1
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Mallick S, Agmon N. Lateral diffusion of ions near membrane surface. Phys Chem Chem Phys 2024; 26:19433-19449. [PMID: 38973628 DOI: 10.1039/d3cp04112c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/09/2024]
Abstract
Biological membranes isolate living cells from their environment, while allowing selective molecular transport between the inner and outer realms. For example, Na+ and K+ permeability through ionic channels contributes to neural conduction. Whether the ionic currents arise directly from cations in the bulk, or from the interface, is currently unclear. There are only scant results concerning lateral diffusion of ions on aquated membrane surfaces (and strong belief that this occurs through binding to a diffusing lipid). We performed classical molecular dynamics (MD) simulations of monovalent ions, Na+, K+, and Cl-, near the surface of the zwitterionic palmitoyl-oleoyl-phosphatidylcholine (POPC) membrane. Realistic force-fields for lipids (Amber's Lipid17 and Lipid21) and water (TIP4P-Ew) are tested for the mass and charge densities and the electrostatic potential across the membrane. These calculations reveal that the chloride can bind to the choline moiety through an intervening water molecule by forming a CH⋯OH hydrogen bond, while cations bind to both the phosphatic and carbonyl oxygens of phosphatidylcholine moieties. Upon transitioning from the bulk to the interface, a cation sheds some of its hydration water, which are replaced by headgroup atoms. Notably, an interfacial cation can bind 1-4 headgroup atoms, which is a key to understanding its surface hopping mechanism. We find that cation binding to three headgroup atoms immobilizes it, while binding to four energizes it. Consequently, the lateral cation diffusion rate is only 15-25 times slower than in the bulk, and 4-5 times faster than lipid self-diffusion. K+ diffusion is notably more anomalous than Na+, switching from sub- to super-diffusion after about 2 ns.
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Affiliation(s)
- Subhasish Mallick
- The Fritz Haber Research Center, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel.
| | - Noam Agmon
- The Fritz Haber Research Center, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel.
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2
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Tamucci JD, Alder NN, May ER. Peptide Power: Mechanistic Insights into the Effect of Mitochondria-Targeted Tetrapeptides on Membrane Electrostatics from Molecular Simulations. Mol Pharm 2023; 20:6114-6129. [PMID: 37904323 PMCID: PMC10841697 DOI: 10.1021/acs.molpharmaceut.3c00480] [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] [Indexed: 11/01/2023]
Abstract
Mitochondrial dysfunction is implicated in nine of the ten leading causes of death in the US, yet there are no FDA-approved therapeutics to treat it. Synthetic mitochondria-targeted peptides (MTPs), including the lead compound SS-31, offer promise, as they have been shown to restore healthy mitochondrial function and treat a variety of common diseases. At the cellular level, research has shown that MTPs accumulate strongly at the inner mitochondrial membrane (IMM), slow energy sinks (e.g., proton leaks), and improve ATP production. Modulation of electrostatic fields around the IMM has been implicated as a key aspect in the mechanism of action (MoA) of these peptides; however, molecular and mechanistic details have remained elusive. In this study, we employed all-atom molecular dynamics simulations (MD) to investigate the interactions of four MTPs with lipid bilayers and calculate their effect on structural and electrostatic properties. In agreement with previous experimental findings, we observed the modulation of the membrane surface and dipole potentials by MTPs. The simulations reveal that the MTPs achieve a reduction in the dipole potential by acting to disorder both lipid head groups and water layers proximal to the bilayer surface. We also find that MTPs decrease the bilayer thickness and increase the membrane's capacitance. These changes suggest that MTPs may enhance how much potential energy can be stored across the IMM at a given transmembrane potential difference. The MTPs also displace cations away from the bilayer surface, modulating the surface potential and offering an alternative mechanism for how these MTPs reduce mitochondrial energy sinks like proton leaks and mitigate Ca2+ accumulation stress. In conclusion, this study highlights the therapeutic potential of MTPs and underlines how interactions of MTPs with lipid bilayers serve as a fundamental component of their MoA.
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Affiliation(s)
- Jeffrey D Tamucci
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Nathan N Alder
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Eric R May
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut 06269, United States
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3
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Biriukov D, Javanainen M. Efficient Simulations of Solvent Asymmetry Across Lipid Membranes Using Flat-Bottom Restraints. J Chem Theory Comput 2023; 19:6332-6341. [PMID: 37651714 PMCID: PMC10537000 DOI: 10.1021/acs.jctc.3c00614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Indexed: 09/02/2023]
Abstract
The routinely employed periodic boundary conditions complicate molecular simulations of physiologically relevant asymmetric lipid membranes together with their distinct solvent environments. Therefore, separating the extracellular fluid from its cytosolic counterpart has often been performed using a costly double-bilayer setup. Here, we demonstrate that the lipid membrane and solvent asymmetry can be efficiently modeled with a single lipid bilayer by applying an inverted flat-bottom potential to ions and other solute molecules, thereby restraining them to only interact with the relevant leaflet. We carefully optimized the parameters of the suggested method so that the results obtained using the flat-bottom and double-bilayer approaches become mutually indistinguishable. Then, we apply the flat-bottom approach to lipid bilayers with various compositions and solvent environments, covering ions and cationic peptides to validate the approach in a realistic use case. We also discuss the possible limitations of the method as well as its computational efficiency and provide a step-by-step guide on how to set up such simulations in a straightforward manner.
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Affiliation(s)
- Denys Biriukov
- Institute
of Organic Chemistry and Biochemistry, Academy of Sciences of the
Czech Republic, Flemingovo
nam. 2, Prague 6 CZ-16610, Czech Republic
- Central
European Institute of Technology, Masaryk
University, Kamenice
5, Brno CZ-62500, Czech Republic
| | - Matti Javanainen
- Institute
of Organic Chemistry and Biochemistry, Academy of Sciences of the
Czech Republic, Flemingovo
nam. 2, Prague 6 CZ-16610, Czech Republic
- Institute
of Biotechnology, University of Helsinki, Helsinki FI-00790, Finland
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4
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Banerjee KK, Maity P, Das S, Karmakar S. Effect of cholesterol on the ion-membrane interaction: Zeta potential and dynamic light scattering study. Chem Phys Lipids 2023; 254:105307. [PMID: 37182823 DOI: 10.1016/j.chemphyslip.2023.105307] [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: 03/30/2023] [Accepted: 05/11/2023] [Indexed: 05/16/2023]
Abstract
Cholesterol in a bio-membrane plays a significant role in many cellular event and is known to regulate the functional activity of protein and ion channel. In this study we report a significant effect of cholesterol on the ion-membrane interaction. We prepare large unilamellar vesicles, composed of zwitterionic lipid DOPC and anionic lipid DOPG with different cholesterol concentration. Electrostatics of anionic membranes containing cholesterol in the presence of NaCl has systematically been explored using dynamic light scattering and zeta potential. Negative zeta potential of the membrane decreases its negative value with increasing ion concentration for all cholesterol concentrations. However, zeta potential itself decreases with increasing cholesterol content even in the absence of monovalent ions. Electrostatic behaviour of the membrane is determined from well-known Gouy Chapmann model. Negative surface charge density of the membrane decreases with increasing cholesterol content. Binding constant, estimated from the electrostatic double layer theory, is found to increase significantly in the presence of cholesterol. Comparison of electrostatic parameters of the membrane in the presence and absence of cholesterol suggests that cholesterol significantly alter the electrostatic behaviour of the membrane.
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Affiliation(s)
- Kalyan Kumar Banerjee
- Soft matter and Biophysics Laboratory, Department of Physics, Jadavpur University, 188, Raja S. C. Mallick Road, Kolkata 700032, India
| | - Pabitra Maity
- Soft matter and Biophysics Laboratory, Department of Physics, Jadavpur University, 188, Raja S. C. Mallick Road, Kolkata 700032, India
| | - Surajit Das
- Soft matter and Biophysics Laboratory, Department of Physics, Jadavpur University, 188, Raja S. C. Mallick Road, Kolkata 700032, India
| | - Sanat Karmakar
- Soft matter and Biophysics Laboratory, Department of Physics, Jadavpur University, 188, Raja S. C. Mallick Road, Kolkata 700032, India.
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5
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Giladi M, Mitra S, Simhaev L, Hiller R, Refaeli B, Strauss T, Baiz CR, Khananshvili D. Exploring the Li + transporting mutant of NCX_Mj for assigning ion binding sites of mitochondrial NCLX. Cell Calcium 2022; 107:102651. [PMID: 36116246 PMCID: PMC10124574 DOI: 10.1016/j.ceca.2022.102651] [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: 07/06/2022] [Revised: 08/14/2022] [Accepted: 09/01/2022] [Indexed: 11/02/2022]
Abstract
The plasma membrane (NCX) and mitochondrial (NCLX) Na+/Ca2+ exchangers are structurally related proteins, although they operate under strictly different ionic conditions and membrane potentials. In contrast with NCX, NCLX can transport either Li+ or Na+ in exchange for Ca2+. Whereas the crystal structure of the archaeal NCX (NCX_Mj) describes the binding sites for alternative binding of 3Na+ or 1Ca2+, these features remain elusive for NCLX due to the lack of structural information. To elucidate the ion-binding features of mitochondrial NCLX, we analyzed here the Li+-transporting NCLX_Mj mutant, produced by replacing the ion-coordinating residues in the archaeal NCX (NCX_Mj) to match the ion-coordinating residues of human NCLX. The NCLX_Mj-mediated Na+/Ca2+ or Li+/Ca2+ exchange rates are insensitive to varying voltage, consistent with an electroneutral ion exchange. Molecular dynamics (MD) simulations revealed that NCLX_Mj contains two novel Li+ binding sites with four ion-coordinating residues, derived from the three Na+ binding sites of NCX_Mj. The ion-coordination modes, observed in the MD simulations, were further supported by two-dimensional infrared (2D IR) spectroscopy and by testing the mutational effects on the ion fluxes. Collectively, our results revealed a structural basis for Li+ binding and electroneutral transport (2Na+/Li+:1Ca2+) by NCLX_Mj, meaning that the NCLX-mediated electroneutral transport may predefine mitochondrial Ca2+ and Na+ signaling to modulate cellular functions.
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Affiliation(s)
- Moshe Giladi
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv 69978, Israel; Tel-Aviv Sourasky Medical Center, Tel Aviv 6423906, Israel
| | - Sunayana Mitra
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712-1224, USA
| | - Luba Simhaev
- Computer-Assisted Drug Design Unit, Blavatnik Center for Drug Discovery, Tel-Aviv University, Tel Aviv 69978, Israel
| | - Reuben Hiller
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv 69978, Israel
| | - Bosmat Refaeli
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv 69978, Israel
| | - Tali Strauss
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv 69978, Israel
| | - Carlos R Baiz
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712-1224, USA.
| | - Daniel Khananshvili
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv 69978, Israel.
