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Maleš P, Nikšić-Franjić I, Wang A, Pem B, Bakarić D. Optical and molecular features of negatively curved surfaces created by POPE lipids: A crucial role of the initial conditions. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 317:124462. [PMID: 38754204 DOI: 10.1016/j.saa.2024.124462] [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: 02/13/2024] [Revised: 05/10/2024] [Accepted: 05/11/2024] [Indexed: 05/18/2024]
Abstract
Membrane fusion is closely related to plasma membrane domains rich in cone-shaped phosphatidylethanolamine (PE) lipids that can reverse membrane curvature under certain conditions. The phase transition of PE-based lipid membranes from the lamellar fluid phase (Lα) to the inverse hexagonal phase (HII) is commonly taken as a general model in reconstructing the membrane fusion pathway, and whose structural features have been mostly described so far using structural and microscopic techniques. The aim of this paper is to decipher the optical and molecular features of Lβ → Lα and especially of Lα → HII transition of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine (POPE) lipids at pH = 7.0 when they are initially prepared in the form of both multi- and unilamellar liposomes (MLVs and LUVs). The distinction between optical properties of MLS- and LUVs-derived HII phase, provided from turbidity-sensitive temperature-dependent UV-Vis spectra, was attributed to different formation mechanisms of HII phase. Most importantly, from FTIR spectroscopic data of POPE lipids in Lβ (15 °C), Lα (50 °C) and HII (85 °C) phases we identified the changes in molecular features of POPE lipids during phase transitions. Among the latter, by far the most significant is different hydration pattern of POPE lipids in MLVs- and LUVs-derived HII phase which extends from the polar-apolar interface all the way to the terminal amino group of the POPE lipid, along with the changes in the conformation of glycerol backbone as evidenced by the signature of α-methylene groups. Molecular dynamics simulations confirmed higher water penetration in HII phase and provided insight into hydrogen bonding patterns.
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Affiliation(s)
- Petra Maleš
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia
| | - Ivana Nikšić-Franjić
- School of Science, Constructor University, Bremen GmbH, Campus Ring 1, 28759 Bremen, Germany
| | - Anna Wang
- School of Chemistry, Australian Centre for Astrobiology, and ARC Centre of Excellence in Synthetic Biology, University of New South Wales Sydney, Bedegal Country, Sydney, NSW 2052, Australia
| | - Barbara Pem
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia
| | - Danijela Bakarić
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia.
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2
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Shikata K, Kasahara K, Watanabe NM, Umakoshi H, Kim K, Matubayasi N. Influence of cholesterol on hydrogen-bond dynamics of water molecules in lipid-bilayer systems at varying temperatures. J Chem Phys 2024; 161:015102. [PMID: 38958163 DOI: 10.1063/5.0208008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Accepted: 06/17/2024] [Indexed: 07/04/2024] Open
Abstract
Cholesterol (Chol) plays a crucial role in shaping the intricate physicochemical attributes of biomembranes, exerting a considerable influence on water molecules proximal to the membrane interface. In this study, we conducted molecular dynamics simulations on the bilayers of two lipid species, dipalmitoylphosphatidylcholine (DPPC) and palmitoyl sphingomyelin; they are distinct with respect to the structures of the hydrogen-bond (H-bond) acceptors. Our investigation focuses on the dynamic properties and H-bonds of water molecules in the lipid-membrane systems, with a particular emphasis on the influence of Chol at varying temperatures. Notably, in the gel phase at 303 K, the presence of Chol extends the lifetimes of H-bonds of the oxygen atoms acting as H-bond acceptors within DPPC with water molecules by a factor of 1.5-2.5. In the liquid-crystalline phase at 323 K, on the other hand, H-bonding dynamics with lipid membranes remain largely unaffected by Chol. This observed shift in H-bonding states serves as a crucial key to unraveling the subtle control mechanisms governing water dynamics in lipid-membrane systems.
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Affiliation(s)
- Kokoro Shikata
- Division of Chemical Engineering, Department of Materials Engineering Science, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Kento Kasahara
- Division of Chemical Engineering, Department of Materials Engineering Science, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Nozomi Morishita Watanabe
- Division of Chemical Engineering, Department of Materials Engineering Science, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Hiroshi Umakoshi
- Division of Chemical Engineering, Department of Materials Engineering Science, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Kang Kim
- Division of Chemical Engineering, Department of Materials Engineering Science, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Nobuyuki Matubayasi
- Division of Chemical Engineering, Department of Materials Engineering Science, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
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3
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Higuchi Y, Saleh MA, Anada T, Tanaka M, Hishida M. Rotational Dynamics of Water near Osmolytes by Molecular Dynamics Simulations. J Phys Chem B 2024; 128:5008-5017. [PMID: 38728154 DOI: 10.1021/acs.jpcb.3c08470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2024]
Abstract
The behavior of water molecules around organic molecules has attracted considerable attention as a crucial factor influencing the properties and functions of soft matter and biomolecules. Recently, it has been suggested that the change in protein stability upon the addition of small organic molecules (osmolytes) is dominated by the change in the water dynamics caused by the osmolyte, where the dynamics of not only the directly interacting water molecules but also the long-range hydration layer affect the protein stability. However, the relation between the long-range structure of hydration water in various solutions and the water dynamics remains unclear at the molecular level. We performed density-functional tight-binding molecular dynamics simulations to elucidate the varying rotational dynamics of water molecules in 15 osmolyte solutions. A positive correlation was observed between the rotational relaxation time and our proposed normalized parameter obtained by dividing the number of hydrogen bonds between water molecules by the number of nearest-neighbor water molecules. For the 15 osmolyte solutions, an increase or a decrease in the value of the normalized parameter for the second hydration shell tended to result in water molecules with slow and fast rotational dynamics, respectively, thus illustrating the importance of the second hydration shell for the rotational dynamics of water molecules. Our simulation results are anticipated to advance the current understanding of water dynamics around organic molecules and the long-range structure of water molecules.
