A comprehensive library of blocked dipeptides reveals intrinsic backbone conformational propensities of unfolded proteins

Proteins: Structure, Function and Bioinformatics

Volumn 80, Issue 4, 2012, Pages 977-990

  Oh, Kwang Im ^a   Lee, Kyung Koo ^a   Park, Eun Kyung ^a   Jung, Youngae ^b   Hwang, Geum Sook ^b   Cho, Minhaeng ^a,b  

^a Korea University   (South Korea)

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

Author keywords

Blocked dipeptide; Peptide conformation; Polyproline II; Unfolded protein structure

Indexed keywords

DIPEPTIDE;

AMINO TERMINAL SEQUENCE; ARTICLE; CARBOXY TERMINAL SEQUENCE; CIRCULAR DICHROISM; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN MOTIF; PROTEIN STRUCTURE;

AMINO ACIDS; CIRCULAR DICHROISM; DIPEPTIDES; HYDROGEN BONDING; MAGNETIC RESONANCE SPECTROSCOPY; PEPTIDE LIBRARY; PROTEIN CONFORMATION; PROTEIN STABILITY; PROTEIN UNFOLDING; SOLVENTS; STATIC ELECTRICITY; WATER;

EID: 84857783671     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.24000     Document Type: Article

References (55)

1. Tiffany ML, Krimm S. Circular dichroism of poly-L-proline in an unordered conformation. Biopolymers 1968; 6: 1767-1770.
2. Shi ZS, Woody RW, Kallenbach NR. Is polyproline II a major backbone conformation in unfolded proteins? Adv Protein Chem 2002; 62: 163-240.
3. Shi ZS, Olson CA, Rose GD, Baldwin RL, Kallenbach NR. Polyproline II structure in a sequence of seven alanine residues. Proc Natl Acad Sci USA 2002; 99: 9190-9195.
4. 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.
5. Avbelj F, Grdadolnik SG, Grdadolnik J, Baldwin RL. Intrinsic backbone preferences are fully present in blocked amino acids. Proc Natl Acad Sci USA 2006; 103: 1272-1277.
6. Zanni MT, Stenger J, Asplund MC, Hochstrasser RM. Solvent dependent conformational dynamics of dipeptides studied with two-dimensional infrared spectroscopy. Biophys J 2001; 80: 8A-9A.
7. Hagarman A, Measey TJ, Mathieu D, Schwalbe H, Schweitzer-Stenner R. Intrinsic propensities of amino acid residues in GxG peptides inferred from amide I′ band profiles and NMR scalar coupling constants. J Am Chem Soc 2010; 132: 540-551.
8. 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.
9. 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.
10. 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. JChem Phys 2004; 121: 1849-1865.
11. Dukor RK, Keiderling TA. Reassessment of the random coil conformation-Vibrational Cd study of proline oligopeptides and related polypeptides. Biopolymers 1991; 31: 1747-1761.
12. Oh KI, Lee KK, Park EK, Yoo DG, Hwang GS, Cho M. Circular dichroism eigenspectra of polyproline II and beta-strand conformers of trialanine in water: singular value decomposition analysis. Chirality 2010; 22: E186-E201.
13. Wright PE, Dyson HJ, Lerner RA. Conformation of peptide-fragments of proteins in aqueous-solution-implications for initiation of protein folding. Biochemistry 1988; 27: 7167-7175.
14. Shortle D, Ackerman MS. Persistence of native-like topology in a denatured protein in 8 M urea. Science 2001; 293: 487-489.
15. 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 USA 2007; 104: 6649-6654.
16. Schweitzer-Stenner R, Hagarman A, Mathieu D, Toal S, Measey TJ, Schwalbe H. Amino acids with hydrogen-bonding side chains have an intrinsic tendency to sample various turn conformations in aqueous solution. Chem Eur J 2011; 17: 6789-6797.
17. 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.
18. Zagrovic B, Lipfert J, Sorin EJ, Millettt IS, van Gunsteren WF, Doniach S, Pande VS. Unusual compactness of a polyproline type II structure. Proc Natl Acad Sci USA 2005; 102: 11698-11703.
19. Jha AK, Colubri A, Freed KF, Sosnick TR. Statistical coil model of the unfolded state: resolving the reconciliation problem. Proc Natl Acad Sci USA 2005; 102: 13099-13104.
20. Bartlett GJ, Choudhary A, Raines RT, Woolfson DN. n ->pi* interactions in proteins. Nat Chem Biol 2010; 6: 615-620.
21. Anfinsen CB. Principles that govern folding of protein chains. Science 1973; 181: 223-230.
22. Swindells MB, Macarthur MW, Thornton JM. Intrinsic Phi, Psi propensities of amino-acids, derived from the coil regions of known structures. Nat Struct Biol 1995; 2: 596-603.
23. Serrano L. Comparison between the Phi distribution of the amino-acids in the protein database and Nmr data indicates that amino-acids have various phi propensities in the random coil conformation. J Mol Biol 1995; 254: 322-333.
24. Oneil KT, Degrado WF. A Thermodynamic scale for the helix-forming tendencies of the commonly occurring amino-acids. Science 1990; 250: 646-651.
25. Kim CWA, Berg JM. Thermodynamic beta-sheet propensities measured using a zinc-finger host peptide. Nature 1993; 362: 267-270.
26. Saudek V, Wormald MR, Williams RJP, Boyd J, Stefani M, Ramponi G. Identification and description of beta-structure in horse muscle acylphosphatase by nuclear magnetic-resonance spectroscopy. J Mol Biol 1989; 207: 405-415.
