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Gholizadeh M, Shareghi B, Farhadian S. Revealing the interaction between alpha-chymotrypsin and eugenol: An integrated multi-spectral and dynamic simulation approach. Int J Biol Macromol 2024; 277:134504. [PMID: 39116971 DOI: 10.1016/j.ijbiomac.2024.134504] [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: 11/24/2023] [Revised: 07/26/2024] [Accepted: 08/03/2024] [Indexed: 08/10/2024]
Abstract
The study aims to explore the effects of Eugenol (EUG) as an antioxidant on α-Chymotrypsin (α-Chy) and its interaction mechanism, with potential implications for new therapy development. The interaction between EUG and α-Chy was demonstrated through ultraviolet (UV) spectroscopy, which resulted in a shift in absorption with docking energies of -22.76 kJ/mol. An increase in fluorescence intensity indicated that the Trp residues moved to a less polar environment, which is consistent with the changes in accessible surface area (ASA) values. The presence of EUG led to a decrease in α-helix, β-turn, and random coil structures as shown by circular dichroism (CD) and Fourier-transform infrared (FTIR) analysis. Additionally, there was a slight increase in β-sheet structures, indicating a decrease in enzyme stability. However, tests for thermal stability showed a decrease in folding upon the introduction of EUG, which contradicted the results obtained from molecular dynamics (MD) simulations. The docking studies revealed that EUG forms hydrogen bonds and van der Waals forces with the enzyme, indicating the interaction mechanism. Kinetic studies confirmed that EUG acts as a mixed inhibitor. However, further research involving live organisms is necessary to fully understand its potential.
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Affiliation(s)
- Mohammad Gholizadeh
- Department of Biology, Faculty of Science, Shahrekord University, Shahrekord, P. O. Box.115, Iran; Central Laboratory, Shahrekord University, Shahrekord, Iran
| | - Behzad Shareghi
- Department of Biology, Faculty of Science, Shahrekord University, Shahrekord, P. O. Box.115, Iran; Central Laboratory, Shahrekord University, Shahrekord, Iran.
| | - Sadegh Farhadian
- Department of Biology, Faculty of Science, Shahrekord University, Shahrekord, P. O. Box.115, Iran; Central Laboratory, Shahrekord University, Shahrekord, Iran.
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Li T, Zhang Y, Shao J, Hou R, Zhang Z, Ye C, Wang H, Zhu B, Zhang Y. Enhancement of non-covalent interaction between soy protein isolate and quercetin by sodium alginate. Food Chem 2024; 460:140422. [PMID: 39068794 DOI: 10.1016/j.foodchem.2024.140422] [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: 03/19/2024] [Revised: 06/16/2024] [Accepted: 07/09/2024] [Indexed: 07/30/2024]
Abstract
Effects of sodium alginate (SA) on the non-covalent interaction between soybean protein isolate (SPI) and quercetin (Que) were investigated by multispectral technology, molecular docking and dynamics simulation technology. Structural alterations of the binary complexes were observed after SA addition, characterized by a red shift of maximum fluorescence emission wavelength. The introduction of 0.1% (w/v) SA led to a reduction of 12.3% in the α-helix and β-sheet structures, accompanied by 12.6% increase in the β-turn and random coil conformations. The binding of SA to SPI provided electrostatic interactions and facilitated the subsequent binding of SPI to Que. Molecular docking confirmed that hydrophobic interactions and electrostatic interactions were also the main driving force. Molecular dynamics simulation emphasized that the ternary complexes with SA exhibited greater stability compared to the binary ones. The foaming and emulsifying properties of SPI-Que complexes were enhanced by 33.76% and 68.28%, respectively, due to the addition of SA.
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Affiliation(s)
- Taoran Li
- College of Public Health and Health Sciences, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Yubo Zhang
- College of Public Health and Health Sciences, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Juanjuan Shao
- Department of Science and Technology, Hebei Agricultural University, Hebei 061100, China
| | - Ruiyang Hou
- College of Public Health and Health Sciences, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Zifan Zhang
- College of Public Health and Health Sciences, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Chengxiang Ye
- College of Public Health and Health Sciences, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Hongwu Wang
- College of Public Health and Health Sciences, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Beibei Zhu
- College of Chinese Medicine Pharmaceutical Engineering, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Yating Zhang
- College of Public Health and Health Sciences, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China.
