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Zhang J, Lin L, Wei W, Wei D. Identification, Characterization, and Computer-Aided Rational Design of a Novel Thermophilic Esterase from Geobacillus subterraneus, and Application in the Synthesis of Cinnamyl Acetate. Appl Biochem Biotechnol 2024; 196:3553-3575. [PMID: 37713064 DOI: 10.1007/s12010-023-04697-2] [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] [Accepted: 08/16/2023] [Indexed: 09/16/2023]
Abstract
Investigation of a novel thermophilic esterase gene from Geobacillus subterraneus DSMZ 13552 indicated a high amino acid sequence similarity of 25.9% to a reported esterase from Geobacillus sp. A strategy that integrated computer-aided rational design tools was developed to select mutation sites. Six mutants were selected from four criteria based on the simulated saturation mutation (including 19 amino acid residues) results. Of these, the mutants Q78Y and G119A were found to retain 87% and 27% activity after incubation at 70 °C for 20 min, compared with the 19% activity for the wild type. Subsequently, a double-point mutant (Q78Y/G119A) was obtained and identified with optimal temperature increase from 65 to 70 °C and a 41.51% decrease in Km. The obtained T1/2 values of 42.2 min (70 °C) and 16.9 min (75 °C) for Q78Y/G119A showed increases of 340% and 412% compared with that in the wild type. Q78Y/G119A was then employed as a biocatalyst to synthesize cinnamyl acetate, for which the conversion rate reached 99.40% with 0.3 M cinnamyl alcohol at 60 °C. The results validated the enhanced enzymatic properties of the mutant and indicated better prospects for industrial application as compared to that in the wild type. This study reported a method by which an enzyme could evolve to achieve enhanced thermostability, thereby increasing its potential for industrial applications, which could also be expanded to other esterases.
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Affiliation(s)
- Jin Zhang
- State Key Laboratory of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, People's Republic of China
| | - Lin Lin
- School of Chemical and Environmental Engineering, Shanghai Institute of Technology, Shanghai, 201418, People's Republic of China
- Research Laboratory for Functional Nanomaterial, National Engineering Research Center for Nanotechnology, Shanghai, 200241, People's Republic of China
| | - Wei Wei
- State Key Laboratory of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, People's Republic of China.
| | - Dongzhi Wei
- State Key Laboratory of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, People's Republic of China
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2
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Guo M, Wu Y, Yao Y, Wu Y, Ni K, Zheng B, Guan Y. Imaging metabolic mechanisms and the binding behavior of nutrients/transporters of edible Matricaria flowers VOCs. Food Res Int 2024; 178:113857. [PMID: 38309891 DOI: 10.1016/j.foodres.2023.113857] [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: 11/01/2023] [Revised: 12/06/2023] [Accepted: 12/14/2023] [Indexed: 02/05/2024]
Abstract
To promote the consumption of flowers and to utilize the nutritional value of proteins, the efficacy of the beneficial components of flowers has been intensively studied. Anthemis nobilis was used as the study object, and all its volatile components (VOCs) were fingerprinted using headspace solid-phase micro-extraction gas-mass spectrometry (HS-SPME/GC-MS). GC-MS fingerprints of five parts of Anthemis nobilis were established using three proteins, bovine lactoferrin (BLF), bovine lactoglobulin (β-Lg), and human serum albumin (HSA), as nutrient transporters. The interactions between the volatile components from different parts of the mother chrysanthemum plant and the nutrient/transport proteins were investigated. The results of fingerprinting showed that the flavor components were dominated by alkenes. In addition, this study revealed that among the three nutrient transporters, the strongest binding to the adsorbed volatile components was HSA, followed by BLF, and β-Lg was second. In addition, a characteristic molecule, camphene, was screened. Integrated molecular simulation using fluorescence spectroscopy was used to validate the results of the interaction of the nutrient/transport proteins systems with characteristic molecule. The properties of the characteristic molecules such as absorption, distribution, metabolism, excretion and toxicity in vivo were analyzed using ADMET to provide a theoretical basis for the preparation of flower-flavored dairy products.
