Article
Biochemistry & Molecular Biology
Shaowei Zhang, Alan R. F. Godwin, Aoife Taylor, Samantha J. O. Hardman, Thomas A. Jowitt, Linus O. Johannissen, Sam Hay, Clair Baldock, Derren J. Heyes, Nigel S. Scrutton
Summary: Research shows that protochlorophyllide oxidoreductase (POR) plays a crucial role in chlorophyll biosynthesis and plant development. It was found that the binding of Pchlide triggers the formation of large oligomers of POR, likely driven by interactions of amino acid residues in the highly conserved lid regions.
Article
Biochemistry & Molecular Biology
Cillian Variot, Daniel Capule, Xhulio Arolli, Jackson Baumgartner, Cory Reidl, Charles Houseman, Miguel A. Ballicora, Daniel P. Becker, Misty L. Kuhn
Summary: In this study, we investigated how the PA3944 enzyme from Pseudomonas aeruginosa recognizes different acceptor substrates and identified critical residues for substrate specificity. By mutating seven amino acid residues to alanine, we determined their effects on the kinetic parameters of PA3944. We found that certain residues improved the affinity and catalytic efficiency of PA3944 towards NANMO and/or polymyxin B. Additionally, one mutant (R106A) showed substrate inhibition towards NANMO, and we propose potential reasons for this inhibition based on further substrate docking studies with R106A.
Review
Plant Sciences
Wenli Sun, Mohamad H. Shahrajabian, Qi Cheng
Summary: This article provides an overview of the functional studies in chlorophyll biosynthesis, focusing on the action mechanisms of two catalysts - DPOR and LPOR. It also discusses the possible future research directions for LPOR and DPOR in the biosynthesis of chlorophyll.
NOTULAE BOTANICAE HORTI AGROBOTANICI CLUJ-NAPOCA
(2021)
Article
Microbiology
Yilin Pang, Jing Wang, Xueping Gao, Mengyao Jiang, Lifei Zhu, Feng Liang, Mengxiang Liang, Xiaolin Wu, Xianxian Xu, Xiaojun Ren, Ting Xie, Wu Wang, Qianqian Sun, Xiaojun Xiong, Jianxin Lyu, Jianghui Li, Guoqiang Tan
Summary: In this study, the fusion of IscS N-terminus with NFS1 C-terminus was conducted, revealing that SUMO-EH-IscS exhibits significant growth recovery and NADH-dehydrogenase I activity in deficient cells. The mutation of IscS resulted in different absorption peaks during the enzyme reaction, indicating that the conserved active site residues play a key role in substrate entry and enzymatic regulation.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Chemistry, Organic
Anwei Hou, Jeroen S. Dickschat
Summary: The study conducted site-directed mutagenesis experiments on the sesterterpene synthase SmTS1 from Streptomyces mobaraensis, revealing diverse effects of mutations on catalytic activity and enzyme function switch. Rational explanations were provided for these findings, offering insights into protein engineering of terpene synthases for improved efficiency or altered functions.
BEILSTEIN JOURNAL OF ORGANIC CHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Mariel Claudia Gerrard Wheeler, Cintia Lucia Arias, Juliana da Fonseca Rezende Mello, Nuria Cirauqui Diaz, Carlos Rangel Rodrigues, Maria Fabiana Drincovich, Alessandra Mendonca Teles de Souza, Clarisa Ester Alvarez
Summary: In this study, the researchers characterized the structural determinants necessary for fumarate allosteric regulation of NADP-ME2 from Arabidopsis thaliana using molecular modeling, molecular docking, normal mode analysis, and mutagenesis. The results provide new insights for enzyme optimization by understanding the allosteric regulation mechanisms.
PLANT MOLECULAR BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Amy E. Medlock, Wided Najahi-Missaoui, Mesafint T. Shiferaw, Angela N. Albetel, William N. Lanzilotta, Harry A. Dailey
Summary: Ferrochelatase is an important enzyme involved in catalyzing heme synthesis in humans, serving a regulatory and catalytic role in the pathway. Studies on its crystal structures, kinetic properties, and catalytic cycle have provided insights into its functions. However, questions regarding metal ion delivery, active site residue roles, and the catalytic mechanism remain open for further investigation.
BIOCHEMICAL JOURNAL
(2021)
Article
Biochemistry & Molecular Biology
Amalie Carnbring Bonde, Sofie Rosenorn Hansen, Eva Johansson, Jais Rose Bjelke, Jacob Lund
Summary: This study investigates the conversion of zymogen Factor X to an active protease and reveals the importance of proline residues in efficient proteolysis. It also identifies essential interaction sites for Factor IXa and the intrinsic tenase complex, as well as the role of a carbohydrate chain in activator specificity.
