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Krah, Alexander (author), Vogelaar, Timothy (author), de Jong, S.I. (author), Claridge, Jolyon K. (author), Bond, Peter J. (author), McMillan, D.G.G. (author)It is a conjecture that the ε subunit regulates ATP hydrolytic function of the F1Fo ATP synthase in bacteria. This has been proposed by the ε subunit taking an extended conformation, with a terminal helix probing into the central architecture of the hexameric catalytic domain, preventing ATP hydrolysis. The ε subunit takes a contracted...journal article 2023
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de Jong, S.I. (author), Sorokin, Dimitry Y. (author), van Loosdrecht, Mark C.M. (author), Pabst, Martin (author), McMillan, D.G.G. (author)Proteomics has greatly advanced the understanding of the cellular biochemistry of microorganisms. The thermoalkaliphile Caldalkalibacillus thermarum TA2.A1 is an organism of interest for studies into how alkaliphiles adapt to their extreme lifestyles, as it can grow from pH 7.5 to pH 11. Within most classes of microbes, the membrane-bound...journal article 2023
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Godoy Hernandez, A. (author), Asseri, Amer H. (author), Purugganan, Aiden J. (author), Jiko, Chimari (author), de Ram, C. (author), Lill, Holger (author), Pabst, Martin (author), Mitsuoka, Kaoru (author), Gerle, Christoph (author), Bald, Dirk (author), McMillan, D.G.G. (author)Functional reintegration into lipid environments represents a major challenge for in vitro investigation of integral membrane proteins (IMPs). Here, we report a new approach, termed LMNG Auto-insertion Reintegration (LAiR), for reintegration of IMPs into lipid bilayers within minutes. The resulting proteoliposomes displayed an unprecedented...journal article 2023
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Marsden, S.R. (author), Wijma, Hein J. (author), Mohr, M.K.F. (author), Justo, Inês (author), Hagedoorn, P.L. (author), Laustsen, Jesper (author), Mestrom, L. (author), McMillan, D.G.G. (author), Hanefeld, U. (author)Regulation of enzyme activity is vital for living organisms. In metalloenzymes, far-reaching rearrangements of the protein scaffold are generally required to tune the metal cofactor's properties by allosteric regulation. Here structural analysis of hydroxyketoacid aldolase from Sphingomonas wittichii RW1 (SwHKA) revealed a dynamic movement of...journal article 2022
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Krah, Alexander (author), van der Hoeven, Bas (author), Mestrom, L. (author), Tonin, F. (author), Knobel, Kirsten C.C. (author), Bond, Peter J. (author), McMillan, D.G.G. (author)Background: Prediction of ligand binding and design of new function in enzymes is a time-consuming and expensive process. Crystallography gives the impression that proteins adopt a fixed shape, yet enzymes are functionally dynamic. Molecular dynamics offers the possibility of probing protein movement while predicting ligand binding....journal article 2021
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Boes, Deborah M. (author), Godoy Hernandez, A. (author), McMillan, D.G.G. (author)Membrane proteins can be classified into two main categories—integral and peripheral membrane proteins—depending on the nature of their membrane interaction. Peripheral membrane proteins are highly unique amphipathic proteins that interact with the membrane indirectly, using electrostatic or hydrophobic interactions, or directly, using...journal article 2021
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Godoy Hernandez, A. (author), McMillan, D.G.G. (author)Lipids play a pivotal role in cellular respiration, providing the natural environment in which an oxidoreductase interacts with the quinone pool. To date, it is generally accepted that negatively charged lipids play a major role in the activity of quinone oxidoreductases. By changing lipid compositions when assaying a type II NADH:quinone...journal article 2021
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Marsden, S.R. (author), Mestrom, L. (author), Wijma, Hein J. (author), Noordam, Sander J. (author), McMillan, D.G.G. (author), Hanefeld, U. (author)Diastereomers are characterised by an intrinsic energy difference, and thermodynamics dictate their distribution within a dynamic equilibrium. The characteristic mechanistic reversibility and non-ideal stereoselectivity of catalysts therefore simultaneously promote both synthesis and epimerization of products during the formation of...journal article 2021
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Asseri, Amer H. (author), Godoy Hernandez, A. (author), Goojani, Hojjat Ghasemi (author), Lill, Holger (author), Sakamoto, Junshi (author), McMillan, D.G.G. (author), Bald, Dirk (author)Cardiolipin (CL) is a lipid that is found in the membranes of bacteria and the inner membranes of mitochondria. CL can increase the activity of integral membrane proteins, in particular components of respiratory pathways. We here report that CL activated detergent-solubilized cytochrome bd, a terminal oxidase from Escherichia coli. CL...journal article 2021
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Gnaiger, E. (author), McMillan, D.G.G. (author)As the knowledge base and importance of mitochondrial physiology to evolution, health and diseaseexpands, the necessity for harmonizing the terminologyconcerning mitochondrial respiratory states and rates has become increasingly apparent. Thechemiosmotic theoryestablishes the mechanism of energy transformationandcoupling in oxidative...journal article 2020
