Neighboring residue effects in terminally blocked dipeptides: Implications for residual secondary structures in intrinsically unfolded/disordered proteins

Chirality

Volumn 26, Issue 9, 2014, Pages 443-452

  Jung, Young Sang ^a   Oh, Kwang Im ^b   Hwang, Geum Sook ^a   Cho, Minhaeng ^a,b  

^a Korea Basic Science Institute (KBSI)   (South Korea)

^b Korea University   (South Korea)

Author keywords

backbone torsion angle; blocked dipeptide; NMR scalar coupling; NRE (neighboring residue effect); nuclear magnetic resonance (NMR); random coil; unfolded protein

Indexed keywords

AMINO ACID; DIPEPTIDE; GLUTAMINE; GLYCINE; INTRINSICALLY DISORDERED PROTEIN; LEUCINE;

CONFERENCE PAPER; HYDROGEN BOND; INTERMETHOD COMPARISON; NUCLEAR MAGNETIC RESONANCE; PEPTIDE ANALYSIS; PEPTIDE SYNTHESIS; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN SECONDARY STRUCTURE; PROTON NUCLEAR MAGNETIC RESONANCE; UNFOLDED PROTEIN RESPONSE; CHEMISTRY; PROTEIN FOLDING;

DIPEPTIDES; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; PROTEIN FOLDING; PROTEIN STRUCTURE, SECONDARY;

EID: 84906937237     PISSN: 08990042     EISSN: 1520636X     Source Type: Journal    
DOI: 10.1002/chir.22285     Document Type: Conference Paper

References (45)

