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Matsuo T, Yamamoto S, Matsuo K. Phospholipid-induced secondary structural changes of lysozyme polymorphic amyloid fibrils studied using vacuum-ultraviolet circular dichroism. Phys Chem Chem Phys 2024; 26:18943-18952. [PMID: 38952218 DOI: 10.1039/d4cp00965g] [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: 07/03/2024]
Abstract
The hallmark of amyloidosis, such as Alzheimer's disease and Parkinson's disease, is the deposition of amyloid fibrils in various internal organs. The onset of the disease is related to the strength of cytotoxicity caused by toxic amyloid species. Furthermore, amyloid fibrils show polymorphism, where some types of fibrils are cytotoxic while others are not. It is thus essential to understand the molecular mechanism of cytotoxicity, part of which is caused by the interaction between amyloid polymorphic fibrils and cell membranes. Here, using amyloid polymorphs of hen egg white lysozyme, which is associated with hereditary systemic amyloidosis, showing different levels of cytotoxicity and liposomes of DMPC and DMPG, changes in the secondary structure of the polymorphs and the structural state of phospholipid membranes caused by the interaction were investigated using vacuum-ultraviolet circular dichroism (VUVCD) and Laurdan fluorescence measurements, respectively. Analysis has shown that the more cytotoxic polymorph increases the antiparallel β-sheet content and causes more disorder in the membrane structure while the other less cytotoxic polymorph shows the opposite structural changes and causes less structural disorder in the membrane. These results suggest a close correlation between the structural properties of amyloid fibrils and the degree of structural disorder of phospholipid membranes, both of which are involved in the fundamental process leading to amyloid cytotoxicity.
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Affiliation(s)
- Tatsuhito Matsuo
- Institute for Quantum Life Science, National Institutes for Quantum Science and Technology, 4-9-1 Anagawa, Chiba, 263-8555, Japan.
| | - Seigi Yamamoto
- Laboratory of Evolutionary Oncology, Chiba Cancer Center Research Institute, Chiba, Japan
| | - Koichi Matsuo
- Hiroshima Synchrotron Radiation Center, Hiroshima University, Hiroshima, Japan
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Lee D, Song S, Cho G, Dalle Ore LC, Malmstadt N, Fuwad A, Kim SM, Jeon TJ. Elucidating the Molecular Interactions between Lipids and Lysozyme: Evaporation Resistance and Bacterial Barriers for Dry Eye Disease. NANO LETTERS 2023; 23:9451-9460. [PMID: 37842945 DOI: 10.1021/acs.nanolett.3c02936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2023]
Abstract
Dry eye disease (DED) is a chronic condition characterized by ocular dryness and inflammation. The tear film lipid layer (TFLL) is the outermost layer composed of lipids and proteins that protect the ocular surface. However, environmental contaminants can disrupt its structure, potentially leading to DED. Although the importance of tear proteins in the TFLL functionality has been clinically recognized, the molecular mechanisms underlying TFLL-protein interactions remain unclear. In this study, we investigated tear protein-lipid interactions and analyzed their role in the TFLL functionality. The results show that lysozyme (LYZ) increases the stability of the TFLL by reducing its surface tension and increasing its surface pressure, resulting in increased TFLL evaporation and bacterial invasion resistance, with improved wettability and lubrication performance. These findings highlight the critical role of LYZ in maintaining ocular health and provide potential avenues for investigating novel approaches to DED treatment and patient well-being.
