Carbohydrates dynamic modeling

It should be noted that none of these dynamic models is related directly to polysaccharide structures as a basis for describing possible modes of reorientation in a carbohydrate chain. Nevertheless, some of them appear to offer a good approximation for linear polysaccharides (for instance, amylose) as seen in the following sections. 

Table I, which lists a number of mono-, oligo-, and polysaccharides and derivatives whose motional descriptions are available based on qualitative arguments, summarizes the experimental conditions and types of measurements used to obtain those descriptions. Table II deals specifically with those carbohydrates for which a quantitative treatment and dynamic modeling have been undertaken. In naming the compounds listed in Tables I and II, IUPAC rules are used for monosaccharide and less complex oligosaccharide molecules. However, empirical names are used for unusual oligosaccharides involving a complex aglycon substituent and polysaccharides. The gross motional features of a number of the compounds in Table I have been discussed in references 6-8, and will be mentioned here only if necessary for further clarification or for comparison with quantitative results.

The second independent motion requires a suitable dynamic model that reflects the geometric constraints of chain flexibility characteristic of polysaccharides. However, no model is yet available that takes polysaccharide structural details into account or describes possible modes of reorientation in the carbohydrate chain. 

These measurements can then be used to derive dynamic models of carbohydrates and oligosaccharides. It is now generally accepted that carbohydrates are dynamic molecules with internal motions that occur on a time-scale faster than the overall motion of the molecules. 

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. 

Our initial, small models of an isolated cellulose chain ranged from the dimer (cellobiose) to the octamer. The dynamics of these fragments have thus far been simulated only in vacuum, using different potential energy functions such as those of MM2(85) (9) and AMBER (10), with and without contributions from electrostatic terms and hydrogen bonds, etc. (The program DISCOVER, customized for carbohydrates and for operation on the Alliant FX/80 computer, has been used (12).) Generally, the time span for the simulations has been of the order of several hundred picoseconds to 1 nanosecond. 

The modeling of carbohydrates is undergoing rapid development. For example, the first comprehensive conformational mappings of disaccharides with flexible residues and the first molecular dynamics studies of carbohydrates have only recently been published. At the same time, interest in carbohydrates has been increasing dramatically, and there is a need for a publication that gently introduces the uninitiated and provides an overview of current research in the area. We feel that Computer Modeling ( Carbohydrate Molecules meets these needs. 

Alderkamp A-C, Nejstgaard JC, Verity PG, Zirbel MJ, Saz-hin AF, van Rijssel M (2006) Dynamics in carbohydrate composition of Phaeocystis pouchetii colonies during spring blooms in mesocosms. J Sea Res 55 169-181 Anderson TR (2005) Plankton functional type modeling running before we can walk J Plankton Res 27 1073-1081... 

The first structure of human renin was obtained from prorenin produced by expression of its cDNA in transfected mammalian cells. Prorenin was cleaved in the laboratory to renin using the protease trypsin. Because the carbohydrates in renin are not required for bioactivity, oligosaccharides were removed enzymatically. This process facilitates crystallization in some cases and also removes the contribution of the heterogeneous sugar chains to the diffraction pattern. The structure was determined without the use of heavy-atom derivatives, by application of molecular replacement techniques based on the atomic coordinates of porcine pepsinogen as the model. The molecular dynamic method of refinement was used extensively to arrive at a 2.5 A resolution structure. However, some of the loop regions were not well resolved in this structure (Sielecki et al, 1989 Sail et al, 1990). 

Graphical molecular modeling package. MULTIC for molecular mechanics, molecular dynamics, and conformational searching of organic molecules, proteins, nucleic acids, and carbohydrates. AMBER-, MM2-, and MM3-like and OPTS force fields implicit solvation model. Reads Cambridge and Brookhaven PDB files. VAX, Convex, Alliant, Cray, and UNIX workstations. 

The CHARMM (Chemistry at HARvard Macromolecular Mechanics) force field is designed for the modelling (both molecular mechanics and dynamics calculations) of macromolecular systems [67]. A revision for carbohydrates was made by Ha et al. [40]. Kouwijzer and Grootenhuis [68-69] redeveloped the CHEAT force field a CHARMm-based force field for carbohydrates with which a molecule in aqueous solution is mimicked by a simulation of the isolated molecule. 

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