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Laudadio E, Minnelli C, Mobbili G, Sabbatini G, Stipa P, Rusciano D, Galeazzi R. Salt effects on mixed composition membranes containing an antioxidant lipophilic edaravone derivative: a computational-experimental study. Org Biomol Chem 2022; 20:5784-5795. [PMID: 35822625 DOI: 10.1039/d2ob01143c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The protection of lipid membranes against oxidation avoids diseases associated with oxidative stress. As a strategy to contrast it, functionalized lipids with antioxidant activity are used to become part of membranes thus protecting them. For this purpose, a lipophilic edaravone derivative has been synthesized, adding a C18 saturated chain to the original structure. The antioxidant activity of C18-Edv has been demonstrated in our previous work. In this study, molecular dynamics simulations have been performed to define the effects of NaCl, MgCl2, KCl, and CaCl2 salts on a palmitoyl-oleoyl-sn-glycero-phosphocholine (POPC) lipid bilayer encapsulating C18-Edv. The results showed how different salts influence POPC lateral diffusion, and the movements of C18-Edv heads, which are antioxidant moieties, were correlated to the ability of C18-Edv molecules to protect membranes. MgCl2 showed a negative impact leading to C18-Edv clusterization and membrane stretching, while KCl and NaCl showed a moderate influence on the mixed lipid membrane structure. CaCl2 increased the exposure of the C18-Edv heads to the lipid-water interface, resulting in the salt with a higher propensity to guarantee protection against radicals in the aqueous phase. Finally, C18-Edv-POPC liposomes have been prepared following the simulation conditions, and then an experimental Oxygen Radical Absorbance Capacity (ORAC) assay has been performed to confirm the in silico predicted results.
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Affiliation(s)
- Emiliano Laudadio
- Department SIMAU, Università Politecnica delle Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - Cristina Minnelli
- Department DISVA, Università Politecnica delle Marche, Via Brecce Bianche, 60131 Ancona, Italy.
| | - Giovanna Mobbili
- Department DISVA, Università Politecnica delle Marche, Via Brecce Bianche, 60131 Ancona, Italy.
| | - Giulia Sabbatini
- Department DISVA, Università Politecnica delle Marche, Via Brecce Bianche, 60131 Ancona, Italy.
| | - Pierluigi Stipa
- Department SIMAU, Università Politecnica delle Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - Dario Rusciano
- Research Center, Sooft Italia SpA, 95100, Catania, Italy
| | - Roberta Galeazzi
- Department DISVA, Università Politecnica delle Marche, Via Brecce Bianche, 60131 Ancona, Italy.
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7
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Molecular and structural basis of interactions of vitamin D3 hydroxyderivatives with aryl hydrocarbon receptor (AhR): An integrated experimental and computational study. Int J Biol Macromol 2022; 209:1111-1123. [PMID: 35421413 DOI: 10.1016/j.ijbiomac.2022.04.048] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 03/10/2022] [Accepted: 04/06/2022] [Indexed: 12/12/2022]
Abstract
To better understand the molecular and structural basis underlying the interaction of vitamin D3 hydroxyderivatives with AhR, molecular simulation was used to probe the binding of 1,20(OH)2D3, 1,25(OH)2D3, 20,23(OH)2D3 and 20(OH)D3 to AhR. qPCR showed that vitamin D3 derivatives stimulate expression of cyp1A1 and cyp1B1 genes that are downstream targets of AhR signaling. These secosteroids stimulated the translocation of the AhR to the nucleus, as measured by flow cytometry and western blotting. Molecular dynamics simulations were used to model the binding of vitamin D3 derivatives to AhR to examine their influence on the structure, conformation and dynamics of the AhR ligand binding domain (LBD). Binding thermodynamics, conformation, secondary structure, dynamical motion and electrostatic potential of AhR were analyzed. The molecular docking scores and binding free energy were all favorable for the binding of D3 derivatives to the AhR. These established ligands and the D3 derivatives are predicted to have different patterns of hydrogen bond formation with the AhR, and varied residue conformational fluctuations and dynamical motion for the LBD. These changes could alter the shape, size and electrostatic potential distribution of the ligand binding pocket, contributing to the different binding affinities of AhR for the natural ligands and D3 derivatives.
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8
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Song Y, Qayyum S, Greer RA, Slominski RM, Raman C, Slominski AT, Song Y. Vitamin D3 and its hydroxyderivatives as promising drugs against COVID-19: a computational study. J Biomol Struct Dyn 2022; 40:11594-11610. [PMID: 34415218 PMCID: PMC8858339 DOI: 10.1080/07391102.2021.1964601] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The epidemiologic correlation between the poor prognosis of SARS-CoV-2 infection and vitamin D deficiency has been observed worldwide, however, their molecular mechanisms are not fully understood. In this study, we used combined molecular docking, molecular dynamics simulations and binding free energy analyses to investigate the potentials of vitamin D3 and its hydroxyderivatives as TMPRSS2 inhibitor and to inhibit the SARS-CoV-2 receptor binding domain (RBD) binding to angiotensin-converting enzyme 2 (ACE2), as well as to unveil molecular and structural basis of 1,25(OH)2D3 capability to inhibit ACE2 and SARS-CoV-2 RBD interactions. The results show that vitamin D3 and its hydroxyderivatives are favorable to bind active site of TMPRSS2 and the binding site(s) between ACE2 and SARS-CoV2-RBD, which indicate that vitamin D3 and its biologically active hydroxyderivatives can serve as TMPRSS2 inhibitor and can inhibit ACE2 binding of SARS-CoV-2 RBD to prevent SARS-CoV-2 entry. Interaction of 1,25(OH)2D3 with SARS-CoV-2 RBD and ACE2 resulted in the conformation and dynamical motion changes of the binding surfaces between SARS-CoV-2 RBD and ACE2 to interrupt the binding of SARS-CoV-2 RBD with ACE2. The interaction of 1,25(OH)2D3 with TMPRSS2 also caused the conformational and dynamical motion changes of TMPRSS2, which could affect TMPRSS2 to prime SARS-CoV-2 spike proteins. Our results propose that vitamin D3 and its biologically active hydroxyderivatives are promising drugs or adjuvants in the treatment of COVID-19. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Yuwei Song
- Department of Dermatology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Shariq Qayyum
- Department of Dermatology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Rory A. Greer
- Department of Biomedical Engineering, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Radomir M. Slominski
- Department of Dermatology, University of Alabama at Birmingham, Birmingham, AL, USA,Department of Medicine and Microbiology, Division of Clinical Immunology and Rheumatology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Chander Raman
- Department of Dermatology, University of Alabama at Birmingham, Birmingham, AL, USA,Department of Medicine and Microbiology, Division of Clinical Immunology and Rheumatology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Andrzej T. Slominski
- Department of Dermatology, University of Alabama at Birmingham, Birmingham, AL, USA,Comprehensive Cancer Center, Cancer Chemoprevention Program, University of Alabama at Birmingham, Birmingham, AL, USA,Pathology and Laboratory Medicine Service, VA Medical Center, Birmingham, AL, USA
| | - Yuhua Song
- Department of Biomedical Engineering, University of Alabama at Birmingham, Birmingham, AL, USA
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9
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Lin X, Gorfe AA. Transmembrane potential of physiologically relevant model membranes: Effects of membrane asymmetry. J Chem Phys 2021; 153:105103. [PMID: 32933265 DOI: 10.1063/5.0018303] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Transmembrane potential difference (Vm) plays important roles in regulating various biological processes. At the macro level, Vm can be experimentally measured or calculated using the Nernst or Goldman-Hodgkin-Katz equation. However, the atomic details responsible for its generation and impact on protein and lipid dynamics still need to be further elucidated. In this work, we performed a series of all-atom molecular dynamics (MD) simulations of symmetric model membranes of various lipid compositions and cation contents to evaluate the relationship between membrane asymmetry and Vm. Specifically, we studied the impact of the asymmetric distribution of POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-l-serine), PIP2 (phosphatidylinositol 4,5-bisphosphate), as well as Na+ and K+ on Vm using atomically detailed MD simulations of symmetric model membranes. The results suggest that, for an asymmetric POPC-POPC/POPS bilayer in the presence of NaCl, the presence of the monovalent anionic lipid POPS in the inner leaflet polarizes the membrane (ΔVm < 0). Intriguingly, replacing a third of the POPS lipids by the polyvalent anionic signaling lipid PIP2 counteracts this effect, resulting in a smaller negative membrane potential. We also found that replacing Na+ ions in the inner region by K+ depolarizes the membrane (ΔVm > 0). These divergent effects arise from variations in the strength of cation-lipid interactions and are correlated with changes in lipid chain order and head-group orientation.
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Affiliation(s)
- Xubo Lin
- Institute of Single Cell Engineering, Beijing Advanced Innovation Center for Biomedical Engineering, Beihang University, Beijing 100191, China
| | - Alemayehu A Gorfe
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, Texas 77030, USA
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10
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Slominski AT, Kim TK, Qayyum S, Song Y, Janjetovic Z, Oak ASW, Slominski RM, Raman C, Stefan J, Mier-Aguilar CA, Atigadda V, Crossman DK, Golub A, Bilokin Y, Tang EKY, Chen JY, Tuckey RC, Jetten AM, Song Y. Vitamin D and lumisterol derivatives can act on liver X receptors (LXRs). Sci Rep 2021; 11:8002. [PMID: 33850196 PMCID: PMC8044163 DOI: 10.1038/s41598-021-87061-w] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 03/16/2021] [Indexed: 12/11/2022] Open
Abstract
The interactions of derivatives of lumisterol (L3) and vitamin D3 (D3) with liver X receptors (LXRs) were investigated. Molecular docking using crystal structures of the ligand binding domains (LBDs) of LXRα and β revealed high docking scores for L3 and D3 hydroxymetabolites, similar to those of the natural ligands, predicting good binding to the receptor. RNA sequencing of murine dermal fibroblasts stimulated with D3-hydroxyderivatives revealed LXR as the second nuclear receptor pathway for several D3-hydroxyderivatives, including 1,25(OH)2D3. This was validated by their induction of genes downstream of LXR. L3 and D3-derivatives activated an LXR-response element (LXRE)-driven reporter in CHO cells and human keratinocytes, and by enhanced expression of LXR target genes. L3 and D3 derivatives showed high affinity binding to the LBD of the LXRα and β in LanthaScreen TR-FRET LXRα and β coactivator assays. The majority of metabolites functioned as LXRα/β agonists; however, 1,20,25(OH)3D3, 1,25(OH)2D3, 1,20(OH)2D3 and 25(OH)D3 acted as inverse agonists of LXRα, but as agonists of LXRβ. Molecular dynamics simulations for the selected compounds, including 1,25(OH)2D3, 1,20(OH)2D3, 25(OH)D3, 20(OH)D3, 20(OH)L3 and 20,22(OH)2L3, showed different but overlapping interactions with LXRs. Identification of D3 and L3 derivatives as ligands for LXRs suggests a new mechanism of action for these compounds.
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Affiliation(s)
- Andrzej T Slominski
- Department of Dermatology, University of Alabama at Birmingham, 1670 University Blvd, Rm 476, Birmingham, AL, 35249, USA.
- Comprehensive Cancer Center, Cancer Chemoprevention Program, University of Alabama at Birmingham, Birmingham, AL, 35249, USA.
