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Insights into short chain polyethylene penetration of phospholipid bilayers via atomistic molecular dynamics simulations. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2024; 1866:184327. [PMID: 38679310 DOI: 10.1016/j.bbamem.2024.184327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 04/16/2024] [Accepted: 04/23/2024] [Indexed: 05/01/2024]
Abstract
The escalation of global plastic production, reaching an annual output of 400 million tons, has significantly intensified concerns regarding plastic waste management. This has been exacerbated by improper recycling and disposal practices, contributing to the impending crisis of plastic pollution. Predictions indicate that by 2025, the environment will bear the burden of over ten billion metric tons of accumulated plastic waste. This situation has led to the concerning release of microplastics and nanoplastics (NPs) into the environment as plastic materials degrade, thereby posing risks to both ecosystems and human health. Nanoparticle interactions with living organisms have garnered significant attention due to their potential to disrupt vital biological processes. Of particular interest are lipid membranes, acting as crucial gatekeepers, underscoring the importance of comprehending the intricate process of NP penetration. Molecular dynamics (MD) simulations serve as a robust tool, offering molecular-level insights into these intricate interactions. In this study, we leverage all-atom MD simulations to delve into the interactions between lipid bilayers and polyethylene (PETH) chains of varying lengths. The investigation spans diverse lipid bilayer compositions-ranging from pure POPC to POPC:DPPC mixtures-revealing how PETH accommodates itself, adopts extended conformations, and influences membrane structure and ordering. Significantly, while longer PETH chains demonstrate limited passive diffusion, their potential to penetrate bilayers over extended timescales emerges as a significant revelation. Overall, this research significantly advances our comprehension of NP-membrane interactions, shedding light on the potential environmental and health implications that lie ahead.
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Revealing the key structural features promoting the helical conformation in algal polysaccharide carrageenan in solution. Carbohydr Polym 2024; 331:121901. [PMID: 38388044 DOI: 10.1016/j.carbpol.2024.121901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 01/12/2024] [Accepted: 01/30/2024] [Indexed: 02/24/2024]
Abstract
Carrageenans are industrially important polysaccharides with tunable viscoelastic and gelation properties. The function of polysaccharide depends on its conformation and chemical composition. However, the solution conformations of carrageenans are highly debated, and the structure-function relationship remains elusive. Here, we have studied the intrinsic conformational behavior of a series of carrageenan hexamers in solution, using extensive all-atom classical MD and enhanced sampling. Our findings comprehensively delineate that carrageenans containing the 3,6-anhydrous bridge (κ-C, ι-C, θ-C, and non-sulfated β-C) adopt compact helical structures as their predominant conformation in solution, whereas carrageenans without the bridge (μ-C, ν-C, and λ-C) remain as extended loosely packed helices; opposing the 'coil-to-helix' paradigm. Glycosidic linkages access a few allowed orientations. We hypothesize that the 3,6-anhydrous bridge, irrespective of carrageenan's sulfation pattern, is essential for stabilizing the helical conformation at the single-chain level. It provides necessary flexibility to the glycosidic linkage to sample conformations close to the experimentally derived helical structure and also prevents the sugar ring flipping. Sulfate groups mainly modify the chain stiffness due to steric and stereo-electronic effects and participate in hydrogen bonding. Such atomistic insights will be helpful for understanding the differential gelation mechanisms of carrageenans and fine-tuning polysaccharide backbone for various industrial applications.
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Deciphering Lipid Arrangement in Phosphatidylserine/Phosphatidylcholine Mixed Membranes: Simulations and Experiments. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:18995-19007. [PMID: 38096496 PMCID: PMC10753890 DOI: 10.1021/acs.langmuir.3c03061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 11/24/2023] [Accepted: 11/26/2023] [Indexed: 12/27/2023]
Abstract
Phosphatidylserine (PS) exposure on the plasma membrane is crucial for many cellular processes including apoptotic cell recognition, blood clotting regulation, cellular signaling, and intercellular interactions. In this study, we investigated the arrangement of PS headgroups in mixed PS/phosphatidylcholine (PC) bilayers, serving as a simplified model of the outer leaflets of mammalian cell plasma membranes. Combining atomistic-scale molecular dynamics (MD) simulations with Langmuir monolayer experiments, we unraveled the mutual miscibility of POPC and POPS lipids and the intricate intermolecular interactions inherent to these membranes as well as the disparities in position and orientation of PC and PS headgroups. Our experiments revealed micrometer-scale miscibility at all mole fractions of POPC and POPS, marked by modest deviations from ideal mixing with no apparent microscale phase separation. The MD simulations, meanwhile, demonstrated that these deviations were due to strong electrostatic interactions between like-lipid pairs (POPC-POPC and POPS-POPS), culminating in lateral segregation and nanoscale clustering. Notably, PS headgroups profoundly affect the ordering of the lipid acyl chains, leading to lipid elongation and subtle PS protrusion above the zwitterionic membrane. In addition, PC headgroups are more tilted with respect to the membrane normal, while PS headgroups align at a smaller angle, making them more exposed to the surface of the mixed PC/PS membranes. These findings provide a detailed molecular-level account of the organization of mixed PC/PS membranes, corroborated by experimental data. The insights gained here extend our comprehension of the physiological role of PSs.
