Computational models for conformations of cell wall mycolates from Mycobacterium tuberculosis

Abstract

Literature highlights the effects of mycolic acid (MA) fine-structure on biological activity, pathogenicity, virulence and cell wall structure and permeability. Knowledge on MA-structure and how their conformations are dependent on their precise molecular composition becomes essential in exploiting these properties in drug-design and in advancing our understanding of the disease. In our group evidence for a structural or functional relationship between cholesterol and MAs have been discovered. The aim of the experimental part of this work was to study this relationship further by attempting to quantify the interaction between cholesterol and MAs in liposomes on an evanescent field biosensor. The binding profiles that were obtained could not be evaluated with kinetic software and the interaction between cholesterol and MAs was not linearly dependant on the concentration of cholesterol. However, novel insight into the interaction was gained when it was observed that cholesterol only accumulated on MA liposomes when cholesterol liposomes containing concentrations of cholesterol resulting in a suspected liquid ordered phase, were used. This is significant since it implies that cholesterol in membrane rafts of the host cell that exist in a liquid ordered phase would be able to interact with MAs under physiological conditions. The theoretical part of this work represents the first molecular modeling study in which MAs are allowed to fold with no conformational restrictions. It is proposed that MAs fold as a function of their functional groups, stereochemistry, and various chain lengths. It was also investigated whether methylation of the acid group changes conformational preferences. The effect of chain length on cyclopropane structure and the viability of systematic conformational searching in MAs were shown using quantum mechanics. Replicate molecular dynamics simulations were done for 4 ns in vacuo on alpha-; methoxy-; methoxy methyl ester- and keto-MAs. MAs had an open starting conformation without conformational restrictions. Results were analysed using eight distances characteristic of the conformational fold. Using these distances, W-, U- and Z-shaped folds were identified. Principal component analysis (PCA) and self-organising maps (SOMs) were used to evaluate differences and trends in MA-conformations. Quantum chemical results showed that chain length did not affect cyclopropane structure and that the systematic plotting of potential energy surfaces is an effective tool to analyse effects of changes in geometry on the energy of the molecule and to predict favoured conformations. Remarkably, single MAs assumed W-, U- and Z-folds in vacuo during molecular dynamics simulations that have previously been observed in monolayers. PCA and SOM plots showed that keto-MA folded faster than other MAs. Alpha-MA showed the highest frequency of W-, U- and Z-folds. Methoxy-MA did not readily fold at its cis-cyclopropane group. Methylation of the acid group of methoxy-MA did not show remarkable differences in the conformations assumed, but almost doubled the frequency of WUZ-structures obtained as compared to non-esterified methoxy-MA. The inherent structural differences between MA-subclasses clearly affect the trends in structural folds that they assume. Molecular modeling of MAs proved to be a versatile tool for resolving structure-function relationships at the molecular level. Copyright 2008, University of Pretoria. All rights reserved. The copyright in this work vests in the University of Pretoria. No part of this work may be reproduced or transmitted in any form or by any means, without the prior written permission of the University of Pretoria. Please cite as follows: Prinsloo, W 2008, Computational models for conformations of cell wall mycolates from Mycobacterium tuberculosis, MSc dissertation, University of Pretoria, Pretoria, viewed yymmdd < http://upetd.up.ac.za/thesis/available/etd-06122009-114802 / > E1400/gm