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Affiliation(s)
- Ming Guo
- College of Chemistry and Materials Engineering, Zhejiang Agriculture & Forestry University, Hangzhou, Zhejiang 311300, China; Zhejiang Provincial Key Laboratory of Forest Aromatic Plants-based Healthcare Functions, Zhejiang Agriculture & Forestry University, Hangzhou 311300, China.
| | - Yanan Wu
- College of Chemistry and Materials Engineering, Zhejiang Agriculture & Forestry University, Hangzhou, Zhejiang 311300, China
| | - Yecen Yao
- College of Chemistry and Materials Engineering, Zhejiang Agriculture & Forestry University, Hangzhou, Zhejiang 311300, China
| | - Yanlin Wu
- College of Chemistry and Materials Engineering, Zhejiang Agriculture & Forestry University, Hangzhou, Zhejiang 311300, China
| | - Kaijie Ni
- College of Chemistry and Materials Engineering, Zhejiang Agriculture & Forestry University, Hangzhou, Zhejiang 311300, China
| | - Bingsong Zheng
- Zhejiang Provincial Key Laboratory of Forest Aromatic Plants-based Healthcare Functions, Zhejiang Agriculture & Forestry University, Hangzhou 311300, China; College of Forestry and Biotechnology, Zhejiang Agriculture & Forestry University, Hangzhou, Zhejiang 311300, China
| | - Yuge Guan
- College of Food and Health, Zhejiang Agriculture & Forestry University, Hangzhou, Zhejiang 311300, China
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Bonarek P, Mularczyk D, Loch JI, Kurpiewska K, Dziedzicka-Wasylewska M. β-Lactoglobulin variants as potential carriers of pramoxine: Comprehensive structural and biophysical studies. J Mol Recognit 2023; 36:e3052. [PMID: 37610054 DOI: 10.1002/jmr.3052] [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: 04/12/2023] [Revised: 07/24/2023] [Accepted: 08/07/2023] [Indexed: 08/24/2023]
Abstract
β-Lactoglobulin (BLG) is a member of the lipocalin family. As other proteins from this group, BLG can be modified to bind specifically compounds of medical interests. The aim of this study was to evaluate the role of two mutations, L39Y and L58F, in the binding of topical anesthetic pramoxine (PRM) to β-lactoglobulin. Circular dichroism spectroscopy, isothermal titration calorimetry (ITC), and X-ray crystallography were used to understand the mechanisms of BLG-PRM interactions. Studies were performed for three new BLG mutants: L39Y, L58F, and L39Y/L58F. ITC measurements indicated a significant increase in the affinity to the PRM of variants L58F and L39Y. Measurements taken for the double mutant L39Y/L58F showed the additivity of two mutations leading to about 80-fold increase in the affinity to PRM in comparison to natural protein BLG from bovine milk. The determined crystal structures revealed that pramoxine is accommodated in the β-barrel interior of BLG mutants and stabilized by hydrophobic interactions. The observed additive effect of two mutations on drug binding opens the possibility for further designing of new BLG variants with high affinity to selected drugs.
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Affiliation(s)
- Piotr Bonarek
- Faculty of Biochemistry, Biophysics and Biotechnology, Department of Physical Biochemistry, Jagiellonian University, Kraków, Poland
| | - Dorota Mularczyk
- Faculty of Biochemistry, Biophysics and Biotechnology, Department of Physical Biochemistry, Jagiellonian University, Kraków, Poland
| | - Joanna I Loch
- Faculty of Chemistry, Department of Crystal Chemistry and Crystal Physics, Jagiellonian University, Kraków, Poland
| | - Katarzyna Kurpiewska
- Faculty of Chemistry, Department of Crystal Chemistry and Crystal Physics, Jagiellonian University, Kraków, Poland
| | - Marta Dziedzicka-Wasylewska
- Faculty of Biochemistry, Biophysics and Biotechnology, Department of Physical Biochemistry, Jagiellonian University, Kraków, Poland
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Loch JI, Barciszewski J, Śliwiak J, Bonarek P, Wróbel P, Pokrywka K, Shabalin IG, Minor W, Jaskolski M, Lewiński K. New ligand-binding sites identified in the crystal structures of β-lactoglobulin complexes with desipramine. IUCRJ 2022; 9:386-398. [PMID: 35546795 PMCID: PMC9067113 DOI: 10.1107/s2052252522004183] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 04/19/2022] [Indexed: 06/15/2023]
Abstract
The homodimeric β-lactoglobulin belongs to the lipocalin family of proteins that transport a wide range of hydrophobic molecules and can be modified by mutagenesis to develop specificity for novel groups of ligands. In this work, new lactoglobulin variants, FAF (I56F/L39A/M107F) and FAW (I56F/L39A/M107W), were produced and their interactions with the tricyclic drug desipramine (DSM) were studied using X-ray crystallography, calorimetry (ITC) and circular dichroism (CD). The ITC and CD data showed micromolar affinity of the mutants for DSM and interactions according to the classical one-site binding model. However, the crystal structures unambiguously showed that the FAF and FAW dimers are capable of binding DSM not only inside the β-barrel as expected, but also at the dimer interface and at the entrance to the binding pocket. The presented high-resolution crystal structures therefore provide important evidence of the existence of alternative ligand-binding sites in the β-lactoglobulin molecule. Analysis of the crystal structures highlighted the importance of shape complementarity for ligand recognition and selectivity. The binding sites identified in the crystal structures of the FAF-DSM and FAW-DSM complexes together with data from the existing literature are used to establish a systematic classification of the ligand-binding sites in the β-lactoglobulin molecule.