Article
Biochemistry & Molecular Biology
Carolina Conter, Filippo Favretto, Paola Dominici, Luis Alfonso Martinez-Cruz, Alessandra Astegno
Summary: This study explored the role of hydroxyl moieties of S84, Y160, and Y246 residues in determining the L-serine/L-OAS preference in TgCBS. It was found that the triple mutant S84A/Y160F/Y246V behaved like an OCBS, showing beta-replacement activity only with L-OAS. The hydroxyl group of Y246 plays a major role in controlling L-serine preference by efficiently stabilizing its leaving group. These findings provide a better understanding of substrate specificity in TgCBS and have implications for the design of new antimicrobial compounds.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
(2023)
Review
Plant Sciences
Derren J. Heyes, Shaowei Zhang, Aoife Taylor, Linus O. Johannissen, Samantha J. O. Hardman, Sam Hay, Nigel S. Scrutton
Summary: LPOR is a light-activated enzyme essential for chlorophyll biosynthesis and plant greening. It catalyzes the conversion of protochlorophyllide to chlorophyllide, playing a crucial role in early plant development. Through photocatalysis, LPOR acts as a master switch for plant photomorphogenesis, triggering complex molecular and cellular events that lead to plant morphological changes.
Article
Food Science & Technology
Carmen Lammi, Giovanna Boschin, Carlotta Bollati, Anna Arnoldi, Gianni Galaverna, Luca Dellafiora
Summary: Bioactive peptides are short peptides with specific biological activities, crucial for understanding the physiological consequences of food and designing novel food products. The identification of bioactive peptides is challenging and mainly relies on bottom-up approaches. A top-down, computer-assisted and hypothesis-driven method was presented to identify potent angiotensin I converting enzyme inhibitory tripeptides, showing promising results for high-throughput identification of bioactive peptides.
FOOD RESEARCH INTERNATIONAL
(2021)
Article
Biochemistry & Molecular Biology
Moawiah M. Naffaa, David E. Hibbs, Mary Chebib, Jane R. Hanrahan
Summary: This study explores the role of two hydrophilic residues (Serine 168 and Serine 243) of the GABA-p1 receptors in response to the binding of GABA and other studied ligands. The results suggest that Ser168 residue stabilizes either closed state or open conformation depending on the other determinant interactions of each state. On the other hand, Ser243 residue forms different inter-subunit interactions with residues in the adjacent subunit at different states of the channel.
NEUROCHEMISTRY INTERNATIONAL
(2022)
Article
Biotechnology & Applied Microbiology
Diamond Jain, Jyoti Verma, Tejavath Ajith, Amitabha Bhattacharjee, Anindya Sundar Ghosh
Summary: The dissemination of class D OXA-type carbapenemases is a significant cause of beta-lactam resistance in Gram-negative bacteria. We conducted a study to determine the importance of specific amino acid residues in the activity of OXA-23 carbapenemase. Site-directed mutagenesis was used to substitute the residues W165, L166, V167, and D222 with alanine, and the resultant proteins were assessed for changes in activity and stability. Our findings suggest that W165 plays a role in maintaining the integrity of OXA-23, while L166 may be responsible for orientating the antibiotic molecules correctly.
JOURNAL OF ANTIBIOTICS
(2023)
Article
Biochemistry & Molecular Biology
Ian M. Furey, Shrenik C. Mehta, Banumathi Sankaran, Liya Hu, B. V. Venkataram Prasad, Timothy Palzkill
Summary: KPC-2 is a common source of antibiotic resistance in Gram-negative bacterial infections due to its ability to hydrolyze most beta-lactam antibiotics, including carbapenems, rapidly. Mutations that slow down the deacylation rate of carbapenems and affect the structure of the active site loop have been identified in KPC-2. This suggests that alterations in the environment of the general base Glu166 and the conformational stability of the Q214-R220 loop are critical for efficient deacylation of carbapenems by the KPC-2 enzyme.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
David W. Konas, Sarah Cho, Oshane D. Thomas, Maryum M. Bhatti, Katherine Leon Hernandez, Cinthya Moran, Hedda Booter, Thomas Candela, Joseph Lacap, Paige McFadden, Savannah van den Berg, Alyssa M. Welter, Ashley Peralta, Cheryl A. Janson, Jaclyn Catalano, Nina M. Goodey
Summary: This study investigates the roles of conserved active site amino acids in the key enzyme IGPS involved in tryptophan biosynthesis in Mycobacterium tuberculosis. Mutation experiments reveal the significant impact of these amino acids on enzyme activity, and their interactions provide a more comprehensive understanding of the mechanism of this enzyme.
