1
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Rao D, Zhu L, Liu W, Guo Z. Molecular Mechanism of Double-Displacement Retaining β-Kdo Glycosyltransferase WbbB. J Phys Chem B 2024. [PMID: 39051443 DOI: 10.1021/acs.jpcb.4c02073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/27/2024]
Abstract
Glycosyltransferases (GTs) are pivotal enzymes involved in glycosidic bond synthesis, which can lead to either retention or inversion of the glycosyl moiety's anomeric configuration. However, the catalytic mechanism for retaining GTs remains a subject of controversy. In this study, we employ MD and QM/MM metadynamics to investigate the double-displacement catalytic mechanism of the retaining β-Kdo transferase WbbB. Our findings demonstrate that the nucleophile Asp232 initiates the reaction by attacking the sugar ring containing a carboxylate at the anomeric position, forming a covalent adduct. Subsequently, the adduct undergoes a rotational rearrangement, ensuring proper orientation of the anomeric carbon for the acceptor substrate. In the second step, Glu158 acts as the catalytic base to abstract the proton of the acceptor substrate to complete the transglycosylation reaction. Notably, His265 does not function as the anticipated catalytic acid; instead, it stabilizes the phosphate group through H-bonding interactions. Our simulations support the double-displacement mechanism implicated from the crystallographic studies of WbbB. This mechanism deviates from the common SNi-type and retaining glycoside hydrolase mechanisms, thereby expanding our understanding of GT catalytic mechanisms.
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Affiliation(s)
- Deming Rao
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan 430023, People's Republic of China
| | - Lin Zhu
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan 430023, People's Republic of China
| | - Weiqiong Liu
- State Key Laboratory of Food Science and Resources, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, People's Republic of China
- School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, People's Republic of China
- International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, People's Republic of China
| | - Zhiyong Guo
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan 430062, People's Republic of China
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2
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Ramli NA, Adam F, Ries ME, Ibrahim SF. DES-ultrasonication treatment of cellulose nanocrystals and the reinforcement in carrageenan biocomposite. Int J Biol Macromol 2024; 270:132385. [PMID: 38754668 DOI: 10.1016/j.ijbiomac.2024.132385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 04/09/2024] [Accepted: 05/13/2024] [Indexed: 05/18/2024]
Abstract
CNCs are intensively studied to reinforce biocomposites. However, it remains a challenge to homogeneously disperse the CNC in biocomposites for a smooth film surface. Mechanochemical treatment via ultrasonication in deep eutectic solvent (DES) generated a stable dispersion of CNC before incorporation into carrageenan biocomposite. Shifted peaks of choline chloride (ChCl) methylene groups to 3.95-3.98 ppm in 1H NMR indicated a formation of eutectic mixture between the hydrogen bond acceptor (HBA) and hydrogen bond donor (HBD) at the functional group of CH3···OH. The swelling of CNC in the DES was proven by the formation of intermolecular H-bond at a length of 2.46 Å. The use of DES contributed to a good dispersion of CNC in the solution which increased zeta potential by 43.2 % compared to CNC in deionized water. The ultrasonication amplitude and feed concentration were varied for the best parameters of a stable dispersion of CNC. The crystallinity of 1 wt% of CNC at 20 % sonication amplitude improved from 76 to 81 %. The high crystallinity of CNCDES resulted in an increase in film tensile and capsule loop strength of Carra-CNCDES by 20.7 and 19.4 %, respectively. Improved dispersion of CNCDES reduced the surface roughness of the biocomposite by 21.8 %. H-bond network in CNCDES improved the biocomposite properties for an ingenious reinforcement material.
