Andrew C. Warden
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View article: Exploration and comparative visualization of metabolic networks in GEMs with MMINT
Exploration and comparative visualization of metabolic networks in GEMs with MMINT Open
Genome-scale metabolic models (GEMs) are essential tools in systems and engineering biology, enabling the simulation of genome-encoded pathways, predicting metabolic fluxes and emergent phenotypes. GEM network visualization tools can facil…
View article: Resolving the structure and assembly of the honeybee silk heterotetrameric coiled coil
Resolving the structure and assembly of the honeybee silk heterotetrameric coiled coil Open
Coiled coil structures, first proposed by Crick in the 1950s, are protein structural motifs found across diverse biological systems. Honeybee silk was among the earliest identified coiled coils, with X‐ray diffraction studies in the 1960s …
View article: Probing the Microscopic Behavior of PFOS Clustering and Adsorption at LNAPL Interfaces; a PFOS–Water–Cyclohexane System
Probing the Microscopic Behavior of PFOS Clustering and Adsorption at LNAPL Interfaces; a PFOS–Water–Cyclohexane System Open
Per- and polyfluoroalkyl substances (PFAS) are common soil and groundwater contaminants that persist in the environment. Perfluorooctanesulfonic acid (PFOS) has been a key component in aqueous film-forming foams, extensively used for firef…
View article: EMMAi: fast enzyme-allocation constraints in GEMs for improved biomass prediction across carbon sources
EMMAi: fast enzyme-allocation constraints in GEMs for improved biomass prediction across carbon sources Open
Genome-scale metabolic models (GEMs) predict emergent phenotypes by modeling the metabolic networks encoded in genomes. While GEMs have significantly advanced systems biology, metabolic engineering, biomedicine, and environmental science, …
View article: SELFprot: Effective and Efficient Multitask Finetuning Methods for Protein Parameter Prediction
SELFprot: Effective and Efficient Multitask Finetuning Methods for Protein Parameter Prediction Open
Accurately predicting protein-ligand interactions and enzymatic kinetics remains a challenge for computational biology. Here, we present SELFprot, a suite of modular transformer-based machine learning architectures that leverage the ESM2-3…
View article: MMINT: A Metabolic Model Interactive Network Tool for the Exploration and Comparative Visualisation of Metabolic Networks
MMINT: A Metabolic Model Interactive Network Tool for the Exploration and Comparative Visualisation of Metabolic Networks Open
View article: Structural insights into the enzymatic breakdown of azomycin-derived antibiotics by 2-nitroimdazole hydrolase (NnhA)
Structural insights into the enzymatic breakdown of azomycin-derived antibiotics by 2-nitroimdazole hydrolase (NnhA) Open
View article: MMINT: a Metabolic Model Interactive Network Tool for the exploration and comparative visualisation of metabolic networks
MMINT: a Metabolic Model Interactive Network Tool for the exploration and comparative visualisation of metabolic networks Open
Genome-scale metabolic models (GEMs) are essential tools in systems and synthetic biology, enabling the mathematical simulation of metabolic pathways encoded in genomes to predict phenotypes. The complexity of GEMs, however, can often limi…
View article: Structural Characterization of Enzymatic Interactions with Functional Nicotinamide Cofactor Biomimetics
Structural Characterization of Enzymatic Interactions with Functional Nicotinamide Cofactor Biomimetics Open
Synthetic nicotinamide biomimetics (NCBs) have emerged as alternatives to the use of natural cofactors. The relatively low cost and ease of manufacture of NCBs may enable the scaling of biocatalytic reactions to produce bulk chemicals (e.g…
View article: Ion-combination specific effects driving the enzymatic activity of halophilic alcohol dehydrogenase 2 from <i>Haloferax volcanii</i> in aqueous ionic liquid solvent mixtures
Ion-combination specific effects driving the enzymatic activity of halophilic alcohol dehydrogenase 2 from <i>Haloferax volcanii</i> in aqueous ionic liquid solvent mixtures Open
Cooperative ion–ion interactions drive the selectivity of ion–protein interactions for the halophilic protein ADH in aqueous solutions, with water molecules tightly bound to acidic residues playing an influential role.