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Affiliation(s)
- Deborah Lee
- Department of Biological Sciences and Bioengineering, Inha University, 100 Inha-ro, Michuhol-gu, Incheon 22212, Republic of Korea
- Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California 90089, United States
| | - Seoyoon Song
- Department of Biological Sciences and Bioengineering, Inha University, 100 Inha-ro, Michuhol-gu, Incheon 22212, Republic of Korea
- Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California 90089, United States
| | - Geonho Cho
- Department of Biological Sciences and Bioengineering, Inha University, 100 Inha-ro, Michuhol-gu, Incheon 22212, Republic of Korea
| | - Lucia C Dalle Ore
- Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California 90089, United States
| | - Noah Malmstadt
- Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California 90089, United States
| | - Ahmed Fuwad
- Department of Mechanical Engineering, Inha University, 100 Inha-ro, Michuhol-gu, Incheon 22212, Republic of Korea
| | - Sun Min Kim
- Department of Biological Sciences and Bioengineering, Inha University, 100 Inha-ro, Michuhol-gu, Incheon 22212, Republic of Korea
- Department of Mechanical Engineering, Inha University, 100 Inha-ro, Michuhol-gu, Incheon 22212, Republic of Korea
| | - Tae-Joon Jeon
- Department of Biological Sciences and Bioengineering, Inha University, 100 Inha-ro, Michuhol-gu, Incheon 22212, Republic of Korea
- Department of Biological Engineering, Inha University, 100 Inha-ro, Michuhol-gu, Incheon 22212, Republic of Korea
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Islam S, Mukhopadhyay C. Aggregation of Lysozyme in the Presence of a Mixed Bilayer of POPC and POPG. ACS OMEGA 2021; 6:17861-17869. [PMID: 34308021 PMCID: PMC8295997 DOI: 10.1021/acsomega.1c01145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 06/30/2021] [Indexed: 05/04/2023]
Abstract
Understanding the molecular mechanisms by which amyloidogenic proteins interact with membranes is a challenging task. Amyloid accumulates from many human diseases have been observed to contain membrane lipids. In this work, coarse-grained molecular dynamics simulations have been used to inspect hen egg white lysozyme (HEWL) aggregation and membrane association in the presence of a pure POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) bilayer and a POPC and POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylglycerol) mixed bilayer. It was observed that, in both cases, two HEWLs formed aggregates. In the presence of a mixed bilayer, after aggregation, the aggregated system started to interact with the membrane. It has been found that one of the lysozymes which came closer to the mixed bilayer unfolded more. The process of the initial insertion of an aggregated system in the mixed bilayer has been analyzed. The structural rearrangements of the protein and lipids were analyzed as well along the course of the simulation. Although with a pure POPC bilayer, aggregation was observed, the aggregated system moved away from the membrane. We believe that our study will provide considerable insights into lysozyme aggregation in the presence of a membrane environment.
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Affiliation(s)
- Shahee Islam
- Department of Chemistry, University
of Calcutta, 92, A. P. C. Road, Kolkata 700009, India
| | - Chaitali Mukhopadhyay
- Department of Chemistry, University
of Calcutta, 92, A. P. C. Road, Kolkata 700009, India
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Duran T, Minatovicz B, Bai J, Shin D, Mohammadiarani H, Chaudhuri B. Molecular Dynamics Simulation to Uncover the Mechanisms of Protein Instability During Freezing. J Pharm Sci 2021; 110:2457-2471. [PMID: 33421436 DOI: 10.1016/j.xphs.2021.01.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 12/07/2020] [Accepted: 01/03/2021] [Indexed: 11/19/2022]
Abstract
Freezing is a common process applied in the pharmaceutical industry to store and transport biotherapeutics. Herewith, multi-scale molecular dynamics simulations of Lactate dehydrogenase (LDH) protein in phosphate buffer with/without ice formation performed to uncover the still poorly understood mechanisms and molecular details of protein destabilization upon freezing. Both fast and slow ice growing conditions were simulated at 243 K from one or two-side of the simulation box, respectively. The rate of ice formation at all-atom simulations was crucial to LDH stability, as faster freezing rates resulted in enhanced structural stability maintained by a higher number of intramolecular hydrogen bonds, less flexible protein's residues, lower solvent accessibility and greater structural compactness. Further, protein aggregation investigated by coarse-grained simulations was verified to be initiated by extended protein structures and retained by electrostatic interactions of the salt bridges between charged residues and hydrogen bonds between polar residues of the protein. Lastly, the study of free energy of dissociation through steered molecular dynamics simulation revealed LDH was destabilized by the solvation of the hydrophobic core and the loss of hydrophobic interactions. For the first time, experimentally validated molecular simulations revealed the detailed mechanisms of LDH destabilization upon ice formation and cryoconcentration of solutes.
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Affiliation(s)
- Tibo Duran
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, CT, 06269, USA
| | - Bruna Minatovicz
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, CT, 06269, USA
| | - Jun Bai
- Department of Computer Sciences and Engineering, University of Connecticut, Storrs, CT, 06269, USA
| | - Dongkwan Shin
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, CT, 06269, USA
| | - Hossein Mohammadiarani
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, CT, 06269, USA
| | - Bodhisattwa Chaudhuri
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, CT, 06269, USA; Institute of Material Sciences (IMS), University of Connecticut, Storrs, CT, USA; Department of Chemical & Biomolecular Engineering, University of Connecticut, Storrs, CT 06269, USA.