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Affiliation(s)
- Nur Amalina Ramli
- Faculty of Chemical and Process Engineering Technology, Universiti Malaysia Pahang Al-Sultan Abdullah, 26300 Kuantan, Pahang, Malaysia
| | - Fatmawati Adam
- Faculty of Chemical and Process Engineering Technology, Universiti Malaysia Pahang Al-Sultan Abdullah, 26300 Kuantan, Pahang, Malaysia; Centre for Research in Advanced Fluid and Processes, Universiti Malaysia Pahang Al-Sultan Abdullah, 26300 Kuantan, Pahang, Malaysia.
| | - Michael E Ries
- School of Physics and Astronomy, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - S Fatimah Ibrahim
- School of Chemical and Process Engineering, University of Leeds, Leeds LS2 9JT, United Kingdom
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3
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Sagiroglugil M, Yasar F. Catalytic Reaction Mechanism of Bacterial GH92 α-1,2-Mannosidase: A QM/MM Metadynamics Study. Chemphyschem 2023; 24:e202300628. [PMID: 37782219 DOI: 10.1002/cphc.202300628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 09/23/2023] [Accepted: 10/01/2023] [Indexed: 10/03/2023]
Abstract
The catalytic mechanism of aC a + 2 ${C{a}^{+2}}$ -dependent family 92 α ${{\rm \alpha }}$ -mannosidase, which is abundantly present in human gut flora and malfunctions leading to the lysosomal storage disease α-mannosidosis, has been investigated using quantum mechanics/molecular mechanics and metadynamics methods. Computational efforts show that the enzyme follows a conformational itinerary of and theC a + 2 ${C{a}^{+2}}$ ion serves a dual purpose, as it not only distorts the sugar ring but also plays a crucial role in orchestrating the arrangement of catalytic residues. This orchestration, in turn, contributes to the facilitation of O S 2 ${{{\rm \ }}^{{\rm O}}{{\rm S}}_{2}}$ conformers for the ensuing reaction. This mechanistic insight is well-aligned with the experimental predictions of the catalytic pathway, and the computed energies are of the same order of magnitude as the experimental estimations. Hence, our results extend the mechanistic understanding of glycosidases.
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Affiliation(s)
- Mert Sagiroglugil
- Department of Physics Engineering, Hacettepe University, Üniversiteler Mahallesi Beytepe Kampüsü, 06800, Ankara, Turkey
- Current Address: Departament de Química Inorgànica i Orgànica (Seccióde Química Orgànica), Institut de Química Teòrica i Computacional (IQTCUB) Universitat de Barcelona, Carrer de Martí i Franquès, 1, 08028, Barcelona, Spain
| | - Fatih Yasar
- Department of Physics Engineering, Hacettepe University, Üniversiteler Mahallesi Beytepe Kampüsü, 06800, Ankara, Turkey
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4
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Morais MAB, Nin-Hill A, Rovira C. Glycosidase mechanisms: Sugar conformations and reactivity in endo- and exo-acting enzymes. Curr Opin Chem Biol 2023; 74:102282. [PMID: 36931022 DOI: 10.1016/j.cbpa.2023.102282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 01/19/2023] [Accepted: 02/09/2023] [Indexed: 03/17/2023]
Abstract
The enzymatic breakdown of carbohydrates plays a critical role in several biological events and enables the development of sustainable processes to obtain bioproducts and biofuels. In this scenario, the design of efficient inhibitors for glycosidases that can act as drug targets and the engineering of carbohydrate-active enzymes with tailored catalytic properties is of remarkable importance. To guide rational approaches, it is necessary to elucidate enzyme molecular mechanisms, in particular understanding how the microenvironment modulates the conformational space explored by the substrate. Computer simulations, especially those based on ab initio methods, have provided a suitable atomic description of carbohydrate conformations and catalytic reactions in several glycosidase families. In this review, we will focus on how the active-site topology (pocket or cleft) and mode of cleavage (endo or exo) can affect the catalytic mechanisms adopted by glycosidases, in particular the substrate conformations along the reaction coordinate.
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Affiliation(s)
- Mariana Abrahão Bueno Morais
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas 13083-100, Brazil
| | - Alba Nin-Hill
- Departament de Química Inorgànica i Orgànica & Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, Barcelona 08028, Spain
| | - Carme Rovira
- Departament de Química Inorgànica i Orgànica & Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, Barcelona 08028, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona 08010, Spain.