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Affiliation(s)
- Yuji Higuchi
- Research Institute for Information Technology, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Md Abu Saleh
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu University, Fukuoka 819-0395, Japan
| | - Takahisa Anada
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu University, Fukuoka 819-0395, Japan
- Institute for Materials Chemistry and Engineering, Kyushu University, Fukuoka 819-0395, Japan
| | - Masaru Tanaka
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu University, Fukuoka 819-0395, Japan
- Institute for Materials Chemistry and Engineering, Kyushu University, Fukuoka 819-0395, Japan
| | - Mafumi Hishida
- Department of Chemistry, Faculty of Science, Tokyo University of Science, 1-3 Kagurazaka, Shinjuku, Tokyo 162-8601, Japan
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4
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Chandra A, Kayal A, Das B, Chandra A. Dynamical Crossover of Interfacial Water upon Melting of a Lipid Bilayer: Influence of Different Parts of the Headgroups. J Phys Chem B 2023. [PMID: 38032152 DOI: 10.1021/acs.jpcb.3c04792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2023]
Abstract
All-atom molecular dynamics simulations of a 1,2-dimyristoyl-sn-glycero-3-phosphocholine bilayer in contact with liquid water were performed at different temperatures ranging from 285 to 320 K. We have investigated the heterogeneity and dynamical transitions in interfacial water as the lipid bilayer undergoes a melting transition. Results are obtained for water at the outer surface of the bilayer and for those buried more deeply in the lipid chains of the bilayer. It is found that lipid bilayer melting influences both the structure and dynamics of interfacial water. The number of interfacial water molecules shows a jump in the melting of the bilayer. The temperature dependence of the diffusivity and orientational relaxation of interfacial water molecules exhibits a dynamical crossover upon melting of the bilayer. The extent of dynamical crossover is found to be rather strong with significant changes in activation barriers for interfacial water around the carbonyl groups, which are deeply buried toward the lipid chains of the bilayer. The dynamical crossover gradually decreases as one moves further away from the outer surface, and it essentially vanishes for water in the region of 5-10 Å from the outer surface. It is found that the lipid melting-induced dynamical crossover of interfacial water is significant only for water that is in close proximity to the bilayer surface or deeply buried into it. The current results reveal that water molecules in different parts of the interface respond differently on melting of the bilayer. The current study also shows that the carbonyl-bound water molecules can play an important role in the phase transition of the bilayer as the temperature is raised through its melting point.
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Affiliation(s)
- Abhilash Chandra
- Department of Chemistry, Indian Institute of Technology Kanpur, Uttar Pradesh 208016, India
| | - Abhijit Kayal
- Department of Chemistry, Indian Institute of Technology Kanpur, Uttar Pradesh 208016, India
| | - Banshi Das
- Department of Chemistry, Indian Institute of Technology Kanpur, Uttar Pradesh 208016, India
| | - Amalendu Chandra
- Department of Chemistry, Indian Institute of Technology Kanpur, Uttar Pradesh 208016, India
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5
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Jain H, Karathanou K, Bondar AN. Graph-Based Analyses of Dynamic Water-Mediated Hydrogen-Bond Networks in Phosphatidylserine: Cholesterol Membranes. Biomolecules 2023; 13:1238. [PMID: 37627303 PMCID: PMC10452392 DOI: 10.3390/biom13081238] [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: 06/20/2023] [Revised: 08/03/2023] [Accepted: 08/07/2023] [Indexed: 08/27/2023] Open
Abstract
Phosphatidylserine lipids are anionic molecules present in eukaryotic plasma membranes, where they have essential physiological roles. The altered distribution of phosphatidylserine in cells such as apoptotic cancer cells, which, unlike healthy cells, expose phosphatidylserine, is of direct interest for the development of biomarkers. We present here applications of a recently implemented Depth-First-Search graph algorithm to dissect the dynamics of transient water-mediated lipid clusters at the interface of a model bilayer composed of 1-palmytoyl-2-oleoyl-sn-glycero-2-phosphatidylserine (POPS) and cholesterol. Relative to a reference POPS bilayer without cholesterol, in the POPS:cholesterol bilayer there is a somewhat less frequent sampling of relatively complex and extended water-mediated hydrogen-bond networks of POPS headgroups. The analysis protocol used here is more generally applicable to other lipid:cholesterol bilayers.
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Affiliation(s)
- Honey Jain
- Faculty of Physics, University of Bucharest, Atomiștilor 405, 077125 Măgurele, Romania
- Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | | | - Ana-Nicoleta Bondar
- Faculty of Physics, University of Bucharest, Atomiștilor 405, 077125 Măgurele, Romania
- IAS-5/INM-9, Forschungszentrum Jülich, Institute of Computational Biomedicine, Wilhelm-Johnen Straße, 52428 Jülich, Germany
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6
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Higuchi Y, Bohinc K, Reščič J, Shimokawa N, Ito H. Coarse-grained molecular dynamics simulation of cation distribution profiles on negatively charged lipid membranes during phase separation. SOFT MATTER 2023; 19:3640-3651. [PMID: 37162535 DOI: 10.1039/d3sm00222e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Revealing the ion distributions on a charged lipid membrane in aqueous solution under the influence of long-range interactions is essential for understanding the origin of the stability of the bilayer structure and the interaction between biomembranes and various electrolytes. However, the ion distributions and their dynamics associated with the phase separation process of the lipid bilayer membrane are still unclear. We perform coarse-grained molecular dynamics simulations to reveal the Na+ and Cl- distributions on charged phospholipid bilayer membranes during phase separation. During the phase separation, cations closely follow the position of negatively charged lipids on a microsecond timescale and are rapidly redistributed parallel to the lipid bilayer. In the homogenous mixture of zwitterionic and negatively charged lipids, cations weakly follow negatively charged lipids, indicating the strong interaction between cations and negatively charged lipids. We also compare cation concentrations as a function of surface charge density obtained by our simulation with those obtained by a modified Poisson-Boltzmann theory. Including the ion finite size makes the statistical results consistent, suggesting the importance of the ion-ion interactions in aqueous solution. Our simulation results advance our understanding of ion distribution during phase separation.
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Affiliation(s)
- Yuji Higuchi
- Research Institute for Information Technology, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan.
| | - Klemen Bohinc
- Faculty of Health Sciences, University of Ljubljana, Zdravstvena 5, SI 1000 Ljubljana, Slovenia
| | - Jurij Reščič
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Vecna pot 113, 1000 Ljubljana, Slovenia
| | - Naofumi Shimokawa
- School of Materials Science, Japan Advanced Institute of Science and Technology, Ishikawa 923-1292, Japan
| | - Hiroaki Ito
- Department of Physics, Graduate School of Science, Chiba University, Chiba 263-8522, Japan
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7
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Bolmatov D, Collier CP, Zav’yalov D, Egami T, Katsaras J. Real Space and Time Imaging of Collective Headgroup Dipole Motions in Zwitterionic Lipid Bilayers. MEMBRANES 2023; 13:442. [PMID: 37103869 PMCID: PMC10142431 DOI: 10.3390/membranes13040442] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 04/05/2023] [Accepted: 04/14/2023] [Indexed: 06/19/2023]
Abstract
Lipid bilayers are supramolecular structures responsible for a range of processes, such as transmembrane transport of ions and solutes, and sorting and replication of genetic materials, to name just a few. Some of these processes are transient and currently, cannot be visualized in real space and time. Here, we developed an approach using 1D, 2D, and 3D Van Hove correlation functions to image collective headgroup dipole motions in zwitterionic phospholipid bilayers. We show that both 2D and 3D spatiotemporal images of headgroup dipoles are consistent with commonly understood dynamic features of fluids. However, analysis of the 1D Van Hove function reveals lateral transient and re-emergent collective dynamics of the headgroup dipoles-occurring at picosecond time scales-that transmit and dissipate heat at longer times, due to relaxation processes. At the same time, the headgroup dipoles also generate membrane surface undulations due a collective tilting of the headgroup dipoles. A continuous intensity band of headgroup dipole spatiotemporal correlations-at nanometer length and nanosecond time scales-indicates that dipoles undergo stretching and squeezing elastic deformations. Importantly, the above mentioned intrinsic headgroup dipole motions can be externally stimulated at GHz-frequency scale, enhancing their flexoelectric and piezoelectric capabilities (i.e., increased conversion efficiency of mechanical energy into electric energy). In conclusion, we discuss how lipid membranes can provide molecular-level insights about biological learning and memory, and as platforms for the development of the next generation of neuromorphic computers.