- Pathology and Laboratory Medicine Service, VA Medical Center, Birmingham, AL, 35249, USA.
| | - Tae-Kang Kim
- Department of Dermatology, University of Alabama at Birmingham, 1670 University Blvd, Rm 476, Birmingham, AL, 35249, USA
| | - Shariq Qayyum
- Department of Dermatology, University of Alabama at Birmingham, 1670 University Blvd, Rm 476, Birmingham, AL, 35249, USA
| | - Yuwei Song
- Department of Dermatology, University of Alabama at Birmingham, 1670 University Blvd, Rm 476, Birmingham, AL, 35249, USA
| | - Zorica Janjetovic
- Department of Dermatology, University of Alabama at Birmingham, 1670 University Blvd, Rm 476, Birmingham, AL, 35249, USA
| | - Allen S W Oak
- Department of Dermatology, University of Alabama at Birmingham, 1670 University Blvd, Rm 476, Birmingham, AL, 35249, USA
| | - Radomir M Slominski
- Department of Dermatology, University of Alabama at Birmingham, 1670 University Blvd, Rm 476, Birmingham, AL, 35249, USA
| | - Chander Raman
- Department of Dermatology, University of Alabama at Birmingham, 1670 University Blvd, Rm 476, Birmingham, AL, 35249, USA
| | - Joanna Stefan
- Department of Dermatology, University of Alabama at Birmingham, 1670 University Blvd, Rm 476, Birmingham, AL, 35249, USA
- Department of Oncology, Nicolaus Copernicus University Medical College, Romanowskiej str. 2, 85-796, Bydgoszcz, Poland
| | - Carlos A Mier-Aguilar
- Department of Dermatology, University of Alabama at Birmingham, 1670 University Blvd, Rm 476, Birmingham, AL, 35249, USA
| | - Venkatram Atigadda
- Department of Dermatology, University of Alabama at Birmingham, 1670 University Blvd, Rm 476, Birmingham, AL, 35249, USA
- Department of Chemistry, University of Alabama at Birmingham, Birmingham, AL, 35249, USA
| | - David K Crossman
- Department of Genetics, Genomics Core Facility, University of Alabama at Birmingham, Birmingham, AL, 35249, USA
| | | | | | - Edith K Y Tang
- School of Molecular Sciences, The University of Western Australia, Perth, WA, Australia
| | - Jake Y Chen
- Informatics Institute, University of Alabama at Birmingham, Birmingham, AL, 35249, USA
| | - Robert C Tuckey
- School of Molecular Sciences, The University of Western Australia, Perth, WA, Australia
| | - Anton M Jetten
- Cell Biology Section, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA
| | - Yuhua Song
- Department of Biomedical Engineering, University of Alabama at Birmingham, Shelby 803, Birmingham, AL, 35249, USA.
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11
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Božič A, Kanduč M. Relative humidity in droplet and airborne transmission of disease. J Biol Phys 2021; 47:1-29. [PMID: 33564965 PMCID: PMC7872882 DOI: 10.1007/s10867-020-09562-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 12/22/2020] [Indexed: 02/06/2023] Open
Abstract
A large number of infectious diseases are transmitted by respiratory droplets. How long these droplets persist in the air, how far they can travel, and how long the pathogens they might carry survive are all decisive factors for the spread of droplet-borne diseases. The subject is extremely multifaceted and its aspects range across different disciplines, yet most of them have only seldom been considered in the physics community. In this review, we discuss the physical principles that govern the fate of respiratory droplets and any viruses trapped inside them, with a focus on the role of relative humidity. Importantly, low relative humidity-as encountered, for instance, indoors during winter and inside aircraft-facilitates evaporation and keeps even initially large droplets suspended in air as aerosol for extended periods of time. What is more, relative humidity affects the stability of viruses in aerosol through several physical mechanisms such as efflorescence and inactivation at the air-water interface, whose role in virus inactivation nonetheless remains poorly understood. Elucidating the role of relative humidity in the droplet spread of disease would permit us to design preventive measures that could aid in reducing the chance of transmission, particularly in indoor environment.
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Affiliation(s)
- Anže Božič
- Department of Theoretical Physics, Jožef Stefan Institute, Ljubljana, Slovenia
| | - Matej Kanduč
- Department of Theoretical Physics, Jožef Stefan Institute, Ljubljana, Slovenia
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12
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Gschwend GC, Girault HH. Discrete Helmholtz model: a single layer of correlated counter-ions. Metal oxides and silica interfaces, ion-exchange and biological membranes. Chem Sci 2020; 11:10304-10312. [PMID: 34094294 PMCID: PMC8162434 DOI: 10.1039/d0sc03748f] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 09/09/2020] [Indexed: 01/31/2023] Open
Abstract
The mechanism by which interfaces in solution can be polarised depends on the nature of the charge carriers. In the case of a conductor, the charge carriers are electrons and the polarisation is homogeneous in the plane of the electrode. In the case of an insulator covered by ionic moieties, the polarisation is inhomogeneous and discrete in the plane of the interface. Despite these fundamental differences, these systems are usually treated in the same theoretical framework that relies on the Poisson-Boltzmann equation for the solution side. In this perspective, we show that interfaces polarised by discrete charge distributions are rather ubiquitous and that their associated potential drop significantly differs from those of conductor-electrolyte interfaces. We show that these configurations, spanning liquid-liquid interfaces, charged silica-water interfaces, metal oxide interfaces, supercapacitors, ion-exchange membranes and even biological membranes can be uniformly treated under a common "Discrete Helmholtz" model where the discrete charges are compensated by a single layer of correlated counter-ions, thereby generating a sharp potential drop at the interface.
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Affiliation(s)
- Grégoire C Gschwend
- Laboratoire d'Electrochimie Physique et Analytique (LEPA), École Polytechnique Fédérale de Lausanne (EPFL) Rue de l'Industrie 17 CH-1951 Sion Switzerland
| | - Hubert H Girault
- Laboratoire d'Electrochimie Physique et Analytique (LEPA), École Polytechnique Fédérale de Lausanne (EPFL) Rue de l'Industrie 17 CH-1951 Sion Switzerland
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13
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Xu H, Yan C, Fu Q, Xiao K, Yu Y, Han D, Wang W, Cheng J. Possible environmental effects on the spread of COVID-19 in China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 731:139211. [PMID: 32402910 PMCID: PMC7204718 DOI: 10.1016/j.scitotenv.2020.139211] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Revised: 05/02/2020] [Accepted: 05/02/2020] [Indexed: 04/13/2023]
Abstract
At the end of 2019, a novel coronavirus, designated as SARS-CoV-2, emerged in Wuhan, China and was identified as the causal pathogen of COVID-19. The epidemic scale of COVID-19 has increased dramatically, with confirmed cases increasing across China and globally. Understanding the potential affecting factors involved in COVID-19 transmission will be of great significance in containing the spread of the epidemic. Environmental and meteorological factors might impact the occurrence of COVID-19, as these have been linked to various diseases, including severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS), whose causative pathogens belong to the same virus family as SARS-CoV-2. We collected daily data of COVID-19 confirmed cases, air quality and meteorological variables of 33 locations in China for the outbreak period of 29 January 2020 to 15 February 2020. The association between air quality index (AQI) and confirmed cases was estimated through a Poisson regression model, and the effects of temperature and humidity on the AQI-confirmed cases association were analyzed. The results show that the effect of AQI on confirmed cases associated with an increase in each unit of AQI was statistically significant in several cities. The lag effect of AQI on the confirmed cases was statistically significant on lag day 1 (relative risk (RR) = 1.0009, 95% confidence interval (CI): 1.0004, 1.0013), day 2 (RR = 1.0007, 95% CI: 1.0003, 1.0012) and day 3 (RR = 1.0008, 95% CI: 1.0003, 1.0012). The AQI effect on the confirmed cases might be stronger in the temperature range of 10 °C ≤ T < 20 °C than in other temperature ranges, while the RR of COVID-19 transmission associated with AQI was higher in the relative humidity (RH) range of 10% ≤ RH < 20%. Results may suggest an enhanced impact of AQI on the COVID-19 spread under low RH.
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Affiliation(s)
- Hao Xu
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Chonghuai Yan
- Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200092, China
| | - Qingyan Fu
- Shanghai Environmental Monitoring Center, Shanghai 200233, China
| | - Kai Xiao
- Wuhan Environmental Protection Science Academy, Wuhan 430015, China
| | - Yamei Yu
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Deming Han
- School of Environmental, Tsinghua University, Beijing 100084, China
| | - Wenhua Wang
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jinping Cheng
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, China.
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14
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Andoh Y, Hayakawa S, Okazaki S. Molecular dynamics study of lipid bilayers modeling outer and inner leaflets of plasma membranes of mouse hepatocytes. I. Differences in physicochemical properties between the two leaflets. J Chem Phys 2020; 153:035105. [PMID: 32716170 DOI: 10.1063/5.0012676] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Outer and inner leaflets of plasma cell membranes have different lipid compositions, and the membrane properties of each leaflet can differ from each other significantly due to these composition differences. However, because of the experimental difficulty in measuring the membrane properties for each leaflet separately, the differences are not well understood at a molecular level. In this study, we constructed two lipid bilayer systems, modeling outer and inner leaflets of plasma membranes of mouse hepatocytes based on experimental composition data. The ion concentration in the interlamellar water phase was also set to match the concentration in extra- and intracellular fluids. The differences in physical properties between the outer and inner leaflets of mouse hepatocyte cell membrane models were investigated by performing 1.2 μs-long all-atomistic molecular dynamics calculations under physiological temperature and pressure conditions (310.15 K and 1 atm). The calculated electron density profiles along the bilayer normal for each model bilayer system captured well the asymmetric feature of the experimental electron density profile across actual cell plasma membranes, indicating that our procedure of modeling the outer and inner leaflets of the cell plasma membranes was satisfactory. We found that compared to the outer leaflet model, the inner leaflet model had a very bulky and soft structure in the lateral direction. To confirm the differences, membrane fluidity was measured from the lateral diffusivity and relaxation times. The fluidity was significantly higher in the inner leaflet model than in the outer leaflet model. We also discuss two topics that are of wide interest in biology, i.e., the interdigitation of acyl tails of lipid molecules between two monolayers and the lateral concentration fluctuation of lipid molecules in the bilayers.
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Affiliation(s)
- Yoshimichi Andoh
- Center for Computational Science, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
| | - Shiho Hayakawa
- Department of Materials Chemistry, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
| | - Susumu Okazaki
- Department of Materials Chemistry, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
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15
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Cao Z, Liu L, Hu G, Bian Y, Li H, Wang J, Zhou Y. Interplay of hydrophobic and hydrophilic interactions in sequence-dependent cell penetration of spontaneous membrane-translocating peptides revealed by bias-exchange metadynamics simulations. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183402. [PMID: 32569587 DOI: 10.1016/j.bbamem.2020.183402] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Revised: 06/14/2020] [Accepted: 06/16/2020] [Indexed: 12/29/2022]
Abstract
Spontaneous Membrane Translocating Peptides (SMTPs) can translocate silently across the bilayer and, thus, have the best potential to improve the delivery of therapeutic molecules to cells without toxicity. However, how their translocation mechanisms are affected by a specific peptide sequence remains poorly understood. Here, bias-exchange metadynamics simulations were employed to investigate the translocation mechanisms of five SMTPs with the same composition of amino acids (LLRLR, LRLLR, LLLRR, RLLLR, and LRLRL). Simulation results yield sequence-dependent free energy barrier using the FESs along the z-directional distance. An in-depth analysis of sequence-dependent interactions in different regions of the bilayers indicates that the free-energy barrier height of a specific sequence is resulted from the accessibility balance of isolated or clustered hydrophobic residues (L) and hydrophilic residues (R) that leads to different levels of resistance for moving of a peptide into the hydrophobic center of the membrane. At the maximal of the free-energy barrier, all peptides have a conformation parallel to the membrane surface with the barrier height determined by their affinity to the hydrophobic region. The appropriate bilayer perturbation and GDM+ pairing are beneficial for peptide translocation. These results provide an improved microscopic understanding of how peptide sequence influences the translocation efficiency and mechanism.