View article: Ion-combination specific effects driving enzymatic activity of halophilic Alcohol Dehydrogenase 2 from Haloferax volcanii in aqueous ionic liquid solvent mixtures
Ion-combination specific effects driving enzymatic activity of halophilic Alcohol Dehydrogenase 2 from Haloferax volcanii in aqueous ionic liquid solvent mixtures Open
Biocatalysis in ionic liquids enables novel routes for bioprocessing. Enzymes derived from extremophiles promise greater stability and activity under ionic liquid (IL) influence. Here, we probe the enzyme Alcohol Dehydrogenase 2 from the h…
View article: The structural components of the Azotobacter vinelandii iron-only nitrogenase, AnfDKG, form a protein complex within the plant mitochondrial matrix
The structural components of the Azotobacter vinelandii iron-only nitrogenase, AnfDKG, form a protein complex within the plant mitochondrial matrix Open
View article: Exploring the potential application of alternative nuclei in NMR based metabolomics
Exploring the potential application of alternative nuclei in NMR based metabolomics Open
Introduction Nuclear magnetic resonance (NMR) is widely used in metabolomics but it focusses on 1 H over other NMR-active nuclei. Objectives To evaluate the potential of alternative NMR-sensitive nuclei to generate useful metabolomic data.…
View article: The structural components of the Azotobacter vinelandii iron-only nitrogenase, AnfDKG, form a protein complex within the plant mitochondrial matrix
The structural components of the Azotobacter vinelandii iron-only nitrogenase, AnfDKG, form a protein complex within the plant mitochondrial matrix Open
A long-held goal of synthetic biology has been the transfer of a bacterial nitrogen-fixation pathway into plants to reduce the use of chemical fertiliser on crops such as rice, wheat and maize. There are three classes of bacterial nitrogen…
View article: Observations on populations of a small insectivorous bird, Malurus leucopterus leuconotus Dumont, after an application of two ultra-low-volume (ULV) insecticides, fenitrothion and fipronil, in arid Australia
Observations on populations of a small insectivorous bird, Malurus leucopterus leuconotus Dumont, after an application of two ultra-low-volume (ULV) insecticides, fenitrothion and fipronil, in arid Australia Open
The use of chemical pesticides to manage locust populations in natural ecosystems is likely to impact non-target arthropods and their predators. However, the relative effects of different locust control applications on Australian birds are…
View article: Testing the Suitability of Preserved Insect Collections for Biodiscovery Using Liquid Chromatography Mass Spectrometry
Testing the Suitability of Preserved Insect Collections for Biodiscovery Using Liquid Chromatography Mass Spectrometry Open
Small metabolites and venom metabolites produced by insects are known to exhibit biological activity. These metabolites could be used to develop natural product-based therapeutics. To screen for these metabolites, insects must be collected…
View article: Sensitivity of the stripe-faced dunnart, Sminthopsis macroura (Gould 1845), to the insecticide, fipronil; implications for pesticide risk assessments in Australia
Sensitivity of the stripe-faced dunnart, Sminthopsis macroura (Gould 1845), to the insecticide, fipronil; implications for pesticide risk assessments in Australia Open
A lack of toxicity data quantifying responses of Australian native mammals to agricultural pesticides prompted an investigation into the sensitivity of the stripe-faced dunnart, Sminthopsis macroura (Gould 1845) to the insecticide, fiproni…
View article: Identifying medically relevant xenon protein targets by in silico screening of the structural proteome
Identifying medically relevant xenon protein targets by in silico screening of the structural proteome Open
In a previous study, in silico screening of the binding of almost all proteins in the Protein Data Bank to each of the five noble gases xenon, krypton, argon, neon, and helium was reported. This massive and rich data set requires analysis …
View article: Sensitivity of The Stripe-Faced Dunnart, Sminthopsis Macroura (Gould 1845), To The Phenyl Pyrazole Insecticide, Fipronil, Toxicological Signs And Implications For Pesticide Risk Assessments In Australia
Sensitivity of The Stripe-Faced Dunnart, Sminthopsis Macroura (Gould 1845), To The Phenyl Pyrazole Insecticide, Fipronil, Toxicological Signs And Implications For Pesticide Risk Assessments In Australia Open
A lack of toxicity data quantifying responses of Australian native mammals to agricultural pesticides prompted an investigation into the sensitivity of the stripe-faced dunnart, Sminthopsis macroura (Gould 1845) to the insecticide, fiproni…
View article: Towards a Systems Biology Approach to Understanding the Lichen Symbiosis: Opportunities and Challenges of Implementing Network Modelling
