NMR Spectroscopy and Computer Modeling of Carbohydrates: Recent Advances

by Johannes F. G. Vliegenthart, Robert J. Woods

Overview

In the past ten years, the interest in the functional and structural aspects of carbohydrates and glycoconjugates has increased enormously. Great insights have been made into the mode of action of glycans in cells, tissues, organs and organisms. As more and more information becomes known implicating carbohydrates in biological function, increasing pressure is placed on all aspects of biophysical methods to adapt and advance in order to provide structural insight into the biology of carbohydrates and conjugated glycans. Many existing tools that have served admirably to probe structure-function relationships in proteins are difficult or impossible to apply to complex glycans and glycoproteins. Established structural methods, such as X-ray diffraction or NMR spectroscopy also face enormous challenges when applied to the study of biologically relevant glycans in glycoproteins. Because of the challenges and limitations of traditional experimental methods, computational techniques can contribute unique insight into the relationship between oligosaccharide structure and biological function. Perhaps in no other field can biomolecular calculations make as major a contribution; whether they serve to provide models to assist in the interpretation of otherwise insufficient experimental data, or to provide a priory models for the structure of oligosaccharides, or insight into the mechanisms of carbohydrate recognition. From the application of quantum mechanics in the study of carbohydrate-processing enzymes, to the classical dynamics simulation of oligosaccharides and their protein complexes, the range of systems being examined theoretically is rapidly expanding. Given the structural diversity and flexibility of carbohydrates, it is not surprising that both experimental and theoretical methods face many unique challenges. Contained within this text are examples of the latest NMR and computational methods applied to oligosaccharides and their complexes with proteins.

Product Details

ISBN-13:	9780841239531
Publisher:	American Chemical Society
Publication date:	03/17/2006
Series:	ACS Symposium Series , #930
Pages:	378
Product dimensions:	9.10(w) x 6.10(h) x 1.00(d)

About the Author

Utrecht University

University of Georgia

Table of Contents

1. Introduction to NMR of Carbohydrates, Johannes F.G. Vliegenthart
2. Conformational Dynamics of Oligosaccharides, Jennie L.M. Jansson, Arnold Maliniak and Göran Widmalm
3. Structure and Dynamics of Carbohydrates using Residual Dipolar Couplings, James H. Prestegard and Xiaobing
4. Protein-Carbohydrate Interactions: A Combined Theoretical and NMR Experimental Approach on Carbohydrate-Aromatic Interactions and on Pyranose Ring Distortion, Jesús Jiménez-Barbero, F. Javier Cañada, Gabriel Cuevas, Juan L. Asensio, Nuria Aboitiz, Angeles Canales, M. Isabel Chávez, M. Carmen Fernández-Alonso, Alicia García-Herrero, Silvia Mari, and Paloma Vidal
5. Structural Analysis of inter- and intramolecular Interactions: Laser Photo CIDNP Technique as a tool, Hans-Christian Siebert, Emald Tajkhorshid, Johannes F.G. Vliegenthart, Claus-Wilhelm von der Lieth, Sabine André and Hans-Joachim Gabius
6. Hydroxy Protons in Structural Studies of Carbohydrates by NMR Spectroscopy, Corine Sandström and Lennart Kenne
7. Oligosaccharides and Cellulose Crystal Surfaces, Bas R. Leeflang, J. Albert van Kuik and Loes M.J. Kroon-Batenburg
8. Biomolecular dynamics: testing microscopic predictions against macroscopic experiments, Andrew Almond
9. Structural Insights towards a molecular comprehension of the GH13 Amylase Specificity, Gwénaëlle André-Leroux
10. Simulations in Carbohydrates, Richard A. Bryce, Muslim, A.-M., McNamara, J.P., Abdel-Aal, H., and Hillier
11. Predicting the 3D Structures of Anti-Carbohydrate Antibodies: Combining Comparative Modeling and MD Simulations, Jane Dannow Dyekjær and R.J Woods
12. .Carbohydrate Structure from NMR Residual Diploar Couplings, Daron I. Freedberg, Ano, S.O., Norris, S.E., and Venable, R.M
13. Incorporation of Carbohydrates into Macromolecular Force Fields, Sarah M. Tschampel, Kirschner, K.N. and Woods, R.J
14. Molecular modeling of carbohydrates with no charges, no hydrogen bonds and no atoms, Alain Laederach,
15. Docking of Carbohydrates to proteins: Empirical free energy functions, Valeria Molinero and Goddard III, W.A.
16. Molecular modeling of retaining glycosyltransferases, Igor Tvaroska
17. Two Unexpected Effects Found with 2, 3, 4, 6-Tetra-O-methyl-D-Gluco- and Mannopyranosyl Oxacarbenium ions: An O-2 Pseudo-equatorial Preference and a large H-2-C-2-O-2-CH3 syn Preference, Dennis M. Whitfield, Ionescu, A., Wang, L., Zgierski, M.Z., and Nukada, T.