Lytic polysaccharide monooxygenases (LPMOs) are enzymes that bind polysaccharides followed by an (oxidative) disruption of the polysaccharide surface, thereby boosting depolymerization. The binding process between the LPMO catalytic domain and polysaccharide is key to the mechanism and establishing structure-function relationships for this binding is therefore crucial. The hyperfine coupling constants (HFCs) from EPR spectroscopy have proven useful for this purpose. Unfortunately, EPR does not provide direct structural data and therefore the experimental EPR parameters have to be supported with parameters calculated with density functional theory. Yet, calculated HFCs are extremely sensitive to the employed computational setup. Using the LPMO (AA9)A catalytic domain, we here quantify the importance of several choices in the computational setup, ranging from the use of specialized basis, the underlying structures, and the employed exchange-correlation functional. We show that specialized basis sets are an absolute necessity, and also that care has to be taken in the optimization of the underlying structure: only by allowing large parts of the protein around the active site to structurally relax could we obtain results that uniformly reproduced experimental trends. We compare our results to previously published X-ray structures and experimental HFCs for (AA9)A as well as to recent experimental/theoretical results for another (AA10) family of LPMOs.
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http://dx.doi.org/10.1016/j.csbj.2020.12.014 | DOI Listing |
BMC Microbiol
January 2025
Center of Infectious Diseases, West China Hospital, Sichuan University, Guoxuexiang 37, Chengdu, 610041, China.
Background: Carbapenem-resistant Klebsiella pneumoniae (CRKP) is a severe threat for human health and urgently needs new therapeutic approaches. Lytic bacteriophages (phages) are promising clinically viable therapeutic options against CRKP. We attempted to isolate lytic phages against CRKP of sequence type 11 and capsular type 64 (ST11-KL64), the predominant type in China.
View Article and Find Full Text PDFEur J Inorg Chem
May 2024
Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States.
Lytic polysaccharide monooxygenases (LPMOs) are Cu-dependent metalloenzymes that catalyze the hydroxylation of strong C-H bonds in polysaccharides using O or HO as oxidants (monooxygenase/peroxygenase). In the absence of C-H substrate, LPMOs reduce O to HO (oxidase) and HO to HO (peroxidase) using proton/electron donors. This rich oxidative reactivity is promoted by a mononuclear Cu center in which some of the amino acid residues surrounding the metal might can accept and donate protons and/or electrons during O and HO reduction.
View Article and Find Full Text PDFInt J Biol Macromol
January 2025
Forest Product Biotechnology/Bioenergy Group, Department of Wood Science, University of British Columbia, 2424 Main Mal, Vancouver V6T 1Z4, Canada. Electronic address:
Modern enzyme cocktails often include lytic polysaccharide monooxygenase (LPMO) as an accessory enzyme that enhances cellulose accessibility during hydrolysis. Although lignin is known to generally impede cellulose hydrolysis, previous research has demonstrated lignin's potential to act as a co-factor in boosting LPMO activity and that the negative impact of lignin limiting enzyme accessibility can be mitigated by sulfonated. When sulphonated lignin was added to microcrystalline cellulose (Avicel) the activity of the lytic polysaccharide monooxygenase (LPMO) was boosted, as determined when using a quartz crystal microbalance and dissipation monitoring (QCM-D).
View Article and Find Full Text PDFBMC Biotechnol
January 2025
Department of Microbiology and Immunology, Faculty of Pharmacy, Beni-Suef University, Beni-Suef, 62511, Egypt.
Background: Successful treatment of pathogenic bacteria like Enterobacter Cloacae with bacteriophage (phage) counteract some hindrance such as phage stability and immunological clearance. Our research is focused on the encapsulation of phage HK6 within chitosan nanoparticles.
Result: Encapsulation significantly improves stability, efficacy, and delivery of phages.
J Appl Microbiol
January 2025
VBlab-Laboratory of Bacterial Viruses, University of Sorocaba, 18023-000 Sorocaba, SP, Brazil.
Aims: In this study, we report the use of two novel lytic polyvalent phages as a cocktail in in planta assays and their efficacy in the control of bacterial halo blight (BHB) caused by Pseudomonas coronafaciens pv. garcae (Pcg) in coffee plants.
Methods And Results: Phages were isolated from samples of coffee plant leaves collected at two different locations in Brazil.
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