Conformations of intrinsically disordered proteins are influenced by linear sequence distributions of oppositely charged residues

Proceedings of the National Academy of Sciences of the United States of America

Volumn 110, Issue 33, 2013, Pages 13392-13397

  Das, Rahul K ^a   Pappu, Rohit V ^a  

^a WASHINGTON UNIVERSITY IN ST LOUIS   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CONNECTIN; PRION PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; LINEAR SYSTEM; PHENOMENOLOGY; PRIORITY JOURNAL; PROTEIN CONFORMATION; SCALE UP; SEGREGATION ANALYSIS; SEQUENCE ALIGNMENT; STATIC ELECTRICITY;

AMINO ACID SEQUENCE; BUFFERS; MARKOV CHAINS; MODELS, CHEMICAL; MOLECULAR DYNAMICS SIMULATION; MOLECULAR SEQUENCE DATA; MONTE CARLO METHOD; PROTEIN CONFORMATION; PROTEINS; STATIC ELECTRICITY; TEMPERATURE;

EID: 84882364963     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1304749110     Document Type: Article

References (43)

1. Dyson HJ, Wright PE (2005) Intrinsically unstructured proteins and their functions. Nat Rev Mol Cell Biol 6(3):197-208.
2. Tantos A, Han KH, Tompa P (2012) Intrinsic disorder in cell signaling and gene transcription. Mol Cell Endocrinol 348(2):457-465.
3. Uversky VN (2002) What does it mean to be natively unfolded? Eur J Biochem 269(1): 2-12.
4. Bright JN, Woolf TB, Hoh JH (2001) Predicting properties of intrinsically unstructured proteins. Prog Biophys Mol Biol 76(3):131-173.
5. Mukhopadhyay S, Krishnan R, Lemke EA, Lindquist S, Deniz AA (2007) A natively unfolded yeast prion monomer adopts an ensemble of collapsed and rapidly fluctuating structures. Proc Natl Acad Sci USA 104(8):2649-2654.
6. Wells M, et al. (2008) Structure of tumor suppressor p53 and its intrinsically disordered N-terminal transactivation domain. Proc Natl Acad Sci USA 105(15):5762-5767.
7. Mao AH, Crick SL, Vitalis A, Chicoine CL, Pappu RV (2010) Net charge per residue modulates conformational ensembles of intrinsically disordered proteins. Proc Natl Acad Sci USA 107(18):8183-8188.
8. Müller-Späth S, et al. (2010) From the Cover: Charge interactions can dominate the dimensions of intrinsically disordered proteins. Proc Natl Acad Sci USA 107(33): 14609-14614.
9. Marsh JA, Forman-Kay JD (2010) Sequence determinants of compaction in intrinsically disordered proteins. Biophys J 98(10):2383-2390.
10. Potoyan DA, Papoian GA (2011) Energy landscape analyses of disordered histone tails reveal special organization of their conformational dynamics. J Am Chem Soc 133(19): 7405-7415.
11. Zhang WH, Ganguly D, Chen JH (2012) Residual structures, conformational fluctuations, and electrostatic interactions in the synergistic folding of two intrinsically disordered proteins. PLoS Comput Biol 8(1):e1002353.
12. Mao AH, Lyle N, Pappu RV (2013) Describing sequence-ensemble relationships for intrinsically disordered proteins. Biochem J 449(2):307-318.
13. Sickmeier M, et al. (2007) DisProt: The database of disordered proteins. Nucleic Acids Res 35(Database issue):D786-D793.
14. Higgs PG, Joanny JF (1991) Theory of polyampholyte solutions. J Chem Phys 94(2): 1543-1554.
15. Fu XD (1995) The superfamily of arginine/serine-rich splicing factors. RNA 1(7): 663-680.
16. Forbes JG, et al. (2005) Titin PEVK segment: Charge-driven elasticity of the open and flexible polyampholyte. J Muscle Res Cell Motil 26(6-8):291-301.
17. Vitalis A, Pappu RV (2009) ABSINTH: A new continuum solvation model for simulations of polypeptides in aqueous solutions. J Comput Chem 30(5):673-699.
18. Das RK, Crick SL, Pappu RV (2012) N-terminal segments modulate the α-helical propensities of the intrinsically disordered basic regions of bZIP proteins. J Mol Biol 416(2):287-299.