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Affiliation(s)
- Joanna I. Loch
- Department of Crystal Chemistry and Crystal Physics, Faculty of Chemistry, Jagiellonian University, Kraków, Poland
| | - Jakub Barciszewski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Joanna Śliwiak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Piotr Bonarek
- Department of Physical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland
| | - Paulina Wróbel
- Department of Crystal Chemistry and Crystal Physics, Faculty of Chemistry, Jagiellonian University, Kraków, Poland
| | - Kinga Pokrywka
- Department of Crystal Chemistry and Crystal Physics, Faculty of Chemistry, Jagiellonian University, Kraków, Poland
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Ivan G. Shabalin
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
| | - Wladek Minor
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
| | - Mariusz Jaskolski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
- Department of Crystallography, Faculty of Chemistry, A. Mickiewicz University, Poznan, Poland
| | - Krzysztof Lewiński
- Department of Crystal Chemistry and Crystal Physics, Faculty of Chemistry, Jagiellonian University, Kraków, Poland
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Probing the ligand-binding pocket of recombinant β-lactoglobulin: Calorimetric and spectroscopic studies. Biophys Chem 2022; 283:106770. [DOI: 10.1016/j.bpc.2022.106770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 01/24/2022] [Accepted: 01/26/2022] [Indexed: 11/23/2022]
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Rana N, Singh AK, Shuaib M, Gupta S, Habiballah MM, Alkhanani MF, Haque S, Reshi MS, Kumar S. Drug Resistance Mechanism of M46I-Mutation-Induced Saquinavir Resistance in HIV-1 Protease Using Molecular Dynamics Simulation and Binding Energy Calculation. Viruses 2022; 14:v14040697. [PMID: 35458427 PMCID: PMC9031992 DOI: 10.3390/v14040697] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 03/05/2022] [Accepted: 03/07/2022] [Indexed: 02/06/2023] Open
Abstract
Drug-resistance-associated mutation in essential proteins of the viral life cycle is a major concern in anti-retroviral therapy. M46I, a non-active site mutation in HIV-1 protease has been clinically associated with saquinavir resistance in HIV patients. A 100 ns molecular dynamics (MD) simulation and MM-PBSA calculations were performed to study the molecular mechanism of M46I-mutation-based saquinavir resistance. In order to acquire deeper insight into the drug-resistance mechanism, the flap curling, closed/semi-open/open conformations, and active site compactness were studied. The M46I mutation significantly affects the energetics and conformational stability of HIV-1 protease in terms of RMSD, RMSF, Rg, SASA, and hydrogen formation potential. This mutation significantly decreased van der Waals interaction and binding free energy (∆G) in the M46I–saquinavir complex and induced inward flap curling and a wider opening of the flaps for most of the MD simulation period. The predominant open conformation was reduced, but inward flap curling/active site compactness was increased in the presence of saquinavir in M46I HIV-1 protease. In conclusion, the M46I mutation induced structural dynamics changes that weaken the protease grip on saquinavir without distorting the active site of the protein. The produced information may be utilized for the discovery of inhibitor(s) against drug-resistant HIV-1 protease.
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Affiliation(s)
- Nilottam Rana
- Molecular Signaling & Drug Discovery Laboratory, Department of Biochemistry, Central University of Punjab, Bathinda 151401, Punjab, India; (N.R.); (A.K.S.); (M.S.)
| | - Atul Kumar Singh
- Molecular Signaling & Drug Discovery Laboratory, Department of Biochemistry, Central University of Punjab, Bathinda 151401, Punjab, India; (N.R.); (A.K.S.); (M.S.)
| | - Mohd Shuaib
- Molecular Signaling & Drug Discovery Laboratory, Department of Biochemistry, Central University of Punjab, Bathinda 151401, Punjab, India; (N.R.); (A.K.S.); (M.S.)