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5
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Mechanism of Chiral-Selective Aminoacylation of an RNA Minihelix Explored by QM/MM Free-Energy Simulations. Life (Basel) 2023; 13:life13030722. [PMID: 36983877 PMCID: PMC10057131 DOI: 10.3390/life13030722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 03/03/2023] [Accepted: 03/03/2023] [Indexed: 03/10/2023] Open
Abstract
Aminoacylation of a primordial RNA minihelix composed of D-ribose shows L-amino acid preference over D-amino acid without any ribozymes or enzymes. This preference in the amino acylation reaction likely plays an important role in the establishment of homochirality in L-amino acid in modern proteins. However, molecular mechanisms of the chiral selective reaction remain unsolved mainly because of difficulty in direct observation of the reaction at the molecular scale by experiments. For seeking a possible mechanism of the chiral selectivity, quantum mechanics/molecular mechanics (QM/MM) umbrella sampling molecular dynamics (MD) simulations of the aminoacylation reactions in a modeled RNA were performed to investigate differences in their free-energy profiles along the reactions for L- and D-alanine and its physicochemical origin. The reaction is initiated by approaching a 3′-oxygen of the RNA minihelix to the carbonyl carbon of an aminoacyl phosphate oligonucleotide. The QM/MM umbrella sampling MD calculations showed that the height of the free-energy barrier for L-alanine aminoacylation reaction was 17 kcal/mol, which was 9 kcal/mol lower than that for the D-alanine system. At the transition state, the distance between the negatively charged 3′-oxygen and the positively charged amino group of L-alanine was shorter than that of D-alanine, which was caused by the chirality difference of the amino acid. These results indicate that the transition state for L-alanine is more electrostatically stabilized than that for D-alanine, which would be a plausible mechanism previously unexplained for chiral selectivity in the RNA minihelix aminoacylation.
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Cho G, Lee J, Kim J. Identification of a novel 5-aminomethyl-2-thiouridine methyltransferase in tRNA modification. Nucleic Acids Res 2023; 51:1971-1983. [PMID: 36762482 PMCID: PMC9976899 DOI: 10.1093/nar/gkad048] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 01/07/2023] [Accepted: 01/18/2023] [Indexed: 02/11/2023] Open
Abstract
The uridine at the 34th position of tRNA, which is able to base pair with the 3'-end codon on mRNA, is usually modified to influence many aspects of decoding properties during translation. Derivatives of 5-methyluridine (xm5U), which include methylaminomethyl (mnm-) or carboxymethylaminomethyl (cmnm-) groups at C5 of uracil base, are widely conserved at the 34th position of many prokaryotic tRNAs. In Gram-negative bacteria such as Escherichia coli, a bifunctional MnmC is involved in the last two reactions of the biosynthesis of mnm5(s2)U, in which the enzyme first converts cmnm5(s2)U to 5-aminomethyl-(2-thio)uridine (nm5(s2)U) and subsequently installs the methyl group to complete the formation of mnm5(s2)U. Although mnm5s2U has been identified in tRNAs of Gram-positive bacteria and plants as well, their genomes do not contain an mnmC ortholog and the gene(s) responsible for this modification is unknown. We discovered that MnmM, previously known as YtqB, is the methyltransferase that converts nm5s2U to mnm5s2U in Bacillus subtilis through comparative genomics, gene complementation experiments, and in vitro assays. Furthermore, we determined X-ray crystal structures of MnmM complexed with anticodon stem loop of tRNAGln. The structures provide the molecular basis underlying the importance of U33-nm5s2U34-U35 as the key determinant for the specificity of MnmM.
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Affiliation(s)
- Gyuhyeok Cho
- Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
| | - Jangmin Lee
- Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
| | - Jungwook Kim
- Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
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7
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Qin Y, Qin B, Zhang J, Fu Y, Li Q, Luo F, Luo Y, He H. Purification and enzymatic properties of a new thermostable endoglucanase from Aspergillus oryzae HML366. INTERNATIONAL MICROBIOLOGY : THE OFFICIAL JOURNAL OF THE SPANISH SOCIETY FOR MICROBIOLOGY 2023:10.1007/s10123-023-00322-8. [PMID: 36705789 DOI: 10.1007/s10123-023-00322-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 11/02/2022] [Accepted: 01/04/2023] [Indexed: 01/28/2023]
Abstract
Aspergillus oryzae HML366 is a newly screened cellulase-producing strain. The endoglucanase HML ED1 from A. oryzae HML366 was quickly purified by a two-step method that combines ammonium sulfate precipitation and strong anion exchange column. SDS-PAGE electrophoresis indicated that the molecular weight of the enzyme was 68 kDa. The optimum temperature of the purified endoglucanase was 60 ℃ and the enzyme activity was stable below 70 ℃. The optimum pH was 6.5, and the enzyme activity was stable at pH between 4.5 and 9.0. The analysis indicated that additional Na+, K+, Ca2+, and Zn2+ reduced the catalytic ability of enzyme to the substrate, but Mn2+ enhanced its catalytic ability to the substrate.The Km and Vmax of the purified endoglucanase were 8.75 mg/mL and 60.24 μmol/min·mg, respectively. In this study, we report for the first time that A. oryzae HML366 can produce a heat-resistant and wide pH tolerant endoglucanase HML ED1, which has potential industrial application value in bioethanol, paper, food, textile, detergent, and pharmaceutical industries.
