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Wang F, Qi H, Li H, Ma X, Gao X, Li C, Lu F, Mao S, Qin HM. State-of-the-art strategies and research advances for the biosynthesis of D-amino acids. Crit Rev Biotechnol 2024; 44:495-513. [PMID: 37160372 DOI: 10.1080/07388551.2023.2193861] [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: 09/01/2022] [Accepted: 02/09/2023] [Indexed: 05/11/2023]
Abstract
D-amino acids (D-AAs) are the enantiomeric counterparts of L-amino acids (L-AAs) and important functional factors with a wide variety of physiological activities and applications in the food manufacture industry. Some D-AAs, such as D-Ala, D-Leu, and D-Phe, have been favored by consumers as sweeteners and fragrances because of their unique flavor. The biosynthesis of D-AAs has attracted much attention in recent years due to their unique advantages. In this review, we comprehensively analyze the structure-function relationships, biosynthesis pathways, multi-enzyme cascade and whole-cell catalysis for the production of D-AAs. The state-of-the-art strategies, including immobilization, protein engineering, and high-throughput screening, are summarized. Future challenges and perspectives of strategies-driven by bioinformatics technologies and smart computing technologies, as well as enzyme immobilization, are also discussed. These new approaches will promote the commercial production and application of D-AAs in the food industry by optimizing the key enzymes for industrial biocatalysts.
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Affiliation(s)
- Fenghua Wang
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, P.R. China
| | - Hongbin Qi
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, P.R. China
| | - Huimin Li
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, P.R. China
| | - Xuanzhen Ma
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, P.R. China
| | - Xin Gao
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, P.R. China
| | - Chao Li
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, P.R. China
| | - Fuping Lu
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, P.R. China
| | - Shuhong Mao
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, P.R. China
| | - Hui-Min Qin
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, P.R. China
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Bowling PE, Dasgupta S, Herbert JM. Eliminating Imaginary Vibrational Frequencies in Quantum-Chemical Cluster Models of Enzymatic Active Sites. J Chem Inf Model 2024; 64:3912-3922. [PMID: 38648614 DOI: 10.1021/acs.jcim.4c00221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2024]
Abstract
In constructing finite models of enzyme active sites for quantum-chemical calculations, atoms at the periphery of the model must be constrained to prevent unphysical rearrangements during geometry relaxation. A simple fixed-atom or "coordinate-lock" approach is commonly employed but leads to undesirable artifacts in the form of small imaginary frequencies. These preclude evaluation of finite-temperature free-energy corrections, limiting thermochemical calculations to enthalpies only. Full-dimensional vibrational frequency calculations are possible by replacing the fixed-atom constraints with harmonic confining potentials. Here, we compare that approach to an alternative strategy in which fixed-atom contributions to the Hessian are simply omitted. While the latter strategy does eliminate imaginary frequencies, it tends to underestimate both the zero-point energy and the vibrational entropy while introducing artificial rigidity. Harmonic confining potentials eliminate imaginary frequencies and provide a flexible means to construct active-site models that can be used in unconstrained geometry relaxations, affording better convergence of reaction energies and barrier heights with respect to the model size, as compared to models with fixed-atom constraints.
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Affiliation(s)
- Paige E Bowling
- Biophysics Graduate Program, The Ohio State University, Columbus, Ohio 43210, United States
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Saswata Dasgupta
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
- Department of Chemistry and Biochemistry, University of California-San Diego, La Jolla, California 92093, United States
| | - John M Herbert
- Biophysics Graduate Program, The Ohio State University, Columbus, Ohio 43210, United States
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
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Wang S, Li Y, Wang B. Synthesis and properties of unsymmetrical porphyrins possessing an isonicotinic acid moiety and phenyl, methoxyphenyl, or chlorophenyl groups. JOURNAL OF CHEMICAL RESEARCH 2021. [DOI: 10.1177/17475198211032835] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The isonicotinic acid containing porphyrin compounds 5-{4-[3-(4-pyridylcarbonyloxy)propoxy]phenyl}-10,15,20-triphenylporphyrin, 5-{4-[3-(4-pyridylcarbonyloxy)propoxy]phenyl}-10,15,20-tri(4-methoxyphenyl)porphyrin, and 5-{4-[3-(4-pyridylcarbonyloxy)propoxy]phenyl}-10,15,20-tri(4-chlorophenyl)porphyrin are prepared and characterized by 1H NMR, 13C NMR, MS, elemental analysis, IR, and UV-Vis. In addition, their spectroscopic properties are investigated through using the Raman spectroscopy, fluorescence, and surface photovoltage measurements. The influence of different substituents on Raman spectra is small, but their impact on the fluorescence spectra and surface photovoltage measurements is significant. Molecular dynamic simulations and UV-Vis diffuse-reflectance spectra show that these porphyrin compounds are potential semiconductor materials.