1. 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: 289-302.
2. Shen Y, Lange O, Delaglio F, Rossi P, Aramini JM, Liu GH, Eletsky A, Wu YB, Singarapu KK, Lemak A, Ignatchenko A, Arrowsmith CH, Szyperski T, Montelione GT, Baker D, Bax A,. Consistent blind protein structure generation from NMR chemical shift data. Proc Natl Acad Sci U S A 2008; 105: 4685-4690.
3. Plaxco KW, Morton CJ, Grimshaw SB, Jones JA, Pitkeathly M, Campbell ID, Dobson CM,. The effects of guanidine hydrochloride on the 'random coil' conformations and NMR chemical shifts of the peptide series GGXGG. J Biomol NMR 1997; 10: 221-230.
4. McDonald CC, Phillips WD,. Proton magnetic resonance spectra of proteins in random-coil configurations. J Am Chem Soc 1969; 91: 1513-1521.
5. Schwarzinger S, Kroon GJA, Foss TR, Chung J, Wright PE, Dyson HJ,. Sequence-dependent correction of random coil NMR chemical shifts. J Am Chem Soc 2001; 123: 2970-2978.
6. 15N chemical shifts of backbone amides in bovine pancreatic trypsin inhibitor and apamin. J Am Chem Soc 1989; 111: 7716-7722.
7. 15N «random coil» chemical shifts. J Am Chem Soc 1994; 116: 8466-8469.
8. 15N random coil NMR chemical shifts of the common amino-acids. I. Investigations of nearest-neighbor effects. J Biomol NMR 1995; 5: 67-81.
9. Wang YJ, Jardetzky O,. Investigation of the neighboring residue effects on protein chemical shifts. J Am Chem Soc 2002; 124: 14075-14084.
10. van der Spoel D., The solution conformations of amino acids from molecular dynamics simulations of Gly-X-Gly peptides: comparison with NMR parameters. Biochem Cell Biol 1998; 76: 164-170.
11. Richarz R, Wüthrich K,. Carbon-13 NMR chemical shifts of the common amino acid residues measured in aqueous solutions of linear tetrapeptides H-Gly-Gly-X-L-Ala-OH. Biopolymers 1978; 17: 2133-2141.
12. 1H NMR parameters of the common amino acid residues measured in aqueous-solutions of the linear tetrapeptides H-Gly-Gly-X-L-Ala-OH. Biopolymers 1979; 18: 285-297.
13. 1H chemical-shifts obtained as a function of temperature and trifluoroethanol concentration for the peptide series GGXGG. J Biomol NMR 1995; 5: 14-24.
14. Keim P, Vigna RA, Marshall RC, Gurd FRN,. Carbon 13 nuclear magnetic resonance of pentapeptides of glycine containing central residues of aliphatic amino acids. J Biol Chem 1973; 248: 6104-6113.
15. Keim P, Vigna RA, Morrow JS, Marshall RC, Gurd FRN,. Carbon 13 nuclear magnetic resonance of pentapeptides of glycine containing central residues of serine, threonine, aspartic and glutamic acids, asparagine, and glutamine. J Biol Chem 1973; 248: 7811-7818.
16. Keim P, Vigna RA, Nigen AM, Morrow JS, Gurd FRN,. Carbon 13 nuclear magnetic resonance of pentapeptides of glycine containing central residues of methionine, proline, arginine, and lysine. J Biol Chem 1974; 249: 4149-4156.
17. Kjaergaard M, Poulsen FM,. Sequence correction of random coil chemical shifts: correlation between neighbor correction factors and changes in the Ramachandran distribution. J Biomol NMR 2011; 50: 157-165.
18. Oh KI, Jung YS, Hwang GS, Cho M,. Conformational distributions of denatured and unstructured proteins are similar to those of 20 x 20 blocked dipeptides. J Biomol NMR 2012; 53: 25-41.
19. β carbon-13 chemical shifts in proteins from an empirical database. J Biomol NMR 1999; 13: 199-211.
20. Penkett CJ, Redfield C, Dodd I, Hubbard J, McBay DL, Mossakowska DE, Smith RAG, Dobson CM, Smith LJ,. NMR analysis of main-chain conformational preferences in an unfolded fibronectin-binding protein. J Mol Biol 1997; 274: 152-159.
21. Wishart DS, Sykes BD, Richards FM,. Relationship between nuclear magnetic resonance chemical shift and protein secondary structure. J Mol Biol 1991; 222: 311-333.
22. Wang YJ, Jardetzky O,. Probability-based protein secondary structure identification using combined NMR chemical-shift data. Protein Sci 2002; 11: 852-861.
23. Schwarzinger S, Kroon GJA, Foss TR, Wright PE, Dyson HJ,. Random coil chemical shifts in acidic 8 M urea: Implementation of random coil shift data in NMRView. J Biomol NMR 2000; 18: 43-48.
24. Carlisle EA, Holder JL, Maranda AM, de Alwis AR, Selkie EL, McKay SL,. Effect of pH, urea, peptide length, and neighboring amino acids on alanine α-proton random coil chemical shifts. Biopolymers 2007; 85: 72-80.
