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Krivoshchapov NV, Medvedev MG. Accurate and Efficient Conformer Sampling of Cyclic Drug-Like Molecules with Inverse Kinematics. J Chem Inf Model 2024; 64:4542-4552. [PMID: 38776465 DOI: 10.1021/acs.jcim.3c02040] [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: 05/25/2024]
Abstract
Identification of all of the influential conformers of biomolecules is a crucial step in many tasks of computational biochemistry. Specifically, molecular docking, a key component of in silico drug development, requires a comprehensive set of conformations for potential candidates in order to generate the optimal ligand-receptor poses and, ultimately, find the best drug candidates. However, the presence of flexible cycles in a molecule complicates the initial search for conformers since exhaustive sampling algorithms via torsional random and systematic searches become very inefficient. The devised inverse-kinematics-based Monte Carlo with refinement (MCR) algorithm identifies independently rotatable dihedral angles in (poly)cyclic molecules and uses them to perform global conformational sampling, outperforming popular alternatives (MacroModel, CREST, and RDKit) in terms of speed and diversity of the resulting conformer ensembles. Moreover, MCR quickly and accurately recovers naturally occurring macrocycle conformations for most of the considered molecules.
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Affiliation(s)
- Nikolai V Krivoshchapov
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow 119991, Russian Federation
| | - Michael G Medvedev
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow 119991, Russian Federation
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2
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Jin SB, Kim HA, Shin JA, Jung NH, Park SY, Hong S, Kong KH. Recombinant expression and tryptophan-assisted analysis of human sweet taste receptor T1R3's extracellular domain in sweetener interaction studies. Prep Biochem Biotechnol 2024:1-8. [PMID: 38578840 DOI: 10.1080/10826068.2024.2336985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2024]
Abstract
The human palate can discern multiple tastes; however, it predominantly perceives five fundamental flavors: sweetness, saltiness, sourness, bitterness, and umami. Sweetness is primarily mediated through the sweet taste receptor, a membrane-bound heterodimeric structure comprising T1R2-T1R3. However, unraveling the structural and mechanistic intricacies of the sweet taste receptor has proven challenging. This study aimed to address this knowledge gap by expressing an extracellular N-terminal domain encompassing the cysteine-rich domain of human hT1R3 (hT1R3-TMD) in Escherichia coli. The expressed protein was obtained as inclusion bodies, purified by metal affinity chromatography, and refolded using the dilution-refolding method. Through rigorous analysis, we confirmed the successful refolding of hT1R3-TMD and elucidated its structural characteristics using circular dichroism spectroscopy. Notably, the refolded protein was found to exist as either a monomer or a dimer, depending on its concentration. A tryptophan fluorescence quenching assay revealed that the dissociation constants for sucrose, sucralose, and brazzein were >9500 μM, 2380 μM and 14.3 μM, respectively. Our findings highlight the utility of this E. coli expression system for producing functional hT1R3-TMD for investigations and demonstrate the efficacy of the tryptophan fluorescence quenching assay in revealing complex interactions between sweet taste receptors and various sweeteners.