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Affiliation(s)
- Dima Bolmatov
- Department of Physics and Astronomy, University of Tennessee, Knoxville, TN 37996, USA
- Shull-Wollan Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - C. Patrick Collier
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Dmitry Zav’yalov
- Department of Physics, Volgograd State Technical University, Volgograd 400005, Russia
| | - Takeshi Egami
- Department of Physics and Astronomy, University of Tennessee, Knoxville, TN 37996, USA
- Shull-Wollan Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Department of Materials Science and Engineering, The University of Tennessee, Knoxville, TN 37916, USA
- Materials Science and Technology Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - John Katsaras
- Department of Physics and Astronomy, University of Tennessee, Knoxville, TN 37996, USA
- Shull-Wollan Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Sample Environment Group, Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
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8
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Malik S, Karmakar S, Debnath A. Relaxation time scales of interfacial water upon fluid to ripple to gel phase transitions of bilayers. J Chem Phys 2023; 158:114503. [PMID: 36948835 DOI: 10.1063/5.0138681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2023] Open
Abstract
The slow relaxation of interface water (IW) across three primary phases of membranes is relevant to understand the influence of IW on membrane functions at supercooled conditions. To this objective, a total of ∼16.26μs all-atom molecular dynamics simulations of 1,2-dimyristoyl-sn-glycerol-3-phosphocholine lipid membranes are carried out. A supercooling-driven drastic slow-down in heterogeneity time scales of the IW is found at the fluid to the ripple to the gel phase transitions of the membranes. At both fluid-to-ripple-to-gel phase transitions, the IW undergoes two dynamic crossovers in Arrhenius behavior with the highest activation energy at the gel phase due to the highest number of hydrogen bonds. Interestingly, the Stokes-Einstein (SE) relation is conserved for the IW near all three phases of the membranes for the time scales derived from the diffusion exponents and the non-Gaussian parameters. However, the SE relation breaks for the time scale obtained from the self-intermediate scattering functions. The behavioral difference in different time scales is universal and found to be an intrinsic property of glass. The first dynamical transition in the α relaxation time of the IW is associated with an increase in the Gibbs energy of activation of hydrogen bond breaking with locally distorted tetrahedral structures, unlike the bulk water. Thus, our analyses unveil the nature of the relaxation time scales of the IW across membrane phase transitions in comparison with the bulk water. The results will be useful to understand the activities and survival of complex biomembranes under supercooled conditions in the future.
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Affiliation(s)
- Sheeba Malik
- Department of Chemistry, IIT Jodhpur, Jodhpur, Rajasthan, India
| | - Smarajit Karmakar
- Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research, Hyderabad, India
| | - Ananya Debnath
- Department of Chemistry, IIT Jodhpur, Jodhpur, Rajasthan, India
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9
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Kumar C, Srivastava S. Structural and Dynamical Studies of a Lipid-Nanoclay Composite Layer at the Air-Water Interface. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:10400-10411. [PMID: 35973133 DOI: 10.1021/acs.langmuir.2c00987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
We modulate the adsorption affinities of nanoclay particles for the air-water interface by changing the cationic surface charge composition of the lipid monolayer and thereby tune the attractive electrostatic interaction between the positively charged lipid layer and the zwitterionic nanoclay particles in the water subphase. Our findings emphasize the significance of electrostatic interaction between lipids and the nanoclay, as well as its impact on the structural and viscoelastic features of the composite layer. We use surface pressure (Π)-mean molecular area (A) isotherms, atomic force microscope (AFM), Brewster angle microscopy (BAM), and energy dispersive X-ray spectrsocopy (EDXS) measurements to analyze the structure phases of lipid and lipid-nanoclay composite interfacial layer. The Π-A isotherm curve shows that the lipid-nanoclay composite layer has a larger lift-off area than the neat lipid layer, indicating that nanoparticles adsorb at the lipid layer via electrostatic interaction between lipid and nanoclay molecules. The surface density of the adsorbed nanoclay particles increases with an increase in the composition of the cationic lipid molecules. The stress relaxation response of the composite layer, measured using step compression measurements, exhibits exponential decay and ubiquitous dependence on the cationic dimyristoy-trimethylammonium propane (DMTAP) composition in the lipid layer with crossover to faster relaxation dynamics at DMTAP > 0.75. The power-law study of the frequency-dependent dynamic viscoelastic responses of the interfacial layer, measured using the barrier oscillation method, reveals a transition from glass-like response from neat lipid layer to gel-like dynamic response for the lipid-nanoclay composite layer. A solid-like behavior is evident for all the interface layers with dilation elastic modulus (E') > dilational viscous modulus (E″); however, the dynamic response of the neat layer is largely frequency-independent, whereas lipid-nanoclay composite layers with DMTAP > 0.75 reveal a frequency-dependent dynamic responses. The frequency-dependent power-law exponent of E', E″ increases on increasing the fractional composition of cationic DMTAP from 0.1 to 1.0, which forms a saturated interface of laponite particles and behaves as a viscoelastic gel in 2D.
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Affiliation(s)
- Chandan Kumar
- Soft Matter and Nanomaterials Laboratory, Department of Physics, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Sunita Srivastava
- Soft Matter and Nanomaterials Laboratory, Department of Physics, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
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10
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Hryc J, Szczelina R, Markiewicz M, Pasenkiewicz-Gierula M. Lipid/water interface of galactolipid bilayers in different lyotropic liquid-crystalline phases. Front Mol Biosci 2022; 9:958537. [PMID: 36046609 PMCID: PMC9423040 DOI: 10.3389/fmolb.2022.958537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 07/11/2022] [Indexed: 11/13/2022] Open
Abstract
In this study, carried out using computational methods, the organisation of the lipid/water interface of bilayers composed of galactolipids with both α-linolenoyl acyl chains is analysed and compared in three different lyotropic liquid-crystalline phases. These systems include the monogalactosyldiglyceride (MGDG) and digalactosyldiglyceride (DGDG) bilayers in the lamellar phase, the MGDG double bilayer during stalk phase formation and the inverse hexagonal MGDG phase. For each system, lipid-water and direct and water-mediated lipid-lipid interactions between the lipids of one bilayer leaflet and those of two apposing leaflets at the onset of new phase (stalk) formation, are identified. A network of interactions between DGDG molecules and its topological properties are derived and compared to those for the MGDG bilayer.
