Theoretical studies of Membrane Proteins : Properties, Prediction Methods and Genome-wide analysis

Membrane proteins are a large and important class of proteins. They are responsible for several of the key functions in a living cell, e.g. transport of nutrients and ions, cell-cell signaling, and cell-cell adhesion. Despite their importance it has not been possible to study their structure and organization in much detail because of the difficulty to obtain 3D structures. In this thesis theoretical studies of membrane protein sequences and structures have been carried out by analyzing existing experimental data. The data comes from several sources including sequence databases, genome sequencing projects, and 3D structures. Prediction of the membrane spanning regions by hydrophobicity analysis is a key technique used in several of the studies. A novel method for this is also presented and compared to other methods. The primary questions addressed in the thesis are: What properties are common to all membrane proteins? What is the overall architecture of a membrane protein? What properties govern the integration into the membrane? How many membrane proteins are there and how are they distributed in different organisms? Several of the findings have now been backed up by experiments. An analysis of the large family of G-protein coupled receptors pinpoints differences in length and amino acid composition of loops between proteins with and without a signal peptide and also differences between extra- and intracellular loops. Known 3D structures of membrane proteins have been studied in terms of hydrophobicity, distribution of secondary structure and amino acid types, position specific residue variability, and differences between loops and membrane spanning regions. An analysis of several fully and partially sequenced genomes from eukaryotes, prokaryotes, and archaea has been carried out. Several differences in the membrane protein content between organisms were found, the most important being the total number of membrane proteins and the distribution of membrane proteins with a given number of transmembrane segments. Of the properties that were found to be similar in all organisms, the most obvious is the bias in the distribution of positive charges between the extra- and intracellular loops. Finally, an analysis of homologues to membrane proteins with known topology uncovered two related, multi-spanning proteins with opposite predicted orientations. The predicted topologies were verified experimentally, providing a first example of "divergent topology evolution".

Spark Plasma Sintering of Si3N4-based Ceramics : Sintering mechanism-Tailoring microstructure-Evaluationg properties

Spark Plasma Sintering (SPS) is a promising rapid consolidation technique that allows a better understanding and manipulating of sintering kinetics and therefore makes it possible to obtain Si3N4-based ceramics with tailored microstructures, consisting of grains with either equiaxed or elongated morphology. The presence of an extra liquid phase is necessary for forming tough interlocking microstructures in Yb/Y-stabilised α-sialon by HP. The liquid is introduced by a new method, namely by increasing the O/N ratio in the general formula RExSi12-(3x+n)Al3x+nOnN16-n while keeping the cation ratios of RE, Si and Al constant. Monophasic α-sialon ceramics with tailored microstructures, consisting of either fine equiaxed or elongated grains, have been obtained by using SPS, whether or not such an extra liquid phase is involved. The three processes, namely densification, phase transformation and grain growth, which usually occur simultaneously during conventional HP consolidation of Si3N4-based ceramics, have been precisely followed and separately investigated in the SPS process. The enhanced densification is attributed to the non-equilibrium nature of the liquid phase formed during heating. The dominating mechanism during densification is the enhanced grain boundary sliding accompanied by diffusion- and/or reaction-controlled processes. The rapid grain growth is ascribed to a dynamic ripening mechanism based on the formation of a liquid phase that is grossly out of equilibrium, which in turn generates an extra chemical driving force for mass transfer. Monophasic α-sialon ceramics with interlocking microstructures exhibit improved damage tolerance. Y/Yb- stabilised monophasic α-sialon ceramics containing approximately 3 vol% liquid with refined interlocking microstructures have excellent thermal-shock resistance, comparable to the best β-sialon ceramics with 20 vol% additional liquid phase prepared by HP. The obtained sialon ceramics with fine-grained microstructure show formidably improved superplasticity in the presence of an electric field. The compressive strain rate reaches the order of 10-2 s-1 at temperatures above 1500oC, that is, two orders of magnitude higher than that has been realised so far by any other conventional approaches. The high deformation rate recorded in this work opens up possibilities for making ceramic components with complex shapes through super-plastic forming.