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Simoens L, Fijalkowski I, Van Damme P. Exposing the small protein load of bacterial life. FEMS Microbiol Rev 2023; 47:fuad063. [PMID: 38012116 PMCID: PMC10723866 DOI: 10.1093/femsre/fuad063] [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: 05/09/2023] [Revised: 11/10/2023] [Accepted: 11/24/2023] [Indexed: 11/29/2023] Open
Abstract
The ever-growing repertoire of genomic techniques continues to expand our understanding of the true diversity and richness of prokaryotic genomes. Riboproteogenomics laid the foundation for dynamic studies of previously overlooked genomic elements. Most strikingly, bacterial genomes were revealed to harbor robust repertoires of small open reading frames (sORFs) encoding a diverse and broadly expressed range of small proteins, or sORF-encoded polypeptides (SEPs). In recent years, continuous efforts led to great improvements in the annotation and characterization of such proteins, yet many challenges remain to fully comprehend the pervasive nature of small proteins and their impact on bacterial biology. In this work, we review the recent developments in the dynamic field of bacterial genome reannotation, catalog the important biological roles carried out by small proteins and identify challenges obstructing the way to full understanding of these elusive proteins.
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Affiliation(s)
- Laure Simoens
- iRIP Unit, Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, 9000 Ghent, Belgium
| | - Igor Fijalkowski
- iRIP Unit, Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, 9000 Ghent, Belgium
| | - Petra Van Damme
- iRIP Unit, Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, 9000 Ghent, Belgium
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Fermon L, Burel A, Ostyn E, Dréano S, Bondon A, Chevance S, Pinel-Marie ML. Mechanism of action of sprG1-encoded type I toxins in Staphylococcus aureus: from membrane alterations to mesosome-like structures formation and bacterial lysis. Front Microbiol 2023; 14:1275849. [PMID: 37854335 PMCID: PMC10579593 DOI: 10.3389/fmicb.2023.1275849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 09/11/2023] [Indexed: 10/20/2023] Open
Abstract
sprG1/SprF1 is a type I toxin-antitoxin system located on Staphylococcus aureus prophage. It has previously been shown that the two toxins, SprG131 and SprG144, encoded by the sprG1 gene, are two membrane-associated peptides structured in a single α-helix. Overexpression of these two peptides leads to growth inhibition and even S. aureus death. In this study, we investigated the involvement of each peptide in this toxicity, the sequence requirements necessary for SprG131 toxicity, and the mechanism of action of these two peptides. Our findings show that both peptides, when expressed individually, are able to stop growth, with higher toxicity observed for SprG131. The combination of a hydrophobic domain and a charged domain located only at the C-terminus is necessary for this toxicity, likely to retain the orientation of the transmembrane domain. A net cationic charge for SprG131 is not essential to induce a growth defect in S. aureus. Furthermore, we established a chronology of toxic events following overexpression to gain insights into the mode of action of SprG144 and SprG131. We demonstrated that mesosome-like structures are already formed when membrane is depolarized, about 20 min after peptides induction. This membrane depolarization occurs concomitantly with a depletion of intracellular ATP, leading to S. aureus growth arrest. Moreover, we hypothesized that SprG144 and SprG131 do not form large pores in the S. aureus membrane, as ATP is not excreted into the extracellular medium, and membrane permeabilization is delayed relative to membrane depolarization. The next challenge is to identify the conditions under which SprG144 and SprG131 are naturally expressed, and to uncover their potential roles during staphylococcal growth, colonization, and infection.
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Affiliation(s)
- Laurence Fermon
- Univ Rennes, INSERM, BRM – UMR_S 1230, Rennes, France
- Univ Rennes, CNRS, ISCR – UMR 6226, Rennes, France
| | - Agnès Burel
- Univ Rennes, CNRS, INSERM, BIOSIT – UAR 3480, US_S 018, Rennes, France
| | - Emeline Ostyn
- Univ Rennes, INSERM, BRM – UMR_S 1230, Rennes, France
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Frolikova M, Sur VP, Novotny I, Blazikova M, Vondrakova J, Simonik O, Ded L, Valaskova E, Koptasikova L, Benda A, Postlerova P, Horvath O, Komrskova K. Juno and CD9 protein network organization in oolemma of mouse oocyte. Front Cell Dev Biol 2023; 11:1110681. [PMID: 37635875 PMCID: PMC10450504 DOI: 10.3389/fcell.2023.1110681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 07/18/2023] [Indexed: 08/29/2023] Open
Abstract
Juno and CD9 protein, expressed in oolemma, are known to be essential for sperm-oocyte binding and fusion. Although evidence exists that these two proteins cooperate, their interaction has not yet been demonstrated. Here in, we present Juno and CD9 mutual localization over the surface of mouse metaphase II oocytes captured using the 3D STED super-resolution technique. The precise localization of examined proteins was identified in different compartments of oolemma such as the microvillar membrane, planar membrane between individual microvilli, and the membrane of microvilli-free region. Observed variance in localization of Juno and CD9 was confirmed by analysis of transmission and scanning electron microscopy images, which showed a significant difference in the presence of proteins between selected membrane compartments. Colocalization analysis of super-resolution images based on Pearson's correlation coefficient supported evidence of Juno and CD9 mutual position in the oolemma, which was identified by proximity ligation assay. Importantly, the interaction between Juno and CD9 was detected by co-immunoprecipitation and mass spectrometry in HEK293T/17 transfected cell line. For better understanding of experimental data, mouse Juno and CD9 3D structure were prepared by comparative homology modelling and several protein-protein flexible sidechain dockings were performed using the ClusPro server. The dynamic state of the proteins was studied in real-time at atomic level by molecular dynamics (MD) simulation. Docking and MD simulation predicted Juno-CD9 interactions and stability also suggesting an interactive mechanism. Using the multiscale approach, we detected close proximity of Juno and CD9 within microvillar oolemma however, not in the planar membrane or microvilli-free region. Our findings show yet unidentified Juno and CD9 interaction within the mouse oolemma protein network prior to sperm attachment. These results suggest that a Juno and CD9 interactive network could assist in primary Juno binding to sperm Izumo1 as a prerequisite to subsequent gamete membrane fusion.