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Affiliation(s)
- Soo-Bin Jin
- Department of Chemistry, College of Natural Sciences, Chung-Ang University, Seoul, Korea
| | - Hyun-A Kim
- Department of Chemistry, College of Natural Sciences, Chung-Ang University, Seoul, Korea
| | - Ji-Ae Shin
- Department of Chemistry, College of Natural Sciences, Chung-Ang University, Seoul, Korea
| | - Na-Hee Jung
- Department of Chemistry, College of Natural Sciences, Chung-Ang University, Seoul, Korea
| | - Seo-Young Park
- Department of Chemistry, College of Natural Sciences, Chung-Ang University, Seoul, Korea
| | - Sungguan Hong
- Department of Chemistry, College of Natural Sciences, Chung-Ang University, Seoul, Korea
| | - Kwang-Hoon Kong
- Department of Chemistry, College of Natural Sciences, Chung-Ang University, Seoul, Korea
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Yuan Y, Yiasmin MN, Tristanto NA, Chen Y, Liu Y, Guan S, Wang Z, Hua X. Computational simulations on the taste mechanism of steviol glycosides based on their interactions with receptor proteins. Int J Biol Macromol 2024; 255:128110. [PMID: 37981277 DOI: 10.1016/j.ijbiomac.2023.128110] [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: 08/28/2023] [Revised: 11/13/2023] [Accepted: 11/13/2023] [Indexed: 11/21/2023]
Abstract
Steviol glycoside (SG) is a potential natural sugar substitute. The taste of various SG structures differ significantly, while their mechanism has not been thoroughly investigated. To investigate the taste mechanism, molecular docking simulations of SGs with sweet taste receptor TAS1R2 and bitter taste receptor TAS2R4 were conducted. The result suggested that four flexible coils (regions) in TAS1R2 constructed a geometry open pocket in space responsible for the binding of sweeteners. Amino acids that form hydrogen bonds with sweeteners are located in different receptor regions. In bitterness simulation, fewer hydrogen bonds were formed with the increased size of SG molecules. Particularly, there was no interaction between RM and TAS2R4 due to its size, which explains the non-bitterness of RM. Molecular dynamics simulations further indicated that the number of hydrogen bonds between SGs and TAS1R2 was maintained during a simulation time of 50 ns, while sucrose was gradually released from the binding site, leading to the break of interaction. Conclusively, the high sweetness intensity of SG can be attributed to its durative concurrent interaction with the receptor's binding site, and such behavior was determined by the structure feature of SG.
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Affiliation(s)
- Yuying Yuan
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Mst Nushrat Yiasmin
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | | | - Yujie Chen
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China; Jiangsu Sevtia Biotechnology Co., Ltd., Wuxi 214181, China
| | - Yaxian Liu
- Department of Biotechnology and Enzyme Science, University of Hohenheim, Institute of Food Science and Biotechnology, Garbenstr. 25, 70599 Stuttgart, Germany
| | - Shuyi Guan
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Zijie Wang
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Xiao Hua
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China.
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Nicholas Chua B, Mei Guo W, Teng Wong H, Siak-Wei Ow D, Leng Ho P, Koh W, Koay A, Tian Wong F. A sweeter future: Using protein language models for exploring sweeter brazzein homologs. Food Chem 2023; 426:136580. [PMID: 37331142 DOI: 10.1016/j.foodchem.2023.136580] [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: 02/28/2023] [Revised: 05/23/2023] [Accepted: 06/06/2023] [Indexed: 06/20/2023]
Abstract
With growing concerns over the health impact of sugar, brazzein offers a viable alternative due to its sweetness, thermostability, and low risk profile. Here, we demonstrated the ability of protein language models to design new brazzein homologs with improved thermostability and potentially higher sweetness, resulting in new diverse optimized amino acid sequences that improve structural and functional features beyond what conventional methods could achieve. This innovative approach resulted in the identification of unexpected mutations, thereby generating new possibilities for protein engineering. To facilitate the characterization of the brazzein mutants, a simplified procedure was developed for expressing and analyzing related proteins. This process involved an efficient purification method using Lactococcus lactis (L. lactis), a generally recognized as safe (GRAS) bacterium, as well as taste receptor assays to evaluate sweetness. The study successfully demonstrated the potential of computational design in producing a more heat-resistant and potentially more palatable brazzein variant, V23.
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Affiliation(s)
- Bryan Nicholas Chua
- Molecular Engineering Laboratory, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, #07-06, Proteos, Singapore 138673, Republic of Singapore
| | - Wei Mei Guo
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, #02-01, Nanos, Singapore 138669, Republic of Singapore
| | - Han Teng Wong
- Molecular Engineering Laboratory, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, #07-06, Proteos, Singapore 138673, Republic of Singapore
| | - Dave Siak-Wei Ow
- Bioprocessing Technology Institute (BTI), Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, #06-01, Centros, Singapore 138668, Republic of Singapore
| | - Pooi Leng Ho
- Bioprocessing Technology Institute (BTI), Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, #06-01, Centros, Singapore 138668, Republic of Singapore
| | - Winston Koh
- Institute of Bioengineering and Bioimaging (IBB), Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, #07-01, Nanos, Singapore 138669, Republic of Singapore; Bioinformatics Institute (BII), Agency of Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01, Matrix, Singapore 138671, Republic of Singapore.
