N-Acetylated amino sugars: the dependence of NMR 3 J (HNH2)-couplings on conformation, dynamics and solvent

Density functional theory (DFT) calculations are used to determine the angular dependence of scalar couplings (Karplus equation) for N-acetylated amino sugars and an equation derived that can estimate bond libration from experimental measurements.

[1]  L. Johnson.  The crystal structure of N-acetyl-a-D-glycosamine , 1966 .

[2]  I. Roberts.  The biochemistry and genetics of capsular polysaccharide production in bacteria. , 1996, Annual review of microbiology.

[3]  A. Imberty,et al.  Structure and conformation of complex carbohydrates of glycoproteins, glycolipids, and bacterial polysaccharides. , 1999, Annual review of biophysics and biomolecular structure.

[4]  V. Barone,et al.  Solvent Effects on Nuclear Magnetic Resonance 2J(C,Hf) and 1J(C,Hf) Spin–Spin Coupling Constants in Acetaldehyde , 2003 .

[5]  I. Carmichael,et al.  Geminal 2JCCH spin-spin coupling constants as probes of the phi glycosidic torsion angle in oligosaccharides. , 2005, Journal of the American Chemical Society.

[6]  J. P. Zikakis,et al.  Chitin: New facets of research. , 1981, Science.

[7]  S. Grzesiek,et al.  NMRPipe: A multidimensional spectral processing system based on UNIX pipes , 1995, Journal of biomolecular NMR.

[8]  I. Carmichael,et al.  {sup 2}J{sub COC} spin-spin coupling constants across glycosidic linkages exhibit a valence bond-angle dependence , 2000 .

[9]  R. J. Abraham,et al.  Conformational analysis. Part 40: a theoretical and NMR investigation of the conformations of cis‐ and trans‐cyclopentane‐1,3‐diol , 2003 .

[10]  D. Case,et al.  Adding Harmonic Motion to the Karplus Relation for Spin-Spin Coupling , 1994 .

[11]  B. Schneider,et al.  The effect of water on NMR spin–spin couplings in DNA: Improvement of calculated values by application of two solvent models , 2003 .

[12]  K. Frimand,et al.  Use of vibrational spectroscopy to study protein and DNA structure, hydration, and binding of biomolecules: A combined theoretical and experimental approach , 2006 .

[13]  Ad Bax,et al.  Quantitative J correlation: a new approach for measuring homonuclear three-bond J(HNH.alpha.) coupling constants in 15N-enriched proteins , 1993 .

[14]  Göran Widmalm,et al.  Hydroxymethyl group conformation in saccharides: structural dependencies of (2)J(HH), (3)J(HH), and (1)J(CH) spin-spin coupling constants. , 2002, The Journal of organic chemistry.

[15]  T. Halgren,et al.  Merck molecular force field. V. Extension of MMFF94 using experimental data, additional computational data, and empirical rules , 1996 .

[16]  B. Coxon.  Deuterium isotope effects in carbohydrates revisited. Cryoprobe studies of the anomerization and NH to ND deuterium isotope induced 13C NMR chemical shifts of acetamidodeoxy and aminodeoxy sugars. , 2005, Carbohydrate research.

[17]  T. Helgaker,et al.  The performance of hybrid density functional theory for the calculation of indirect nuclear spin–spin coupling constants in substituted hydrocarbons , 2004, Magnetic resonance in chemistry : MRC.

[18]  A. Varki.  Nothing in Glycobiology Makes Sense, except in the Light of Evolution , 2006, Cell.

[19]  M. Karplus,et al.  CHARMM: A program for macromolecular energy, minimization, and dynamics calculations , 1983 .

[20]  A. Almond,et al.  Hyaluronan: the absence of amide-carboxylate hydrogen bonds and the chain conformation in aqueous solution are incompatible with stable secondary and tertiary structure models. , 2006, The Biochemical journal.

[21]  Jesús Jiménez-Barbero,et al.  New insights into alpha-GalNAc-Ser motif: influence of hydrogen bonding versus solvent interactions on the preferred conformation. , 2006, Journal of the American Chemical Society.

[22]  A. Bax,et al.  Determination of the Backbone Dihedral Angles φ in Human Ubiquitin from Reparametrized Empirical Karplus Equations , 1996 .

[23]  B. M. Pinto,et al.  Structure and dynamics of oligosaccharides: NMR and modeling studies. , 1996, Current opinion in structural biology.

[24]  P. DeAngelis.  Evolution of glycosaminoglycans and their glycosyltransferases: Implications for the extracellular matrices of animals and the capsules of pathogenic bacteria , 2002, The Anatomical record.

[25]  A. Almond,et al.  Use of 15N-NMR to resolve molecular details in isotopically-enriched carbohydrates: sequence-specific observations in hyaluronan oligomers up to decasaccharides. , 2004, Glycobiology.

[26]  Martin Karplus,et al.  Vicinal Proton Coupling in Nuclear Magnetic Resonance , 1963 .

[27]  J H Prestegard,et al.  NMR structures of biomolecules using field oriented media and residual dipolar couplings , 2000, Quarterly Reviews of Biophysics.

[28]  D. Case,et al.  Static and Dynamic Effects on Vicinal Scalar J Couplings in Proteins and Peptides: A MD/DFT Analysis , 2000 .

[29]  Barbara Imperiali,et al.  Asparagine-linked protein glycosylation: from eukaryotic to prokaryotic systems. , 2006, Glycobiology.

[30]  J. Flippen,et al.  N‐Acetyl‐α‐d‐galactosamine. An amino sugar , 1974 .

[31]  R. Sasisekharan,et al.  The Sweet Science of Glycobiology , 2003, American Scientist.

[32]  O. Malkina,et al.  Chemical Shifts and Spin−Spin Coupling Constants in Me α-d-Xylopyranoside: A DFT Approach , 2001 .

[33]  Karl N. Kirschner,et al.  Solvent interactions determine carbohydrate conformation , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[34]  James R Cheeseman,et al.  Calculation of Nuclear Spin-Spin Coupling Constants of Molecules with First and Second Row Atoms in Study of Basis Set Dependence. , 2006, Journal of chemical theory and computation.

[35]  V. Bystrov.  Spin—spin coupling and the conformational states of peptide systems , 1976 .

[36]  Andrew Almond,et al.  Towards understanding the interaction between oligosaccharides and water molecules. , 2005, Carbohydrate research.

[37]  D R Salahub,et al.  Conformational dynamics of an alanine dipeptide analog: an ab initio molecular dynamics study. , 2001, Physical review. E, Statistical, nonlinear, and soft matter physics.

[38]  Andrew Almond,et al.  Hyaluronan: the local solution conformation determined by NMR and computer modeling is close to a contracted left-handed 4-fold helix. , 2006, Journal of molecular biology.