• Development of genetic algorithm for optimisation of predicted membrane protein structures

      Minaji-Moghaddam, Noushin (University of BedfordshireUniversity of Bedfordshire, 2007-03)
      Due to the inherent problems with their structural elucidation in the laboratory, the computational prediction of membrane protein structure is an essential step toward understanding the function of these leading targets for drug discovery. In this work, the development of a genetic algorithm technique is described that is able to generate predictive 3D structures of membrane proteins in an ab initio fashion that possess high stability and similarity to the native structure. This is accomplished through optimisation of the distances between TM regions and the end-on rotation of each TM helix. The starting point for the genetic algorithm is from the model of general TM region arrangement predicted using the TMRelate program. From these approximate starting coordinates, the TMBuilder program is used to generate the helical backbone 3D coordinates. The amino acid side chains are constructed using the MaxSprout algorithm. The genetic algorithm is designed to represent a TM protein structure by encoding each alpha carbon atom starting position, the starting atom of the initial residue of each helix, and operates by manipulating these starting positions. To evaluate each predicted structure, the SwissPDBViewer software (incorporating the GROMOS force field software) is employed to calculate the free potential energy. For the first time, a GA has been successfully applied to the problem of predicting membrane protein structure. Comparison between newly predicted structures (tests) and the native structure (control) indicate that the developed GA approach represents an efficient and fast method for refinement of predicted TM protein structures. Further enhancement of the performance of the GA allows the TMGA system to generate predictive structures with comparable energetic stability and reasonable structural similarity to the native structure.
    • Investigation of the colorimetric measurement of pH and metal ions by using reagents doped in sol-gel glasses for potential on-line monitoring

      Javaid, Muhammad Azhar (University of BedfordshireUniversity of Bedfordshire, 1998-07)
      Sol-gel porous glasses have been doped with indicator molecules for colorimetric measurements of pH and metal ions in solution. pH measurements were made in real time (20 seconds) to a wide pH range 3-8 by using bromophenol blue doped in sol-gel thin films. New methods of sol-gel coating on the inside of test tubes and tubing have been introduced for simple, non invasive, on the spot chemical sensing. pH indicator doped films were also successfully autoclaved for biological applications without affecting their chemical and physical properties. The pore structure of thin films has been controlled for minimising the effect of ageing on response time by introducing dimethyl formamide (DMF). The effect of light, temperature and salt on thin films have been studied. The results show that they are relatively stable between 20-31' C and less affected « 0.03 absorbance unit decrease in 3 weeks) by light. However their response to pH is changed by adding salt in solution with concentration higher than O.OlM. Fourier transform infra red (FTIR) study of films has been conducted to elucidate the effect of ageing, DMF and autoclaving on their chemical structures. It was found that ageing continues after four weeks of fabrication and addition of DMF helps to reduce ageing and increase porosity. The long term stability of these pH indicator doped films in various solvents has been established. Thin films on microscope slides were deposited by using a newly designed spin coater and have been demonstrated as reusable pH slides. Sol-gel films were also doped by different metal reagents. Eriochrome cyanine doped thin films were found to be sensitive to copper ions in solution. Copper (Cu++) was measured to a low concentration of 0.6 ppm. The effect of light and temperature on Eriochrome copper complex was studied. Interferences of other metal ions were examined. A fibre-optic pH sensor has been demon.strated by coating an optical fibre with a sol-gel film (0.8 J.1m thick) doped with bromophenol blue. The sensor has shown fast response (5 seconds) to pH changes from pH 3 to 8 and no leaching or cracking during repeated use. It is simple to fabricate and easy to use as an interchangeable pH fibre probe. It has potential application in biological processes as an integral part of an online monitoring system.