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Affiliation(s)
- Yongling Qin
- College of Chemistry and Biological Engineering, Hechi University, Yizhou, 546300, China. .,Guangxi Colleges Universities Key Laboratory of Exploitation and Utilization of Microbial and Botanical Resources, Yizhou, 546300, China. .,Application and Research Center of Agricultural Biotechnology, Hechi University, Yizhou, 546300, China.
| | - Baoshan Qin
- College of Chemistry and Biological Engineering, Hechi University, Yizhou, 546300, China.,Guangxi Colleges Universities Key Laboratory of Exploitation and Utilization of Microbial and Botanical Resources, Yizhou, 546300, China.,Application and Research Center of Agricultural Biotechnology, Hechi University, Yizhou, 546300, China
| | - Jian Zhang
- Guangxi Medical College, Nanning, 530023, China
| | - Yue Fu
- College of Chemistry and Biological Engineering, Hechi University, Yizhou, 546300, China.,Guangxi Colleges Universities Key Laboratory of Exploitation and Utilization of Microbial and Botanical Resources, Yizhou, 546300, China.,Application and Research Center of Agricultural Biotechnology, Hechi University, Yizhou, 546300, China
| | - Qiqian Li
- College of Chemistry and Biological Engineering, Hechi University, Yizhou, 546300, China.,Guangxi Colleges Universities Key Laboratory of Exploitation and Utilization of Microbial and Botanical Resources, Yizhou, 546300, China.,Application and Research Center of Agricultural Biotechnology, Hechi University, Yizhou, 546300, China
| | - Fengfeng Luo
- College of Chemistry and Biological Engineering, Hechi University, Yizhou, 546300, China.,Guangxi Colleges Universities Key Laboratory of Exploitation and Utilization of Microbial and Botanical Resources, Yizhou, 546300, China.,Application and Research Center of Agricultural Biotechnology, Hechi University, Yizhou, 546300, China
| | - Yanmei Luo
- College of Chemistry and Biological Engineering, Hechi University, Yizhou, 546300, China
| | - Haiyan He
- College of Chemistry and Biological Engineering, Hechi University, Yizhou, 546300, China. .,Guangxi Colleges Universities Key Laboratory of Exploitation and Utilization of Microbial and Botanical Resources, Yizhou, 546300, China. .,Application and Research Center of Agricultural Biotechnology, Hechi University, Yizhou, 546300, China.
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8
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Delle Piane M, Pesce L, Cioni M, Pavan GM. Reconstructing reactivity in dynamic host-guest systems at atomistic resolution: amide hydrolysis under confinement in the cavity of a coordination cage. Chem Sci 2022; 13:11232-11245. [PMID: 36320487 PMCID: PMC9517058 DOI: 10.1039/d2sc02000a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 08/28/2022] [Indexed: 11/21/2022] Open
Abstract
Spatial confinement is widely employed by nature to attain unique efficiency in controlling chemical reactions. Notable examples are enzymes, which selectively bind reactants and exquisitely regulate their conversion into products. In an attempt to mimic natural catalytic systems, supramolecular metal-organic cages capable of encapsulating guests in their cavity and of controlling/accelerating chemical reactions under confinement are attracting increasing interest. However, the complex nature of these systems, where reactants/products continuously exchange in-and-out of the host, makes it often difficult to elucidate the factors controlling the reactivity in dynamic regimes. As a case study, here we focus on a coordination cage that can encapsulate amide guests and enhance their hydrolysis by favoring their mechanical twisting towards reactive molecular configurations under confinement. We designed an advanced multiscale simulation approach that allows us to reconstruct the reactivity in such host-guest systems in dynamic regimes. In this way, we can characterize amide encapsulation/expulsion in/out of the cage cavity (thermodynamics and kinetics), coupling such host-guest dynamic equilibrium with characteristic hydrolysis reaction constants. All computed kinetic/thermodynamic data are then combined, obtaining a statistical estimation of reaction acceleration in the host-guest system that is found in optimal agreement with the available experimental trends. This shows how, to understand the key factors controlling accelerations/variations in the reaction under confinement, it is necessary to take into account all dynamic processes that occur as intimately entangled in such host-guest systems. This also provides us with a flexible computational framework, useful to build structure-dynamics-property relationships for a variety of reactive host-guest systems.