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Affiliation(s)
- Jakub Hryc
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Robert Szczelina
- Faculty of Mathematics and Computer Science, Jagiellonian University, Krakow, Poland
| | - Michal Markiewicz
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
- *Correspondence: Marta Pasenkiewicz-Gierula, ; Michal Markiewicz,
| | - Marta Pasenkiewicz-Gierula
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
- *Correspondence: Marta Pasenkiewicz-Gierula, ; Michal Markiewicz,
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11
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Domínguez-Arca V, Sabín J, García-Río L, Bastos M, Taboada P, Barbosa S, Prieto G. On the structure and stability of novel cationic DPPC liposomes doped with gemini surfactants. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.120230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
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12
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Gilbert J, Ermilova I, Nagao M, Swenson J, Nylander T. Effect of encapsulated protein on the dynamics of lipid sponge phase: a neutron spin echo and molecular dynamics simulation study. NANOSCALE 2022; 14:6990-7002. [PMID: 35470842 DOI: 10.1039/d2nr00882c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Lipid membranes are highly mobile systems with hierarchical, time and length scale dependent, collective motions including thickness fluctuations, undulations, and topological membrane changes, which play an important role in membrane interactions. In this work we have characterised the effect of encapsulating two industrially important enzymes, β-galactosidase and aspartic protease, in lipid sponge phase nanoparticles on the dynamics of the lipid membrane using neutron spin echo (NSE) spectroscopy and molecular dynamics (MD) simulations. From NSE, reduced membrane dynamics were observed upon enzyme encapsulation, which were dependent on the enzyme concentration and type. By fitting the intermediate scattering functions (ISFs) with a modified Zilman and Granek model including nanoparticle diffusion, an increase in membrane bending rigidity was observed, with a larger effect for β-galactosidase than aspartic protease at the same concentration. MD simulations for the system with and without aspartic protease showed that the lipids relax more slowly in the system with protein due to the replacement of the lipid carbonyl-water hydrogen bonds with lipid-protein hydrogen bonds. This indicates that the most likely cause of the increase in membrane rigidity observed in the NSE measurements was dehydration of the lipid head groups. The dynamics of the protein itself were also studied, which showed a stable secondary structure of protein over the simulation, indicating no unfolding events occurred.
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Affiliation(s)
- Jennifer Gilbert
- Division of Physical Chemistry, Department of Chemistry, Naturvetarvägen 14, Lund University, 22362 Lund, Sweden.
- NanoLund, Lund University, Professorsgatan 1, 223 63 Lund, Sweden
| | - Inna Ermilova
- Department of Physics, Chalmers University of Technology, 412 96 Gothenburg, Sweden
| | - Michihiro Nagao
- NIST Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA
- Department of Materials Science and Engineering, University of Maryland, College Park, Maryland 20742, USA
- Department of Physics and Astronomy, University of Delaware, Newark, Delaware 19716, USA
| | - Jan Swenson
- Department of Physics, Chalmers University of Technology, 412 96 Gothenburg, Sweden
| | - Tommy Nylander
- Division of Physical Chemistry, Department of Chemistry, Naturvetarvägen 14, Lund University, 22362 Lund, Sweden.
- NanoLund, Lund University, Professorsgatan 1, 223 63 Lund, Sweden
- Lund Institute of Advanced Neutron and X-Ray Science, Scheelevägen 19, 223 70 Lund, Sweden
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13
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Karathanou K, Bondar AN. Algorithm to catalogue topologies of dynamic lipid hydrogen-bond networks. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2022; 1864:183859. [PMID: 34999081 DOI: 10.1016/j.bbamem.2022.183859] [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: 08/30/2021] [Revised: 12/21/2021] [Accepted: 12/31/2021] [Indexed: 06/14/2023]
Abstract
Lipid membrane interfaces host reactions essential for the functioning of cells. The hydrogen-bonding environment at the membrane interface is particularly important for binding of proteins, drug molecules, and ions. We present here the implementation and applications of a depth-first search algorithm that analyzes dynamic lipid interaction networks. Lipid hydrogen-bond networks sampled transiently during simulations of lipid bilayers are clustered according to main types of topologies that characterize three-dimensional arrangements of lipids connected to each other via short water bridges. We characterize the dynamics of hydrogen-bonded lipid clusters in simulations of model POPE and POPE:POPG membranes that are often used for bacterial membrane proteins, in a model of the Escherichia coli membrane with six different lipid types, and in POPS membranes. We find that all lipids sample dynamic hydrogen-bonded networks with linear, star, or circular arrangements of the lipid headgroups, and larger networks with combinations of these three types of topologies. Overall, linear lipid-water bridges tend to be short. Water-mediated lipid clusters in all membranes with PE lipids tend to be somewhat small, with about four lipids in all membranes studied here. POPS membranes allow circular arrangements of three POPS lipids to be sampled frequently, and complex arrangements of linear, star, and circular paths may also be sampled. These findings suggest a molecular picture of the membrane interface whereby lipid molecules transiently connect in clusters with somewhat small spatial extension.
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Affiliation(s)
- Konstantina Karathanou
- Freie Universität Berlin, Department of Physics, Theoretical Molecular Biophysics, Arnimallee 14, D-14195 Berlin, Germany
| | - Ana-Nicoleta Bondar
- Freie Universität Berlin, Department of Physics, Theoretical Molecular Biophysics, Arnimallee 14, D-14195 Berlin, Germany; University of Bucharest, Faculty of Physics, Str. Atomiştilor 405, Bucharest-Măgurele 077125, Romania; Institute for Neuroscience and Medicine and Institute for Advanced Simulations (IAS-5/INM-9), Computational Biomedicine, Forschungszentrum Jülich, 52425 Jülich, Germany.
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14
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Malik S, Debnath A. Structural Changes of Interfacial Water upon Fluid-Ripple-Gel Phase Transitions of Bilayers. Chem Phys Lett 2022. [DOI: 10.1016/j.cplett.2022.139613] [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]
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15
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Hande VR, Chakrabarty S. How Far Is "Bulk Water" from Interfaces? Depends on the Nature of the Surface and What We Measure. J Phys Chem B 2022; 126:1125-1135. [PMID: 35104127 DOI: 10.1021/acs.jpcb.1c08603] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Using systematic molecular dynamics (MD) simulations, we revisit the question: At what distance from an interface do the properties of "bulk water" get recovered? We have considered three different kinds of interfaces: nonpolar (hydrophobic; isooctane-water interface), charged (negative; AOT bilayer), and polar (zwitterionic; POPC bilayer). In order to interrogate the extent of perturbation of the interfacial water molecules as a function of the distance from the interface, we utilize a diverse range of structural and dynamical parameters. To capture the structural perturbations, we look into local density (translational order), local tetrahedral order parameter, and dipolar orientation of the water molecules. We also explore the anisotropic diffusion of the water molecules in the direction perpendicular to the interface as well as the planar diffusion parallel to the interface in a distance dependent manner. In addition, the orientational time correlation functions have been computed to understand the extent of slowdown in the rotational dynamics. As expected, the electrostatic field emanating from the charged AOT interface seems to have the highest long-range effect on the orientational order and dynamics of the water molecules, whereas specific interactions like hydrogen bonding and electrostatic interaction lead to significant trapping and kinetic slowdown for both AOT and POPC (zwitterionic) very close to the interface. Our analysis highlights that not only the length-scale of perturbation depends on the nature of the interfaces and specific interactions but also the type of water property that we measure/calculate. Different water properties seem to have widely different length-scale of perturbation. Orientational order parameters seem to be perturbed to a much longer length-scale as compared to translational order parameters. The global orientational order of water can be perturbed even up to ∼4-5 nm near the negatively charged AOT surface in the absence of any extra electrolyte. This observation has significant implication toward the interpretation of experimental measurements as well since different spectroscopic techniques would probe different parameters or water properties with possible mutual disagreement and inconsistency between different types of measurements. Thus, our study provides a broader and unifying perspective toward the aspect of "context dependent" structural and dynamical perturbation of "interfacial water".