19. Dobrynin AV, Rubinstein M (1995) Flory theory of a polyampholyte chain. Journale de Physique II France 5(5):677-695.
20. Pappu RV, Wang X, Vitalis A, Crick SL (2008) A polymer physics perspective on driving forces and mechanisms for protein aggregation. Arch Biochem Biophys 469(1): 132-141.
21. Dima RI, Thirumalai D (2004) Asymmetry in the shapes of folded and denatured states of proteins. J Phys Chem B 108(21):6564-6570.
22. Bernadó P, Svergun DI (2012) Analysis of intrinsically disordered proteins by smallangle X-ray scattering. Methods Mol Biol 896:107-122.
23. Steinhauser MO (2005) A molecular dynamics study on universal properties of polymer chains in different solvent qualities. Part I. A review of linear chain properties. J Chem Phys 122(9):094901.
24. Yamakov V, et al. (2000) Conformations of random polyampholytes. Phys Rev Lett 85(20):4305-4308.
25. Schäfer L (1999) Excluded Volume Effects in Polymer Solutions as Explained by the Renormalization Group (Springer, Berlin).
26. Tanaka M, Tanaka T (2000) Clumps of randomly charged polymers: Molecular dynamics simulation of condensation, crystallization, and swelling. Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics 62(3 Pt B):3803-3816.
27. Nettels D, et al. (2009) Single-molecule spectroscopy of the temperature-induced collapse of unfolded proteins. Proc Natl Acad Sci USA 106(49):20740-20745.
28. Hofmann H, et al. (2012) Polymer scaling laws of unfolded and intrinsically disordered proteins quantified with single-molecule spectroscopy. Proc Natl Acad Sci USA 109(40):16155-16160.
29. Takahashi M, et al. (2010) Polyglutamine tract-binding protein-1 binds to U5-15kD via a continuous 23-residue segment of the C-terminal domain. Biochim Biophys Acta 1804(7):1500-1507.
30. Rees M, et al. (2012) Solution model of the intrinsically disordered polyglutamine tract-binding protein-1. Biophys J 102(7):1608-1616.
31. Edwards SF, King PR, Pincus P (1980) Phase-changes in polyampholytes. Ferroelectrics 30(1-4):3-6.
32. Dobrynin AV, Colby RH, Rubinstein M (2004) Polyampholytes. J Polym Sci B 42(19): 3513-3538.
33. Kantor Y, Kardar M (1995) Randomly charged polymers: An exact enumeration study. Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics 52(1):835-846.
34. Gutin AM, Shakhnovich EI (1994) Effect of a net charge on the conformation of polyampholytes. Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics 50(5): R3322-R3325.
35. Srivastava D, Muthukumar M (1996) Sequence dependence of conformations of polyampholytes. Macromolecules 29(6):2324-2326.
36. Sanchez IC (1979) Phase transition behavior of the isolated polymer chain. Macromolecules 12(5):980-988.
37. Borg M, et al. (2007) Polyelectrostatic interactions of disordered ligands suggest a physical basis for ultrasensitivity. Proc Natl Acad Sci USA 104(23):9650-9655.
38. Kumar S, Hoh JH (2004) Modulation of repulsive forces between neurofilaments by sidearm phosphorylation. Biochem Biophys Res Commun 324(2):489-496.
39. Buljan M, et al. (2012) Tissue-specific splicing of disordered segments that embed binding motifs rewires protein interaction networks. Mol Cell 46(6):871-883.
40. Vuzman D, Levy Y (2012) Intrinsically disordered regions as affinity tuners in protein- DNA interactions. Mol Biosyst 8(1):47-57.
41. Mitsutake A, Sugita Y, Okamoto Y (2003) Replica-exchange multicanonical and multicanonical replica-exchange Monte Carlo simulations of peptides. II. Application to a more complex system. J Chem Phys 118(14):6676-6688.
42. Chen AA, Marucho M, Baker NA, Pappu RV (2009) Simulations of RNA interactions with monovalent ions. Methods Enzymol 469:411-432.
43. Uversky VN, Gillespie JR, Fink AL (2000) Why are "natively unfolded" proteins unstructured under physiologic conditions? Proteins 41(3):415-427.