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Hashemzadeh H, Javadi H, Darvishi MH. Study of Structural stability and formation mechanisms in DSPC and DPSM liposomes: A coarse-grained molecular dynamics simulation. Sci Rep 2020; 10:1837. [PMID: 32020000 PMCID: PMC7000798 DOI: 10.1038/s41598-020-58730-z] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 01/19/2020] [Indexed: 01/09/2023] Open
Abstract
Liposomes or biological vesicles can be created from cholesterol, phospholipid, and water. Their stability is affected by their phospholipid composition which can influence disease treatment and drug delivery efficacy. In this study, the effect of phospholipid type on the formation and stability of liposomes using coarse-grained molecular dynamics simulations is investigated. For this purpose, the simulation study of the DSPC (1,2-distearoyl-sn-glycero-3-phosphocholine) and DPSM (Egg sphingomyelin) lipids were considered. All simulations were carried out using the Gromacs software and Martini force field 2.2. Energy minimization (3000 steps) model, equilibrium at constant volume to adjust the temperature at 400 Kelvin and equilibrium at constant pressure to adjust the pressure, at atmospheric pressure (1 bar) have been validated. Microsecond simulations, as well as formation analysis including density, radial distribution function, and solvent accessible surface area, demonstrated spherical nanodisc structures for the DPSM and DSPC liposomes. The results revealed that due to the cylindrical geometric structure and small-size head group, the DSPC lipid maintained its perfectly spherical structure. However, the DPSM lipid showed a conical geometric structure with larger head group than other lipids, which allows the liposome to form a micelle structure. Although the DSPC and DPSM lipids used in the laboratory tests exhibit liposome and micelle behaviors, the simulation results revealed their nanodisc structures. Energy analysis including overall energy, Van der Waals interaction energy, and electrostatic interaction energy showed that DPSM liposome is more stable than DSPC liposome.
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Affiliation(s)
- H Hashemzadeh
- Nanobiotechnology Department, Faculty of Bioscience, Tarbiat Modares University, Tehran, Iran
| | - H Javadi
- Nanobiotechnology Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - M H Darvishi
- Nanobiotechnology Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran.
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Ji M, Ding Y, Li X, Mao N, Chen J. Computational investigation of a ternary model of SnoN-SMAD3-SMAD4 complex. Comput Biol Chem 2019; 83:107159. [PMID: 31743832 DOI: 10.1016/j.compbiolchem.2019.107159] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 10/28/2019] [Accepted: 11/03/2019] [Indexed: 12/18/2022]
Abstract
The transforming growth factor β (TGFβ) plays an essential role in the regulation of cellular processes such as cell proliferation, migration, differentiation, and apoptosis by association with SMAD transcriptional factors that are regulated by the transcriptional regulator SnoN. The crystal structure of SnoN-SMAD4 reveals that SnoN can adopt two binding modes, the open and closed forms, at the interfaces of SMAD4 subunits. Accumulating evidence indicates that SnoN can interact with both SMAD3 and SMAD4 to form a ternary SnoN-SMAD3-SMAD4 complex in the TGFβ signaling pathway. However, how the interaction of SnoN with the SMAD3 and SMAD4 remains unclear. Here, molecular dynamics (MD) simulations and molecular modeling methods were performed to figure out this issue. The simulations reveal that SnoNopen exists in two, open and semi-closed, conformations. Molecular modeling and MD simulation studies suggest that the SnoNclosed form interferes with the SMAD3-SMAD4 protein; in contract, the SnoNopen can form a stable SnoN-SMAD3-SMAD4 complex. These mechanistic mechanisms may help elucidate the detailed engagement of SnoN with two SMAD3 and SMAD4 transcriptional factors in the regulation of TGFβ signaling pathway.