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Zika virus prM protein contains cholesterol binding motifs required for virus entry and assembly. Nat Commun 2023; 14:7344. [PMID: 37957166 PMCID: PMC10643666 DOI: 10.1038/s41467-023-42985-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 10/25/2023] [Indexed: 11/15/2023] Open
Abstract
For successful infection of host cells and virion production, enveloped viruses, including Zika virus (ZIKV), extensively rely on cellular lipids. However, how virus protein-lipid interactions contribute to the viral life cycle remains unclear. Here, we employ a chemo-proteomics approach with a bifunctional cholesterol probe and show that cholesterol is closely associated with the ZIKV structural protein prM. Bioinformatic analyses, reverse genetics alongside with photoaffinity labeling assays, and atomistic molecular dynamics simulations identified two functional cholesterol binding motifs within the prM transmembrane domain. Loss of prM-cholesterol association has a bipartite effect reducing ZIKV entry and leading to assembly defects. We propose a model in which membrane-resident M facilitates cholesterol-supported lipid exchange during endosomal entry and, together with cholesterol, creates a platform promoting virion assembly. In summary, we identify a bifunctional role of prM in the ZIKV life cycle by mediating viral entry and virus assembly in a cholesterol-dependent manner.
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In Vitro and In Silico Studies of Functionalized Polyurethane Surfaces toward Understanding Biologically Relevant Interactions. ACS Biomater Sci Eng 2023; 9:6112-6122. [PMID: 37909715 PMCID: PMC10646850 DOI: 10.1021/acsbiomaterials.3c01367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 10/18/2023] [Indexed: 11/03/2023]
Abstract
The solid-aqueous boundary formed upon biomaterial implantation provides a playground for most biochemical reactions and physiological processes involved in implant-host interactions. Therefore, for biomaterial development, optimization, and application, it is essential to understand the biomaterial-water interface in depth. In this study, oxygen plasma-functionalized polyurethane surfaces that can be successfully utilized in contact with the tissue of the respiratory system were prepared and investigated. Through experiments, the influence of plasma treatment on the physicochemical properties of polyurethane was investigated by atomic force microscopy, attenuated total reflection infrared spectroscopy, differential thermal analysis, X-ray photoelectron spectroscopy, secondary ion mass spectrometry, and contact angle measurements, supplemented with biological tests using the A549 cell line and two bacteria strains (Staphylococcus aureus and Pseudomonas aeruginosa). The molecular interpretation of the experimental findings was achieved by molecular dynamics simulations employing newly developed, fully atomistic models of unmodified and plasma-functionalized polyurethane materials to characterize the polyurethane-water interfaces at the nanoscale in detail. The experimentally obtained polar and dispersive surface free energies were consistent with the calculated free energies, verifying the adequacy of the developed models. A 20% substitution of the polymeric chain termini by their oxidized variants was observed in the experimentally obtained plasma-modified polyurethane surface, indicating the surface saturation with oxygen-containing functional groups.
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How Neuromembrane Lipids Modulate Membrane Proteins: Insights from G-Protein-Coupled Receptors (GPCRs) and Receptor Tyrosine Kinases (RTKs). Cold Spring Harb Perspect Biol 2023; 15:a041419. [PMID: 37487628 PMCID: PMC10547395 DOI: 10.1101/cshperspect.a041419] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/26/2023]
Abstract
Lipids play a diverse and critical role in cellular processes in all tissues. The unique lipid composition of nerve membranes is particularly interesting because it contains, among other things, polyunsaturated lipids, such as docosahexaenoic acid, which the body only gets through the diet. The crucial role of lipids in neurological processes, especially in receptor-mediated cell signaling, is emphasized by the fact that in many neuropathological diseases there are significant deviations in the lipid composition of nerve membranes compared to healthy individuals. The lipid composition of neuromembranes can significantly affect the function of receptors by regulating the physical properties of the membrane or by affecting specific interactions between receptors and lipids. In addition, it is worth noting that the ligand-binding pocket of many receptors is located inside the cell membrane, due to which lipids can even modulate the binding of ligands to their receptors. These mechanisms highlight the importance of lipids in the regulation of membrane receptor activation and function. In this article, we focus on two major protein families: G-protein-coupled receptors (GPCRs) and receptor tyrosine kinases (RTKs) and discuss how lipids affect their function in neuronal membranes, elucidating the basic mechanisms underlying neuronal function and dysfunction.
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Miscibility of Phosphatidylcholines in Bilayers: Effect of Acyl Chain Unsaturation. MEMBRANES 2023; 13:411. [PMID: 37103838 PMCID: PMC10146409 DOI: 10.3390/membranes13040411] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 04/02/2023] [Accepted: 04/03/2023] [Indexed: 06/19/2023]
Abstract
The miscibility of phospholipids in a hydrated bilayer is an issue of fundamental importance for understanding the organization of biological membranes. Despite research on lipid miscibility, its molecular basis remains poorly understood. In this study, all-atom MD simulations complemented by Langmuir monolayer and DSC experiments have been performed to investigate the molecular organization and properties of lipid bilayers composed of phosphatidylcholines with saturated (palmitoyl, DPPC) and unsaturated (oleoyl, DOPC) acyl chains. The experimental results showed that the DOPC/DPPC bilayers are systems exhibiting a very limited miscibility (strongly positive values of excess free energy of mixing) at temperatures below the DPPC phase transition. The excess free energy of mixing is divided into an entropic component, related to the ordering of the acyl chains, and an enthalpic component, resulting from the mainly electrostatic interactions between the headgroups of lipids. MD simulations showed that the electrostatic interactions for lipid like-pairs are much stronger than that for mixed pairs and temperature has only a slight influence on these interactions. On the contrary, the entropic component increases strongly with increasing temperature, due to the freeing of rotation of acyl chains. Therefore, the miscibility of phospholipids with different saturations of acyl chains is an entropy-driven process.