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Affiliation(s)
- Shiqi Wang
- School of Materials Science and Engineering, Henan Polytechnic University, Jiaozuo, P.R. China
| | - Yao Li
- School of Safety Science and Engineering, Henan Polytechnic University, Jiaozuo, P.R. China
| | - Binbin Wang
- School of Materials Science and Engineering, Henan Polytechnic University, Jiaozuo, P.R. China
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Bellini RG, Coronado MA, Paschoal AR, Gaudencio do Rêgo T, Hungria M, Ribeiro de Vasconcelos AT, Nicolás MF. Structural analysis of a novel N-carbamoyl-d-amino acid amidohydrolase from a Brazilian Bradyrhizobium japonicum strain: In silico insights by molecular modelling, docking and molecular dynamics. J Mol Graph Model 2018; 86:35-42. [PMID: 30336451 DOI: 10.1016/j.jmgm.2018.10.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2018] [Revised: 10/06/2018] [Accepted: 10/08/2018] [Indexed: 10/28/2022]
Abstract
In this work we performed several in silico analyses to describe the relevant structural aspects of an enzyme N-Carbamoyl-d-amino acid amidohydrolase (d-NCAase) encoded on the genome of the Brazilian strain CPAC 15 (=SEMIA 5079) of Bradyrhizobium japonicum, a nonpathogenic species belonging to the order Rhizobiales. d-NCAase has wide applications particularly in the pharmaceutical industry, since it catalyzes the production of d-amino acids such as D-p-hydroxyphenylglycine (D-HPG), an intermediate in the synthesis of β-lactam antibiotics. We applied a homology modelling approach and 50 ns of molecular dynamics simulations to predict the structure and the intersubunit interactions of this novel d-NCAase. Also, in order to evaluate the substrate binding site, the model was subjected to 50 ns of molecular dynamics simulations in the presence of N-Carbamoyl-d-p-hydroxyphenylglycine (Cp-HPG) (a d-NCAase canonical substrate) and water-protein/water-substrate interactions analyses were performed. Overall, the structural analysis and the molecular dynamics simulations suggest that d-NCAase of B. japonicum CPAC-15 has a homodimeric structure in solution. Here, we also examined the substrate specificity of the catalytic site of our model and the interactions with water molecules into the active binding site were comprehensively discussed. Also, these simulations showed that the amino acids Lys123, His125, Pro127, Cys172, Asp174 and Arg176 are responsible for recognition of ligand in the active binding site through several chemical associations, such as hydrogen bonds and hydrophobic interactions. Our results show a favourable environment for a reaction of hydrolysis that transforms N-Carbamoyl-d-p-hydroxyphenylglycine (Cp-HPG) into the active compound D-p-hydroxyphenylglycine (D-HPG). This work envisage the use of d-NCAase from the Brazilian Bradyrhizobium japonicum strain CPAC-15 (=SEMIA 5079) for the industrial production of D-HPG, an important intermediate for semi-synthesis of β-lactam antibiotics such as penicillins, cephalosporins and amoxicillin.
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Affiliation(s)
- Reinaldo G Bellini
- Laboratório Nacional de Computação Científica, Petrópolis, Rio de Janeiro, Brazil
| | - Mônika Aparecida Coronado
- Centro Multiusuário de Inovação Biomolecular, Departamento de Física, Universidade, Estadual Paulista (UNESP), São José do Rio Preto, 15054-000, SP, Brazil.
| | - Alexandre Rossi Paschoal
- Federal University of Technology - Paraná, Avenida Alberto Carazzai, 1640, 86300-000, Cornélio Procópio, PR, Brazil.
| | - Thaís Gaudencio do Rêgo
- Universidade Federal da Paraíba, Centro de Informática, Rua dos Escoteiros, S/N, João Pessoa, PB, 58055-000, Brazil.