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Affiliation(s)
- Mingfei Ji
- Department of Urology, Changzheng Hospital, Naval Military Medical University, Shanghai, 200003, China
| | - Yelei Ding
- Department of Urology, Changzheng Hospital, Naval Military Medical University, Shanghai, 200003, China
| | - Xiaolong Li
- Department of Orthopedics, Changhai Hospital, Naval Military Medical University, Shanghai, 200433, China.
| | - Ningfang Mao
- Department of Orthopedics, Changhai Hospital, Naval Military Medical University, Shanghai, 200433, China.
| | - Jie Chen
- Department of Urology, Changzheng Hospital, Naval Military Medical University, Shanghai, 200003, China.
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Lopes NA, Barreto Pinilla CM, Brandelli A. Antimicrobial activity of lysozyme-nisin co-encapsulated in liposomes coated with polysaccharides. Food Hydrocoll 2019. [DOI: 10.1016/j.foodhyd.2019.02.009] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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9
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Pandey P, Meena NK, Prakash A, Kumar V, Lynn AM, Ahmad F. Characterization of heterogeneous intermediate ensembles on the guanidinium chloride-induced unfolding pathway of β-lactoglobulin. J Biomol Struct Dyn 2019; 38:1042-1053. [PMID: 30880641 DOI: 10.1080/07391102.2019.1593245] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Folding pathway of β-LgA (β-lactoglobulin) evolves through the conformational α→β transition. The α→β transition is a molecular hallmark of various neurodegenerative diseases. Thus, β-LgA may serve as a good model for understanding molecular mechanism of protein aggregation involved in neurodegenerative diseases. Here, we studied the conformational dynamics of β-LgA in 6 M GdmCl at different temperatures using MD simulations. Structural order parameters such as RMSD, Rg, SASA, native contacts (Q), hydrophobic distal-matrix and free-energy landscape (FEL) were used to investigate the conformational transitions. Our results show that GdmCl destabilizes secondary and tertiary structure of β-LgA by weakening the hydrophobic interactions and hydrogen bond network. Multidimensional FEL shows the presence of different unfolding intermediates at 400 K. I1 is long-lived intermediate which has mostly intact native secondary structure, but loose tertiary structure. I2 is structurally compact intermediate formed after the partial loss of secondary structure. The transiently and infrequently buried evolution of W19 shows that intermediate conformational ensembles are structurally heterogeneous. We observed that the intermediate conformations are largely stabilized by non-native H-bonds. The outcome of this work provides the molecular details of intermediates trapped due to non-native interactions that may be regarded as pathogenic conformations involved in neurodegenerative diseases.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Preeti Pandey
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Naveen Kumar Meena
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Amresh Prakash
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Vijay Kumar
- Amity Institute of Neuropsychology & Neurosciences, Amity University, Noida, India
| | - Andrew M Lynn
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Faizan Ahmad
- Jamia Millia Islamia, Centre for Interdisciplinary Research in Basic Sciences, New Delhi, India
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Trusova VM, Gorbenko GP. Membrane interactions of fibrillar lysozyme: Effect of lipid bilayer composition. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2018.10.103] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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Sodeifian G, Razmimanesh F. Diffusional interaction behavior of NSAIDs in lipid bilayer membrane using molecular dynamics (MD) simulation: Aspirin and Ibuprofen. J Biomol Struct Dyn 2018; 37:1666-1684. [PMID: 29695194 DOI: 10.1080/07391102.2018.1464956] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
In this research, for the first time, molecular dynamics (MD) method was used to simulate aspirin and ibuprofen at various concentrations and in neutral and charged states. Effects of the concentration (dosage), charge state, and existence of an integral protein in the membrane on the diffusion rate of drug molecules into lipid bilayer membrane were investigated on 11 systems, for which the parameters indicating diffusion rate and those affecting the rate were evaluated. Considering the diffusion rate, a suitable score was assigned to each system, based on which, analysis of variance (ANOVA) was performed. By calculating the effect size of the indicative parameters and total scores, an optimum system with the highest diffusion rate was determined. Consequently, diffusion rate controlling parameters were obtained: the drug-water hydrogen bond in protein-free systems and protein-drug hydrogen bond in the systems containing protein.
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Affiliation(s)
- Gholamhossein Sodeifian
- a Faculty of Engineering, Department of Chemical Engineering, Modeling and Simulation Centre , University of Kashan , Kashan 87317-53153 , Iran
| | - Fariba Razmimanesh
- a Faculty of Engineering, Department of Chemical Engineering, Modeling and Simulation Centre , University of Kashan , Kashan 87317-53153 , Iran
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