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Dissecting the mechanisms of environment sensitivity of smart probes for quantitative assessment of membrane properties. Biophys J 2023; 122:224a. [PMID: 36783097 DOI: 10.1016/j.bpj.2022.11.1332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023] Open
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9
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Dissecting the mechanisms of environment sensitivity of smart probes for quantitative assessment of membrane properties. Open Biol 2022; 12:220175. [PMID: 36099931 PMCID: PMC9470265 DOI: 10.1098/rsob.220175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
The plasma membrane, as a highly complex cell organelle, serves as a crucial platform for a multitude of cellular processes. Its collective biophysical properties are largely determined by the structural diversity of the different lipid species it accommodates. Therefore, a detailed investigation of biophysical properties of the plasma membrane is of utmost importance for a comprehensive understanding of biological processes occurring therein. During the past two decades, several environment-sensitive probes have been developed and become popular tools to investigate membrane properties. Although these probes are assumed to report on membrane order in similar ways, their individual mechanisms remain to be elucidated. In this study, using model membrane systems, we characterized the probes Pro12A, NR12S and NR12A in depth and examined their sensitivity to parameters with potential biological implications, such as the degree of lipid saturation, double bond position and configuration (cis versus trans), phospholipid headgroup and cholesterol content. Applying spectral imaging together with atomistic molecular dynamics simulations and time-dependent fluorescent shift analyses, we unravelled individual sensitivities of these probes to different biophysical properties, their distinct localizations and specific relaxation processes in membranes. Overall, Pro12A, NR12S and NR12A serve together as a toolbox with a wide range of applications allowing to select the most appropriate probe for each specific research question.
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Maturation of the SARS-CoV-2 virus is regulated by dimerization of its main protease. Comput Struct Biotechnol J 2022; 20:3336-3346. [PMID: 35720615 PMCID: PMC9195460 DOI: 10.1016/j.csbj.2022.06.023] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 06/10/2022] [Accepted: 06/10/2022] [Indexed: 12/01/2022] Open
Abstract
SARS-CoV-2 main protease (Mpro) involved in COVID-19 is required for maturation of the virus and infection of host cells. The key question is how to block the activity of Mpro. By combining atomistic simulations with machine learning, we found that the enzyme regulates its own activity by a collective allosteric mechanism that involves dimerization and binding of a single substrate. At the core of the collective mechanism is the coupling between the catalytic site residues, H41 and C145, which direct the activity of Mpro dimer, and two salt bridges formed between R4 and E290 at the dimer interface. If these salt bridges are mutated, the activity of Mpro is blocked. The results suggest that dimerization of main proteases is a general mechanism to foster coronavirus proliferation, and propose a robust drug-based strategy that does not depend on the frequently mutating spike proteins at the viral envelope used to develop vaccines.
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Abstract
In cell membranes, G protein-coupled receptors (GPCRs) interact with cholesterol, which modulates their assembly, stability, and conformation. Previous studies have shown how cholesterol modulates the structural properties of GPCRs at ambient temperature. Here, we characterized the mechanical, kinetic, and energetic properties of the human β2-adrenergic receptor (β2AR) in the presence and absence of the cholesterol analog cholesteryl hemisuccinate (CHS) at room temperature (25°C), at physiological temperature (37°C), and at high temperature (42°C). We found that CHS stabilized various structural regions of β2AR differentially, which changed nonlinearly with temperature. Thereby, the strongest effects were observed for structural regions that are important for receptor signaling. Moreover, at 37°C, but not at 25° or 42°C, CHS caused β2AR to increase and stabilize conformational substates to adopt to basal activity. These findings indicate that the nonlinear, temperature-dependent action of CHS in modulating the structural and functional properties of this GPCR is optimized for 37°C.
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12
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Dimerization of the pulmonary surfactant protein C in a membrane environment. PLoS One 2022; 17:e0267155. [PMID: 35476695 PMCID: PMC9045638 DOI: 10.1371/journal.pone.0267155] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 04/01/2022] [Indexed: 11/26/2022] Open
Abstract
Surfactant protein C (SP-C) has several functions in pulmonary surfactant. These include the transfer of lipids between different membrane structures, a role in surfactant recycling and homeostasis, and involvement in modulation of the innate defense system. Despite these important functions, the structures of functional SP-C complexes have remained unclear. SP-C is known to exist as a primarily α-helical structure with an apparently unstructured N-terminal region, yet there is recent evidence that the functions of SP-C could be associated with the formation of SP-C dimers and higher oligomers. In this work, we used molecular dynamics simulations, two-dimensional umbrella sampling, and well-tempered metadynamics to study the details of SP-C dimerization. The results suggest that SP-C dimerizes in pulmonary surfactant membranes, forming dimers of different topologies. The simulations identified a dimerization motif region V21xxxVxxxGxxxM33 that is much larger than the putative A30xxxG34 motif that is commonly assumed to control the dimerization of some α-helical transmembrane domains. The results provide a stronger basis for elucidating how SP-C functions in concert with other surfactant proteins.
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13
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Vitamin E acetate alters properties of pulmonary surfactant. Biophys J 2022. [DOI: 10.1016/j.bpj.2021.11.354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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14
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Rigorous Computational Study Reveals What Docking Overlooks: Double Trouble from Membrane Association in Protein Kinase C Modulators. J Chem Inf Model 2020; 60:5624-5633. [PMID: 32915560 DOI: 10.1021/acs.jcim.0c00624] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Increasing protein kinase C (PKC) activity is of potential therapeutic value. Its activation involves an interaction between the C1 domain and diacylglycerol (DAG) at intracellular membrane surfaces; DAG mimetics hold promise as new drugs. We previously developed the isophthalate derivative HMI-1a3, an effective but highly lipophilic (clogP = 6.46) DAG mimetic. Although a less lipophilic pyrimidine analog, PYR-1gP (clogP = 3.30), gave positive results in computational docking, it unexpectedly presented greatly diminished binding to PKC in vitro. Through more rigorous computational molecular modeling, we reveal that, unlike HMI-1a3, PYR-1gP forms an intramolecular hydrogen bond, which both obstructs binding and reorients PYR-1gP in the membrane in a fashion that prevents it from correctly accessing the PKC C1 domain. Our results highlight the great value of molecular dynamics simulations as a key component for the drug design process of ligands targeting weakly membrane-associated proteins, where simulation in the relevant membrane environment is crucial for obtaining biologically applicable results.