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Guan S, Zhao L, Jin H, Shan N, Han W, Wang S, Shan Y. Binding modes of phosphotriesterase-like lactonase complexed with δ-nonanoic lactone and paraoxon using molecular dynamics simulations. J Biomol Struct Dyn 2016; 35:273-286. [DOI: 10.1080/07391102.2016.1142899] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Shanshan Guan
- National Engineering Laboratory For AIDS Vaccine, Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, School of Life Sciences, Jilin University, Changchun 130012, China
- State Key Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun 130023, China
| | - Li Zhao
- National Engineering Laboratory For AIDS Vaccine, Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, School of Life Sciences, Jilin University, Changchun 130012, China
| | - Hanyong Jin
- National Engineering Laboratory For AIDS Vaccine, Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, School of Life Sciences, Jilin University, Changchun 130012, China
| | - Ning Shan
- Editorial Department of Journal of Jilin University (Science Edition), Changchun, China
| | - Weiwei Han
- National Engineering Laboratory For AIDS Vaccine, Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, School of Life Sciences, Jilin University, Changchun 130012, China
| | - Song Wang
- State Key Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun 130023, China
| | - Yaming Shan
- National Engineering Laboratory For AIDS Vaccine, Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, School of Life Sciences, Jilin University, Changchun 130012, China
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de Juan Fernández L, Fuentes de Arriba ÁL, Monleón LM, Rubio OH, Alcázar Montero V, Rubio LS, Morán JR. An Enantioselective Benzofuran-Based Receptor for Dinitrobenzoyl-Substituted Amino Acids. European J Org Chem 2016. [DOI: 10.1002/ejoc.201501457] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Zhan D, Bai A, Yu L, Han W, Feng Y. Characterization of the PH1704 protease from Pyrococcus horikoshii OT3 and the critical functions of Tyr120. PLoS One 2014; 9:e103902. [PMID: 25192005 PMCID: PMC4156298 DOI: 10.1371/journal.pone.0103902] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Accepted: 07/03/2014] [Indexed: 12/02/2022] Open
Abstract
The PH1704 protease from hyperthermophilic archaean Pyrococcus horikoshii OT3 is a member of DJ-1/ThiJ/PfpI superfamily with diverse functional subclasses. The recombinant PH1704 was efficiently purified and was systematically characterized by a combination of substrate specificity analysis, steady-state kinetics study and molecular docking research. The homogeneous protease was obtained as a presumed dodecamer with molecular weight of ∼240 kDa. Iodoacetamide strongly inhibited the peptidase activity, confirming that Cys100 is a nucleophilic residue. The recombinant protein was identified as both an aminopeptidase and an endopeptidase. Experimental data showed that L-R-amc was the best substrate of PH1704. Structural interaction fingerprint analysis (SIFt) indicated the binding pose of PH1704 and showed that Tyr120 is important in substrate binding. Kinetic parameters Kcat and Kcat/Km of the Y120P mutant with L-R-amc was about 7 and 7.8 times higher than that of the wild type (WT). For the endopeptidase Y120P with AAFR-amc, Kcat and Kcat/Km is 10- and 21- fold higher than that of WT. Experimental data indicate the important functions of Tyr120: involvement in enzyme activity to form a hydrogen bond with Cys100 and as an entrance gate of the substrate with Lys43. The results of this study can be used to investigate the DJ-1/ThiJ/PfpI superfamily.
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Affiliation(s)
- Dongling Zhan
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Science, Jilin University, Changchun, China
- College of Food Science and Engineering, Jilin Agricultural University, Changchun, China
| | - Aixi Bai
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Science, Jilin University, Changchun, China
| | - Lei Yu
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Science, Jilin University, Changchun, China
| | - Weiwei Han
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Science, Jilin University, Changchun, China
- * E-mail: (YF); (WH)
| | - Yan Feng
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Science, Jilin University, Changchun, China
- State Key Laboratory of Microbial Metabolism, College of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- * E-mail: (YF); (WH)
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