding modulates the mechanical stability of dihydrofolate reductase Biophys. J. 89 2005 3337 3344
6. G. Arad-Haase, and S.G. Chuartzman Z. Reich Mechanical unfolding of acylphosphatase studied by single-molecule force spectroscopy and MD simulations Biophys. J. 99 2010 238 247
7. M. Bertz, and M. Rief Ligand binding mechanics of maltose binding protein J. Mol. Biol. 393 2009 1097 1105
8. Y. Cao, T. Yoo, and H. Li Single molecule force spectroscopy reveals engineered metal chelation is a general approach to enhance mechanical stability of proteins Proc. Natl. Acad. Sci. USA 105 2008 11152 11157
9. M. Zocher, and C. Zhang D.J. Müller Cholesterol increases kinetic, energetic, and mechanical stability of the human β2-adrenergic receptor Proc. Natl. Acad. Sci. USA 109 2012 E3463 E3472
10. M.M. DuVall, and J.L. Gifford W. Herzog Altered mechanical properties of titin immunoglobulin domain 27 in the presence of calcium Eur. Biophys. J. 42 2013 301 307
11. E. Hann, and N. Kirkpatrick D.J. Brockwell The effect of protein complexation on the mechanical stability of Im9 Biophys. J. 92 2007 L79 L81
12. C. Horejs, and R. Ristl D. Pum Single-molecule force spectroscopy reveals the individual mechanical unfolding pathways of a surface layer protein J. Biol. Chem. 286 2011 27416 27424
13. J. Song, and Z. Zhang Y. Chen Small ubiquitin-like modifier (SUMO) recognition of a SUMO binding motif: a reversal of the bound orientation J. Biol. Chem. 280 2005 40122 40129
14. J.R. Gareau, and C.D. Lima The SUMO pathway: emerging mechanisms that shape specificity, conjugation and recognition Nat. Rev. Mol. Cell Biol. 11 2010 861 871
15. R. Geiss-Friedlander, and F. Melchior Concepts in sumoylation: a decade on Nat. Rev. Mol. Cell Biol. 8 2007 947 956
16. J. Song, and L.K. Durrin Y. Chen Identification of a SUMO-binding motif that recognizes SUMO-modified proteins Proc. Natl. Acad. Sci. USA 101 2004 14373 14378
17. C.S. Seu, and Y. Chen Identification of SUMO-binding motifs by NMR Methods Mol. Biol. 497 2009 121 138
18. J.R. Gareau, D. Reverter, and C.D. Lima Determinants of small ubiquitin-like modifier 1 (SUMO1) protein specificity, E3 ligase, and SUMO-RanGAP1 binding activities of nucleoporin RanBP2 J. Biol. Chem. 287 2012 4740 4751
19. H.C. Kotamarthi, R. Sharma, and S.R. Koti Ainavarapu Single-molecule studies on PolySUMO proteins reveal their mechanical flexibility Biophys. J. 104 2013 2273 2281
20. M. Carrion-Vazquez, and A.F. Oberhauser J.M. Fernandez Mechanical and chemical unfolding of a single protein: a comparison Proc. Natl. Acad. Sci. USA 96 1999 3694 3699
21. V. Aggarwal, and S.R. Kulothungan S.R.K. Ainavarapu Ligand-modulated parallel mechanical unfolding pathways of maltose-binding proteins J. Biol. Chem. 286 2011 28056 28065
22. E.L. Florin, and M. Rief H.E. Gaub Sensing specific molecular interactions with the atomic force microscope Biosens. Bioelectron. 10 1995 895 901
23. C. Bustamante, and J.F. Marko S. Smith Entropic elasticity of lambda-phage DNA Science 265 1994 1599 1600
24. H. Dietz, and F. Berkemeier M. Rief Anisotropic deformation response of single protein molecules Proc. Natl. Acad. Sci. USA 103 2006 12724 12728
25. M. Schlierf, and M. Rief Temperature softening of a protein in single-molecule experiments J. Mol. Biol. 354 2005 497 503
26. A.J. Xu, and T.A. Springer Calcium stabilizes the von Willebrand factor A2 domain by promoting refolding Proc. Natl. Acad. Sci. USA 109 2012 3742 3747
27. M. Bertz, M. Wilmanns, and M. Rief The titin-telethonin complex is a directed, superstable molecular bond in the muscle Z-disk Proc. Natl. Acad. Sci. USA 106 2009 13307 13310
28. M. Rief, J.M. Fernandez, and H.E. Gaub Elastically coupled two-level systems as a model for biopolymer extensibility Phys. Rev. Lett. 81 1998 4764 4767
29. M. Rief, and M. Gautel H.E. Gaub Reversible unfolding of individual titin immunoglobulin domains by AFM Science 276 1997 1109 1112
30. T. Serdiuk, and M.G. Madej D.J. Müller Substrate-induced changes in the structural properties of LacY Proc. Natl. Acad. Sci. USA 111 2014 E1571 E1580
31. M. Carrion-Vazquez, and H. Li J.M. Fernandez The mechanical stability of ubiquitin is linkage dependent Nat. Struct. Biol. 10 2003 738 743
32. A.D. Capili, and C.D. Lima Structure and analysis of a complex between SUMO and Ubc9 illustrates features of a conserved E2-Ubl interaction J. Mol. Biol. 369 2007 608 618
33. D. Baba, and N. Maita M. Shirakawa Crystal structure of thymine DNA glycosylase conjugated to SUMO-1 Nature 435 2005 979 982
34. L. Shen, and M.H. Tatham R.T. Hay SUMO protease SENP1 induces isomerization of the scissile peptide bond Nat. Struct. Mol. Biol. 13 2006 1069 1077