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Affiliation(s)
- Massimo Delle Piane
- Department of Applied Science and Technology, Politecnico di Torino Corso Duca degli Abruzzi 24 10129 Torino Italy
| | - Luca Pesce
- Department of Innovative Technologies, University of Applied Sciences and Arts of Southern Switzerland, Polo Universitario Lugano Campus Est, Via la Santa 1 6962 Lugano-Viganello Switzerland
| | - Matteo Cioni
- Department of Applied Science and Technology, Politecnico di Torino Corso Duca degli Abruzzi 24 10129 Torino Italy
| | - Giovanni M Pavan
- Department of Applied Science and Technology, Politecnico di Torino Corso Duca degli Abruzzi 24 10129 Torino Italy
- Department of Innovative Technologies, University of Applied Sciences and Arts of Southern Switzerland, Polo Universitario Lugano Campus Est, Via la Santa 1 6962 Lugano-Viganello Switzerland
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Coines J, Cuxart I, Teze D, Rovira C. Computer Simulation to Rationalize “Rational” Engineering of Glycoside Hydrolases and Glycosyltransferases. J Phys Chem B 2022; 126:802-812. [PMID: 35073079 PMCID: PMC8819650 DOI: 10.1021/acs.jpcb.1c09536] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
![]()
Glycoside hydrolases
and glycosyltransferases are the main classes
of enzymes that synthesize and degrade carbohydrates, molecules essential
to life that are a challenge for classical chemistry. As such, considerable
efforts have been made to engineer these enzymes and make them pliable
to human needs, ranging from directed evolution to rational design,
including mechanism engineering. Such endeavors fall short and are
unreported in numerous cases, while even success is a necessary but
not sufficient proof that the chemical rationale behind the design
is correct. Here we review some of the recent work in CAZyme mechanism
engineering, showing that computational simulations are instrumental
to rationalize experimental data, providing mechanistic insight into
how native and engineered CAZymes catalyze chemical reactions. We
illustrate this with two recent studies in which (i) a glycoside hydrolase
is converted into a glycoside phosphorylase and (ii) substrate specificity
of a glycosyltransferase is engineered toward forming O-, N-, or S-glycosidic bonds.
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Affiliation(s)
- Joan Coines
- Departament de Química Inorgànica i Orgànica and Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, Barcelona 08028, Spain
| | - Irene Cuxart
- Departament de Química Inorgànica i Orgànica and Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, Barcelona 08028, Spain
| | - David Teze
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby 2800, Denmark
| | - Carme Rovira
- Departament de Química Inorgànica i Orgànica and Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, Barcelona 08028, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys 23, Barcelona 08010, Spain
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10
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Fungal cellulases: protein engineering and post-translational modifications. Appl Microbiol Biotechnol 2021; 106:1-24. [PMID: 34889986 DOI: 10.1007/s00253-021-11723-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Revised: 11/28/2021] [Accepted: 11/30/2021] [Indexed: 12/18/2022]
Abstract
Enzymatic degradation of lignocelluloses into fermentable sugars to produce biofuels and other biomaterials is critical for environmentally sustainable development and energy resource supply. However, there are problems in enzymatic cellulose hydrolysis, such as the complex cellulase composition, low degradation efficiency, high production cost, and post-translational modifications (PTMs), all of which are closely related to specific characteristics of cellulases that remain unclear. These problems hinder the practical application of cellulases. Due to the rapid development of computer technology in recent years, computer-aided protein engineering is being widely used, which also brings new opportunities for the development of cellulases. Especially in recent years, a large number of studies have reported on the application of computer-aided protein engineering in the development of cellulases; however, these articles have not been systematically reviewed. This article focused on the aspect of protein engineering and PTMs of fungal cellulases. In this manuscript, the latest literatures and the distribution of potential sites of cellulases for engineering have been systematically summarized, which provide reference for further improvement of cellulase properties. KEY POINTS: •Rational design based on virtual mutagenesis can improve cellulase properties. •Modifying protein side chains and glycans helps obtain superior cellulases. •N-terminal glutamine-pyroglutamate conversion stabilizes fungal cellulases.