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van Amelrooy, E.F. (author), Schut, H. (author), Egger, Werner (author), Dickmann, Marcel (author), Hugenschmidt, Christoph (author), Mallée, L. (author), Hanefeld, U. (author), McMillan, D.G.G. (author), Eijt, S.W.H. (author)A new method is developed to produce mesoporous titania thin films at room temperature using the enzyme papain in a dip-coating procedure, providing low-cost titania films in a sustainable manner. Quartz crystal microbalance, positron annihilation Doppler broadening and lifetime spectroscopy, scanning electron microscopy, and X-ray...journal article 2020
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Kleikamp, H.B.C. (author), Lin, Y. (author), McMillan, D.G.G. (author), Geelhoed, Jeanine S. (author), Naus-Wiezer, Suzanne N.H. (author), Van Baarlen, Peter (author), Saha, Chinmoy (author), Louwen, Rogier (author), Sorokin, Dimitry Y. (author), van Loosdrecht, Mark C.M. (author), Pabst, Martin (author)Nonulosonic acids, commonly referred to as sialic acids, are a highly important group of nine-carbon sugars common to all domains of life. They all share biosynthetic and structural features, but otherwise display a remarkable chemical diversity. In humans, sialic acids cover all cells which makes them important for processes such as cellular...review 2020
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Mestrom, L. (author), Marsden, S.R. (author), McMillan, D.G.G. (author), Schoevaart, Rob (author), Hagedoorn, P.L. (author), Hanefeld, U. (author)In this case study, we compare the performance of an enzyme immobilised using two different methods: i) as carrier-free catalytically active inclusion bodies or ii) as carrier-attached immobilised enzyme. To make this comparison we used a trehalose transferase from Thermoproteus uzoniensis fused to the fluorescent thermostable protein mCherry...journal article 2020
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Marsden, S.R. (author), McMillan, D.G.G. (author), Hanefeld, U. (author)The synthetic properties of the Thiamine diphosphate (ThDP)-dependent pyruvate dehydrogenase E1 subunit from Escherichia coli (EcPDH E1) was assessed for carboligation reactions with aliphatic ketoacids. Due to its role in metabolism, EcPDH E1 was previously characterised with respect to its biochemical properties, but it was never applied...journal article 2020
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de Jong, S.I. (author), van den Broek, M.A. (author), Merkel, Alexander Y. (author), de la Torre Cortes, Pilar (author), Kalamorz, Falk (author), Cook, Gregory M. (author), van Loosdrecht, Mark C.M. (author), McMillan, D.G.G. (author)The aerobic thermoalkaliphile Caldalkalibacillus thermarum strain TA2.A1 is a member of a separate order of alkaliphilic bacteria closely related to the Bacillales order. Efforts to relate the genomic information of this evolutionary ancient organism to environmental adaptation have been thwarted by the inability to construct a complete...journal article 2020
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Zarco-Zavala, Mariel (author), Watanabe, Ryo (author), McMillan, D.G.G. (author), Suzuki, Toshiharu (author), Ueno, Hiroshi (author), Mendoza-Hoffmann, Francisco (author), García-Trejo, José J. (author), Noji, Hiroyuki (author)The rotation of Paracoccus denitrificans F<sub>1</sub>-ATPase (PdF<sub>1</sub>) was studied using single-molecule microscopy. At all concentrations of adenosine triphosphate (ATP) or a slowly hydrolyzable ATP analog (ATPγS), above or below K<sub>m</sub>, PdF1 showed three dwells per turn, each separated by 120°. Analysis of dwell time between...journal article 2020
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Urbani, Andrea (author), Giorgio, Valentina (author), Carrer, Andrea (author), Franchin, Cinzia (author), Arrigoni, Giorgio (author), Jiko, Chimari (author), Abe, Kazuhiro (author), Bogers, J.F.M. (author), McMillan, D.G.G. (author)The molecular identity of the mitochondrial megachannel (MMC)/permeability transition pore (PTP), a key effector of cell death, remains controversial. By combining highly purified, fully active bovine F-ATP synthase with preformed liposomes we show that Ca2+ dissipates the H+ gradient generated by ATP hydrolysis. After incorporation of the...journal article 2019
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Godoy Hernandez, A. (author), Tate, Daniel J. (author), McMillan, D.G.G. (author)Type-II NADH:quinone oxidoreductases (NDH-2s) are an important element of microbial pathogen electron transport chains and an attractive drug target. Despite being widely studied, its mechanism and catalysis are still poorly understood in a hydrophobic membrane environment. A recent report for the Escherichia coli NDH-2 showed NADH oxidation...journal article 2019
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Marsden, S.R. (author), Mestrom, L. (author), Bento, Isabel (author), Hagedoorn, P.L. (author), McMillan, D.G.G. (author), Hanefeld, U. (author)The class II hydroxy ketoacid aldolase A5VH82 from Sphingomonas wittichii RW1 (SwHKA) accepts hydroxypyruvate as nucleophilic donor substrate, giving access to synthetically challenging 3,4-dihydroxy-α-ketoacids. The crystal structure of holo-SwHKA in complex with hydroxypyruvate revealed CH-π interactions between the C−H bonds at C3 of...journal article 2019
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Marsden, S.R. (author), Mestrom, L. (author), McMillan, D.G.G. (author), Hanefeld, U. (author)The enzymatic synthesis of esters and peptides is unfavoured in aqueous solvent systems due to competing hydrolysis. This can be overcome by using energy rich substrate analogues: elimination of a good leaving group temporarily establishes more favourable equilibrium conditions, allowing for (nearly) complete conversion. While kinetically...review 2019
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