25. Smith LJ, Bolin KA, Schwalbe H, MacArthur MW, Thornton JM, Dobson CM,. Analysis of main chain torsion angles in proteins: Prediction of NMR coupling constants for native and random coil conformations. J Mol Biol 1996; 255: 494-506.
26. Shi ZS, Chen K, Liu ZG, Ng A, Bracken WC, Kallenbach NR,. Polyproline II propensities from GGXGG peptides reveal an anticorrelation with β-sheet scales. Proc Natl Acad Sci U S A 2005; 102: 17964-17968.
27. Avbelj F, Grdadolnik SG, Grdadolnik J, Baldwin RL,. Intrinsic backbone preferences are fully present in blocked amino acids. Proc Natl Acad Sci U S A 2006; 103: 1272-1277.
28. Choi JH, Cho M,. Computational IR spectroscopy of water: OH stretch frequencies, transition dipoles, and intermolecular vibrational coupling constants. J Chem Phys 2013; 138: 174108.
29. Ting D, Wang GL, Shapovalov M, Mitra R, Jordan MI, Dunbrack RL,. Neighbor-dependent ramachandran probability distributions of amino acids developed from a hierarchical dirichlet process model. Plos Comput Biol 2010; 6: e1000763.
30. Shapovalov MV, Dunbrack RL,. A smoothed backbone-dependent rotamer library for proteins derived from adaptive kernel density estimates and regressions. Structure 2011; 19: 844-858.
31. Fiebig KM, Schwalbe H, Buck M, Smith LJ, Dobson CM,. Toward a description of the conformations of denatured states of proteins. Comparison of a random coil model with NMR measurements. J Phys Chem-Us 1996; 100: 2661-2666.
32. Avbelj F, Baldwin RL,. Origin of the neighboring residue effect on peptide backbone conformation. Proc Natl Acad Sci U S A 2004; 101: 10967-10972.
33. Lam SL, Hsu VL,. NMR identification of left-handed polyproline type II helices. Biopolymers 2003; 69: 270-281.
34. Whitten ST, Yang HW, Fox RO, Hilser VJ,. Exploring the impact of polyproline II (P(II)) conformational bias on the binding of peptides to the SEM-5 SH3 domain. Protein Sci 2008; 17: 1200-1211.
35. Avbelj F, Kocjan D, Baldwin RL,. Protein chemical shifts arising from α-helices and β-sheets depend on solvent exposure. Proc Natl Acad Sci U S A 2004; 101: 17394-17397.
36. Dukor RK, Keiderling TA,. Reassessment of the random coil conformation-vibrational CD study of proline oligopeptides and related polypeptides. Biopolymers 1991; 31: 1747-1761.
37. Eker F, Cao XL, Nafie L, Schweitzer-Stenner R,. Tripeptides adopt stable structures in water. A combined polarized visible Raman, FTIR, and VCD spectroscopy study. J Am Chem Soc 2002; 124: 14330-14341.
38. Hahn S, Lee H, Cho M,. Theoretical calculations of infrared absorption, vibrational circular dichroism, and two-dimensional vibrational spectra of acetylproline in liquids water and chloroform. J Chem Phys 2004; 121: 1849-1865.
39. Lee KK, Hahn S, Oh KI, Choi JS, Joo C, Lee H, Han HY, Cho M,. Structure of N-acetylproline amide in liquid water: Experimentally measured and numerically simulated infrared and vibrational circular dichroism spectra. J Phys Chem B 2006; 110: 18834-18843.
40. Lee KK, Joo C, Yang S, Han H, Cho M,. Phosphorylation effect on the GSSS peptide conformation in water: Infrared, vibrational circular dichroism, and circular dichroism experiments and comparisons with molecular dynamics simulations. J Chem Phys 2007; 126: 235102.
41. Makowska J, Rodziewicz-Motowidlo S, Baginska K, Makowski M, Vila JA, Liwo A, Chmurzynski L, Scheraga HA,. Further evidence for the absence of polyproline II stretch in the XAO peptide. Biophys J 2007; 92: 2904-2917.
42. Oh KI, Han J, Lee KK, Hahn S, Han H, Cho M,. Site-specific hydrogen-bonding interaction between N-acetylproline amide and protic solvent molecules: Comparisons of IR and VCD measurements with MD simulations. J Phys Chem A 2006; 110: 13355-13365.
43. Oh KI, Lee KK, Park EK, Yoo DG, Hwang GS, Cho M,. Circular dichroism eigenspectra of polyproline II and β-strand conformers of trialanine in water: Singular value decomposition analysis. Chirality 2010; 22: E186-E201.
44. Schweitzer-Stenner R, Measey TJ,. The alanine-rich XAO peptide adopts a heterogeneous population, including turn-like and polyproline II conformations. Proc Natl Acad Sci U S A 2007; 104: 6649-6654.
45. Shi ZS, Olson CA, Rose GD, Baldwin RL, Kallenbach NR,. Polyproline II structure in a sequence of seven alanine residues. Proc Natl Acad Sci U S A 2002; 99: 9190-9195.