27. Schlorb C, Ackermann K, Richter C, Wirmer J, Schwalbe H. Heterologous expression of hen egg white lysozyme and resonance assignment of tryptophan side chains in its non-native states. J Biomol Nmr 2005; 33: 95-104.
28. Case DA, Darden TA, Cheatham TEIII, Simmerling CL, Wang J, Duke RE, Luo R, Merz KM, Pearlman DA, Crowley M, Walker RC, Zhang W, Wang B, Hayik S, Roitberg A, Seabra G, Wong KF, Paesani F, Wu X, Brozell S, Mathews DH, Schafmeister C, Ross WS, Kollman PA. AMBER 9. San Francisco: University of California; 2006.
29. Darden T, York D, Pedersen L. Particle Mesh Ewald-an N. Log(N) method for Ewald sums in large systems. J Chem Phys 1993; 98: 10089-10092.
30. Karplus M. Contact electron-spin coupling of nuclear magnetic moments. J Chem Phys 1959; 30: 11-15.
31. Avbelj F, Kocjan D, Baldwin RL. Protein chemical shifts arising from alpha-helices and beta-sheets depend on solvent exposure. Proc Natl Acad Sci USA 2004; 101: 17394-17397.
32. Zhang HY, Neal S, Wishart DS. RefDB: a database of uniformly referenced protein chemical shifts. J Biomol Nmr 2003; 25: 173-195.
33. Shi ZS, Chen K, Liu ZG, Ng A, Bracken WC, Kallenbach NR. Polyproline II propensities from GGXGG peptides reveal an anticorrelation with beta-sheet scales. Proc Natl Acad Sci USA 2005; 102: 17964-17968.
34. Patgiri A, Jochim AL, Arora PS. A hydrogen bond surrogate approach for stabilization of short peptide sequences in alpha-helical conformation. Accounts Chem Res 2008; 41: 1289-1300.
35. Graf J, Nguyen PH, Stock G, Schwalbe H. Structure and dynamics of the homologous series of alanine peptides: a joint molecular dynamics/NMR study. J Am Chem Soc 2007; 129: 1179-1189.
36. Grdadolnik J, Mohacek-Grosev V, Baldwin RL, Avbelj F. Populations of the three major backbone conformations in 19 amino acid dipeptides. Proc Natl Acad Sci USA 2011; 108: 1794-1798.
37. Avbelj F, Baldwin RL. Origin of the neighboring residue effect on peptide backbone conformation. Proc Natl Acad Sci USA 2004; 101: 10967-10972.
38. Tanford C. Protein denaturation. Adv Protein Chem 1968; 23: 121-282.
39. Avbelj F, Baldwin RL. Role of backbone solvation and electrostatics in generating preferred peptide backbone conformations: distributions of phi. Proc Natl Acad Sci USA 2003; 100: 5742-5747.
40. Kimura T, Matubayasi N, Sato H, Hirata F, Nakahara M. Enthalpy and entropy decomposition of free-energy changes for side-chain conformations of aspartic acid and asparagine in acidic, neutral, and basic aqueous solutions. J Phys Chem B 2002; 106: 12336-12343.
41. Liu L, Guo QX. Isokinetic relationship, isoequilibrium relationship, and enthalpy-entropy compensation. Chem Rev 2001; 101: 673-695.
42. Krug RR, Hunter WG, Grieger RA. Statistical interpretation of enthalpy-entropy compensation. Nature 1976; 261: 566-567.
43. Kauzmann W, Bodanszky A, Rasper J. Volume changes in protein reactions. II. Comparison of ionization reactions in proteins and small molecules. J Am Chem Soc 1962; 84: 1777-1788.
44. Douglas JF, Dudowicz J, Freed KF. Crowding induced self-assembly and enthalpy-entropy compensation. Phys Rev Lett 2009; 103: 13.
45. Mezei M, Fleming PJ, Srinivasan R, Rose GD. Polyproline II helix is the preferred conformation for unfolded polyalanine in water. Proteins-Struct Funct Bioinformatics 2004; 55: 502-507.
46. Ramachandran GN, Ramakrishnan C, Sasisekharan V. Stereochemistry of polypeptide chain configurations. J Mol Biol 1963; 7: 95-99.
47. Richards FM. Areas, volumes, packing, and protein-structure. Ann Rev Biophys Bioeng 1977; 6: 151-176.
48. Moore PB, Voss NR, Gerstein M, Steitz TA. The geometry of the ribosomal polypeptide exit tunnel. J Mol Biol 2006; 360: 893-906.
49. Dewar MJS, Zoebisch EG, Healy EF, Stewart JJP. The development and use of quantum-mechanical molecular-models 76. Am1-a new general-purpose quantum-mechanical molecular-model. J Am Chem Soc 1985; 107: 3902-3909.
50. Stewart JJP. Optimization of parameters for semiempirical methods. II. Applications. J Comp Chem 1989; 10: 221-264.
51. Stewart JJP. Optimization of parameters for semiempirical methods. I. Method. J Comp Chemistry 1989; 10(2): 209-220.
52. Kwac K, Lee KK, Han JB, Oh KI, Cho M. Classical and quantum mechanical/molecular mechanical molecular dynamics simulations of alanine dipeptide in water: comparisons with IR and vibrational circular dichroism spectra. J Chem Phys 2008; 128: 10.
53. Raines RT, Hinderaker MP. An electronic effect on protein structure. Protein Sci 2003; 12: 1188-1194.
54. Levintha C. Are there pathways for protein folding. J De Chimie Physique Et De Physico-Chimie Biologique 1968; 65: 44-45.
55. Redfield C, Dobson CM. Sequential H-1-Nmr assignments and secondary structure of hen egg-white lysozyme in solution. Biochemistry 1988; 27: 122-136.