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Affiliation(s)
- Zanxia Cao
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China.
| | - Lei Liu
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China; College of Information Management, Dezhou University, Dezhou 253023, China.
| | - Guodong Hu
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China.
| | - Yunqiang Bian
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China.
| | - Haiyan Li
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China; College of Physics and Electronic Information, Dezhou University, Dezhou 253023, China.
| | - Jihua Wang
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China.
| | - Yaoqi Zhou
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China; Institute for Glycomics, School of Information and Communication Technology, Griffith University, Parklands Dr, Southport, QLD 4222, Australia.
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16
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Yang H, Ahmad ZA, Song Y. Molecular insight for the role of key residues of calreticulin in its binding activities: A computational study. Comput Biol Chem 2020; 85:107228. [DOI: 10.1016/j.compbiolchem.2020.107228] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 01/28/2020] [Accepted: 02/01/2020] [Indexed: 12/26/2022]
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17
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Kirch A, Celaschi YM, de Almeida JM, Miranda CR. Brine-Oil Interfacial Tension Modeling: Assessment of Machine Learning Techniques Combined with Molecular Dynamics. ACS APPLIED MATERIALS & INTERFACES 2020; 12:15837-15843. [PMID: 32191023 DOI: 10.1021/acsami.9b22189] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The physical chemistry mechanisms behind the oil-brine interface phenomena are not yet fully clarified. The knowledge of the relation between brine composition and concentration for a given oil may lead to the ionic tuning of the injected solution on geochemical and enhanced oil recovery processes. Thus, it is worth examining the parameters influencing the interfacial properties. In this context, we have combined machine learning (ML) techniques with classical molecular dynamics simulations (MD) to predict oil/brine interfacial tensions (IFT) effectively and compared this process to a linear regression (LR) method. To diversify our data set, we have introduced a new atomistic crude oil model (medium) with 36 different types of hydrocarbon molecules. The MD simulations were performed for mono- and multicomponent (toluene, heptane, Heptol, light, and medium) oil systems interfaced with sulfate and chloride brines with varying cations (Na+, K+, Ca2+, and Mg2+) and salinity concentration. Thus, a consistent IFT data set was built for the ML training and LR fitting at room temperature and pressure conditions, over the feature space considering oil density, oil composition, salinity, and ionic concentrations. On the basis of gradient boosted (GB) algorithms, we have observed that the dominant quantities affecting the IFT are related to the oil attributes and the salinity concentration, and no specific ion dominates the IFT changes. When the obtained LR model was validated against MD and experimental data from the literature, the error varied up to 2% and 9%, respectively, showing a robust and consistent transferability. The combination of MD simulations and ML techniques may provide a fast and cost-effective IFT determination over multiple and complex fluid-fluid and fluid-solid interfaces.
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Affiliation(s)
- Alexsandro Kirch
- Instituto de Fı́sica, DFMT, Universidade de São Paulo, CP 66318, 05315-970 São Paulo, SP, Brazil
| | - Yuri M Celaschi
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, 09210-580 Santo André, SP, Brazil
| | - James M de Almeida
- Instituto de Fı́sica, DFMT, Universidade de São Paulo, CP 66318, 05315-970 São Paulo, SP, Brazil
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, 09210-580 Santo André, SP, Brazil
| | - Caetano R Miranda
- Instituto de Fı́sica, DFMT, Universidade de São Paulo, CP 66318, 05315-970 São Paulo, SP, Brazil
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18
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Dean HB, Roberson ED, Song Y. Neurodegenerative Disease-Associated Variants in TREM2 Destabilize the Apical Ligand-Binding Region of the Immunoglobulin Domain. Front Neurol 2019; 10:1252. [PMID: 32021611 PMCID: PMC6985895 DOI: 10.3389/fneur.2019.01252] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 11/11/2019] [Indexed: 01/22/2023] Open
Abstract
Single nucleotide variations in Triggering Receptor Expressed on Myeloid Cells 2 (TREM2) have been linked to both late-onset Alzheimer's disease and behavioral variant frontotemporal dementia (FTD), the latter presenting either in isolation or with cystic bone lesions in a condition called Nasu-Hakola disease. Models of the extracellular domain of TREM2 show that Nasu-Hakola disease-associated mutations are grossly inactivating by truncation, frameshift, or unfolding, that Alzheimer's disease (AD)-associated variants localize to a putative ligand-interacting region (PLIR) on the extracellular surface, and that FTD-associated variants are found in the hydrophobic core. However, while these disease-associated residues are predicted to play some role in disrupting ligand binding to the extracellular domain of TREM2, how they ultimately lead to disease remains unknown. Here, we used in silico molecular modeling to investigate all-atom models of TREM2 and characterize the effects on conformation and dynamical motion of AD-associated R47H and R62H as well as FTD-associated T96K, D86V, and T66M variants compared to the benign N68K variant and the common variant. Our model, which is based on a published 2.2 Å resolution crystal structure of the TREM2 extracellular domain, finds that both AD- and FTD-associated variants cause localized instability in three loops adjacent to the PLIR that correspond to the complementarity-determining regions (CDRs) of antibodies. This instability ultimately disrupts tethering between these CDRs and the core of the immunoglobulin domain, exposing a group of otherwise-buried, negatively charged residues. This instability and exposure of negatively charged residues is most severe following introduction of the T66M variant that has been described as causing FTD even in the heterozygous state and is less severe following introduction of variants that are less strongly tied to FTD or of those associated with AD. Thus, our results provide further evidence that the proposed loss-of-function caused by neurodegenerative disease-associated variants may be driven by altered conformational stability of the ligand-interacting CDR and, ultimately, loss of affinity or specificity for TREM2 ligands.
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Affiliation(s)
- Hunter B Dean
- Department of Biomedical Engineering, University of Alabama at Birmingham, Birmingham, AL, United States.,Department of Neurology, University of Alabama at Birmingham, Birmingham, AL, United States.,Center for Neurodegeneration and Experimental Therapeutics, University of Alabama at Birmingham, Birmingham, AL, United States.,Alzheimer's Disease Center, University of Alabama at Birmingham, Birmingham, AL, United States.,Medical Scientist Training Program, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Erik D Roberson
- Department of Neurology, University of Alabama at Birmingham, Birmingham, AL, United States.,Center for Neurodegeneration and Experimental Therapeutics, University of Alabama at Birmingham, Birmingham, AL, United States.,Alzheimer's Disease Center, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Yuhua Song
- Department of Biomedical Engineering, University of Alabama at Birmingham, Birmingham, AL, United States
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19
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Ionic transport through a protein nanopore: a Coarse-Grained Molecular Dynamics Study. Sci Rep 2019; 9:15740. [PMID: 31673049 PMCID: PMC6823379 DOI: 10.1038/s41598-019-51942-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 07/17/2019] [Indexed: 11/09/2022] Open
Abstract
The MARTINI coarse-grained (CG) force field is used to test the ability of CG models to simulate ionic transport through protein nanopores. The ionic conductivity of CG ions in solution was computed and compared with experimental results. Next, we studied the electrostatic behavior of a solvated CG lipid bilayer in salt solution under an external electric field. We showed this approach correctly describes the experimental conditions under a potential bias. Finally, we performed CG molecular dynamics simulations of the ionic transport through a protein nanopore (α-hemolysin) inserted in a lipid bilayer, under different electric fields, for 2-3 microseconds. The resulting I - V curve is qualitatively consistent with experiments, although the computed current is one order of magnitude smaller. Current saturation was observed for potential biases over ±350 mV. We also discuss the time to reach a stationary regime and the role of the protein flexibility in our CG simulations.
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20
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Heterogeneity in structure and dynamics of water near bilayers using TIP3P and TIP4P/2005 water models. Chem Phys 2019. [DOI: 10.1016/j.chemphys.2019.110396] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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21
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Deplazes E, White J, Murphy C, Cranfield CG, Garcia A. Competing for the same space: protons and alkali ions at the interface of phospholipid bilayers. Biophys Rev 2019; 11:483-490. [PMID: 31115866 DOI: 10.1007/s12551-019-00541-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 04/29/2019] [Indexed: 10/26/2022] Open
Abstract
Maintaining gradients of solvated protons and alkali metal ions such as Na+ and K+ across membranes is critical for cellular function. Over the last few decades, both the interactions of protons and alkali metal ions with phospholipid membranes have been studied extensively and the reported interactions of these ions with phospholipid headgroups are very similar, yet few studies have investigated the potential interdependence between proton and alkali metal ion binding at the water-lipid interface. In this short review, we discuss the similarities between the proton-membrane and alkali ion-membrane interactions. Such interactions include cation attraction to the phosphate and carbonyl oxygens of the phospholipid headgroups that form strong lipid-ion and lipid-ion-water complexes. We also propose potential mechanisms that may modulate the affinities of these cationic species to the water-phospholipid interfacial oxygen moieties. This review aims to highlight the potential interdependence between protons and alkali metal ions at the membrane surface and encourage a more nuanced understanding of the complex nature of these biologically relevant processes.
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Affiliation(s)
- Evelyne Deplazes
- School of Life Sciences, University of Technology Sydney, Ultimo, NSW, 2007, Australia. .,School of Pharmacy and Biomedical Sciences, Curtin University, Perth, WA, 6845, Australia.
| | - Jacqueline White
- School of Life Sciences, University of Technology Sydney, Ultimo, NSW, 2007, Australia
| | - Christopher Murphy
- School of Life Sciences, University of Technology Sydney, Ultimo, NSW, 2007, Australia
| | - Charles G Cranfield
- School of Life Sciences, University of Technology Sydney, Ultimo, NSW, 2007, Australia
| | - Alvaro Garcia
- School of Life Sciences, University of Technology Sydney, Ultimo, NSW, 2007, Australia.
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22
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Leonard AN, Wang E, Monje-Galvan V, Klauda JB. Developing and Testing of Lipid Force Fields with Applications to Modeling Cellular Membranes. Chem Rev 2019; 119:6227-6269. [DOI: 10.1021/acs.chemrev.8b00384] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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23
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Lin X, Nair V, Zhou Y, Gorfe AA. Membrane potential and dynamics in a ternary lipid mixture: insights from molecular dynamics simulations. Phys Chem Chem Phys 2018; 20:15841-15851. [PMID: 29845130 DOI: 10.1039/c8cp01629a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Transmembrane potential (Vm) plays critical roles in cell signaling and other functions. However, the impact of Vm on the structure and dynamics of membrane lipids and proteins, which are critical for the regulation of signaling, is still an open question. All-atom molecular dynamics (MD) simulation is emerging as a useful technique to address this issue. Previous atomistic MD simulations of pure or binary model membranes indicated that both ion imbalance and electric field can be used to generate Vm, but both approaches failed to yield structural changes in lipids with statistical significance. We hypothesized that a possible reason for this could be oversimplified membrane composition or limited sampling. In this work, we tested if and how Vm modulates the structure and dynamics of lipids in a physiologically relevant model membrane. Using a detailed side-by-side comparison, we first show that while both ion imbalance and electric field generate Vm in our complex membranes, only the latter could produce physiologically relevant Vm. We further show that double bonds in lipid acyl chains have a relatively large sensitivity to Vm. A single-bilayer model with an electric field showed the highest sensitivity in simulations under the isothermal-isobaric (NPT) ensemble, reproducing expected responses of head-group dipoles to Vm and suggesting that this approach may be more suitable for studying the structural effects of Vm. Our findings also shed light on the relationship between the macroscopic Vm and its atomic-level underpinnings.