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Affiliation(s)
- Vrushali R Hande
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Pune 411008, Maharashtra, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Suman Chakrabarty
- Department of Chemical, Biological & Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Kolkata 700106, India
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16
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Sabin J, Alatorre-Meda M, Miñones J, Domínguez-Arca V, Prieto G. New insights on the mechanism of polyethylenimine transfection and their implications on gene therapy and DNA vaccines. Colloids Surf B Biointerfaces 2021; 210:112219. [PMID: 34836707 DOI: 10.1016/j.colsurfb.2021.112219] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Revised: 10/30/2021] [Accepted: 11/12/2021] [Indexed: 12/28/2022]
Abstract
Polyethylenimine (PEI) has been demonstrated as an efficient DNA delivery vehicle both in vitro and in vivo. There is a consensus that PEI-DNA complexes enter the cells by endocytosis and escape from endosomes by the so-called "proton sponge" effect. However, little is known on how and where the polyplexes are de-complexed for DNA transcription and replication to occur inside the cell nucleus. To better understand this issue, we (i) tracked the cell internalization of PEI upon transfection to human epithelial cells and (ii) studied the interaction of PEI with phospholipidic layers mimicking nuclear membranes. Both the biological and physicochemical experiments provided evidence of a strong binding affinity between PEI and the lipidic bilayer. Firstly, confocal microscopy revealed that PEI alone could not penetrate the cell nucleus; instead, it arranged throughout the cytoplasm and formed a sort of aureole surrounding the nuclei periphery. Secondly, surface tension measurements, fluorescence dye leakage assays, and differential scanning calorimetry demonstrated that a combination of hydrophobic and electrostatic interactions between PEI and the phospholipidic monolayers/bilayers led to the formation of stable defects along the model membranes, allowing the intercalation of PEI through the monolayer/bilayer structure. Results are also supported by molecular dynamics simulation of the pore formation in PEI-lipidic bilayers. As discussed throughout the text, these results might shed light on a the mechanism in which the interaction between PEI and the nucleus membrane might play an active role on the DNA release: on the one hand, the PEI-membrane interaction is anticipated to facilitate the DNA disassembly from the polyplex by establishing a competition with DNA for the PEI binding and on the other hand, the forming defects are expected to serve as channels for the entrance of de-complexed DNA into the cell nucleus. A better understanding of the mechanism of transfection of cationic polymers opens paths to development of more efficiency vectors to improve gene therapy treatment and the new generation of DNA vaccines.
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Affiliation(s)
- Juan Sabin
- Biophysics and Interfaces Group, Applied Physics Department, Universidade de Santiago de Compostela, Spain; AFFINImeter-Software 4 Science Developments S.L. Edificio Emprendia s/n Campus Vida, Santiago de Compostela, Spain.
| | - Manuel Alatorre-Meda
- Cátedras CONACyT-Tecnológico Nacional de México/I. T. Tijuana, Centro de Graduados e Investigación en Química-Grupo de Biomateriales y Nanomedicina, Blvd. Alberto Limón Padilla S/N, 22510 Tijuana, BC, Mexico
| | - Jose Miñones
- Department of Physical Chemistry, Faculty of Pharmacy Universidade de Santiago de Compostela, Spain
| | - Vicente Domínguez-Arca
- Biophysics and Interfaces Group, Applied Physics Department, Universidade de Santiago de Compostela, Spain.
| | - Gerardo Prieto
- Biophysics and Interfaces Group, Applied Physics Department, Universidade de Santiago de Compostela, Spain
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17
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Malik S, Debnath A. Dehydration induced dynamical heterogeneity and ordering mechanism of lipid bilayers. J Chem Phys 2021; 154:174904. [PMID: 34241050 DOI: 10.1063/5.0044614] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Understanding the influence of dehydration on the membrane structure is crucial to control membrane functionality related to domain formation and cell fusion under anhydrobiosis conditions. To this end, we perform all-atom molecular dynamic simulations of 1,2-dimyristoyl-sn-glycero-3-phosphocholine dimyristoylphosphatidylcholine lipid membranes at different hydration levels at 308 K. As dehydration increases, the lipid area per head group decreases with an increase in bilayer thickness and lipid order parameters indicating bilayer ordering. Concurrently, translational and rotational dynamics of interfacial water (IW) molecules near membranes slow down. On the onset of bilayer ordering, the IW molecules exhibit prominent features of dynamical heterogeneity evident from non-Gaussian parameters and one-dimensional van Hove correlation functions. At a fully hydrated state, diffusion constants (D) of the IW follow a scaling relation, D∼τα -1, where the α relaxation time (τα) is obtained from self-intermediate scattering functions. However, upon dehydration, the relation breaks and the D of the IW follows a power law behavior as D∼τα -0.57, showing the signature of glass dynamics. τα and hydrogen bond lifetime calculated from intermittent hydrogen bond auto-correlation functions undergo a similar crossover in association with bilayer ordering on dehydration. The bilayer ordering is accompanied with an increase in fraction of caged lipids spanned over the bilayer surface and a decrease in fraction of mobile lipids due to the non-diffusive dynamics. Our analyses reveal that the microscopic mechanism of lipid ordering by dehydration is governed by dynamical heterogeneity. The fundamental understanding from this study can be applied to complex bio-membranes to trap functionally relevant gel-like domains at room temperature.
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Affiliation(s)
- Sheeba Malik
- Department of Chemistry, Indian Institute of Technology Jodhpur, Karwad, Rajasthan, India
| | - Ananya Debnath
- Department of Chemistry, Indian Institute of Technology Jodhpur, Karwad, Rajasthan, India
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18
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Interfacial hydration determines orientational and functional dimorphism of sterol-derived Raman tags in lipid-coated nanoparticles. Proc Natl Acad Sci U S A 2021; 118:2105913118. [PMID: 34389679 DOI: 10.1073/pnas.2105913118] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Lipid-coated noble metal nanoparticles (L-NPs) combine the biomimetic surface properties of a self-assembled lipid membrane with the plasmonic properties of a nanoparticle (NP) core. In this work, we investigate derivatives of cholesterol, which can be found in high concentrations in biological membranes, and other terpenoids, as tunable, synthetic platforms to functionalize L-NPs. Side chains of different length and polarity, with a terminal alkyne group as Raman label, are introduced into cholesterol and betulin frameworks. The synthesized tags are shown to coexist in two conformations in the lipid layer of the L-NPs, identified as "head-out" and "head-in" orientations, whose relative ratio is determined by their interactions with the lipid-water hydrogen-bonding network. The orientational dimorphism of the tags introduces orthogonal functionalities into the NP surface for selective targeting and plasmon-enhanced Raman sensing, which is utilized for the identification and Raman imaging of epidermal growth factor receptor-overexpressing cancer cells.