| | - Sanjay Gupta
- Department of Urology, Pharmacology and Pathology, Case Western Reserve University, Cleveland, OH 44106, USA;
| | - Mahmoud M. Habiballah
- Medical Laboratory Technology Department, Jazan University, Jazan 45142, Saudi Arabia;
- SMIRES for Consultation in Specialized Medical Laboratories, Jazan University, Jazan 45142, Saudi Arabia
| | - Mustfa F. Alkhanani
- Emergency Service Department, College of Applied Sciences, AlMaarefa University, Riyadh 11597, Saudi Arabia;
| | - Shafiul Haque
- Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, Jazan University, Jazan 45142, Saudi Arabia;
| | - Mohd Salim Reshi
- Toxicology and Pharmacology Lab., Department of Zoology, School of Biosciences and Biotechnology, Baba Ghulam Shah Badshah University, Rajouri 185234, Jammu & Kashmir, India;
| | - Shashank Kumar
- Molecular Signaling & Drug Discovery Laboratory, Department of Biochemistry, Central University of Punjab, Bathinda 151401, Punjab, India; (N.R.); (A.K.S.); (M.S.)
- Correspondence:
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7
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Makori SI, Mu TH, Sun HN. Functionalization of sweet potato leaf polyphenols by nanostructured composite β-lactoglobulin particles from molecular level complexations: A review. Food Chem 2022; 372:131304. [PMID: 34655825 DOI: 10.1016/j.foodchem.2021.131304] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 09/25/2021] [Accepted: 09/30/2021] [Indexed: 12/18/2022]
Abstract
Sweet potato leaf polyphenols (SPLPs) have shown potential health benefits in the food and pharmaceutical industries. Nowadays, consumption of SPLPs from animal feeds to foodstuff is becoming a trend worldwide. However, the application of SPLPs is limited by their low bioavailability and stability. β-lactoglobulin (βlg), a highly regarded whey protein, can interact with SPLPs at the molecular level to form reversible or irreversible nanocomplexes (NCs). Consequently, the functional properties and final quality of SPLPs are directly modified. In this review, the composition and structure of SPLPs and βlg, as well as methods of molecular complexation and mechanisms of formation of SPLPsβlgNCs, are revisited. The modified functionalities of SPLPsβlgNCs, especially protein conformational structures, antioxidant activity, solubility, thermal stability, emulsifying, and gelling properties including allergenic potential, digestibility, and practical applications are discussed for SPLPs future development.
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Affiliation(s)
- Shadrack Isaboke Makori
- Laboratory of Food Chemistry and Nutrition Science, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Key Laboratory of Agro-Products Processing, Ministry of Agriculture and Rural Affairs, No. 2 Yuan Ming Yuan West Road, Haidian District, P.O. Box 5109, Beijing 100193, China; Food Technology Division, Kenya Industrial Research and Development Institute (KIRDI), P.O. Box 30650, GPO, Nairobi, Kenya
| | - Tai-Hua Mu
- Laboratory of Food Chemistry and Nutrition Science, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Key Laboratory of Agro-Products Processing, Ministry of Agriculture and Rural Affairs, No. 2 Yuan Ming Yuan West Road, Haidian District, P.O. Box 5109, Beijing 100193, China.
| | - Hong-Nan Sun
- Laboratory of Food Chemistry and Nutrition Science, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Key Laboratory of Agro-Products Processing, Ministry of Agriculture and Rural Affairs, No. 2 Yuan Ming Yuan West Road, Haidian District, P.O. Box 5109, Beijing 100193, China.
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Recent applications of bio-engineering principles to modulate the functionality of proteins in food systems. Trends Food Sci Technol 2021. [DOI: 10.1016/j.tifs.2021.04.055] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Broersen K. Milk Processing Affects Structure, Bioavailability and Immunogenicity of β-lactoglobulin. Foods 2020; 9:foods9070874. [PMID: 32635246 PMCID: PMC7404694 DOI: 10.3390/foods9070874] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 06/24/2020] [Accepted: 06/26/2020] [Indexed: 12/15/2022] Open
Abstract
Bovine milk is subjected to various processing steps to warrant constant quality and consumer safety. One of these steps is pasteurization, which involves the exposure of liquid milk to a high temperature for a limited amount of time. While such heating effectively ameliorates consumer safety concerns mediated by pathogenic bacteria, these conditions also have an impact on one of the main nutritional whey constituents of milk, the protein β-lactoglobulin. As a function of heating, β-lactoglobulin was shown to become increasingly prone to denaturation, aggregation, and lactose conjugation. This review discusses the implications of such heat-induced modifications on digestion and adsorption in the gastro-intestinal tract, and the responses these conformations elicit from the gastro-intestinal immune system.
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Affiliation(s)
- Kerensa Broersen
- Department of Applied Stem Cell Technologies, TechMed Centre, University of Twente, Postbus 217, 7500 AE Enschede, The Netherlands
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