Genome evolution & adaptation of the multinuclear wheat stripe rust fungus. Animals and plants package their genomes into a single nucleus within each cell. In contrast, millions of fungal species accommodate multiple nuclei containing individual haploid genomes. It is currently unknown what the evolutionary implications are for this unusual genome division into multiple nuclei. Here we explore the evolutionary consequences of genome division into multiple nuclei for the first time by applying c ....Genome evolution & adaptation of the multinuclear wheat stripe rust fungus. Animals and plants package their genomes into a single nucleus within each cell. In contrast, millions of fungal species accommodate multiple nuclei containing individual haploid genomes. It is currently unknown what the evolutionary implications are for this unusual genome division into multiple nuclei. Here we explore the evolutionary consequences of genome division into multiple nuclei for the first time by applying cutting edge genome biology tools and algorithms. The economically significant study system is the devastating wheat stripe rust fungus. This pathogen costs Australian farmers over $100 million a year. New understanding is expected to lead to better disease management, reduced fungicide applications, and increased yields.Read moreRead less
Theoretical Studies on the KcsA Potassium Channel and the L-type Calcium Channel. All electrical activities in the brain are regulated by opening and closing of ion channels. Thus, understanding their mechanisms is a fundamental problem in biology. The project is aimed at developing a theoretical model of two important types of ion channels. Using a supercomputer, we will first deduce the shape of the microstructure formed by a protein wall. Then, using a computer simulation technique, we will c ....Theoretical Studies on the KcsA Potassium Channel and the L-type Calcium Channel. All electrical activities in the brain are regulated by opening and closing of ion channels. Thus, understanding their mechanisms is a fundamental problem in biology. The project is aimed at developing a theoretical model of two important types of ion channels. Using a supercomputer, we will first deduce the shape of the microstructure formed by a protein wall. Then, using a computer simulation technique, we will construct a set of physical models of biological ion channels, which will correctly replicate experimental observations. Such a theory will link the structure and function of an ion channel through the fundamental principles of physics.Read moreRead less
Discovery Early Career Researcher Award - Grant ID: DE240100301
Funder
Australian Research Council
Funding Amount
$440,000.00
Summary
Reducing uncertainty in prediction of leaf respiration in a changing world. This project aims to advance our understanding of responses of carbon dioxide (CO2) release by leaf (leaf respiration) to sustained changes in CO2 and temperature. Leaf respiration in terrestrial forests releases yearly CO2 that is two to four times higher than CO2 emitted by human activities, but its response to climate change is not well understood. The project expects to generate new knowledge on mechanisms underlying ....Reducing uncertainty in prediction of leaf respiration in a changing world. This project aims to advance our understanding of responses of carbon dioxide (CO2) release by leaf (leaf respiration) to sustained changes in CO2 and temperature. Leaf respiration in terrestrial forests releases yearly CO2 that is two to four times higher than CO2 emitted by human activities, but its response to climate change is not well understood. The project expects to generate new knowledge on mechanisms underlying responses of leaf respiration to these climate change variables, separately and combined. Expected outcome is to deliver criteria that enable dynamic changes in leaf respiration to be predicted in climate models. Results should benefit improved forecast of feedback between Australian forests' carbon cycling and climate.Read moreRead less
Why is the photosynthetic CO2-fixing enzyme, Rubisco, so inefficient? Dissection of the catalytic chemistry by computational simulation and experimental testing. Fixation of CO2 by the enzyme Rubisco during photosynthesis produces organic compounds which feed all life. Despite this critical role, Rubisco catalyses its reaction sluggishly and, worse, discriminates poorly between CO2 and O2, leading to useless products. Our combined expertise equips us to analyse Rubisco's mechanism using quantum- ....Why is the photosynthetic CO2-fixing enzyme, Rubisco, so inefficient? Dissection of the catalytic chemistry by computational simulation and experimental testing. Fixation of CO2 by the enzyme Rubisco during photosynthesis produces organic compounds which feed all life. Despite this critical role, Rubisco catalyses its reaction sluggishly and, worse, discriminates poorly between CO2 and O2, leading to useless products. Our combined expertise equips us to analyse Rubisco's mechanism using quantum-chemical methods and then test predictions experimentally. We will capitalise on our previous successful studies of Rubisco by addressing emergent issues which are the keys to understanding catalytic efficiency and CO2/O2 selectivity: the roles of a carbamylated lysine; the way CO2 addition is rendered irreversible; and the spin inversion inherent in O2 addition.Read moreRead less
3D Structure determination of biomacromolecular assemblies from sparse data. This project has direct impact on pharmaceutical research: Biomacromolecular interactions are key points for pharmaceutical intervention and detailed structural knowledge of dynamic protein interactions can significantly accelerate drug development. Australia has invested in expensive instrumentation that can be used with new laboratory methods to obtain information on delicately balanced biomacromolecular interactions, ....3D Structure determination of biomacromolecular assemblies from sparse data. This project has direct impact on pharmaceutical research: Biomacromolecular interactions are key points for pharmaceutical intervention and detailed structural knowledge of dynamic protein interactions can significantly accelerate drug development. Australia has invested in expensive instrumentation that can be used with new laboratory methods to obtain information on delicately balanced biomacromolecular interactions, and how they malfunction in disease. This project will provide a computational framework to increase the impact of this investment by integrating measurements from a range of novel technologies and developing understanding of changes in structure of large protein complexes in different functional states.Read moreRead less
TOWARDS A COMPLETE DESCRIPTION OF HOW ENZYMES WORK: development of simulation methods and protocols, blind test predictions, and experimental validation. Enzymes catalyze quite fantastic chemistry under mild physiological conditions. Many special chemical concepts (such as "transition-state stabilization" and "entropy-enthalpy compensation") proposed to explain these powers are unnecessary. Uniquely for a catalyst, these powers are integral to the structure, properties and dynamics of the protei ....TOWARDS A COMPLETE DESCRIPTION OF HOW ENZYMES WORK: development of simulation methods and protocols, blind test predictions, and experimental validation. Enzymes catalyze quite fantastic chemistry under mild physiological conditions. Many special chemical concepts (such as "transition-state stabilization" and "entropy-enthalpy compensation") proposed to explain these powers are unnecessary. Uniquely for a catalyst, these powers are integral to the structure, properties and dynamics of the protein, as constrained and selected by evolution. The question is how do they work? Answering this requires energetic and thermodynamic analysis beyond current experimental techniques, but accessible by computer simulation. We aim to develop a robust toolkit of simulation methods and protocols, blind test them by predicting the mechanism of a new enzyme, with followup experimental validation.