| | - Ann Koay
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, #02-01, Nanos, Singapore 138669, Republic of Singapore.
| | - Fong Tian Wong
- Molecular Engineering Laboratory, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, #07-06, Proteos, Singapore 138673, Republic of Singapore; Institute of Sustainability for Chemicals, Energy and Environment (ISCE(2)), Agency for Science, Technology and Research (A*STAR), 8 Biomedical Grove, Neuros, #07-01, Singapore 138665, Republic of Singapore.
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Saraiva A, Carrascosa C, Ramos F, Raheem D, Pedreiro S, Vega A, Raposo A. Brazzein and Monellin: Chemical Analysis, Food Industry Applications, Safety and Quality Control, Nutritional Profile and Health Impacts. Foods 2023; 12:foods12101943. [PMID: 37238762 DOI: 10.3390/foods12101943] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 04/30/2023] [Accepted: 05/06/2023] [Indexed: 05/28/2023] Open
Abstract
Recently, customers have been keener to buy products manufactured using all-natural ingredients with positive health properties, but without losing flavor. In this regard, the objective of the current study is to review the consumption of brazzein and monellin, their nutritional profiles and health effects, and their potential applications in the food industry. This poses challenges with sustainability and important quality and safety indicators, as well as the chemical processes used to determine them. To better understand the utilization of brazzein and monellin, the chemical analysis of these two natural sweet proteins was also reviewed by placing particular emphasis on their extraction methods, purification and structural characterization. Protein engineering is considered a means to improve the thermal stability of brazzein and monellin to enhance their application in food processing, especially where high temperatures are applied. When the quality and safety of these sweet proteins are well-investigated and the approval from safety authorities is secured, the market for brazzein and monellin as food ingredient substitutes for free sugar will be guaranteed in the future. Ultimately, the review on these two natural peptide sweeteners increases the body of knowledge on alleviating problems of obesity, diabetes and other non-communicable diseases.
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Affiliation(s)
- Ariana Saraiva
- Department of Animal Pathology and Production, Bromatology and Food Technology, Faculty of Veterinary, Universidad de Las Palmas de Gran Canaria, Trasmontaña s/n, 35413 Arucas, Spain
| | - Conrado Carrascosa
- Department of Animal Pathology and Production, Bromatology and Food Technology, Faculty of Veterinary, Universidad de Las Palmas de Gran Canaria, Trasmontaña s/n, 35413 Arucas, Spain
| | - Fernando Ramos
- Faculty of Pharmacy, University of Coimbra, Azinhaga de Santa Comba, 3000-548 Coimbra, Portugal
- Associated Laboratory for Green Chemistry (LAQV) of the Network of Chemistry and Technology (REQUIMTE), Rua D. Manuel II, Apartado 55142, 4051-401 Porto, Portugal
| | - Dele Raheem
- Arctic Centre, University of Lapland, 96101 Rovaniemi, Finland
| | - Sónia Pedreiro
- Faculty of Pharmacy, University of Coimbra, Azinhaga de Santa Comba, 3000-548 Coimbra, Portugal
- Associated Laboratory for Green Chemistry (LAQV) of the Network of Chemistry and Technology (REQUIMTE), Rua D. Manuel II, Apartado 55142, 4051-401 Porto, Portugal
| | - Angelo Vega
- Department of Animal Pathology and Production, Bromatology and Food Technology, Faculty of Veterinary, Universidad de Las Palmas de Gran Canaria, Trasmontaña s/n, 35413 Arucas, Spain
| | - António Raposo
- CBIOS (Research Center for Biosciences and Health Technologies), Universidade Lusófona de Humanidades e Tecnologias, Campo Grande 376, 1749-024 Lisboa, Portugal
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Yu Y, Xu S, He R, Liang G. Application of Molecular Simulation Methods in Food Science: Status and Prospects. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:2684-2703. [PMID: 36719790 DOI: 10.1021/acs.jafc.2c06789] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Molecular simulation methods, such as molecular docking, molecular dynamic (MD) simulation, and quantum chemical (QC) calculation, have become popular as characterization and/or virtual screening tools because they can visually display interaction details that in vitro experiments can not capture and quickly screen bioactive compounds from large databases with millions of molecules. Currently, interdisciplinary research has expanded molecular simulation technology from computer aided drug design (CADD) to food science. More food scientists are supporting their hypotheses/results with this technology. To understand better the use of molecular simulation methods, it is necessary to systematically summarize the latest applications and usage trends of molecular simulation methods in the research field of food science. However, this type of review article is rare. To bridge this gap, we have comprehensively summarized the principle, combination usage, and application of molecular simulation methods in food science. We also analyzed the limitations and future trends and offered valuable strategies with the latest technologies to help food scientists use molecular simulation methods.