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15
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Tail-Oxidized Cholesterol Enhances Membrane Permeability for Small Solutes. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:10438-10447. [PMID: 32804507 PMCID: PMC7482392 DOI: 10.1021/acs.langmuir.0c01590] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 08/16/2020] [Indexed: 06/01/2023]
Abstract
Cholesterol renders mammalian cell membranes more compact by reducing the amount of voids in the membrane structure. Because of this, cholesterol is known to regulate the ability of cell membranes to prevent the permeation of water and water-soluble molecules through the membranes. Meanwhile, it is also known that even seemingly tiny modifications in the chemical structure of cholesterol can lead to notable changes in membrane properties. The question is, how significantly do these small changes in cholesterol structure affect the permeability barrier function of cell membranes? In this work, we applied fluorescence methods as well as atomistic molecular dynamics simulations to characterize changes in lipid membrane permeability induced by cholesterol oxidation. The studied 7β-hydroxycholesterol (7β-OH-chol) and 27-hydroxycholesterol (27-OH-chol) represent two distinct groups of oxysterols, namely, ring- and tail-oxidized cholesterols, respectively. Our previous research showed that the oxidation of the cholesterol tail has only a marginal effect on the structure of a lipid bilayer; however, oxidation was found to disturb membrane dynamics by introducing a mechanism that allows sterol molecules to move rapidly back and forth across the membrane-bobbing. Herein, we show that bobbing of 27-OH-chol accelerates fluorescence quenching of NBD-lipid probes in the inner leaflet of liposomes by dithionite added to the liposomal suspension. Systematic experiments using fluorescence quenching spectroscopy and microscopy led to the conclusion that the presence of 27-OH-chol increases membrane permeability to the dithionite anion. Atomistic molecular dynamics simulations demonstrated that 27-OH-chol also facilitates water transport across the membrane. The results support the view that oxysterol bobbing gives rise to successive perturbations to the hydrophobic core of the membrane, and these perturbations promote the permeation of water and small water-soluble molecules through a lipid bilayer. The observed impairment of permeability can have important consequences for eukaryotic organisms. The effects described for 27-OH-chol were not observed for 7β-OH-chol which represents ring-oxidized sterols.
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Functionalization of the Parylene C Surface Enhances the Nucleation of Calcium Phosphate: Combined Experimental and Molecular Dynamics Simulations Approach. ACS APPLIED MATERIALS & INTERFACES 2020; 12:12426-12435. [PMID: 32098467 PMCID: PMC7497617 DOI: 10.1021/acsami.9b20877] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Accepted: 02/26/2020] [Indexed: 06/10/2023]
Abstract
Interactions at the solid-body fluid interfaces play a vital role in bone tissue formation at the implant surface. In this study, fully atomistic molecular dynamics (MD) simulations were performed to investigate interactions between the physiological components of body fluids (Ca2+, HPO42-, H2PO4-, Na+, Cl-, and H2O) and functionalized parylene C surface. In comparison to the native parylene C (-Cl surface groups), the introduction of -OH, -CHO, and -COOH surface groups significantly enhances the interactions between body fluid ions and the polymeric surface. The experimentally observed formation of calcium phosphate nanocrystals is discussed in terms of MD simulations of the calcium phosphate clustering. Surface functional groups promote the clustering of calcium and phosphate ions in the following order: -OH > -CHO > -Cl (parent parylene C) ≈ -COO-. This promoting role of surface functional groups is explained as stimulating the number of Ca2+ and HPO42- surface contacts as well as ion chemisorption. The molecular mechanism of calcium phosphate cluster formation at the functionalized parylene C surface is proposed.
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Complex Behavior of Phosphatidylcholine-Phosphatidic Acid Bilayers and Monolayers: Effect of Acyl Chain Unsaturation. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:5944-5956. [PMID: 30942590 DOI: 10.1021/acs.langmuir.9b00381] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Phosphatidic acids (PAs) have many biological functions in biomembranes, e.g., they are involved in the proliferation, differentiation, and transformation of cells. Despite decades of research, the molecular understanding of how PAs affect the properties of biomembranes remains elusive. In this study, we explored the properties of lipid bilayers and monolayers composed of PAs and phosphatidylcholines (PCs) with various acyl chains. For this purpose, the Langmuir monolayer technique and atomistic molecular dynamics (MD) simulations were used to study the miscibility of PA and PC lipids and the molecular organization of mixed bilayers. The monolayer experiments demonstrated that the miscibility of membrane components strongly depends on the structure of the hydrocarbon chains and thus on the overall lipid shape. Interactions between PA and PC molecules vary from repulsive, for systems containing lipids with saturated and unsaturated acyl tails (strongly positive values of the excess free energy of mixing), to attractive, for systems in which all lipid tails are saturated (negative values of the excess free energy of mixing). The MD simulations provided atomistic insight into polar interactions (formation of hydrogen bonds and charge pairs) in PC-PA systems. H-bonding between PA monoanions and PCs in mixed bilayers is infrequent, and the lipid molecules interact mainly via electrostatic interactions. However, the number of charge pairs significantly decreases with the number of unsaturated lipid chains in the PA-PC system. The PA dianions weakly interact with the zwitterionic lipids, but their headgroups are more hydrated as compared to the monoanionic form. The acyl chains in all PC-PA bilayers are more ordered compared to single-component PC systems. In addition, depending on the combination of lipids, we observed a deeper location of the PA phosphate groups compared to the PC phosphate groups, which can alter the presentation of PAs for the peripheral membrane proteins, affecting their accessibility for binding.