ACS BIO & MED CHEM AU
(2023)
Review
Chemistry, Physical
Binuraj R. K. Menon, Daniel Richmond, Navya Menon
Summary: Bio-halogenase enzymes have the ability to selectively halogenate molecules during biosynthesis, providing opportunities for C-H activation and functionalization of molecular structures.
CATALYSIS REVIEWS-SCIENCE AND ENGINEERING
(2022)
Article
Biochemistry & Molecular Biology
Tobias M. Hedison, Erik Breslmayr, Muralidharan Shanmugam, Kwankao Karnpakdee, Derren J. Heyes, Anthony P. Green, Roland Ludwig, Nigel S. Scrutton, Daniel Kracher
Summary: Understanding the reaction mechanism of fungal LPMOs with H2O2 is crucial for their application in biotechnological settings. Research shows that a 'priming' electron transfer reaction from the cellobiose dehydrogenase partner protein supports up to 20 catalytic cycles of LPMOs.
Editorial Material
Chemistry, Multidisciplinary
Binuraj R. K. Menon
Review
Biochemistry & Molecular Biology
Harshwardhan Poddar, Derren J. Heyes, Giorgio Schiro, Martin Weik, David Leys, Nigel S. Scrutton
Summary: Dynamic changes in protein structures are crucial for protein function and can be investigated with unprecedented temporal and spatial resolution using X-ray free electron lasers. Light-activated proteins are attractive targets for time-resolved structural studies, as they allow for visualization of early chemical changes and global structural changes.
Article
Chemistry, Physical
Angus J. Robertson, F. Aaron Cruz-Navarrete, Henry P. Wood, Nikita Vekaria, Andrea M. Hounslow, Claudine Bisson, Matthew J. Cliff, Nicola J. Baxter, Jonathan P. Waltho
Summary: Understanding the factors contributing to the high catalytic efficiencies of enzymes is crucial for catalysis and enzyme design. This study investigates the relationship between binding a phosphodianion group in a distal site, adopting a closed enzyme form, and catalytic proficiency. The results suggest that binding of a phosphodianion group in the distal site stimulates domain closure and stabilizes the closed active form, leading to high catalytic efficiencies.
Article
Chemistry, Physical
Navya Menon, Daniel Richmond, Mohammad Rejaur Rahman, Binuraj R. K. Menon
Summary: The development of enzymatic routes for the synthesis of amide and carboxylic acid bonds in bioactive molecular scaffolds under aqueous conditions poses a major challenge for the biopharmaceutical and fine chemical industries. In this study, we characterized and studied the kinetics of two enzymes, tryptophan-2-monooxygenase (iaaM) and indole-3-acetamide hydrolase (iaaH), present in plant microbiomes, which catalyze the conversion of tryptophan to indole-3-acetamide and subsequent hydrolysis to form carboxylic acid. These enzymes have the potential to produce indole-3-acetic acid (IAA), a natural plant hormone and an important synthon for agrochemical and pharmaceutical applications. Additionally, we demonstrated the synthesis of IAA derivatives using a one-pot multienzyme biosynthetic cascade and the de novo biosynthesis of IAA and its derivatives from glucose or indoles in Escherichia coli.
Article
Chemistry, Physical
Angus J. Robertson, Alex L. Wilson, Matthew J. Burn, Matthew J. Cliff, Paul L. A. Popelier, Jonathan P. Waltho
Summary: The study using QM models, experimental NMR measurements, and X-ray structures revealed that the transition of an archetypal phosphoryl transfer enzyme, beta PGM, triggers partial proton transfer and partial dissociation of phosphoryl group. Proton transfer continues but is not completed during the reaction with the enzyme in the TSA conformation. Changes in proton position and electrostatic repulsion stimulate phosphoryl transfer.
Article
Chemistry, Physical
Tobias M. Hedison, Andreea I. Iorgu, Donato Calabrese, Derren J. Heyes, Muralidharan Shanmugam, Nigel S. Scrutton
Summary: This study investigates the structural, dynamical, and functional relationship of copper nitrite reductases (CuNiRs) through combining crystallographic techniques and solution-state approaches. The findings shed light on the catalytic mechanisms of these enzymes and suggest the involvement of protein dynamics. The importance of integrating high-resolution crystallographic techniques and low-resolution solution-state approaches in studying metalloenzymes is emphasized.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2022)
Article
Multidisciplinary Sciences
Jonathan S. Trimble, Rebecca Crawshaw, Florence J. Hardy, Colin W. Levy, Murray J. B. Brown, Douglas E. Fuerst, Derren J. Heyes, Richard Obexer, Anthony P. Green
Summary: The ability to program new modes of catalysis into proteins using genetic code expansion methodology has led to the development of photoenzymes that operate through triplet energy transfer catalysis. This allows for versatile reactivity in organic synthesis that is not possible with current biocatalysis methods. The study demonstrates the successful installation of a genetically encoded photosensitizer into a protein scaffold, resulting in a photoenzyme that can perform cycloadditions with high efficiency and selectivity. The photoenzyme outperforms small-molecule catalysts by being able to operate under aerobic conditions and at ambient temperatures. This research opens up new possibilities for excited-state chemistry in protein active sites and provides a foundation for the development of enantioselective photocatalysts.