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Affiliation(s)
- Xubo Lin
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, Texas 77030, USA
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24
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Ishiyama T, Shirai S, Okumura T, Morita A. Molecular dynamics study of structure and vibrational spectra at zwitterionoic lipid/aqueous KCl, NaCl, and CaCl 2 solution interfaces. J Chem Phys 2018; 148:222801. [PMID: 29907059 DOI: 10.1063/1.5006543] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Molecular dynamics (MD) simulations of KCl, NaCl, and CaCl2 solution/dipalmytoylphosphatidylcholine lipid interfaces were performed to analyze heterodyne-detected vibrational sum frequency generation (HD-VSFG) spectra in relation to the interfacial water structure. The present MD simulation well reproduces the experimental spectra and elucidates a specific cation effect on the interfacial structure. The K+, Na+, and Ca2+ cation species penetrate in the lipid layer more than the anions in this order, due to the electrostatic interaction with negative polar groups of lipid, and the electric double layer between the cations and anions cancels the intrinsic orientation of water at the water/lipid interface. These mechanisms explain the HD-VSFG spectrum of the water/lipid interface and its spectral perturbation by adding the ions. The lipid monolayer reverses the order of surface preference of the cations at the solution/lipid interface from that at the solution/air interface.
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Affiliation(s)
- Tatsuya Ishiyama
- Department of Applied Chemistry, Graduate School of Science and Engineering, University of Toyama, Toyama 930-8555, Japan
| | - Shinnosuke Shirai
- Department of Applied Chemistry, Graduate School of Science and Engineering, University of Toyama, Toyama 930-8555, Japan
| | - Tomoaki Okumura
- Department of Applied Chemistry, Graduate School of Science and Engineering, University of Toyama, Toyama 930-8555, Japan
| | - Akihiro Morita
- Department of Chemistry, Graduate School of Science Tohoku University, Sendai 980-8578, Japan and Elements Strategy Initiative for Catalysts and Batteries (ESICB), Kyoto University, Kyoto 615-8520, Japan
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25
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Ahlstrand E, Zukerman Schpector J, Friedman R. Computer simulations of alkali-acetate solutions: Accuracy of the forcefields in difference concentrations. J Chem Phys 2018; 147:194102. [PMID: 29166095 DOI: 10.1063/1.4985919] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
When proteins are solvated in electrolyte solutions that contain alkali ions, the ions interact mostly with carboxylates on the protein surface. Correctly accounting for alkali-carboxylate interactions is thus important for realistic simulations of proteins. Acetates are the simplest carboxylates that are amphipathic, and experimental data for alkali acetate solutions are available and can be compared with observables obtained from simulations. We carried out molecular dynamics simulations of alkali acetate solutions using polarizable and non-polarizable forcefields and examined the ion-acetate interactions. In particular, activity coefficients and association constants were studied in a range of concentrations (0.03, 0.1, and 1M). In addition, quantum-mechanics (QM) based energy decomposition analysis was performed in order to estimate the contribution of polarization, electrostatics, dispersion, and QM (non-classical) effects on the cation-acetate and cation-water interactions. Simulations of Li-acetate solutions in general overestimated the binding of Li+ and acetates. In lower concentrations, the activity coefficients of alkali-acetate solutions were too high, which is suggested to be due to the simulation protocol and not the forcefields. Energy decomposition analysis suggested that improvement of the forcefield parameters to enable accurate simulations of Li-acetate solutions can be achieved but may require the use of a polarizable forcefield. Importantly, simulations with some ion parameters could not reproduce the correct ion-oxygen distances, which calls for caution in the choice of ion parameters when protein simulations are performed in electrolyte solutions.
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Affiliation(s)
- Emma Ahlstrand
- Department of Chemistry and Biomedical Sciences, Linnæus University, 391 82 Kalmar, Sweden
| | - Julio Zukerman Schpector
- Universidade Federal de São Carlos, Departamento de Química, CP 676, 13565-905 São Carlos, SP, Brazil
| | - Ran Friedman
- Department of Chemistry and Biomedical Sciences, Linnæus University, 391 82 Kalmar, Sweden
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26
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Yadav RK, Singh M, Roy S, Ansari MN, Saeedan AS, Kaithwas G. Modulation of oxidative stress response by flaxseed oil: Role of lipid peroxidation and underlying mechanisms. Prostaglandins Other Lipid Mediat 2018; 135:21-26. [PMID: 29452256 DOI: 10.1016/j.prostaglandins.2018.02.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 02/08/2018] [Accepted: 02/08/2018] [Indexed: 12/13/2022]
Abstract
Polyunsaturated fatty acids (PUFA's) are majorly classified as ω-3 and ω-6 fatty acids. The eicosapentaenoic acid (EPA, ω-3:20-5), docosahexaenoic acid (DHA, ω-3:22-6) and alpha-linolenic acid (ALA, ω-3:18-3) are known ω-3 fatty acids, extracted from animal (e.g fish oil) and plant sources (e.g flaxseed oil). Furthermore, linoleic acid (LA, ω-6:18-2) is recognized as ω-6 fatty acid and the most prominent biological fatty acid with a pro-inflammatory response. Flaxseed oil has variety of biological roles, due to the significant amount of ω-3/ω-6 fatty acids. Numerous studies have reported that ALA (ω-3:18-3) and LA (ω-6:18-2) has diverse pharmacological activities. The ALA (ω-3:18-3) and LA (ω-6:18-2) are recognised to be the pharmacological antagonist. For example, ALA (ω-3:18-3) is recognised as anti-inflammatory, whereas LA (ω-6:18-2) is considered to be pro-inflammatory. PUFA's get oxidized in three ways; firstly, free radical-mediated pathway, secondly non-free radical non-enzymatic metabolism, and lastly enzymatic degradation. The present report is an attempt to summarize various modes of PUFA's metabolism and elaborate biological effects of the associated metabolites concerning flaxseed oil.
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Affiliation(s)
- Rajnish Kumar Yadav
- Department of Pharmaceutical Sciences, School of Biosciences and Biotechnology, Babasaheb Bhimrao Ambedkar University (A Central University), Vidya Vihar, Raebareli Road, Lucknow 226025, UP, India
| | - Manjari Singh
- Department of Pharmaceutical Sciences, School of Biosciences and Biotechnology, Babasaheb Bhimrao Ambedkar University (A Central University), Vidya Vihar, Raebareli Road, Lucknow 226025, UP, India
| | - Subhadeep Roy
- Department of Pharmaceutical Sciences, School of Biosciences and Biotechnology, Babasaheb Bhimrao Ambedkar University (A Central University), Vidya Vihar, Raebareli Road, Lucknow 226025, UP, India
| | - Mohd Nazam Ansari
- Department of Pharmacology, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-Kharj, Saudi Arabia
| | - Abdulaziz S Saeedan
- Department of Pharmacology, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-Kharj, Saudi Arabia
| | - Gaurav Kaithwas
- Department of Pharmaceutical Sciences, School of Biosciences and Biotechnology, Babasaheb Bhimrao Ambedkar University (A Central University), Vidya Vihar, Raebareli Road, Lucknow 226025, UP, India.
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Emelyanova KA, Victorov AI. Driving Force for Spontaneous Perforation of Bilayers Formed by Ionic Amphiphiles in Aqueous Salt. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:13438-13443. [PMID: 29064715 DOI: 10.1021/acs.langmuir.7b02885] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Spontaneous perforation of amphiphilic membranes is important in both living matter and technology because of an impact on functions of biological membranes and shape transitions of self-assembling structures. Nevertheless, no definite molecular mechanism has been established so far even for simple ionic surfactant systems. We show that spontaneous perforation of a bilayer formed by an ionic amphiphile is driven by electrostatics. Creation of large pores with a concave-convex geometry of the rim is promoted by lower electrostatic free energy than that for a flat nonperforated bilayer. The opposite effect comes from the elasticity of the hydrocarbon tails of the amphiphile that prefer flat geometry of a nonperforated bilayer. The balance between electrostatics and tail deformation controls the appearance of pores; this balance is modulated by added salt that screens the electrostatic interactions. We illustrate the proposed mechanism with the aid of classical aggregation model that has been extended by including an analytical description of the electrostatic contribution for the toroidal rim of a pore. Numerical solution of the linearized Poisson-Boltzmann equation confirms the role of electrostatic forces in formation of pores. For the ionic surfactants of CnTAB family, we predict shape transitions including bilayer perforations and formation of branched micellar networks induced by changing salinity or temperature and demonstrate the effect of surfactant's molecular parameters on these transitions.
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Affiliation(s)
- Ksenia A Emelyanova
- St. Petersburg State University , 7/9 Universitetskaya nab., 199034 St. Petersburg, Russia
| | - Alexey I Victorov
- St. Petersburg State University , 7/9 Universitetskaya nab., 199034 St. Petersburg, Russia
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28
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Ma Y, Poole K, Goyette J, Gaus K. Introducing Membrane Charge and Membrane Potential to T Cell Signaling. Front Immunol 2017; 8:1513. [PMID: 29170669 PMCID: PMC5684113 DOI: 10.3389/fimmu.2017.01513] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2017] [Accepted: 10/25/2017] [Indexed: 01/12/2023] Open
Abstract
While membrane models now include the heterogeneous distribution of lipids, the impact of membrane charges on regulating the association of proteins with the plasma membrane is often overlooked. Charged lipids are asymmetrically distributed between the two leaflets of the plasma membrane, resulting in the inner leaflet being negatively charged and a surface potential that attracts and binds positively charged ions, proteins, and peptide motifs. These interactions not only create a transmembrane potential but they can also facilitate the formation of charged membrane domains. Here, we reference fields outside of immunology in which consequences of membrane charge are better characterized to highlight important mechanisms. We then focus on T cell receptor (TCR) signaling, reviewing the evidence that membrane charges and membrane-associated calcium regulate phosphorylation of the TCR–CD3 complex and discuss how the immunological synapse exhibits distinct patterns of membrane charge distribution. We propose that charged lipids, ions in solution, and transient protein interactions form a dynamic equilibrium during T cell activation.