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Multiscale Simulations of Biological Membranes: The Challenge To Understand Biological Phenomena in a Living Substance. Chem Rev 2019; 119:5607-5774. [PMID: 30859819 PMCID: PMC6727218 DOI: 10.1021/acs.chemrev.8b00538] [Citation(s) in RCA: 166] [Impact Index Per Article: 33.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
![]()
Biological
membranes are tricky to investigate. They are complex
in terms of molecular composition and structure, functional
over a wide range of time scales, and characterized
by nonequilibrium conditions. Because of all of these
features, simulations are a great technique to study biomembrane
behavior. A significant part of the functional processes
in biological membranes takes place at the molecular
level; thus computer simulations are the method of
choice to explore how their properties emerge from specific
molecular features and how the interplay among the numerous
molecules gives rise to function over spatial and
time scales larger than the molecular ones. In this
review, we focus on this broad theme. We discuss the current
state-of-the-art of biomembrane simulations that, until
now, have largely focused on a rather narrow picture
of the complexity of the membranes. Given this, we
also discuss the challenges that we should unravel in the
foreseeable future. Numerous features such as the actin-cytoskeleton
network, the glycocalyx network, and nonequilibrium
transport under ATP-driven conditions have so far
received very little attention; however, the potential
of simulations to solve them would be exceptionally high. A
major milestone for this research would be that one day
we could say that computer simulations genuinely research
biological membranes, not just lipid bilayers.
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How to minimize dye-induced perturbations while studying biomembrane structure and dynamics: PEG linkers as a rational alternative. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2018; 1860:2436-2445. [PMID: 30028957 DOI: 10.1016/j.bbamem.2018.07.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 07/03/2018] [Accepted: 07/09/2018] [Indexed: 11/28/2022]
Abstract
Organic dye-tagged lipid analogs are essential for many fluorescence-based investigations of complex membrane structures, especially when using advanced microscopy approaches. However, lipid analogs may interfere with membrane structure and dynamics, and it is not obvious that the properties of lipid analogs would match those of non-labeled host lipids. In this work, we bridged atomistic simulations with super-resolution imaging experiments and biomimetic membranes to assess the performance of commonly used sphingomyelin-based lipid analogs. The objective was to compare, on equal footing, the relative strengths and weaknesses of acyl chain labeling, headgroup labeling, and labeling based on poly-ethyl-glycol (PEG) linkers in determining biomembrane properties. We observed that the most appropriate strategy to minimize dye-induced membrane perturbations and to allow consideration of Brownian-like diffusion in liquid-ordered membrane environments is to decouple the dye from a membrane by a PEG linker attached to a lipid headgroup. Yet, while the use of PEG linkers may sound a rational and even an obvious approach to explore membrane dynamics, the results also suggest that the dyes exploiting PEG linkers interfere with molecular interactions and their dynamics. Overall, the results highlight the great care needed when using fluorescent lipid analogs, in particular accurate controls.
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Physiologically-relevant levels of sphingomyelin, but not GM1, induces a β-sheet-rich structure in the amyloid-β(1-42) monomer. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2018; 1860:1709-1720. [PMID: 29626441 DOI: 10.1016/j.bbamem.2018.03.026] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 03/29/2018] [Accepted: 03/31/2018] [Indexed: 01/07/2023]
Abstract
To resolve the contribution of ceramide-containing lipids to the aggregation of the amyloid-β protein into β-sheet rich toxic oligomers, we employed molecular dynamics simulations to study the effect of cholesterol-containing bilayers comprised of POPC (70% POPC, and 30% cholesterol) and physiologically relevant concentrations of sphingomyelin (SM) (30% SM, 40% POPC, and 30% cholesterol), and the GM1 ganglioside (5% GM1, 70% POPC, and 25% cholesterol). The increased bilayer rigidity provided by SM (and to a lesser degree, GM1) reduced the interactions between the SM-enriched bilayer and the N-terminus of Aβ42 (and also residues Ser26, Asn27, and Lys28), which facilitated the formation of a β-sheet in the normally disordered N-terminal region. Aβ42 remained anchored to the SM-enriched bilayer through hydrogen bonds with the side chain of Arg5. With β-sheets in the at the N and C termini, the structure of Aβ42 in the sphingomyelin-enriched bilayer most resembles β-sheet-rich structures found in higher-ordered Aβ fibrils. Conversely, when bound to a bilayer comprised of 5% GM1, the conformation remained similar to that observed in the absence of GM1, with Aβ42 only making contact with one or two GM1 molecules. This article is part of a Special Issue entitled: Protein Aggregation and Misfolding at the Cell Membrane Interface edited by Ayyalusamy Ramamoorthy.
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Bobbing of Oxysterols: Molecular Mechanism for Translocation of Tail-Oxidized Sterols through Biological Membranes. J Phys Chem Lett 2018; 9:1118-1123. [PMID: 29437399 DOI: 10.1021/acs.jpclett.8b00211] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Translocation of sterols between cellular membrane leaflets is of key importance in membrane organization, dynamics, and signaling. We present a novel translocation mechanism that differs in a unique manner from the established ones. The bobbing mechanism identified here is demonstrated for tail-oxidized sterols, but is expected to be viable for any molecule containing two polar centers at the opposite sides of the molecule. The mechanism renders translocation across a lipid membrane possible without a change in molecular orientation. For tail-oxidized sterols, the bobbing mechanism provides an exceptionally facile means to translocate these signaling molecules across membrane structures and may thus represent an important pathway in the course of their biological action.