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Importance of conformational and electrostatic contributions in simulations of enzyme reaction mechanisms. The research will contribute to the development of biomolecular simulation in Australia by demonstrating its potential to complement experiment, and also promote the effective use of APAC (Australian national supercomputer facilities) resources by providing advanced programs and computational protocols for other researchers. It will assist the diffusion of computational biology technology i ....Importance of conformational and electrostatic contributions in simulations of enzyme reaction mechanisms. The research will contribute to the development of biomolecular simulation in Australia by demonstrating its potential to complement experiment, and also promote the effective use of APAC (Australian national supercomputer facilities) resources by providing advanced programs and computational protocols for other researchers. It will assist the diffusion of computational biology technology into industrial applications such as rational drug design and protein engineering, as, for example, in our associated Linkage project grant, and provide novel insights into protein engineering and other sorts of design, which transcend concepts currently used in biomimetic chemistry.Read moreRead less
Integrating theory and data to model evolution under a changing climate. This project aims to develop an innovative approach that integrates diverse data sources, from genetic sequences to geographic distributions, to improve inference of evolutionary dynamics. This will provide a powerful and efficient new method for understanding species’ responses to climate change, demonstrated by inferring past, current and future climate adaptability in a diverse and ecologically important Australian plant ....Integrating theory and data to model evolution under a changing climate. This project aims to develop an innovative approach that integrates diverse data sources, from genetic sequences to geographic distributions, to improve inference of evolutionary dynamics. This will provide a powerful and efficient new method for understanding species’ responses to climate change, demonstrated by inferring past, current and future climate adaptability in a diverse and ecologically important Australian plant family. Expected outcomes include enrichment of evolutionary theory and software tools to assess species' vulnerability to climate change. These outcomes will bring significant benefits to improve knowledge and protection of Australian biota and maximise returns on Australia's investment in biodiversity databases.Read moreRead less
Metal Complexes for Activation and Scission of Small, Multiply-Bonded Molecules. The immediate outcome of this work is a series of new metal complexes capable of selectively cleaving the strong bonds present in a number of small molecules of industrial and synthetic importance. These outcomes will have a significant impact on the development of both novel transition metal systems for synthetic chemistry and new industrial procedures for the activation and cleavage of multiply-bonded molecules su ....Metal Complexes for Activation and Scission of Small, Multiply-Bonded Molecules. The immediate outcome of this work is a series of new metal complexes capable of selectively cleaving the strong bonds present in a number of small molecules of industrial and synthetic importance. These outcomes will have a significant impact on the development of both novel transition metal systems for synthetic chemistry and new industrial procedures for the activation and cleavage of multiply-bonded molecules such as molecular nitrogen and carbon dioxide. They will lead to new consumer products, better methods of production, and potential downstream applications such as nitric oxide/nitrogen dioxide converters and carbon dioxide emission controls.Read moreRead less
Activation and Scission of Small Molecules using Three-Coordinate Metal Complexes. Chemists have long admired the ease with which such fundamental molecules as nitrogen, oxygen and carbon dioxide are processed in biological systems under mild conditions in contrast to existing industrial processes such as nitrogen 'fixation' which require drastic temperatures and pressures. Our project addresses this inbalance by using powerful computational methods to design highly-tuned chemical systems based ....Activation and Scission of Small Molecules using Three-Coordinate Metal Complexes. Chemists have long admired the ease with which such fundamental molecules as nitrogen, oxygen and carbon dioxide are processed in biological systems under mild conditions in contrast to existing industrial processes such as nitrogen 'fixation' which require drastic temperatures and pressures. Our project addresses this inbalance by using powerful computational methods to design highly-tuned chemical systems based on three-coordinate metal complexes which are specific for the activation and scission of important small molecules possessing multiple bonds.Read moreRead less