Towards a Systems Biology Approach to Understanding the Lichen Symbiosis: Opportunities and Challenges of Implementing Network Modelling Open
Lichen associations, a classic model for successful and sustainable interactions between micro-organisms, have been studied for many years. However, there are significant gaps in our understanding about how the lichen symbiosis operates at…
View article: Plant expression of NifD protein variants resistant to mitochondrial degradation
Plant expression of NifD protein variants resistant to mitochondrial degradation Open
Significance Engineering nitrogenase in plants may help alleviate economic and environmental issues due to the use of nitrogen fertilizer. Mitochondria have shown promise in supporting the function of nitrogenase, including electron donati…
View article: Cellular and Structural Basis of Synthesis of the Unique Intermediate Dehydro-F <sub>420</sub> -0 in Mycobacteria
Cellular and Structural Basis of Synthesis of the Unique Intermediate Dehydro-F <sub>420</sub> -0 in Mycobacteria Open
Mycobacteria are major environmental microorganisms and cause many significant diseases, including tuberculosis. Mycobacteria make an unusual vitamin-like compound, F 420 , and use it to both persist during stress and resist antibiotic tre…
View article: Cellular and structural basis of synthesis of the unique intermediate dehydro-F<sub>420</sub>-0 in mycobacteria
Cellular and structural basis of synthesis of the unique intermediate dehydro-F<sub>420</sub>-0 in mycobacteria Open
F 420 is a low-potential redox cofactor used by diverse bacteria and archaea. In mycobacteria, this cofactor has multiple roles, including adaptation to redox stress, cell wall biosynthesis, and activation of the clinical antitubercular pr…
View article: Cofactor F420-Dependent Enzymes: An Under-Explored Resource for Asymmetric Redox Biocatalysis
Cofactor F420-Dependent Enzymes: An Under-Explored Resource for Asymmetric Redox Biocatalysis Open
The asymmetric reduction of enoates, imines and ketones are among the most important reactions in biocatalysis. These reactions are routinely conducted using enzymes that use nicotinamide cofactors as reductants. The deazaflavin cofactor F…
View article: Cofactor F<sub>420</sub>-Dependent Enzymes: An Under-Explored Resource for Asymmetric Redox Biocatalysis
Cofactor F<sub>420</sub>-Dependent Enzymes: An Under-Explored Resource for Asymmetric Redox Biocatalysis Open
Asymmetric reduction of enoates, imines and ketones are among the most important reactions in biocatalysis. These reactions are routinely conducted using enzymes that use nicotinamide cofactors as reductants. The deazaflavin cofactor F420 …
View article: Engineering a functional NifDK polyprotein resistant to mitochondrial degradation
Engineering a functional NifDK polyprotein resistant to mitochondrial degradation Open
To engineer Mo dependent nitrogenase function in plants expression of proteins NifD and NifK will be an absolute requirement. Although mitochondria have been established as a suitable eukaryotic environment for biosynthesis of oxygen-sensi…
View article: A Miniature Gas Sampling Interface with Open Microfluidic Channels: Characterization of Gas-to-Liquid Extraction Efficiency of Volatile Organic Compounds
A Miniature Gas Sampling Interface with Open Microfluidic Channels: Characterization of Gas-to-Liquid Extraction Efficiency of Volatile Organic Compounds Open
Chemosensory protein based olfactory biosensors are expected to play a significant role in next-generation volatile organic compound (VOC) detection systems due to their ultra-high sensitivity and selectivity. As these biosensors can perfo…
View article: Engineered Enzymes that Retain and Regenerate their Cofactors Enable Continuous-Flow Biocatalysis
Engineered Enzymes that Retain and Regenerate their Cofactors Enable Continuous-Flow Biocatalysis Open
Biocatalysis is used for many chemical syntheses due to its high catalytic rates, specificities and operation under ambient conditions [1][1], [2][2]. Continuous-flow chemistry offers advantages to biocatalysis, avoiding process issues cau…
View article: Computer-Guided Surface Engineering for Enzyme Improvement
Computer-Guided Surface Engineering for Enzyme Improvement Open
Protein engineering strategies are often guided by our understanding of how the structure of a protein determines its function. However, our understanding is generally restricted to small regions of a protein, namely the active site and it…
View article: Isolation of the (+)-Pinoresinol-Mineralizing Pseudomonas sp. Strain SG-MS2 and Elucidation of Its Catabolic Pathway
Isolation of the (+)-Pinoresinol-Mineralizing Pseudomonas sp. Strain SG-MS2 and Elucidation of Its Catabolic Pathway Open
Pinoresinol is a dimer of two β-β′-linked coniferyl alcohol molecules. It is both a plant defense molecule synthesized through the shikimic acid pathway and a representative of several β-β-linked dimers produced during the microbial degrad…