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19
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Voloshin VP, Medvedev NN. ORIENTATION OF WATER MOLECULES NEAR A GLOBULAR PROTEIN. J STRUCT CHEM+ 2021. [DOI: 10.1134/s002247662105005x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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20
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Higuchi Y, Asano Y, Kuwahara T, Hishida M. Rotational Dynamics of Water at the Phospholipid Bilayer Depending on the Head Groups Studied by Molecular Dynamics Simulations. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:5329-5338. [PMID: 33881324 DOI: 10.1021/acs.langmuir.1c00417] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Hydration states are a crucial factor that affect the self-assembly and properties of soft materials and biomolecules. Although previous experiments have revealed that the hydration state strongly depends on the chemical structure of lipid molecules, the mechanisms at the molecular level remain unknown. Classical and density-functional tight-binding (DFTB) molecular dynamics (MD) simulations are employed to determine the mechanisms underlying dissimilar water dynamics between lipid membranes with phosphatidylcholine (PC) and phosphatidylethanolamine (PE) head groups. The classical MD simulation shows that rotational relaxations of water are faster on the PE lipid than on the PC lipid, which is consistent with a previous experimental study using terahertz spectroscopy. Furthermore, DFTB-MD simulation of N(CH3)4+ and NH4+ ions, which correspond to the different head groups in PC and PE, respectively, shows qualitative agreement with the classical MD simulation. Remarkably, the PE lipids and the NH4+ ions break hydrogen bonds between water molecules in the secondary hydration shell. In contrast, the PC lipids and the N(CH3)4+ ions bind water molecules weakly in both the primary and secondary hydration shells and increase hydrogen bonds between water. Our atomistic simulations show that these changes in the hydrogen-bond network of water molecules cause the different rotational relaxation of water molecules between the two lipids.
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Affiliation(s)
- Yuji Higuchi
- Institute for Solid State Physics, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8581, Japan
| | - Yuta Asano
- Institute for Solid State Physics, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8581, Japan
| | - Takuya Kuwahara
- MicroTribology Center μTC, Fraunhofer IWM, Wöhlerstraße 11, Freiburg 79108, Germany
| | - Mafumi Hishida
- Department of Chemistry, Faculty of Pure and Applied Sciences, University of Tsukuba, Tsukuba 305-8571, Ibaraki, Japan
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21
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Mondal D, Malik S, Banerjee P, Kundu N, Debnath A, Sarkar N. Modulation of Membrane Fluidity to Control Interfacial Water Structure and Dynamics in Saturated and Unsaturated Phospholipid Vesicles. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:12423-12434. [PMID: 33035065 DOI: 10.1021/acs.langmuir.0c02736] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The structure and dynamics of interfacial water in biological systems regulate the biochemical reactions. But, it is still enigmatic how the behavior of the interfacial water molecule is controlled. Here, we have investigated the effect of membrane fluidity on the structure and dynamics of interfacial water molecules in biologically relevant phopholipid vesicles. This study delineates that modulation of membrane fluidity through interlipid separation and unsaturation not only mitigate membrane rigidity but also disrupt the strong hydrogen bond (H-bond) network around the lipid bilayer interface. As a result, a disorder in H-bonding between water molecules arises several layers beyond the first hydration shell of the polar headgroup, which essentially modifies the interfacial water structure and dynamics. Furthermore, we have also provided evidence of increasing transportation through these modulated membranes, which enhance the membrane mediated isomerization reaction rate.
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Affiliation(s)
- Dipankar Mondal
- Department of Chemistry, Indian Institute of Technology Kharagpur Kharagpur 721302, West Bengal, India
| | - Sheeba Malik
- Department of Chemistry, Indian Institute of Technology Jodhpur, Jodhpur 342037, Rajasthan, India
| | - Pavel Banerjee
- Department of Chemistry, Indian Institute of Technology Kharagpur Kharagpur 721302, West Bengal, India
| | - Niloy Kundu
- Department of Chemistry, Indian Institute of Technology Kharagpur Kharagpur 721302, West Bengal, India
- Environment Research Group, R&D and Scientific Services Department, Tata Steel Ltd., Jamshedpur 831007, India
| | - Ananya Debnath
- Department of Chemistry, Indian Institute of Technology Jodhpur, Jodhpur 342037, Rajasthan, India
| | - Nilmoni Sarkar
- Department of Chemistry, Indian Institute of Technology Kharagpur Kharagpur 721302, West Bengal, India
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22
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Bolmatov D, Kinnun JJ, Katsaras J, Lavrentovich MO. Phonon-mediated lipid raft formation in biological membranes. Chem Phys Lipids 2020; 232:104979. [PMID: 32980352 DOI: 10.1016/j.chemphyslip.2020.104979] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 09/21/2020] [Accepted: 09/21/2020] [Indexed: 10/23/2022]
Abstract
Short-wavelength collective molecular motions, also known as phonons, have recently attracted much interest in revealing dynamic properties of biological membranes through the use of neutron and X-ray scattering, infrared and Raman spectroscopies, and molecular dynamics simulations. Experimentally detecting unique vibrational patterns such as, shear phonon excitations, viscoelastic crossovers, transverse acoustic phonon gaps, and continuous and truncated optical phonon modes in cellular membranes, to name a few, has proven non-trivial. Here, we review recent advances in liquid thermodynamics that have resulted in the development of the phonon theory of liquids. The theory has important predictions regarding the shear vibrational spectra of fluids, namely the emergence of viscoelastic crossovers and transverse acoustic phonon gaps. Furthermore, we show that these vibrational patterns are common in soft (non-crystalline) materials, including, but not limited to liquids, colloids, liquid crystals (mesogens), block copolymers, and biological membranes. The existence of viscoelastic crossovers and acoustic phonon gaps define the self-diffusion properties of cellular membranes and provide a molecular picture of the transient nature of lipid rafts (Bolmatov et al., 2020). Importantly, the timescales (picoseconds) for the formation and dissolution of transient lipid rafts match the lifetime of the formation and breakdown of interfacial water hydrogen bonds. Apart from acoustic propagating phonon modes, biological membranes can also support more energetic non-propagating optical phonon excitations, also known as standing waves or breathing modes. Importantly, optical phonons can be truncated due to the existence of finite size nanodomains made up of strongly correlated lipid-cholesterol molecular pairs. These strongly coupled molecular pairs can serve as nucleation centers for the formation of stable rafts at larger length scales, due to correlations of spontaneous fluctuations (Onsager's regression hypothesis). Finally and importantly, molecular level viscoelastic crossovers, acoustic phonon gaps, and continuous and truncated optical phonon modes may offer insights as to how lipid-lipid and lipid-protein interactions enable biological function.
