UCT CS Research Document Archive

Force-extension of the Amylose Polysaccharide

van den Berg, Rudolf (2010) Force-extension of the Amylose Polysaccharide. MSc, Department of Computer Science, University of Cape Town.

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Abstract

Atomic Force Microscopy (AFM) single-molecule stretching experiments have been used in a number of studies to characterise the elasticity of single polysaccharide molecules. Steered molecular dynamics (SMD) simulations can reproduce the force-extension behaviour of polysaccharides, while allowing for investigation of the molecular mechanisms behind the macroscopic behaviour. Various stretching experiments on single amylose molecules, using AFM combined with SMD simulations have shown that the molecular elasticity in saccharides is a function of both rotational motion about the glycosidic bonds and the flexibility of individual sugar rings. This study investigates the molecular mechanisms that determine the elastic properties exhibited by amylose when subjected to deformations with the use of constant force SMD simulations. Amylose is a linear polysaccharide of glucose linked mainly by (14) bonds. The elastic properties of amylose are explored by investigating the effect of both stretching speed and strand length on the force-extension profile. On the basis of this work, we confirm that the elastic behaviour of amylose is governed by the mechanics of the pyranose rings and their force-induced conformational transitions. The molecular mechanism can be explained by a combination of syn and anti-parallel conformations of the dihedral angles and chair-to-boat transitional changes. Almost half the chair-to-boat transitional changes of the pyranose rings occur in quick succession in the first part of the force-extension profile (cooperatively) and then the rest follow later (anti-cooperatively) at higher forces, with a much greater interval between them. At low forces, the stretching profile is characterised by the transition of the dihedral angles to the anti-conformation, with low elasticities measured for all the chain lengths. Chair-to-boat transitional changes of the pyranose rings of the shorter chains only occurred anti-cooperatively at high stretching forces, whereas much lower forces were recorded for the same conformational change in the longer chains. For the shorter chains most of these conversions produced the characteristic “shoulder" in the amylose stretching curve. Faster ramping rates were found to increase the force required to reach a particular extension of an amylose fragment. The transitions were similar in shape, but occur at lower forces, proving that decreasing the ramping rate lowers the expected force. The mechanism was also essentially the same, with very little change between the simulations. Simulations performed with slower ramping rates were found to be adequate for reproduction of the experimental curve.

EPrint Type:Electronic Thesis or Dissertation
Keywords:carbohydrates simulation modelling
Subjects:J Computer Applications: J.2 PHYSICAL SCIENCES AND ENGINEERING
I Computing Methodologies: I.6 SIMULATION AND MODELING
ID Code:619
Deposited By:Kuttel, Michelle
Deposited On:23 September 2010