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Affiliation(s)
- Yuanqing Ma
- EMBL Australia Node in Single Molecule Science, School of Medical Sciences, University of New South Wales, Sydney, NSW, Australia.,ARC Centre of Excellence in Advanced Molecular Imaging, University of New South Wales, Sydney, NSW, Australia
| | - Kate Poole
- EMBL Australia Node in Single Molecule Science, School of Medical Sciences, University of New South Wales, Sydney, NSW, Australia.,ARC Centre of Excellence in Advanced Molecular Imaging, University of New South Wales, Sydney, NSW, Australia
| | - Jesse Goyette
- EMBL Australia Node in Single Molecule Science, School of Medical Sciences, University of New South Wales, Sydney, NSW, Australia.,ARC Centre of Excellence in Advanced Molecular Imaging, University of New South Wales, Sydney, NSW, Australia
| | - Katharina Gaus
- EMBL Australia Node in Single Molecule Science, School of Medical Sciences, University of New South Wales, Sydney, NSW, Australia.,ARC Centre of Excellence in Advanced Molecular Imaging, University of New South Wales, Sydney, NSW, Australia
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29
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Non-thermal effects of microwave in sodium chloride aqueous solution: Insights from molecular dynamics simulations. J Mol Liq 2017. [DOI: 10.1016/j.molliq.2016.11.126] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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30
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31
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Wang L, Peng JB. Phosphorylation of KLHL3 at serine 433 impairs its interaction with the acidic motif of WNK4: a molecular dynamics study. Protein Sci 2016; 26:163-173. [PMID: 27727489 DOI: 10.1002/pro.3063] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Revised: 09/09/2016] [Accepted: 10/09/2016] [Indexed: 12/17/2022]
Abstract
Interaction between the acidic motif (AM) of protein kinase WNK4 and the Kelch domain of KLHL3 are involved in the pathogenesis of pseudohypoaldosteronism type II, a hereditary form of hypertension. This interaction is disrupted by some disease-causing mutations in either WNK4 or KLHL3, or by angiotensin II- and insulin-induced phosphorylation of KLHL3 at serine 433, which is also a site frequently mutated in patients. However, the mechanism by which this phosphorylation disrupts the interaction is unclear. In this study, we approached this problem using molecular dynamics simulation with structural, dynamical and energetic analyses. Results from independent simulations indicate that when S433 was phosphorylated, the electrostatic potential became more negative in the AM binding site of KLHL3 and therefore was unfavorable for binding with the negatively charged AM. In addition, the intermolecular hydrogen bond network that kept the AM stable in the binding site of KLHL3 was disrupted, and the forces for the hydrophobic interactions between the AM of WNK4 and KLHL3 were also reduced. As a result, the weakened interactions were no longer capable of holding the AM of WNK4 at its binding site in KLHL3. In conclusion, phosphorylation of KLHL3 at S433 disrupts the hydrogen bonds, hydrophobic and electrostatic interactions between the Kelch domain of KLHL3 and the AM of WNK4. This study provides a key molecular understanding of the KLHL3-mediated regulation of WNK4, which is an integrative regulator of electrolyte homeostasis and blood pressure regulation in the kidney. Significances Statement: WNK4 is an integrative regulator of electrolyte homeostasis, which is important in the blood pressure regulation by the kidney. Interaction between WNK4 and KLHL3 is a key physiological process that is impaired in a hereditary form of hypertension. This study provides substantial new insights into the role of phosphorylation of KLHL3 in regulating the interaction with WNK4, and therefore advances our understanding of molecular pathogenesis of hypertension and the mechanism of blood pressure regulation.
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Affiliation(s)
- Lingyun Wang
- Division of Nephrology, Department of Medicine, Nephrology Research and Training Center, University of Alabama at Birmingham, Birmingham, AL, 35294
| | - Ji-Bin Peng
- Division of Nephrology, Department of Medicine, Nephrology Research and Training Center, University of Alabama at Birmingham, Birmingham, AL, 35294.,Department of Urology, University of Alabama at Birmingham, Birmingham, AL, 35294
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32
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Pineda De Castro LF, Dopson M, Friedman R. Biological Membranes in Extreme Conditions: Anionic Tetraether Lipid Membranes and Their Interactions with Sodium and Potassium. J Phys Chem B 2016; 120:10628-10634. [PMID: 27668511 DOI: 10.1021/acs.jpcb.6b06206] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Archaea such as Sulfolobus acidocaldarius tolerate extreme temperatures and high acidity and can grow in the presence of toxic metals and low concentrations of Na+ or K+. It is believed that their unique tetraether membranes protect them from harsh environments and allow their survival under such conditions. We used molecular dynamics simulations to study membranes comprising glycerol dialkylnonitol tetraether lipids, which are the main component of S. acidocaldarius membranes, in solutions containing different concentrations of NaCl and KCl or with Na+ or K+ counterions (trace cations, 0 M). Anionic binding sites on the membranes were almost 50% occupied in the presence of counterions. The free energy of cation-phosphate complexation and the residence times of ions near the membranes were found to be both ion- and concentration-dependent. Sodium ions had more favorable interactions with the membranes and a longer residence time, whereas higher cation concentrations led to shorter ion residence times. When only counterions were present in the solutions, large residence times suggested that the membrane may function as a cation-attracting reservoir. The results suggested that the ions can be easily transferred to the cytoplasm as needed, explaining the growth curves of S. acidocaldarius under different salinities and pH.
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Affiliation(s)
- Luis Felipe Pineda De Castro
- Computational Chemistry and Biochemistry Research Group (CCBG), Department of Chemistry and Biomedical Sciences, ‡Centre of Excellence "Biomaterials Chemistry", and §Linnaeus University Centre for Ecology and Evolution in Microbial model Systems (EEMiS), Linnæus University , 391 82 Kalmar, Sweden
| | - Mark Dopson
- Computational Chemistry and Biochemistry Research Group (CCBG), Department of Chemistry and Biomedical Sciences, ‡Centre of Excellence "Biomaterials Chemistry", and §Linnaeus University Centre for Ecology and Evolution in Microbial model Systems (EEMiS), Linnæus University , 391 82 Kalmar, Sweden
| | - Ran Friedman
- Computational Chemistry and Biochemistry Research Group (CCBG), Department of Chemistry and Biomedical Sciences, ‡Centre of Excellence "Biomaterials Chemistry", and §Linnaeus University Centre for Ecology and Evolution in Microbial model Systems (EEMiS), Linnæus University , 391 82 Kalmar, Sweden
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33
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Pineda De Castro LF, Dopson M, Friedman R. Biological Membranes in Extreme Conditions: Simulations of Anionic Archaeal Tetraether Lipid Membranes. PLoS One 2016; 11:e0155287. [PMID: 27167213 PMCID: PMC4864297 DOI: 10.1371/journal.pone.0155287] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Accepted: 03/29/2016] [Indexed: 01/25/2023] Open
Abstract
In contrast to the majority of organisms that have cells bound by di-ester phospholipids, archaeal membranes consist of di- and tetraether phospholipids. Originating from organisms that withstand harsh conditions (e.g., low pH and a wide range of temperatures) such membranes have physical properties that make them attractive materials for biological research and biotechnological applications. We developed force-field parameters based on the widely used Generalized Amber Force Field (GAFF) to enable the study of anionic tetraether membranes of the model archaean Sulfolobus acidocaldarius by computer simulations. The simulations reveal that the physical properties of these unique membranes depend on the number of cyclopentane rings included in each lipid unit, and on the size of cations that are used to ensure charge neutrality. This suggests that the biophysical properties of Sulfolobus acidocaldarius cells depend not only on the compositions of their membranes but also on the media in which they grow.
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Affiliation(s)
- Luis Felipe Pineda De Castro
- Computational Chemistry and Biochemistry research Group (CCBG), Department of Chemistry and Biomedical Sciences, Linnæus University, 391 82 Kalmar, Sweden
- Centre of Excellence “Biomaterials Chemistry”, Linnæus University, 391 82 Kalmar, Sweden
| | - Mark Dopson
- Systems Biology of Microorganisms Research Group (SBMR), Centre for Ecology and Evolution in Microbial model Systems (EEMiS), Linnæus University, 391 82 Kalmar, Sweden
| | - Ran Friedman
- Computational Chemistry and Biochemistry research Group (CCBG), Department of Chemistry and Biomedical Sciences, Linnæus University, 391 82 Kalmar, Sweden
- Centre of Excellence “Biomaterials Chemistry”, Linnæus University, 391 82 Kalmar, Sweden
- * E-mail:
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34
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Melcr J, Bonhenry D, Timr Š, Jungwirth P. Transmembrane Potential Modeling: Comparison between Methods of Constant Electric Field and Ion Imbalance. J Chem Theory Comput 2016; 12:2418-25. [DOI: 10.1021/acs.jctc.5b01202] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Josef Melcr
- Institute of Organic
Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo
nám. 2, 16610 Prague 6, Czech Republic
| | - Daniel Bonhenry
- Institute of Organic
Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo
nám. 2, 16610 Prague 6, Czech Republic
| | - Štěpán Timr
- Institute of Organic
Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo
nám. 2, 16610 Prague 6, Czech Republic
| | - Pavel Jungwirth
- Institute of Organic
Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo
nám. 2, 16610 Prague 6, Czech Republic
- Department of Physics, Tampere University of Technology, P.O. Box 692, FI-33101 Tampere, Finland
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35
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Maity P, Saha B, Kumar GS, Karmakar S. Binding of monovalent alkali metal ions with negatively charged phospholipid membranes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:706-14. [DOI: 10.1016/j.bbamem.2016.01.012] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Revised: 01/15/2016] [Accepted: 01/18/2016] [Indexed: 11/30/2022]
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36
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Yang H, Song Y. Structural Insight for Roles of DR5 Death Domain Mutations on Oligomerization of DR5 Death Domain-FADD Complex in the Death-Inducing Signaling Complex Formation: A Computational Study. J Mol Model 2016; 22:89. [PMID: 26995783 DOI: 10.1007/s00894-016-2941-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Accepted: 02/22/2016] [Indexed: 12/14/2022]
Abstract
Death receptor 5 (DR5)-induced apoptosis that prioritizes the death of tumor cells has been proposed as one of the promising cancer therapies. In this process, oligomerized DR5 death domain (DD) binding to Fas-associated death domain (FADD) leads to FADD activating caspase-8, which marks the formation of the death-inducing signaling complex (DISC) that initiates apoptosis. DR5 DD mutations found in cancer cells have been suggested to play an important pathological role, the mechanism through which those mutants prevent the DR5-activated DISC formation is not clear yet. This study sought to provide structural and molecular insight for the roles of four selected DR5 DD mutations (E355K, E367K, K415N, and L363F) in the oligomerization of DR5 DD-FADD complex during the DISC formation. Results from the molecular dynamics simulations show that the simulated mutants induce conformational, dynamical motions and interactions changes in the DR5 DD-FADD tetramer complex, including changes in a protein's backbone flexibility, less exposure of FADD DED's caspase-8 binding site, reduced H-bonding and hydrophobic contacts at the DR5 DD-FADD DD binding, altered distribution of the electrostatic potentials and correlated motions of residues, and reduced binding affinity of DR5 DD binding to FADD. This study provides structural and molecular insight for the influence of DR5 DD mutations on oligomerization of DR5 DD-FADD complex, which is expected to foster understanding of the DR5 DD mutants' resistance mechanism against DR5-activated DISC formation.
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Affiliation(s)
- Hongyi Yang
- Department of Chemistry, The University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Yuhua Song
- Department of Biomedical Engineering, The University of Alabama at Birmingham, 803 Shelby Interdisciplinary Biomedical Research Building, 1825 University Boulevard, Birmingham, AL, 35294, USA.
