|CCL 16.12.02 PhD scholarships in computational biophysics and protein structure modelling, Perth, Australia|
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Date: Fri Dec 2 03:13:33 2016
Subject: 16.12.02 PhD scholarships in computational biophysics and protein structure modelling, Perth, Australia
The Biomolecular Modelling Group at Curtin University (Perth, Australia) has two PhD scholarships available for two different projects as outlined below in (1) understanding protein translation in the ribosome, and (2) the prediction of new fungal effector-like proteins. These PhD positions are available immediately. PROJECT 1: PREDICTION OF NEW FUNGAL EFFECTOR-LIKE PROTEINS. The primary means by which microbial pathogens thrive is through the externalisation of effectors, which are imported into host cells, interfere with their biological processes and promote disease. The discovery of effectors is of high importance to agriculture, facilitating the screening of cultivars for disease resistance; however, this is not a simple process. Fungal effector proteins exhibit little to no amino acid sequence homology to other known proteins. There is, however, growing evidence that some types of effector proteins share similar 3D structures despite having very different amino acid sequences. This project will shed much necessary light into these effector proteins through the following specific aims: (1) augment existing bioinformatics pipelines to predict the 3D structure of fungal protein effectors from publicly available fungal and plant genome/proteome datasets; (2) discover new fungal effector-like proteins through searching for similar 3D structures to known effectors; and (3) discover and characterise new effector-like proteins through the prediction of their interactions with target plant proteins. This project will be co-supervised by Prof. Ricardo Mancera (R.Mancera^-^curtin.edu.au; School of Biomedical Sciences and Curtin Institute for Computation) and Dr. James Hane (James.Hane^-^curtin.edu.au; Centre for Crop and Disease Management, Department of Environment & Agriculture) at Curtin University. This project would suit someone with an undergraduate and/or Masters degree in biology, bioinformatics, biotechnology, chemistry or related field with demonstrable experience in bioinformatics and/or molecular modelling. PROJECT 2: UNDERSTANDING PROTEIN TRANSLATION IN THE RIBOSOME. During translation, amino acids are brought to the ribosome by transfer RNA (tRNA) molecules through a diffusive process. Consequently the time that a ribosome spends at a specific codon is mainly determined by the time that the cognate tRNA needs to arrive, ultimately governing the speed at which the ribosome can advance along the mRNA and, therefore, the rate at which the specific protein is produced. Mathematical models of the process of translation represent mRNA as a one-dimensional lattice, with each site of the lattice representing a codon of the mRNA. Ribosomes are represented as particles that can bind to the lattice, hop stochastically along the lattice, and hop off the lattice at the last site, all at different rates. The internal mechanochemical cycle of the ribosome and the fact that all mRNAs in the cell share the same pool of main translation resources, such as tRNAs and ribosomes, is also considered. These models, however, neglect to incorporate the effect that the crowded environment in the cell cytoplasm has on the diffusion of tRNAs to the ribosomes. As a consequence, normal diffusion assumptions underlying the estimation of average waiting times associated to each codon are not valid in general, and it remains largely unclear how the control of timing of protein synthesis and regulation of protein production rates are affected. Increasing our ability to accurately model the underlying mechanisms that govern translation dynamics will impact the use of recombinant gene expression in biotechnology to produce a range of therapeutic agents as well as our understanding of certain diseases arising from malfunctioning of the regulation mechanisms of translation. This project will focus on how to describe the hopping rates along the mRNA in a more accurate manner: since tRNAs cannot freely diffuse in the cytoplasm, the average time spent by a ribosome on a codon cannot be assumed to be proportional to the corresponding tRNA concentration. Molecular dynamics and Brownian simulations of the effects of macromolecular crowding on the diffusion of tRNAs will improve the modelling of hopping rates, going beyond the oversimplified assumption that they are constant and proportional to tRNA abundance. This project will be co-supervised by Prof. Ricardo Mancera (R.Mancera^-^curtin.edu.au; School of Biomedical Sciences and Curtin Institute for Computation) and Dr. Maria Carmen Romano (M.Romano^-^abdn.ac.uk; Institute for Complex Systems and Mathematical Biology, Department of Physics, University of Aberdeen, UK). The student will be expected to spend the first six months of this project at Aberdeen (UK), followed by two years in Perth (Australia), and then a further 6 months at Aberdeen to complete the project. This project would suit someone with an undergraduate and/or Masters degree in physics, chemistry, biotechnology or related field with demonstrable experience in molecular dynamics simulations. For both PhD positions the student will be required to apply for admission and enrol at Curtin University (http://www.curtin.edu.au). Curtin is the largest university in Western Australia and is ranked amongst the top universities in Australia and within the top 2% in the world. The Biomolecular Modelling Group, headed by Prof. Ricardo Mancera, is one of the major users of the newly established Pawsey Supercomputing Centre in Perth, which houses the fastest supercomputer in the southern hemisphere. In addition, living in the state capital Perth offers a great lifestyle due to Western Australias superb weather, beaches and outdoors activities. For project 2 the student will also be expected to apply for admission and co-enrol at the University of Aberdeen (http://www.abdn.ac.uk). Aberdeen is one of the oldest universities in the UK and ranked within the top 1% in the world. Applicants whose academic qualifications were not obtained from an English- language speaking country will need to satisfy English language requirements by attaining 7.0 in all bands of the IELTS or an overall score of 94 in the TOEFL (with a minimum of 27 in writing and 24 in other areas). Only applicants that fulfil these requirements need apply by submitting a copy of their full CV to Professor Ricardo Mancera (R.Mancera^-^curtin.edu.au), including full details of all academic degrees obtained, research skills and experience, any publications and conference presentations, and the names of 2-3 referees.NOTE THAT E-MAIL ADDRESSES HAVE BEEN MODIFIED!!!
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