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22
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Oxysterol Translocation through Lipid Bilayers. Biophys J 2018. [DOI: 10.1016/j.bpj.2017.11.1517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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Abstract
Folding and packing of membrane proteins are highly influenced by the lipidic component of the membrane. Here, we explore how the hydrophobic mismatch (the difference between the hydrophobic span of a transmembrane protein region and the hydrophobic thickness of the lipid membrane around the protein) influences transmembrane helix packing in a cellular environment. Using a ToxRED assay in Escherichia coli and a Bimolecular Fluorescent Complementation approach in human-derived cells complemented by atomistic molecular dynamics simulations we analyzed the dimerization of Glycophorin A derived transmembrane segments. We concluded that, biological membranes can accommodate transmembrane homo-dimers with a wide range of hydrophobic lengths. Hydrophobic mismatch and its effects on dimerization are found to be considerably weaker than those previously observed in model membranes, or under in vitro conditions, indicating that biological membranes (particularly eukaryotic membranes) can adapt to structural deformations through compensatory mechanisms that emerge from their complex structure and composition to alleviate membrane stress. Results based on atomistic simulations support this view, as they revealed that Glycophorin A dimers remain stable, despite of poor hydrophobic match, using mechanisms based on dimer tilting or local membrane thickness perturbations. Furthermore, hetero-dimers with large length disparity between their monomers are also tolerated in cells, and the conclusions that one can draw are essentially similar to those found with homo-dimers. However, large differences between transmembrane helices length hinder the monomer/dimer equilibrium, confirming that, the hydrophobic mismatch has, nonetheless, biologically relevant effects on helix packing in vivo.
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Oxysterols Versus Cholesterol in Model Neuronal Membrane. I. The Case of 7-Ketocholesterol. The Langmuir Monolayer Study. J Membr Biol 2017; 250:553-564. [PMID: 28861595 PMCID: PMC5613072 DOI: 10.1007/s00232-017-9984-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 08/21/2017] [Indexed: 01/30/2023]
Abstract
Oxysterols are products of cholesterol oxidation. They can be formed endogenously (in both enzymatic and non-enzymatic reactions) as well as exogenously (delivered with food). Recent studies clearly demonstrate cytotoxic properties of these compounds, being mainly due to their incorporation into natural lipid bilayers. This process can influence mechanical and physicochemical properties of biomembrane—mainly by modifying the interactions between its components, which may result in the disruption of proper functioning of cell membrane and could lead to its degradation. Therefore, it can be assumed that oxysterols may affect the initiation of neurodegenerative diseases, including Alzheimer’s disease. However, the mode of action of these molecules at the molecular level is not fully known. To get a better understanding of the role of oxysterols in neurodegeneration, it is of great importance to examine mutual interactions between oxysterols and neuronal membrane components. One of the most promising techniques that can be used to analyze such interactions is the Langmuir monolayer technique. In this work, we have prepared an artificial neuronal membrane modeled as multicomponent Langmuir monolayer built up with cholesterol, 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC), and sphingomyelin (SM). To examine whether there are any changes in the membrane properties under oxidative stress, in this paper we have investigated the impact of the representative ring-oxidized oxysterol: 7-ketocholesterol (7-KC). Our results show that replacing cholesterol with 7-KC increases the interaction between molecules in the model membrane.
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Molecular Dynamics Insights into Water-Parylene C Interface: Relevance of Oxygen Plasma Treatment for Biocompatibility. ACS APPLIED MATERIALS & INTERFACES 2017; 9:16685-16693. [PMID: 28459527 DOI: 10.1021/acsami.7b03265] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Solid-water interfaces play a vital role in biomaterials science because they provide a natural playground for most biochemical reactions and physiological processes. In the study, fully atomistic molecular dynamics simulations were performed to investigate interactions between water molecules and several surfaces modeling for unmodified and modified parylene C surfaces. The introduction of -OH, -CHO, and -COOH to the surface and alterations in their coverage significantly influence the energetics of interactions between water molecules and the polymer surface. The theoretical studies were complemented with experimental measurements of contact angle, surface free energy, and imaging of osteoblast cells adhesion. Both MD simulations and experiments demonstrate that the optimal interface, in terms of biocompatibility, is obtained when 60% of native -Cl groups of parylene C surface is exchanged for -OH groups. By exploring idealized models of bare and functionalized parylene C, we obtained a unique insight into molecular interactions at the water-polymer interface. The calculated values of interaction energy components (electrostatic and dispersive) correspond well with the experimentally determined values of surface free energy components (polar and dispersive), revealing their optimal ratio for cells adhesion. The results are discussed in the context of controllable tuning and functionalization of implant polymeric coating toward improved biocompatibility.
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Mechanism of allosteric regulation of β 2-adrenergic receptor by cholesterol. eLife 2016; 5. [PMID: 27897972 PMCID: PMC5182060 DOI: 10.7554/elife.18432] [Citation(s) in RCA: 105] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 11/28/2016] [Indexed: 11/13/2022] Open
Abstract
There is evidence that lipids can be allosteric regulators of membrane protein structure and activation. However, there are no data showing how exactly the regulation emerges from specific lipid-protein interactions. Here we show in atomistic detail how the human β2-adrenergic receptor (β2AR) - a prototypical G protein-coupled receptor - is modulated by cholesterol in an allosteric fashion. Extensive atomistic simulations show that cholesterol regulates β2AR by limiting its conformational variability. The mechanism of action is based on the binding of cholesterol at specific high-affinity sites located near the transmembrane helices 5-7 of the receptor. The alternative mechanism, where the β2AR conformation would be modulated by membrane-mediated interactions, plays only a minor role. Cholesterol analogues also bind to cholesterol binding sites and impede the structural flexibility of β2AR, however cholesterol generates the strongest effect. The results highlight the capacity of lipids to regulate the conformation of membrane receptors through specific interactions.