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Affiliation(s)
- Yuandong Yu
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, Bioengineering College, Chongqing University, Chongqing400030, China
| | - Shiqi Xu
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, Bioengineering College, Chongqing University, Chongqing400030, China
| | - Ran He
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, Bioengineering College, Chongqing University, Chongqing400030, China
| | - Guizhao Liang
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, Bioengineering College, Chongqing University, Chongqing400030, China
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Ponnusamy V, Subramanian G, Muthuswamy K, Shanmugamprema D, Krishnan V, Velusamy T, Subramaniam S. Genetic variation in sweet taste receptors and a mechanistic perspective on sweet and fat taste sensation in the context of obesity. Obes Rev 2022; 23:e13512. [PMID: 36282093 DOI: 10.1111/obr.13512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 09/14/2022] [Accepted: 10/05/2022] [Indexed: 11/30/2022]
Abstract
Taste sensation enables humans to make nutritionally important decisions such as food preference and consumption. It functions as deterministic factors for unpropitious eating behavior, leading to overweight and obesity. The hedonistic feeling on consumption of fat and sugar-rich meals, in particular, has a negative influence on health. In addition, impairment in the taste receptors alters the downstream signaling of taste transduction pathway. Hence, genetic polymorphism in typical taste receptors is a predictor of taste sensitivity variance across individuals. The present review summarizes the effect of a single nucleotide polymorphism (SNP) in sweet taste receptors (T1R2/T1R3) on taste perception among individuals of various body mass index (BMI). Furthermore, in the context of obesity, we discussed the possibility of crosstalk between fat and sweet receptors as well as taste dysfunction in diseased individuals. In overall, a greater understanding of the physiological relationship between taste receptors, altered taste sensitivity, and genetic polymorphisms should lead to more effective obesity prevention approaches.
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Affiliation(s)
- Vinithra Ponnusamy
- Molecular Physiology Laboratory, Department of Biochemistry, Bharathiar University, Coimbatore, Tamilnadu, India, 641046
| | - Gowtham Subramanian
- Molecular Physiology Laboratory, Department of Biochemistry, Bharathiar University, Coimbatore, Tamilnadu, India, 641046
| | - Karthi Muthuswamy
- Molecular Physiology Laboratory, Department of Biochemistry, Bharathiar University, Coimbatore, Tamilnadu, India, 641046
| | - Deepankumar Shanmugamprema
- Molecular Physiology Laboratory, Department of Biochemistry, Bharathiar University, Coimbatore, Tamilnadu, India, 641046
| | - Vasanth Krishnan
- Molecular Biology Laboratory, Department of Botany, School of Life Sciences, Bharathiar University, Coimbatore, Tamilnadu, India, 641046
| | - Thirunavukkarasu Velusamy
- Department of Biotechnology, School of Biotechnology and Genetic Engineering, Bharathiar University, Coimbatore, Tamilnadu, India, 641046
| | - Selvakumar Subramaniam
- Molecular Physiology Laboratory, Department of Biochemistry, Bharathiar University, Coimbatore, Tamilnadu, India, 641046
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