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Affiliation(s)
- Dima Bolmatov
- Large Scale Structures Group, Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, United States; Shull-Wollan Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831, United States; Department of Physics and Astronomy, University of Tennessee, Knoxville, TN 37996, United States.
| | - Jacob J Kinnun
- Large Scale Structures Group, Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, United States; Shull-Wollan Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831, United States.
| | - John Katsaras
- Shull-Wollan Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831, United States; Department of Physics and Astronomy, University of Tennessee, Knoxville, TN 37996, United States; Sample Environment Group, Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, United States.
| | - Maxim O Lavrentovich
- Shull-Wollan Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831, United States; Department of Physics and Astronomy, University of Tennessee, Knoxville, TN 37996, United States.
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23
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Gavish L, Hoffer O, Rabin N, Halak M, Shkilevich S, Shayovitz Y, Weizman G, Haim O, Gavish B, Gertz SD, Ovadia‐Blechman Z. Microcirculatory Response to Photobiomodulation—Why Some Respond and Others Do Not: A Randomized Controlled Study. Lasers Surg Med 2020; 52:863-872. [DOI: 10.1002/lsm.23225] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/01/2020] [Indexed: 12/18/2022]
Affiliation(s)
- Lilach Gavish
- The Institute for Research in Military Medicine (IRMM) Faculty of Medicine of The Hebrew University of Jerusalem and Israel Defense Forces Medical Corps Ein Kerem, POB 12272 Jerusalem 9112001 Israel
- Institute for Medical Research‐Israel‐Canada (IMRIC) Faculty of Medicine of The Hebrew University of Jerusalem Ein Kerem, POB 12272 Jerusalem 9112001 Israel
| | - Oshrit Hoffer
- School of Electrical Engineering Afeka Tel‐Aviv Academic College of Engineering 38 Mivtza Kadesh St. Tel‐Aviv 6910717 Israel
| | - Neta Rabin
- Unit of Mathematics Afeka Tel‐Aviv Academic College of Engineering 38 Mivtza Kadesh St. Tel‐Aviv 6910717 Israel
- Department of Industrial Engineering, The Iby and Aladar Fleischman Faculty of Engineering Tel‐Aviv University P.O.B 39040, Ramat Aviv Tel‐Aviv 6997801 Israel
| | - Moshe Halak
- Department of Vascular Surgery Sheba Medical Center Ramat‐Gan 5265601 Israel
| | - Simon Shkilevich
- School of Medical Engineering Afeka Tel‐Aviv Academic College of Engineering 8 Mivtza Kadesh St. Tel‐Aviv 6910717 Israel
| | - Yuval Shayovitz
- School of Medical Engineering Afeka Tel‐Aviv Academic College of Engineering 8 Mivtza Kadesh St. Tel‐Aviv 6910717 Israel
| | - Gal Weizman
- School of Medical Engineering Afeka Tel‐Aviv Academic College of Engineering 8 Mivtza Kadesh St. Tel‐Aviv 6910717 Israel
| | - Ortal Haim
- School of Electrical Engineering Afeka Tel‐Aviv Academic College of Engineering 38 Mivtza Kadesh St. Tel‐Aviv 6910717 Israel
| | | | - S. David Gertz
- The Institute for Research in Military Medicine (IRMM) Faculty of Medicine of The Hebrew University of Jerusalem and Israel Defense Forces Medical Corps Ein Kerem, POB 12272 Jerusalem 9112001 Israel
- Institute for Medical Research‐Israel‐Canada (IMRIC) Faculty of Medicine of The Hebrew University of Jerusalem Ein Kerem, POB 12272 Jerusalem 9112001 Israel
| | - Zehava Ovadia‐Blechman
- School of Medical Engineering Afeka Tel‐Aviv Academic College of Engineering 8 Mivtza Kadesh St. Tel‐Aviv 6910717 Israel
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Srivastava A, Malik S, Karmakar S, Debnath A. Dynamic coupling of a hydration layer to a fluid phospholipid membrane: intermittency and multiple time-scale relaxations. Phys Chem Chem Phys 2020; 22:21158-21168. [DOI: 10.1039/d0cp02803g] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Understanding the coupling of a hydration layer and a lipid membrane is crucial to gaining access to membrane dynamics and understanding its functionality towards various biological processes.
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Affiliation(s)
- Abhinav Srivastava
- Department of Chemistry
- Indian Institute of Technology Jodhpur
- Rajasthan
- India
| | - Sheeba Malik
- Department of Chemistry
- Indian Institute of Technology Jodhpur
- Rajasthan
- India
| | - Smarajit Karmakar
- Centre for Interdisciplinary Sciences
- Tata Institute of Fundamental Research
- Hyderabad 500107
- India
| | - Ananya Debnath
- Department of Chemistry
- Indian Institute of Technology Jodhpur
- Rajasthan
- India
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25
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Srivastava A, Karmakar S, Debnath A. Quantification of spatio-temporal scales of dynamical heterogeneity of water near lipid membranes above supercooling. SOFT MATTER 2019; 15:9805-9815. [PMID: 31746927 DOI: 10.1039/c9sm01725a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
A hydrated 1,2-dimyristoyl-sn-glycero-3-phosphorylcholine (DMPC) lipid membrane is investigated using an all atom molecular dynamics simulation at 308 K to determine the physical sources of universal slow relaxations of hydration layers and length-scale of the spatially heterogeneous dynamics. Continuously residing interface water (IW) molecules hydrogen bonded to different moieties of lipid heads in the membrane are identified. The non-Gaussian parameters of all classes of IW molecules show a cross-over from cage vibration to translational diffusion. A significant non-Gaussianity is observed for the IW molecules exhibiting large length correlations in translational van Hove functions. Two time-scales for the ballistic motions and hopping transitions are obtained from the self intermediate scattering functions of the IW molecules with an additional long relaxation, which disappears for bulk water. The long relaxation time-scales for the IW molecules obtained from the self intermediate scattering functions are in good accordance with the hydrogen bond relaxation time-scales irrespective of the nature of the chemical confinement and the confinement lifetime. Employing a block analysis approach, the length-scale of dynamical heterogeneities is captured from a transition from non-Gaussianity to Gaussianity in van Hove correlation functions of the IW molecules. The heterogeneity length-scale is comparable to the wave-length of the small and weak undulations of the membrane calculated by Fourier transforms of lipid tilts. This opens up a new avenue towards a possible correlation between heterogeneity length-scale and membrane curvature more significant for rippled membranes. Thus, our analyses provide a measure towards the spatio-temporal scale of dynamical heterogeneity of confined water near membranes.
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Affiliation(s)
- Abhinav Srivastava
- Department of Chemistry, Indian Institute of Technology Jodhpur, Jodhpur 342037, India.
