Construction of the Midge History Match Model

Imperial Users onl

Mechanistic behaviour and molecular interactions of heat shock protein 47 (HSP47)

This project involves the study of heat shock protein 47 (HSP47), which is a molecular chaperone crucial for collagen biosynthesis. It exhibits a high degree of sequence homology with members of the serine protease inhibitor (serpin) superfamily, though HSP47 does not possess the inhibitory activity. It is a single-substrate chaperone, and binds only to collagen. ‘Knock-out’ of the hsp47 gene impairs the secretion of correctly folded collagen triple helix molecules leading to embryonic lethality in mice. Thus the aim of this project was to elucidate the specific mechanism that governs the binding to and release from collagen at the molecular level, known as the ‘pH-switch mechanism’. Emphasis is given on histidine (His) residues as the HSP47-collagen dissociation pH is similar to the pKa of the imidazole side chain of His residues. Site directed mutagenesis was used to mutate surface His residues, based on a mouse HSP47 homology model. The effects of the mutations on the behaviour of HSP47 were then assessed by collagen binding assays and structural analyses with circular dichroism (CD). All mutants were found to have good solubility and retain their binding ability to collagen like wild-type HSP47 in batch assay, but perturbed behaviour was seen in column experiment. Mutation of His residue at position 191 (H191) causes the shift in the collagen dissociation pH, while mutation of H197 and/or 198 disrupt the specific HSP47-collagen interaction. H191, 197 and 198 are predicted to be located in the region near the C-terminus of strand 3 of β-sheet A (s3A) in the homology model, a region specifically known as the ‘breach cluster’ in serpin nomenclature. The extent of conformational rearrangement of this region was further investigated by means of intrinsic tryptophan fluorescence spectroscopy using a series of single tryptophan (Trp) mutants. Results from analyses performed on the mutants did not contradict the observation seen in His mutational work, as Trp residues in the ‘breach’ cluster are likely to be located in the dynamic region of HSP47 pH-triggered conformational change. In conclusion, this study establishes the importance of His residues in the ‘breach cluster’ to HSP47 pH-switch behaviour. Finally, a model for HSP47 pH-switch mechanism was proposed from data obtained via mutagenesis experiments. The model is hoped to assist future research into HSP47 cellular behaviour and will also be of great use in therapeutic applications involving the molecular chaperone

Effect of reconstituted method on shear strength properties of peat

Peat is an organic soil contains more than 75% organic content. Shear strength of the soil is one of the most important parameters in engineering design, especially during the pre-construction and post-construction periods, since used to evaluate the foundation and slope stability of soil. Peat normally known as a soil that has very low shear strength and to determine and understand the shear strength of the peat is difficult in geotechnical engineering because of a few factors such as the origin of the soil, water content, organic matter and the degree of humification. The aim of this study was to determine the effective undrained shear strength properties of reconstituted peat. All the reconstituted peat samples were of the size that passing opening sieve 0.425mm, 1.000mm, 2.360mm and 3.350mm and were preconsolidated at pressures of 50 kPa, 80 kPa and 100 kPa. The relationship deviator stress- strain, σdmax and excess pore water pressure, Δu, shows that in both of reconstituted and undisturbed peat gradually increased when confining pressure, σ’ and pre- consolidation pressure, σc increased. As a conclusion, the undrained shear strength properties result obtained shows that the RS3.350 has higher strength than RS0.425, RS1.000 and RS2.360. However, the entire reconstituted peat sample shows the increment value of the shear strength with the increment of peat size and pre- consolidation pressure. For comparison purposes, the undrained shear strength properties result obtained shows that the reconstituted peat has higher strength than undisturbed peat. The factors that contributed to the higher shear strength properties in this study are segregation of peat size, pre- consolidation pressure, initial void ratio and also the physical properties such as initial water content, fiber content and liquid limit

Soil compaction of peat under the influence of electrokinetic stabilization (EKS) treatment

This study aims to enhance the properties of peat such as, (shear strength, compressibility, permeability and liquid limit). Peat is considered as one of the problematic soil in construction projects all over the world, which covers about 4% land of the whole world while 8% of the total area of Malaysia and about (5.86%) of peat soil existing in Johor state. Low shear strength of peat may lead to massive loss of various sectors contributing toward any economic activities such as construction & agriculture projects. There are several issues related to peat stabilization which has become a priority to ensure that soft soil is stable & capable of supporting a load after treated by a suitable soil stabilization method. The problem can be finally reduced by applying stabilization treatment to enhance its properties. One of the known technique Electrokinetic Stabilization treatment, by applying an electric potential to stabilize soft soil. In this method, aluminum was used as an electrode with various voltage potential in the range of 110 to 150 V was applied on both cathode and anode electrode for the duration of 3 and 6 hours at the testing condition without & with a load of (50 kg). Soil parameters such as, shear strength