Populations of the three major backbone conformations in 19 amino acid dipeptides

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

Volumn 108, Issue 5, 2011, Pages 1794-1798

  Grdadolnik, Joze ^a   Mohacek Grosev, Vlasta ^b   Baldwin, Robert L ^c   Avbelj, Franc ^a  

^a NATIONAL INSTITUTE OF CHEMISTRY   (Slovenia)

^b RUDER BO KOVI INSTITUTE   (Croatia)

^c STANFORD UNIVERSITY   (United States)

Author keywords

Aqueous solution; Backbone conformations; Spectral populations; Vibrational spectroscopy

Indexed keywords

ALANINE; AMIDE; AMINO ACID; DIPEPTIDE; LEUCINE; PEPTIDE; SOLVENT;

ABSORPTION; ARTICLE; ATTENUATED TOTAL REFLECTION SPECTROSCOPY; HUMAN; IONIZATION; NUCLEAR MAGNETIC RESONANCE; PRIORITY JOURNAL; PROTEIN CONFORMATION; RAMAN SPECTROMETRY; SPECTROSCOPY; TEMPERATURE DEPENDENCE;

DIPEPTIDES; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; PROTEIN CONFORMATION; SPECTRUM ANALYSIS;

EID: 79952141708     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1017317108     Document Type: Article

References (21)

1. Hu H, Elstner M, Hermans J (2003) Comparison of a QM/MM force field and molecular mechanics force fields in simulations of alanine and glycine dipeptides (Ace-Ala-Nme and Ace-Gly-Nme) in water in relation to the problem of modeling the unfolded peptide backbone in solution. Proteins: Struct, Funct, Genet 50:451-463.
2. Lovell SC, et al. (2003) Structure validation by Cα geometry: φ, ψ and Cβ deviation. Proteins: Struct, Funct, Genet 50:437-450.
3. Avbelj FA, Baldwin RL (2003) Role of backbone solvation and electrostatics in generating preferred peptide backbone conformations: Distributions of phi. Proc Natl Acad Sci USA 100:5742-5747.
4. Jha AK, et al. (2005) Helix, sheet and polyproline II frequencies and strong nearestneighbor effects in a restricted coil library. Biochemistry 44:9691-9702. (Pubitemid 40994363)
5. Fitzkee NC, Fleming PJ, Rose GD (2005) The Protein Coil Library: A structural database of nonhelix, nonstrand fragments derived from the PDB. Proteins: Struct, Funct, Bioinf 58:852-854. (Pubitemid 40271250)
6. Perskie LL, Street TO, Rose GD (2008) Structures, basins and energies: A deconstruction of the Protein Coil Library. Protein Sci 17:1151-1161. (Pubitemid 351930913)
7. Avbelj F, Golic Grdadolnik S, Grdadolnik J, Baldwin RL (2006) Intrinsic backbone preferences are fully present in blocked amino acids. Proc Natl Acad Sci USA 103:1272-1277. (Pubitemid 43191155)
8. Plaxco KW, et al. (1997) The effects of guanidine hydrochloride on the "random coil" conformations and NMR chemical shifts of the peptide series GGXGG. J Biomol NMR 10:221-230.
9. Penkett CJ, et al. (1997) NMR analysis of main-chain conformational preferences in an unfolded fibronectin-binding protein. J Mol Biol 274:152-159. (Pubitemid 27520602)
10. Avbelj F, Baldwin RL (2004) Origin of the neighboring residue effect on peptide backbone conformation. Proc Natl Acad Sci USA 101:10967-10972. (Pubitemid 38989568)
11. Chen K, Liu Z, Zhou C, Shi Z, Kallenbach NR (2005) Neighbor effect on PPII conformation in alanine peptides. J Am Chem Soc 127:10146-10147. (Pubitemid 41045462)
12. Mu Y, Kosov DS, Stock G (2003) Conformational dynamics of trialanine in water. 2. Comparison of AMBER, CHARMM, GROMOS and OPLS force fields to NMR and infrared experiments. J Phys Chem B 107:5064-5073.
13. Grdadolnik J, Golic Grdadolnik S, Avbelj F (2008) Determination of conformational preferences of dipeptides using vibrational spectroscopy. J Phys Chem B 112:2712-2718. (Pubitemid 351472981)
14. McColl IH, et al. (2004) Vibrational Raman optical activity characterization of poly (L-proline) II helix. J Am Chem Soc 126:5076-5077. (Pubitemid 38509458)
15. Mikhonin AV, Bykov SV, Myshkina NS, Asher SA (2006) Peptide secondary structure folding reaction coordinate: Correlation between UV Raman amide III frequency, ψ Ramachandran angle, and hydrogen bonding. J Phys Chem B 110:1928-1943. (Pubitemid 43235795)
16. Shi Z, Olson CA, Rose GD, Baldwin RL, Kallenbach NR (2002) Polyproline II structure in a sequence of seven alanine residues. Proc Natl Acad Sci USA 99:9190-9195. (Pubitemid 34764589)
17. Madison V, Kopple KD (1980) Solvent-dependent conformational distributions of some dipeptides. J Am Chem Soc 102:4855-4863.
18. 13C-H coupling constants for the conformational analysis of N-acetyl-N′-methylamides of aliphatic amino acids. Int J Pept Protein Res 35:473-480.
19. Takekiyo T, Imai T, Kato M, Taniguchi Y (2004) Temperature and pressure effects on conformational equilibria of alanine dipeptide in aqueous solution. Biopolymers 73:283-290. (Pubitemid 38220384)
20. Schweitzer-Stenner R (2009) Distribution of conformations sampled by the central amino acid residue in tripeptides inferred from amide I band profiles and NMR scalar coupling constants. J Phys Chem B 113:2922-2932.
21. Hagarman A, Measy TJ, Mathieu D, Schwalbe H, Schweitzer-Stenner R (2010) Intrinsic propensities of amino acid residues in GxG peptides inferred from amide I′ band profiles and NMR scalar coupling constants. J Am Chem Soc 132:540-551.