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Affiliation(s)
- Michaela Frolikova
- Laboratory of Reproductive Biology, Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Vestec, Czechia
| | - Vishma Pratap Sur
- Laboratory of Reproductive Biology, Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Vestec, Czechia
| | - Ivan Novotny
- Light Microscopy Core Facility, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czechia
| | - Michaela Blazikova
- Light Microscopy Core Facility, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czechia
| | - Jana Vondrakova
- Laboratory of Reproductive Biology, Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Vestec, Czechia
| | - Ondrej Simonik
- Laboratory of Reproductive Biology, Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Vestec, Czechia
| | - Lukas Ded
- Laboratory of Reproductive Biology, Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Vestec, Czechia
| | - Eliska Valaskova
- Laboratory of Reproductive Biology, Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Vestec, Czechia
| | - Lenka Koptasikova
- Imaging Methods Core Facility at BIOCEV, Faculty of Science, Charles University, Vestec, Czechia
| | - Ales Benda
- Imaging Methods Core Facility at BIOCEV, Faculty of Science, Charles University, Vestec, Czechia
| | - Pavla Postlerova
- Laboratory of Reproductive Biology, Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Vestec, Czechia
- Department of Veterinary Sciences, Faculty of Agrobiology, Food and Natural Resources, University of Life Sciences Prague, Prague, Czechia
| | - Ondrej Horvath
- Light Microscopy Core Facility, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czechia
| | - Katerina Komrskova
- Laboratory of Reproductive Biology, Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Vestec, Czechia
- Department of Zoology, Faculty of Science, Charles University, Prague, Czechia
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Guo Y, Chen X, Yu X, Wan J, Cao X. Prediction and validation of monoclonal antibodies separation in aqueous two-phase system using molecular dynamic simulation. J Chromatogr A 2023; 1694:463921. [PMID: 36940643 DOI: 10.1016/j.chroma.2023.463921] [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: 11/19/2022] [Revised: 02/19/2023] [Accepted: 03/07/2023] [Indexed: 03/16/2023]
Abstract
In order to predict how mAbs partition in 20% ethylene oxide/80% propylene oxide (v/v) random copolymer (EO20PO80)/water aqueous two-phase system (ATPS), a molecular dynamic simulation model was developed using Gromacs and then validated by experiments. The ATPS was applied with seven kinds of salt, including buffer salt and strong dissociation salt that were commonly employed in the purification of protein. Na2SO4 was shown to have the best effects on lowering EO20PO80 content in the aqueous phase and enhancing recovery. The content of EO20PO80 in the sample solution was decreased to 0.62%±0.25% and the recovery of rituximab increased to 97.88%±0.95% by adding 300 mM Na2SO4 into back extraction ATPS. The viability determined by ELISA was 95.57% at the same time. A strategy for constructing a prediction model for the distribution of mAbs in ATPS was proposed in consideration of this finding. Partition of trastuzumab in ATPS was predicted by the model created using this method and the prediction result was further validated by experiments. The recovery of trastuzumab reached 95.63%±2.86% under the ideal extraction conditions suggested by the prediction model.
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Affiliation(s)
- Yibo Guo
- State Key Laboratory of Bioreactor Engineering, Department of Bioengineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237 China
| | - Xi Chen
- State Key Laboratory of Bioreactor Engineering, Department of Bioengineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237 China
| | - Xue Yu
- Shandong Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou, 253023, P.R. China
| | - Junfen Wan
- State Key Laboratory of Bioreactor Engineering, Department of Bioengineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237 China.
| | - Xuejun Cao
- State Key Laboratory of Bioreactor Engineering, Department of Bioengineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237 China.
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