Carbohydrates, molecular dynamics simulations

J. W. Brady and R. K. Schmidt, /. Phys. Chem., 97, 958 (1993). The Role of Hydrogen Bonding in Carbohydrates Molecular Dynamics Simulations of Maltose in Aqueous Solu-... 

With the advent of molecular dynamics simulations applied to carbohydrates, one can anticipate the direct computation of more conceptually appealmg surfaces of V in 0s) space from a given U( qint,qext)) in the near future. Monte Carlo integration over (qext) and (b,x, 0h) for fix (0s) provides an alternative procedure, but one which is probably less attractive in terms of efficiency than the molecular dynamics approach. A second alternative, known as adiabatic mapping, provides an approximation to V((0s ), and applications of this method to carbohydrates have recently begun to appear. 12,13 in this approach the conformational... 

Molecular Dynamics Simulations of Carbohydrates and Their Solvation... 

Molecular dynamics (MD) simulations are a class of molecular mechanics calculation which directly model the motions of molecular systems, often providing considerable information which cannot be obtained by any other technique, theoretical or experimental. MD simulations have only recently been applied to problems of carbohydrate conformation and motions, but it is likely that this technique will be widely used for modeling carbohydrates in the future. This paper introduces the basic techniques of MD simulations and illustrates the types of information which can be gained from such simulations by discussing the results of several simulations of sugars. The importance of solvation in carbohydrate systems will also be discussed, and procedures for including solvation in molecular dynamics simulations will be introduced and again illustrated from carbohydrate studies. 

The first reported molecular dynamics simulations of carbohydrates began to appear in 1986, with the publication of studies of the vacutim motions of a-D-glucopyranose (9), discussed below, and the dynamics of a hexa-NAG substrate bound to lysozyme (IQ), which are described in greater detail in the chapter by Post, et al. in this voltime. Since that time, simulations of the dynamics of many more carbohydrate molecules have been undertaken. A number of these studies are described in subsequent chapters of this voltime. The introduction of this well developed technique to problems of carbohydrate structure and function could contribute substantially to the understanding of this class of molecules, as has been the case for proteins and related biopolymers. 

P R E CONTENTS Preface. Stable-Isotope Assisted Protein NMR Spectroscopy in Solution, Brian J. Stockman and John L. Mar-kley. 31P and 1H Two-Dimensional NMR and NOESY-Dis-tance Restrained Molecular Dynamics Methodologies for Defining Sequence-Specific Variations in Duplex Oligonucleotides, David G. Gorenstein, Robert P. Meadows, James T. Metz, Edward Nikonowcz and Carol Beth Post. NMR Study of B- and Z-DNA Hairpins of d[(CG) 3T4(CG)3] in Solution, Sa-toshi Ikuta and Yu-Sen Wang. Molecular Dynamics Simulations of Carbohydrate Molecules, J.W. Brady. Diversity in the Structure of Hemes, Russell Timkovich and Laureano L. Bon-doc. Index. Volume 2,1991, 180 pp. 112.50/E72.50 ISBN 1-55938-396-8... 

A molecular dynamics simulation of the crystal structures of a-cyclodextrin hexahydrate and / -cyclodextrin dodecahydrate was more successful. In both hydrates, the carbohydrate atomic positions and two third of the water positions were reproduced within the experimental accuracy, and most of the O-H 0 hydrogen bonds that had been determined by neutron diffraction studies (Part III, Chap. 18) also showed up in the simulation [360, 361]. 

J. Kohler, Molecular Dynamics Simulations of Carbohydrates in Molecular Dynamics, Applications in Molecular Biology, J.M. Goodfellow (ed) MacMillan, London, 1991. 

Roberts, C.J. and Debenedetti, P.G. Structure and dynamics in concentrated, amorphous carbohydrate-water systems by molecular dynamics simulation, /. Phys. Chem. B, 103, 7308,1999. 

Numerous reports have been published about the three-dimensional structure of proteins determined by X-ray crystallography and/or NMR, and by computational chemical calculation from the results of amino acid sequencing. An empirical approach to identifying catalytic sites, the location of metal ion and carbohydrate binding sites, and folding and unfolding, has been studied with molecular dynamics simulations. Once the binding site of a protein, the structure of the protein-small molecule interaction, is... 

Carbohydrates. The conformational flexibility of lactose in solution has been investigated by residual dipolar couplings. One-bond carbon-proton and proton-proton coupling constants have been measured in two oriented media and interpreted in combination with molecular dynamics simulations. Two different approaches have been used to determine the alignment tensor from a... 

Galema, S.A., Howard, E., Engberts, J.B.F.N. and Grigera, J.R., The effect of stereochemistry upon carbohydrate hydration. A molecular dynamics simulation of beta-n-galactopyranose and (alpha,beta)-D-talopyranose, Carhohydr. Res., 1994, 265, 215-225. 

The topic of hydrogen bonding of carbohydrates and hydrate inclusion compounds has been surveyed as have the topics of intramolecular hydrogen bonding and molecular association in monosaccharides and natural cellulose. Other reviews on physical aspects of carbohydrates have dealt with liquid crystal compounds and with molecular dynamics simulations in the field. ... 

Higher Oligosacdiarides and C-Glyco es. - Following the previous section, not only di-, but tri- and tetrasaccharide complexes of rainbow trout lysozyme have been characterized by X-ray analysis. The orientation of the (a 1- 6) mannosyl arm of a heptasaccharide and hexasacchatide (and disaccharide fragments) has been studied by molecular dynamics simulations and compared with protein-carbohydrate complex crystal structures. ... 

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