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Cholesterol oxidation products and their biological importance. Chem Phys Lipids 2016; 199:144-160. [DOI: 10.1016/j.chemphyslip.2016.03.001] [Citation(s) in RCA: 98] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Revised: 03/02/2016] [Accepted: 03/03/2016] [Indexed: 12/14/2022]
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How To Minimize Artifacts in Atomistic Simulations of Membrane Proteins, Whose Crystal Structure Is Heavily Engineered: β₂-Adrenergic Receptor in the Spotlight. J Chem Theory Comput 2016; 11:3432-45. [PMID: 26575777 DOI: 10.1021/acs.jctc.5b00070] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Atomistic molecular dynamics (MD) simulations are used extensively to elucidate membrane protein properties. These simulations are based on three-dimensional protein structures that in turn are often based on crystallography. The protein structures resolved in crystallographic studies typically do not correspond to pristine proteins, however. Instead the crystallized proteins are commonly engineered, including structural modifications (mutations, replacement of protein sequences by antibodies, bound ligands, etc.) whose impact on protein structure and dynamics is largely unknown. Here we explore this issue through atomistic MD simulations (∼5 μs in total), focusing on the β2-adrenergic receptor (β2AR) that is one of the most studied members of the G-protein coupled receptor superfamily. Starting from an inactive-state crystal structure of β2AR, we remove the many modifications in β2AR systematically one at a time, in six consecutive steps. After each step, we equilibrate the system and simulate it quite extensively. The results of this step-by-step approach highlight that the structural modifications used in crystallization can affect ligand and G-protein binding sites, packing at the transmembrane-helix interface region, and the dynamics of connecting loops in β2AR. When the results of the systematic step-by-step approach are compared to an all-at-once technique where all modifications done on β2AR are removed instantaneously at the same time, it turns out that the step-by-step method provides results that are superior in terms of maintaining protein structural stability. The results provide compelling evidence that for membrane proteins whose 3D structure is based on structural engineering, the preparation of protein structure for atomistic MD simulations is a delicate and sensitive process. The results show that most valid results are found when the structural modifications are reverted slowly, one at a time.
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Protocol to Avoid Possible Artifacts in Atomistic Simulation of GPCR Proteins whose Crystal Structure is Heavily Engineered. Biophys J 2016. [DOI: 10.1016/j.bpj.2015.11.386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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Toward Atomistic Resolution Structure of Phosphatidylcholine Headgroup and Glycerol Backbone at Different Ambient Conditions. J Phys Chem B 2015; 119:15075-88. [PMID: 26509669 PMCID: PMC4677354 DOI: 10.1021/acs.jpcb.5b04878] [Citation(s) in RCA: 90] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Revised: 10/19/2015] [Indexed: 11/28/2022]
Abstract
Phospholipids are essential building blocks of biological membranes. Despite a vast amount of very accurate experimental data, the atomistic resolution structures sampled by the glycerol backbone and choline headgroup in phoshatidylcholine bilayers are not known. Atomistic resolution molecular dynamics simulations have the potential to resolve the structures, and to give an arrestingly intuitive interpretation of the experimental data, but only if the simulations reproduce the data within experimental accuracy. In the present work, we simulated phosphatidylcholine (PC) lipid bilayers with 13 different atomistic models, and compared simulations with NMR experiments in terms of the highly structurally sensitive C-H bond vector order parameters. Focusing on the glycerol backbone and choline headgroups, we showed that the order parameter comparison can be used to judge the atomistic resolution structural accuracy of the models. Accurate models, in turn, allow molecular dynamics simulations to be used as an interpretation tool that translates these NMR data into a dynamic three-dimensional representation of biomolecules in biologically relevant conditions. In addition to lipid bilayers in fully hydrated conditions, we reviewed previous experimental data for dehydrated bilayers and cholesterol-containing bilayers, and interpreted them with simulations. Although none of the existing models reached experimental accuracy, by critically comparing them we were able to distill relevant chemical information: (1) increase of choline order parameters indicates the P-N vector tilting more parallel to the membrane, and (2) cholesterol induces only minor changes to the PC (glycerol backbone) structure. This work has been done as a fully open collaboration, using nmrlipids.blogspot.fi as a communication platform; all the scientific contributions were made publicly on this blog. During the open research process, the repository holding our simulation trajectories and files ( https://zenodo.org/collection/user-nmrlipids ) has become the most extensive publicly available collection of molecular dynamics simulation trajectories of lipid bilayers.
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Effect of Phosphatidic Acid on Biomembrane: Experimental and Molecular Dynamics Simulations Study. J Phys Chem B 2015; 119:10042-51. [DOI: 10.1021/acs.jpcb.5b03604] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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Cholesterol under oxidative stress-How lipid membranes sense oxidation as cholesterol is being replaced by oxysterols. Free Radic Biol Med 2015; 84:30-41. [PMID: 25795515 DOI: 10.1016/j.freeradbiomed.2015.03.006] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Revised: 03/06/2015] [Accepted: 03/09/2015] [Indexed: 02/06/2023]
Abstract
The behavior of oxysterols in phospholipid membranes and their effects on membrane properties were investigated by means of dynamic light scattering, fluorescence spectroscopy, NMR, and extensive atomistic simulations. Two families of oxysterols were scrutinized-tail-oxidized sterols, which are mostly produced by enzymatic processes, and ring-oxidized sterols, formed mostly via reactions with free radicals. The former family of sterols was found to behave similar to cholesterol in terms of molecular orientation, roughly parallel to the bilayer normal, leading to increasing membrane stiffness and suppression of its membrane permeability. In contrast, ring-oxidized sterols behave quantitatively differently from cholesterol. They acquire tilted orientations and therefore disrupt the bilayer structure with potential implications for signaling and other biochemical processes in the membranes.