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37
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Wu YY, Bao L, Zhang X, Tan ZJ. Flexibility of short DNA helices with finite-length effect: From base pairs to tens of base pairs. J Chem Phys 2016; 142:125103. [PMID: 25833610 DOI: 10.1063/1.4915539] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Flexibility of short DNA helices is important for the biological functions such as nucleosome formation and DNA-protein recognition. Recent experiments suggest that short DNAs of tens of base pairs (bps) may have apparently higher flexibility than those of kilo bps, while there is still the debate on such high flexibility. In the present work, we have studied the flexibility of short DNAs with finite-length of 5-50 bps by the all-atomistic molecular dynamics simulations and Monte Carlo simulations with the worm-like chain model. Our microscopic analyses reveal that short DNAs have apparently high flexibility which is attributed to the significantly strong bending and stretching flexibilities of ∼6 bps at each helix end. Correspondingly, the apparent persistence length lp of short DNAs increases gradually from ∼29 nm to ∼45 nm as DNA length increases from 10 to 50 bps, in accordance with the available experimental data. Our further analyses show that the short DNAs with excluding ∼6 bps at each helix end have the similar flexibility with those of kilo bps and can be described by the worm-like chain model with lp ∼ 50 nm.
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Affiliation(s)
- Yuan-Yan Wu
- Department of Physics and Key Laboratory of Artificial Micro and Nano-structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan 430072, China
| | - Lei Bao
- Department of Physics and Key Laboratory of Artificial Micro and Nano-structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan 430072, China
| | - Xi Zhang
- Department of Physics and Key Laboratory of Artificial Micro and Nano-structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan 430072, China
| | - Zhi-Jie Tan
- Department of Physics and Key Laboratory of Artificial Micro and Nano-structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan 430072, China
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38
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Wang L, Holmes RP, Peng JB. Molecular Modeling of the Structural and Dynamical Changes in Calcium Channel TRPV5 Induced by the African-Specific A563T Variation. Biochemistry 2016; 55:1254-64. [PMID: 26837804 DOI: 10.1021/acs.biochem.5b00732] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Transient receptor potential cation channels, vanilloid subfamily, member 5 (TRPV5) plays a key role in active Ca(2+) reabsorption in the kidney. Variations in TRPV5 occur at high frequency in African populations and may contribute to their higher efficiency of Ca(2+) reabsorption. One of the African specific variations, A563T, exhibits increased Ca(2+) transport ability. However, it is unclear how this variation influences the channel pore. On the basis of the structure of TRPV1, a TRPV5 model was generated to simulate the structural and dynamical changes induced by the A563T variation. On the basis of this model, amino acid residue 563 interacts with V540, which is one residue away from the key residue, D542, involved in Ca(2+) selectivity and Mg(2+) blockade. The A563T variation increases secondary structure stability and reduces dynamical motion of D542. In addition, the A563T variation alters the electrostatic potential of the outer surface of the pore. Differences in contact between selective filter residues and residue 563 and in electrostatic potential between the two TRPV5 variants were also observed in another model derived from an alternative alignment in the selective filters between TRPV5 and TRPV1. These findings indicate that the A563T variation induces structural, dynamical, and electrostatic changes in the TRPV5 pore, providing structural insight into the functional alterations associated with the A563T variation.
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Affiliation(s)
- Lingyun Wang
- Division of Nephrology, Department of Medicine, Nephrology Research and Training Center and ‡Department of Urology, University of Alabama at Birmingham , Birmingham, Alabama 35294, United States
| | - Ross P Holmes
- Division of Nephrology, Department of Medicine, Nephrology Research and Training Center and ‡Department of Urology, University of Alabama at Birmingham , Birmingham, Alabama 35294, United States
| | - Ji-Bin Peng
- Division of Nephrology, Department of Medicine, Nephrology Research and Training Center and ‡Department of Urology, University of Alabama at Birmingham , Birmingham, Alabama 35294, United States
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39
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Pasenkiewicz-Gierula M, Baczynski K, Markiewicz M, Murzyn K. Computer modelling studies of the bilayer/water interface. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:2305-2321. [PMID: 26825705 DOI: 10.1016/j.bbamem.2016.01.024] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Revised: 01/18/2016] [Accepted: 01/21/2016] [Indexed: 01/24/2023]
Abstract
This review summarises high resolution studies on the interface of lamellar lipid bilayers composed of the most typical lipid molecules which constitute the lipid matrix of biomembranes. The presented results were obtained predominantly by computer modelling methods. Whenever possible, the results were compared with experimental results obtained for similar systems. The first and main section of the review is concerned with the bilayer-water interface and is divided into four subsections. The first describes the simplest case, where the interface consists only of lipid head groups and water molecules and focuses on interactions between the lipid heads and water molecules; the second describes the interface containing also mono- and divalent ions and concentrates on lipid-ion interactions; the third describes direct inter-lipid interactions. These three subsections are followed by a discussion on the network of direct and indirect inter-lipid interactions at the bilayer interface. The second section summarises recent computer simulation studies on the interactions of antibacterial membrane active compounds with various models of the bacterial outer membrane. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg.
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Affiliation(s)
- Marta Pasenkiewicz-Gierula
- Department of Computational Biophysics and Bioinformatics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland.
| | - Krzysztof Baczynski
- Department of Computational Biophysics and Bioinformatics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Michal Markiewicz
- Department of Computational Biophysics and Bioinformatics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Krzysztof Murzyn
- Department of Computational Biophysics and Bioinformatics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
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40
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Ganesan SJ, Xu H, Matysiak S. Effect of lipid head group interactions on membrane properties and membrane-induced cationic β-hairpin folding. Phys Chem Chem Phys 2016; 18:17836-50. [DOI: 10.1039/c5cp07669b] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Stages in membrane induced SVS-1 folding.
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Affiliation(s)
- Sai J. Ganesan
- Fischell Department of Bioengineering
- University of Maryland
- College Park
- USA
| | - Hongcheng Xu
- Biophysics Program
- University of Maryland
- College Park
- USA
| | - Silvina Matysiak
- Fischell Department of Bioengineering
- University of Maryland
- College Park
- USA
- Biophysics Program
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41
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Maity P, Saha B, Kumar GS, Karmakar S. Effect of counterions on the binding affinity of Na+ ions with phospholipid membranes. RSC Adv 2016. [DOI: 10.1039/c6ra17056k] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
We have systematically investigated the effect of counterions on the interaction of the Na+ ion with phospholipid membranes using dynamic light scattering, zeta potential, isothermal titration calorimetry and fluorescence spectroscopy techniques.
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Affiliation(s)
- Pabitra Maity
- Department of Physics
- Jadavpur University
- Kolkata 700032
- India
| | - Baishakhi Saha
- Biophysical Chemistry Laboratory
- Organic and Medicinal Chemistry Division
- CSIR-Indian Institute of Chemical Biology
- Kolkata 700 032
- India
| | - Gopinatha Suresh Kumar
- Biophysical Chemistry Laboratory
- Organic and Medicinal Chemistry Division
- CSIR-Indian Institute of Chemical Biology
- Kolkata 700 032
- India
| | - Sanat Karmakar
- Department of Physics
- Jadavpur University
- Kolkata 700032
- India
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42
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Cordomí A, Edholm O, Perez JJ. Effect of Force Field Parameters on Sodium and Potassium Ion Binding to Dipalmitoyl Phosphatidylcholine Bilayers. J Chem Theory Comput 2015; 5:2125-34. [PMID: 26613152 DOI: 10.1021/ct9000763] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
The behavior of electrolytes in molecular dynamics simulations of zwitterionic phospholipid bilayers is very sensitive to the force field parameters used. Here, several 200 ns molecular dynamics of simulations of dipalmitoyl phosphotidylcholine (PC) bilayers in 0.2 M sodium or potassium chloride using various common force field parameters for the cations are presented. All employed parameter sets give a larger number of Na(+) ions than K(+) ions that bind to the lipid heads, but depending on the parameter choice quite different results are seen. A wide range of coordination numbers for the Na(+) and K(+) ions is also observed. These findings have been analyzed and compared to published experimental data. Some simulations produce aggregates of potassium chloride, indicating (in accordance with published simulations) that these force fields do not reproduce the delicate balance between salt and solvated ions. The differences between the force fields can be characterized by one single parameter, the electrostatic radius of the ion, which is correlated to σMO (M represents Na(+)/K(+)), the Lennard-Jones radius. When this parameter exceeds a certain threshold, binding to the lipid heads is no longer observed. One would, however, need more accurate experimental data to judge or rank the different force fields precisely. Still, reasons for the poor performance of some of the parameter sets are clearly demonstrated, and a quality control procedure is provided.
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Affiliation(s)
- Arnau Cordomí
- Department d'Enginyeria Química, Technical University of Catalonia (UPC), Avenue Diagonal 647, 08028 Barcelona, Spain, and, Theoretical Biological Physics, Royal Institute of Technology (KTH), SE-10691 Stockholm, Sweden
| | - Olle Edholm
- Department d'Enginyeria Química, Technical University of Catalonia (UPC), Avenue Diagonal 647, 08028 Barcelona, Spain, and, Theoretical Biological Physics, Royal Institute of Technology (KTH), SE-10691 Stockholm, Sweden
| | - Juan J Perez
- Department d'Enginyeria Química, Technical University of Catalonia (UPC), Avenue Diagonal 647, 08028 Barcelona, Spain, and, Theoretical Biological Physics, Royal Institute of Technology (KTH), SE-10691 Stockholm, Sweden
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43
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Wolf MG, Grubmüller H, Groenhof G. Anomalous surface diffusion of protons on lipid membranes. Biophys J 2015; 107:76-87. [PMID: 24988343 DOI: 10.1016/j.bpj.2014.04.062] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Revised: 01/06/2014] [Accepted: 04/07/2014] [Indexed: 11/30/2022] Open
Abstract
The cellular energy machinery depends on the presence and properties of protons at or in the vicinity of lipid membranes. To asses the energetics and mobility of a proton near a membrane, we simulated an excess proton near a solvated DMPC bilayer at 323 K, using a recently developed method to include the Grotthuss proton shuttling mechanism in classical molecular dynamics simulations. We obtained a proton surface affinity of -13.0 ± 0.5 kJ mol(-1). The proton interacted strongly with both lipid headgroup and linker carbonyl oxygens. Furthermore, the surface diffusion of the proton was anomalous, with a subdiffusive regime over the first few nanoseconds, followed by a superdiffusive regime. The time- and distance dependence of the proton surface diffusion coefficient within these regimes may also resolve discrepancies between previously reported diffusion coefficients. Our simulations show that the proton anomalous surface diffusion originates from restricted diffusion in two different surface-bound states, interrupted by the occasional bulk-mediated long-range surface diffusion. Although only a DMPC membrane was considered in this work, we speculate that the restrictive character of the on-surface diffusion is highly sensitive to the specific membrane conditions, which can alter the relative contributions of the surface and bulk pathways to the overall diffusion process. Finally, we discuss the implications of our findings for the energy machinery.
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Affiliation(s)
- Maarten G Wolf
- Computational Biomolecular Chemistry Group, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany; Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Helmut Grubmüller
- Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Gerrit Groenhof
- Computational Biomolecular Chemistry Group, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.