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Zhao X, Meng X, Ragauskas AJ, Lai C, Ling Z, Huang C, Yong Q. Unlocking the secret of lignin-enzyme interactions: Recent advances in developing state-of-the-art analytical techniques. Biotechnol Adv 2021; 54:107830. [PMID: 34480987 DOI: 10.1016/j.biotechadv.2021.107830] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 08/07/2021] [Accepted: 08/29/2021] [Indexed: 02/08/2023]
Abstract
Bioconversion of renewable lignocellulosics to produce liquid fuels and chemicals is one of the most effective ways to solve the problem of fossil resource shortage, energy security, and environmental challenges. Among the many biorefinery pathways, hydrolysis of lignocellulosics to fermentable monosaccharides by cellulase is arguably the most critical step of lignocellulose bioconversion. In the process of enzymatic hydrolysis, the direct physical contact between enzymes and cellulose is an essential prerequisite for the hydrolysis to occur. However, lignin is considered one of the most recalcitrant factors hindering the accessibility of cellulose by binding to cellulase unproductively, which reduces the saccharification rate and yield of sugars. This results in high costs for the saccharification of carbohydrates. The various interactions between enzymes and lignin have been explored from different perspectives in literature, and a basic lignin inhibition mechanism has been proposed. However, the exact interaction between lignin and enzyme as well as the recently reported promotion of some types of lignin on enzymatic hydrolysis is still unclear at the molecular level. Multiple analytical techniques have been developed, and fully unlocking the secret of lignin-enzyme interactions would require a continuous improvement of the currently available analytical techniques. This review summarizes the current commonly used advanced research analytical techniques for investigating the interaction between lignin and enzyme, including quartz crystal microbalance with dissipation (QCM-D), surface plasmon resonance (SPR), attenuated total reflectance-Fourier transform infrared (ATR-FTIR) spectroscopy, atomic force microscopy (AFM), nuclear magnetic resonance (NMR) spectroscopy, fluorescence spectroscopy (FLS), and molecular dynamics (MD) simulations. Interdisciplinary integration of these analytical methods is pursued to provide new insight into the interactions between lignin and enzymes. This review will serve as a resource for future research seeking to develop new methodologies for a better understanding of the basic mechanism of lignin-enzyme binding during the critical hydrolysis process.
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Affiliation(s)
- Xiaoxue Zhao
- Co-Innovation Center for Efficient Processing and Utilization of Forest Resources, Department of Bioengineering, Nanjing Forestry University, Nanjing 210037, China
| | - Xianzhi Meng
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, TN 37996, USA
| | - Arthur J Ragauskas
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, TN 37996, USA; Center for Renewable Carbon, Department of Forestry, Wildlife and Fisheries, University of Tennessee, Knoxville, TN 37996, USA; Joint Institute for Biological Sciences, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Chenhuan Lai
- Co-Innovation Center for Efficient Processing and Utilization of Forest Resources, Department of Bioengineering, Nanjing Forestry University, Nanjing 210037, China
| | - Zhe Ling
- Co-Innovation Center for Efficient Processing and Utilization of Forest Resources, Department of Bioengineering, Nanjing Forestry University, Nanjing 210037, China
| | - Caoxing Huang
- Co-Innovation Center for Efficient Processing and Utilization of Forest Resources, Department of Bioengineering, Nanjing Forestry University, Nanjing 210037, China.
| | - Qiang Yong
- Co-Innovation Center for Efficient Processing and Utilization of Forest Resources, Department of Bioengineering, Nanjing Forestry University, Nanjing 210037, China.
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