Article
Biochemistry & Molecular Biology
Laszlo L. P. Hosszu, Daljit Sangar, Mark Batchelor, Emmanuel Risse, Andrea M. Hounslow, John Collinge, Jonathan P. Waltho, Jan Bieschke
Summary: In prion replication, the conversion of cellular form of prion protein (PrPC) to its disease-associated fibrillar form is achieved through a full conformational transition. Transmembrane forms of PrP play a role in this structural conversion. Removing residues 119-136 of PrP, which includes the first β-strand and a large portion of the conserved hydrophobic region associated with the ER membrane, resulted in an open native-like conformer of PrPC with increased solvent exposure and enhanced fibril formation. These findings suggest a stepwise folding transition initiated by the conformational switch to this open form of PrPC.
JOURNAL OF MOLECULAR BIOLOGY
(2023)
Article
Multidisciplinary Sciences
Harshwardhan Poddar, Ronald Rios-Santacruz, Derren J. J. Heyes, Muralidharan Shanmugam, Adam Brookfield, Linus O. O. Johannissen, Colin W. W. Levy, Laura N. N. Jeffreys, Shaowei Zhang, Michiyo Sakuma, Jacques-Philippe Colletier, Sam Hay, Giorgio Schiro, Martin Weik, Nigel S. S. Scrutton, David Leys
Summary: This study provides insights into the mechanism of CarH, a photoreceptor involved in transcriptional regulation. The authors show that the response of CarH to light integrates both B-12 photochemistry and redox changes to drive large-scale conformational changes.
NATURE COMMUNICATIONS
(2023)
Article
Chemistry, Multidisciplinary
Mary Ortmayer, Florence J. Hardy, Matthew G. Quesne, Karl Fisher, Colin Levy, Derren J. Heyes, C. Richard A. Catlow, Sam P. de Visser, Stephen E. J. Rigby, Sam Hay, Anthony P. Green
Summary: This study utilizes an expanded genetic code to investigate the impact of hydrogen bonding interactions on ferryl heme structure and reactivity, revealing that modifications to the active site amino acid Trp51 can significantly affect the reactivity of ferryl heme intermediates and regulate catalytic function.
Article
Chemistry, Multidisciplinary
Ines S. Camacho, Rachelle Black, Derren J. Heyes, Linus O. Johannissen, Lennart A. I. Ramakers, Bruno Bellina, Perdita E. Barran, Sam Hay, Alex R. Jones
Summary: A study using molecular dynamics simulations, native ion mobility mass spectrometry and time-resolved spectroscopy has revealed the mechanism of B-12-dependent photoreceptor CarH in the dark and how B-12 drives domain assembly in CarH. When B-12 is in excess, it can form head-to-tail dimers that quickly combine to form tetramers; while when B-12 is scarce, tetramers can still form without a complete B-12 complement to each dimer.
Review
Plant Sciences
Derren J. Heyes, Shaowei Zhang, Aoife Taylor, Linus O. Johannissen, Samantha J. O. Hardman, Sam Hay, Nigel S. Scrutton
Summary: LPOR is a light-activated enzyme essential for chlorophyll biosynthesis and plant greening. It catalyzes the conversion of protochlorophyllide to chlorophyllide, playing a crucial role in early plant development. Through photocatalysis, LPOR acts as a master switch for plant photomorphogenesis, triggering complex molecular and cellular events that lead to plant morphological changes.
Article
Chemistry, Multidisciplinary
Henry P. Wood, Nicola J. Baxter, F. Aaron Cruz-Navarrete, Clare R. Trevitt, Andrea M. Hounslow, Jonathan P. Waltho
Summary: The study demonstrated an efficient enzymatic synthesis method for anomer-specific beta G16BP using the D170N variant of beta PGM. The perturbation of catalytic magnesium ion coordination by the substitution at residue 170 in the enzyme was found to contribute to the accumulation of beta G16BP. The purification process employed a simple and environmentally friendly precipitation procedure, resulting in a high purity and yield of the beta G16BP product.