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44
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Zarzycki P. Interfacial water screens the protein-induced transmembrane voltage. J Phys Chem B 2015; 119:1474-82. [PMID: 25563965 DOI: 10.1021/jp509329u] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Transmembrane proteins are crucial in cellular traffic, signal transduction, and energy storage in a form of transmembrane voltage. These proteins are stabilized by hydrophobic and hydrophilic interactions, in which cytoplasmic and exoplasmic water plays a special role. Water structural ordering generates the dipole potential that typically overcompensates for an intrinsic membrane-protein potential gradient, and thus it modifies and sustains an overall cellular electrostatics. Although the transmembrane voltage has been extensively studied, the dipole potential has attracted very little attention. Here, by using molecular dynamics, we examined water electrostatic response to the transmembrane charge, field, and potential asymmetry introduced by the presence of four integral membrane proteins: typical of inner (α-helix) and outer membrane (β-barrel). In all cases, the protein presence introduces electrostatic directionality in the transmembrane dipole field and voltage. In particular, water generates a deep potential sink if strongly polar residues are densely packed on one side of bilayer, as frequently occurs in a selectivity filter of the K(+) channel. We also found that protein secondary structure is less important than the polar residue distribution along the protein channel. Our findings are relevant for understanding the driving force behind biomembrane conductivity: the ability of biological water to electrostatically screen the transmembrane voltage.
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Affiliation(s)
- Piotr Zarzycki
- Institute of Physical Chemistry, Polish Academy of Sciences , Warsaw, Poland
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45
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Wang N, Zhou S, Kekenes-Huskey PM, Li B, McCammon JA. Poisson-Boltzmann versus Size-Modified Poisson-Boltzmann Electrostatics Applied to Lipid Bilayers. J Phys Chem B 2014; 118:14827-32. [PMID: 25426875 PMCID: PMC4280115 DOI: 10.1021/jp511702w] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
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Mean-field
methods, such as the Poisson–Boltzmann equation
(PBE), are often used to calculate the electrostatic properties of
molecular systems. In the past two decades, an enhancement of the
PBE, the size-modified Poisson–Boltzmann equation (SMPBE),
has been reported. Here, the PBE and the SMPBE are reevaluated for
realistic molecular systems, namely, lipid bilayers, under eight different
sets of input parameters. The SMPBE appears to reproduce the molecular
dynamics simulation results better than the PBE only under specific
parameter sets, but in general, it performs no better than the Stern
layer correction of the PBE. These results emphasize the need for
careful discussions of the accuracy of mean-field calculations on
realistic systems with respect to the choice of parameters and call
for reconsideration of the cost-efficiency and the significance of
the current SMPBE formulation.
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Affiliation(s)
- Nuo Wang
- Department of Chemistry and Biochemistry, ‡Department of Mathematics, §Department of Pharmacology, ⊥Howard Hughes Medical Institute, University of California-San Diego , La Jolla, California 92093, United States
| | - Shenggao Zhou
- Department of Chemistry and Biochemistry, ‡Department of Mathematics, §Department of Pharmacology, ⊥Howard Hughes Medical Institute, University of California-San Diego , La Jolla, California 92093, United States
| | - Peter M Kekenes-Huskey
- Department of Chemistry and Biochemistry, ‡Department of Mathematics, §Department of Pharmacology, ⊥Howard Hughes Medical Institute, University of California-San Diego , La Jolla, California 92093, United States
| | - Bo Li
- Department of Chemistry and Biochemistry, ‡Department of Mathematics, §Department of Pharmacology, ⊥Howard Hughes Medical Institute, University of California-San Diego , La Jolla, California 92093, United States
| | - J Andrew McCammon
- Department of Chemistry and Biochemistry, ‡Department of Mathematics, §Department of Pharmacology, ⊥Howard Hughes Medical Institute, University of California-San Diego , La Jolla, California 92093, United States
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46
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Wang L, Murphy-Ullrich JE, Song Y. Molecular insight into the effect of lipid bilayer environments on thrombospondin-1 and calreticulin interactions. Biochemistry 2014; 53:6309-22. [PMID: 25260145 DOI: 10.1021/bi500662v] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Thrombospondin-1 (TSP1) binding to cell surface calreticulin (CRT) stimulates the association of CRT with low-density lipoprotein (LDL) receptor-related protein (LRP1) to signal focal adhesion disassembly and engagement of cellular activities. A recent study demonstrated that membrane rafts are necessary for TSP1-mediated focal adhesion disassembly, but the molecular role of membrane rafts in mediating TSP1-CRT-LRP1 signaling is unknown. In this study, we investigated the effect of lipid bilayer environments on TSP1 and CRT interactions via atomically detailed molecular dynamics simulations. Results showed that the microscopic structural properties of lipid molecules and mesoscopic mechanical properties and electrostatic potential of the bilayer were significantly different between a 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) bilayer and a raftlike lipid bilayer [a POPC/cholesterol (CHOL) raftlike lipid bilayer or a POPC/CHOL/sphingomyelin (SM) raftlike lipid bilayer], and the difference was enhanced by SM lipids in a raftlike lipid bilayer. These bilayer property differences affect the interactions of CRT with the bilayer, further influencing CRT conformation and TSP1-CRT interactions. A raftlike lipid bilayer stabilized CRT conformation as compared to a POPC bilayer environment. TSP1 binding to CRT resulted in a conformation for the CRT N-domain more "open" than that of the CRT P-domain in a raftlike lipid bilayer environment, which could facilitate binding of CRT to LRP1 to engage downstream signaling. The open conformational changes of CRT by binding to TSP1 in a raftlike lipid bilayer were enhanced by SM lipids in a lipid bilayer. The direct interactions of both the N- and P-domains of CRT with the bilayer contribute to the more open conformation of CRT in the TSP1-CRT complex on a raftlike lipid bilayer as compared to that on a POPC bilayer. The interactions of CRT or the TSP1-CRT complex with the lipid bilayer also caused CHOL molecules and/or lipids to be more coordinated and to aggregate into patchlike regions in the raftlike lipid bilayers. The lipid and CHOL molecule coordination and aggregation could in turn affect the interactions of CRT with the membrane raft, thereby altering TSP1-CRT interactions and CRT conformational changes that potentially regulate its interactions with LRP1. This study provides molecular insights into the role of lipid bilayer environments in TSP1-CRT interactions and in the CRT conformational changes that are predicted to facilitate binding of CRT to LRP1 to engage downstream signaling events.
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Affiliation(s)
- Lingyun Wang
- Department of Biomedical Engineering and ‡Department of Pathology, The University of Alabama at Birmingham , Birmingham, Alabama 35294, United States
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47
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Gongadze E, Velikonja A, Perutkova Š, Kramar P, Maček-Lebar A, Kralj-Iglič V, Iglič A. Ions and water molecules in an electrolyte solution in contact with charged and dipolar surfaces. Electrochim Acta 2014. [DOI: 10.1016/j.electacta.2013.07.147] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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48
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Vermaas JV, Tajkhorshid E. A microscopic view of phospholipid insertion into biological membranes. J Phys Chem B 2013; 118:1754-64. [PMID: 24313792 DOI: 10.1021/jp409854w] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Understanding the process of membrane insertion is an essential step in developing a detailed mechanism, for example, for peripheral membrane protein association and membrane fusion. The highly mobile membrane mimetic (HMMM) has been used to accelerate the membrane association and binding of peripheral membrane proteins in simulations by increasing the lateral diffusion of phospholipid headgroups while retaining an atomistic description of the interface. Through a comparative study, we assess the difference in insertion rate of a free phospholipid into an HMMM as well as into a conventional phospholipid bilayer and develop a detailed mechanistic model of free phospholipid insertion into biological membranes. The mechanistic insertion model shows that successful irreversible association of the free phospholipid to the membrane interface, which results in its insertion, is the rate-limiting step. Association is followed by independent, sequential insertion of the acyl tails of the free phospholipid into the membrane, with splayed acyl tail intermediates. Use of the HMMM is found to replicate the same intermediate insertion states as in the full phospholipid bilayer; however, it accelerates overall insertion by approximately a factor of 3, with the probability of successful association of phospholipid to the membrane being significantly enhanced.
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Affiliation(s)
- Josh V Vermaas
- Center for Biophysics and Computational Biology, Department Biochemistry, College of Medicine, and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
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49
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Chen Z, Mao Y, Yang J, Zhang T, Zhao L, Yu K, Zheng M, Jiang H, Yang H. Characterizing the binding of annexin V to a lipid bilayer using molecular dynamics simulations. Proteins 2013; 82:312-22. [DOI: 10.1002/prot.24389] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2013] [Revised: 07/07/2013] [Accepted: 08/01/2013] [Indexed: 11/09/2022]
Affiliation(s)
- Zhuxi Chen
- Drug Discovery and Design Center; State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences; Shanghai 201203 China
| | - Yanyan Mao
- Drug Discovery and Design Center; State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences; Shanghai 201203 China
| | - Jing Yang
- Drug Discovery and Design Center; State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences; Shanghai 201203 China
| | - Tao Zhang
- Drug Discovery and Design Center; State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences; Shanghai 201203 China
| | - Lifen Zhao
- Drug Discovery and Design Center; State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences; Shanghai 201203 China
| | - Kunqian Yu
- Drug Discovery and Design Center; State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences; Shanghai 201203 China
| | - Mingyue Zheng
- Drug Discovery and Design Center; State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences; Shanghai 201203 China
| | - Hualiang Jiang
- Drug Discovery and Design Center; State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences; Shanghai 201203 China
| | - Huaiyu Yang
- Drug Discovery and Design Center; State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences; Shanghai 201203 China
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50
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Hu Y, Ou S, Patel S. Free energetics of arginine permeation into model DMPC lipid bilayers: coupling of effective counterion concentration and lateral bilayer dimensions. J Phys Chem B 2013; 117:11641-53. [PMID: 23888915 DOI: 10.1021/jp404829y] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Mechanisms and underlying thermodynamic determinants of translocation of charged cationic peptides such as cell-penetrating peptides across the cellular membrane continue to receive much attention. Two widely held views include endocytotic and non-endocytotic (diffusive) processes of permeant transfer across the bilayer. Considering a purely diffusive process, we consider the free energetics of translocation of a monoarginine peptide mimic across a model DMPC bilayer. We compute potentials of mean force for the transfer of a charged monoarginine peptide unit from water to the center of a 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) model lipid bilayer. We use fully atomistic molecular dynamics simulations coupled with the adaptive biasing force (ABF) method for free energy estimation. The estimated potential of mean force difference from bulk to bilayer center is 6.94 ± 0.28 kcal/mol. The order of magnitude of this prediction is consistent with past experimental estimates of arginine partitioning into physiological bilayers in the context of translocon-based experiments, though the correlation between the bench and computer experiments is not unambiguous. Moreover, the present value is roughly one-half of previous estimates based on all-atom molecular dynamics free energy calculations. We trace the differences between the present and earlier calculations to system sizes used in the simulations and the dependence of the contributions to the free energy from various system components (water, lipids, ions, peptide) on overall system size. By varying the bilayer lateral dimensions in simulations using only sufficient numbers of counterions to maintain overall system charge neutrality, we find the possibility of an inherent convergent transfer free energy value.
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Affiliation(s)
- Yuan Hu
- Department of Chemistry and Biochemistry, University of Delaware , Newark, Delaware 19716, United States
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