13C NMR reveals no evidence of n-π* interactions in proteins

PLoS ONE

Volumn 7, Issue 8, 2012, Pages

  Worley, Bradley ^a   Richard, Georgia ^a   Harbison, Gerard S ^a   Powers, Robert ^a  

^a UNIVERSITY OF NEBRASKA LINCOLN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CARBONYL DERIVATIVE; CARBON; PROTEIN;

ARTICLE; CARBON NUCLEAR MAGNETIC RESONANCE; CRYSTAL STRUCTURE; DIPOLE; ENERGY TRANSFER; EXCITATION; HYDROGEN BOND; MOLECULAR INTERACTION; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN INTERACTION; PROTEIN STABILITY; STRUCTURE ACTIVITY RELATION; STRUCTURE ANALYSIS; CHEMICAL STRUCTURE; CHEMISTRY; NUCLEAR MAGNETIC RESONANCE;

CARBON ISOTOPES; HYDROGEN BONDING; MODELS, MOLECULAR; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; PROTEINS;

EID: 84864484028     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0042075     Document Type: Article

References (32)

1. Knudsen M, Wiuf C, ((2010)) The cath database. Hum Genomics 4:: 207--212.
2. Rost B, ((1999)) Twilight zone of protein sequence alignments. Protein Engineering 12:: 85--94.
3. Zhang Y, ((2009)) Protein structure prediction: when is it useful? Curr Opin Struct Biol 19:: 145--155.
4. Robertson AD, Murphy KP, ((1997)) Protein structure and the energetics of protein stability. Chem Rev 97:: 1251--1267.
5. Dill KA, ((1990)) Dominant forces in protein folding. Biochemistry 29:: 7133--7155.
6. Kauzmann W, ((1959)) Some factors in the interpretation of protein denaturation. Advances in Protein Chem 14:: 1--63.
7. Pace CN, ((2009)) Energetics of protein hydrogen bonds. Nat Struct Mol Biol 16:: 681--682.
8. Gao J, Bosco DA, Powers ET, Kelly JW, ((2009)) Localized thermodynamic coupling between hydrogen bonding and microenvironment polarity substantially stabilizes proteins. Nat Struct Mol Biol 16:: 684--690.
9. Shakhnovich E, ((2009)) Protein folding roller coaster, one molecule at a time. Proc Natl Acad Sci U S A 106:: 11823--11824.
10. Shaw DE, Maragakis P, Lindorff-Larsen K, Piana S, Dror RO, et al. ((2010)) Atomic-level characterization of the structural dynamics of proteins. Science 330:: 341--346.
11. Bartlett GJ, Choudhary A, Raines RT, Woolfson DN, ((2010)) n- pi* interactions in proteins. Nat Chem Biol 6:: 615--620.
12. Mera H, Stokbro K, ((2009)) Using kohn-sham density functional theory to describe charged excitations in finite systems. Phys Rev B 79:: 125109.
13. Burgi HB, Dunitz JD, Shefter E, ((1973)) Geometrical reaction coordinates.2. nucleophilic addition to a carbonyl group. J Am Chem Soc 95:: 5065--5067.
14. Ramsey NF, ((1950)) Magnetic shielding of nuclei in molecules. Physical Review 78:: 699--703.
15. Abragam A, ((1961)) The Principles of Nuclear Magnetism. Clarendon Press.
16. Savitsky GB, Namikawa K, Zweifel G, ((1965)) A relationship between carbon-13 carbonyl chemical shifts and n-pi transition energies in cyclic and bicyclic ketones. Journal of Physical Chemistry 69:: 3105--3109.
17. De JWH, ((1970)) Relation between carbon-13 and oxygen-17 carbonyl chemical shifts for n - n* transition energies. Mol Phys 18:: 31--37.
18. Choudhary A, Gandla D, Krow GR, Raines RT, ((2009)) Nature of amide carbonyl-carbonyl interactions in proteins. J Am Chem Soc 131:: 7244--7246.
19. Wang Y, Jardetzky O, ((2002)) Probability-based protein secondary structure identification using combined nmr chemical-shift data. Protein Science 11:: 852--861.
20. de Dios AC, Pearson JG, Oldfield E, ((1993)) Secondary and tertiary structural effects on protein nmr chemical shifts: an ab initio approach. Science 260:: 1491--1496.
21. Asakawa N, Kuroki S, Kurosu H, Ando I, Shoji A, et al. ((1992)) Hydrogen-bonding effect on c-13 nmr chemical-shifts of l-alanine residue carbonyl carbons of peptides in the solid state. J Am Chem Soc 114:: 3261--3265.
22. Wylie BJ, Sperling LJ, Frericks HL, Shah GJ, Franks WT, et al. ((2007)) Chemical-shift anisotropy measurements of amide and carbonyl resonances in a microcrystalline protein with slow magic-angle spinning nmr spectroscopy. J Am Chem Soc 129:: 5318--5319.
23. Cisnetti F, Loth K, Pelupessy P, Bodenhausen G, ((2004)) Determination of chemical shift anisotropy tensors of carbonyl nuclei in proteins through cross-correlated relaxation in nmr. ChemPhysChem 5:: 807--814.
24. Neal S, Nip AM, Zhang H, Wishart DS, ((2003)) Rapid and accurate calculation of protein 1h, 13c and 15n chemical shifts. J Biomol NMR 26:: 215--240.
25. Markwick PRL, Sattler M, ((2004)) Site-specific variations of carbonyl chemical shift anisotropies in proteins. J Am Chem Soc 126:: 11424--11425.
26. Wang G, R L Dunbrack J, ((2003)) Pisces: a protein sequence culling server. Bioinformatics 19:: 1589--1591.
27. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, et al. ((2000)) The protein data bank. Nucleic Acids Res 28:: 235--242.
28. Ulrich EL, Akutsu H, Doreleijers JF, Harano Y, Ioannidis YE, et al. ((2008)) Biomagresbank. Nucleic Acids Res 36:: D402--D408.
29. Pearson WR, ((2000)) Flexible sequence similarity searching with the fasta3 program package. Methods in Molecular Biology 132:: 185--219.
30. Wishart DS, Zhang HY, Neal S, ((2003)) Refdb: A database of uniformly referenced protein chemical shifts. Journal of Biomol NMR 25:: 173--195.
31. Krissinel E, Henrick K, ((2007)) Inference of macromolecular assemblies from crystalline state. Journal of Molecular Biology 372:: 774--797.
32. Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, et al. ((2009)) Gaussian-09, revision a.02.