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Experimental determination and computational interpretation of biophysical properties of lipid bilayers enriched by cholesteryl hemisuccinate. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1848:422-32. [DOI: 10.1016/j.bbamem.2014.10.032] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Revised: 10/06/2014] [Accepted: 10/20/2014] [Indexed: 10/24/2022]
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Deciphering the infrared spectrum of the protonated water pentamer and the hybrid Eigen-Zundel cation. Phys Chem Chem Phys 2014; 16:4933-41. [PMID: 24477279 DOI: 10.1039/c3cp54029d] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Traditionally, infrared band assignment for the protonated water clusters, such as H(+)(H2O)5, is based on their lowest energy isomer. Recent experiments extend the observation spectral window to lower frequencies, for which such assignment appears to be inadequate. Because this hydrogen-bonded system is highly anharmonic, harmonic spectral calculations are insufficient for reliable interpretation. Consequently, we have calculated the IR spectrum of several isomers of the protonated water pentamer using an inherently anharmonic methodology, utilizing dipole and velocity autocorrelation functions computed from ab initio molecular dynamic trajectories. While the spectrum of H(+)(H2O)5 is universally assumed to represent the branched Eigen isomer, we find a better agreement for a mixture of a ring and linear isomers. The first has an Eigen core and contributes at high frequencies, whereas the latter accounts for all prominent low-frequency bands. Interestingly, its core is neither a classical Eigen nor a Zundel cation, but rather has hybrid geometry. Such an isomer may play a role in proton conductance along short proton wires.
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Both Zundel and Eigen Isomers Contribute to the IR Spectrum of the Gas-Phase H9O4+ Cluster. J Phys Chem B 2013; 118:278-86. [DOI: 10.1021/jp410446d] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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37
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A ‘clusters-in-liquid’ method for calculating infrared spectra identifies the proton-transfer mode in acidic aqueous solutions. Nat Chem 2012; 5:29-35. [DOI: 10.1038/nchem.1503] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2012] [Accepted: 10/12/2012] [Indexed: 12/24/2022]
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38
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Excited-state polarizability in crystalline sexithiophene: Charge-transfer and vibronic effects. Chem Phys Lett 2012. [DOI: 10.1016/j.cplett.2012.01.038] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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39
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Intermediate vibronic coupling in charge transfer states: Comprehensive calculation of electronic excitations in sexithiophene crystal. J Chem Phys 2011; 134:224505. [DOI: 10.1063/1.3597607] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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40
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Steric and Electronic Effects in the Host−Guest Hydrogen Bonding in Clathrate Hydrates. J Phys Chem A 2011; 115:6149-54. [DOI: 10.1021/jp111245z] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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41
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Reactivity of a sodium atom in vibrationally excited water clusters: An ab initio molecular dynamics study. Chem Phys Lett 2008. [DOI: 10.1016/j.cplett.2008.05.075] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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42
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A sodium atom in a large water cluster: electron delocalization and infrared spectra. J Chem Phys 2008; 128:154306. [PMID: 18433208 DOI: 10.1063/1.2902970] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Ab initio molecular dynamics simulations modeling low-energy collisions of a sodium atom with a cluster with more than 30 water molecules are presented. We follow the dynamics of the atom-cluster interaction and the delocalization of the valence electron of sodium together with the changes in the electron binding energy. This electron tends to be shared by the nascent sodium cation and the water cluster. IR spectra of the sodium-water cluster are both computationally and experimentally obtained, with a good agreement between the two approaches.
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Unbound exciton–phonon states in oligothiophene crystals – A model approach for spectroscopic purposes. Chem Phys 2008. [DOI: 10.1016/j.chemphys.2007.10.025] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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44
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Biliäre Fe-, Cu-, Mn-Exkretion und Galleflußrate bei enteralen oder bei parenteralen Fe-Zulagen. J Anim Physiol Anim Nutr (Berl) 1991. [DOI: 10.1111/j.1439-0396.1991.tb00243.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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45
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Biliary flow rate and concentration of Fe, Cu and Mn as affected by enteral or parenteral Ni supply. JOURNAL OF TRACE ELEMENTS AND ELECTROLYTES IN HEALTH AND DISEASE 1990; 4:175-82. [PMID: 2136135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Five and three bile duct cannulated 45 kg pigs were used in two experiments to evaluate the effects of nickel on the biliary excretion of iron, copper and manganese. In control periods the animals consumed 1.5 mg Ni per day (1 mg/kg diet), and in the respective treatment periods they further received 90 mg Ni per day (60 mg/kg diet) orally or 1.5 mg Ni per day intravenously. Oral supplementation of nickel had no significant effect on biliary iron, whereas the secretion rate of copper was increased by about 50%, and manganese secretion was reduced to about 50% of the control value. Parenteral administration of nickel had no significant effect on biliary iron, copper and manganese secretion. Iron and copper secretion rates were highest after feeding, whereas the pattern of manganese secretion was characterized by a predominant noctural peak irrespective of the treatments in both experiments.
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Effects of the hypocholesterolemic compound K12.148 on bile flow and bile composition in pigs. J Anim Physiol Anim Nutr (Berl) 1990. [DOI: 10.1111/j.1439-0396.1990.tb00125.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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47
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Effects of the hypocholesterolemic compound K12.148 on serum lipids and parameters of clinical chemistry of pigs. J Anim Physiol Anim Nutr (Berl) 1990. [DOI: 10.1111/j.1439-0396.1990.tb00124.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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48
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Zur Messung von Galleflußrate und Gallelipiden an gallengangskanülierten Schweinen mittels einer vollautomatischen Rückfuhrapparatur. J Anim Physiol Anim Nutr (Berl) 1989. [DOI: 10.1111/j.1439-0396.1989.tb00821.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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