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26
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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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27
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Singha N, Srivastava A, Pramanik B, Ahmed S, Dowari P, Chowdhuri S, Das BK, Debnath A, Das D. Unusual confinement properties of a water insoluble small peptide hydrogel. Chem Sci 2019; 10:5920-5928. [PMID: 31360397 PMCID: PMC6566298 DOI: 10.1039/c9sc01754b] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 05/04/2019] [Indexed: 12/18/2022] Open
Abstract
Unlike polymeric hydrogels, in the case of supramolecular hydrogels, the cross-linked network formation is governed by non-covalent forces. Hence, in these cases, the gelator molecules inside the network retain their characteristic physicochemical properties as no covalent modification is involved. Supramolecular hydrogels thus get dissolved easily in aqueous medium as the dissolution leads to a gain in entropy. Thus, any supramolecular hydrogel, insoluble in bulk water, is beyond the present understanding and hitherto not reported as well. Herein, we present a peptide-based (PyKC) hydrogel which remained insoluble in water for more than a year. Moreover, in the gel state, any movement of solvent or solute to and from the hydrogel is highly restricted resulting in a high degree of compartmentalization. The hydrogel could be re-dissolved in the presence of some biomolecules which makes it a prospective material for in vivo applications. Experimental studies and all atom molecular dynamics simulations revealed that a cysteine containing gelator forms dimers through disulfide linkage which self-assemble into PyKC layers with a distinct PyKC-water interface. The hydrogel is stabilized by intra-molecular hydrogen bonds within the peptide-conjugates and the π-π stacking of the pyrene rings. The unique confinement ability of the hydrogel is attributed to the slow dynamics of water which remains confined in the core region of PyKC via hydrogen bonds. The hydrogen bonds present in the confined water need activation energies to move through the water depleted hydrophobic environment of pyrene rings which significantly reduces water transport across the hydrogel. The compartmentalizing ability is effectively used to protect enzymes for a long time from denaturing agents like urea, heat or methanol. Overall, the presented system shows unique insolubility and confinement properties that could be a milestone in the research of soft-materials.
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Affiliation(s)
- Nilotpal Singha
- Department of Chemistry , Indian Institute of Technology Guwahati , Assam 781039 , India .
| | - Arpita Srivastava
- Department of Chemistry , Indian Institute of Technology Jodhpur , Rajasthan 342037 , India .
| | - Bapan Pramanik
- Department of Chemistry , Indian Institute of Technology Guwahati , Assam 781039 , India .
| | - Sahnawaz Ahmed
- Department of Chemistry , Indian Institute of Technology Guwahati , Assam 781039 , India .
| | - Payel Dowari
- Department of Chemistry , Indian Institute of Technology Guwahati , Assam 781039 , India .
| | - Sumit Chowdhuri
- Department of Chemistry , Indian Institute of Technology Guwahati , Assam 781039 , India .
| | - Basab Kanti Das
- Department of Chemistry , Indian Institute of Technology Guwahati , Assam 781039 , India .
| | - Ananya Debnath
- Department of Chemistry , Indian Institute of Technology Jodhpur , Rajasthan 342037 , India .
| | - Debapratim Das
- Department of Chemistry , Indian Institute of Technology Guwahati , Assam 781039 , India .
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Das K, Roy B, Satpathi S, Hazra P. Impact of Topology on the Characteristics of Water inside Cubic Lyotropic Liquid Crystalline Systems. J Phys Chem B 2019; 123:4118-4128. [DOI: 10.1021/acs.jpcb.9b01559] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Konoya Das
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune Dr. Homi Bhabha Road, Pashan, Pune, India 411008
| | - Bibhisan Roy
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune Dr. Homi Bhabha Road, Pashan, Pune, India 411008
| | - Sagar Satpathi
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune Dr. Homi Bhabha Road, Pashan, Pune, India 411008
| | - Partha Hazra
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune Dr. Homi Bhabha Road, Pashan, Pune, India 411008
- Centre for Energy Science, Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune, India 411008
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Päslack C, Smith JC, Heyden M, Schäfer LV. Hydration-mediated stiffening of collective membrane dynamics by cholesterol. Phys Chem Chem Phys 2019; 21:10370-10376. [DOI: 10.1039/c9cp01431d] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Hydration water governs the cholesterol-induced changes in collective headgroup dynamics in lipid bilayers.
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Affiliation(s)
- Christopher Päslack
- Theoretical Chemistry
- Faculty of Chemistry and Biochemistry
- Ruhr University Bochum
- D-44780 Bochum
- Germany
| | - Jeremy C. Smith
- Center for Molecular Biophysics
- Oak Ridge National Laboratory
- Oak Ridge
- USA
- Department of Biochemistry and Cellular and Molecular Biology
| | - Matthias Heyden
- School of Molecular Sciences
- Arizona State University
- Tempe
- USA
| | - Lars V. Schäfer
- Theoretical Chemistry
- Faculty of Chemistry and Biochemistry
- Ruhr University Bochum
- D-44780 Bochum
- Germany
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Franck JM, Han S. Overhauser Dynamic Nuclear Polarization for the Study of Hydration Dynamics, Explained. Methods Enzymol 2018; 615:131-175. [PMID: 30638529 DOI: 10.1016/bs.mie.2018.09.024] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
We outline the physical properties of hydration water that are captured by Overhauser Dynamic Nuclear Polarization (ODNP) relaxometry and explore the insights that ODNP yields about the water and the surface that this water is coupled to. As ODNP relies on the pairwise cross-relaxation between the electron spin of a spin probe and a proton nuclear spin of water, it captures the dynamics of single-particle diffusion of an ensemble of water molecules moving near the spin probe. ODNP principally utilizes the same physics as other nuclear magnetic resonance (NMR) relaxometry (i.e., relaxation measurement) techniques. However, in ODNP, electron paramagnetic resonance (EPR) excites the electron spins probes and their high net polarization acts as a signal amplifier. Furthermore, it renders ODNP parameters highly sensitive to water moving at rates commensurate with the EPR frequency of the spin probe (typically 10GHz). Also, ODNP selectively enhances the NMR signal contributions of water moving within close proximity to the spin label. As a result, ODNP can capture ps-ns movements of hydration waters with high sensitivity and locality, even in samples with protein concentrations as dilute as 10 µM. To date, the utility of the ODNP technique has been demonstrated for two major applications: the characterization of the spatial variation in the properties of the hydration layer of proteins or other surfaces displaying topological diversity, and the identification of structural properties emerging from highly disordered proteins and protein domains. The former has been shown to correlate well with the properties of hydration water predicted by MD simulations and has been shown capable of evaluating the hydrophilicity or hydrophobicity of a surface. The latter has been demonstrated for studies of an interhelical loop of proteorhodopsin, the partial structure of α-synuclein embedded at the lipid membrane surface, incipient structures adopted by tau proteins en route to fibrils, and the structure and hydration profile of a transmembrane peptide. This chapter focuses on offering a mechanistic understanding of the ODNP measurement and the molecular dynamics encoded in the ODNP parameters. In particular, it clarifies how the electron-nuclear dipolar coupling encodes information about the molecular dynamics in the nuclear spin self-relaxation and, more importantly, the electron-nuclear spin cross-relaxation rates. The clarification of the molecular dynamics underlying ODNP should assist in establishing a connection to theory and computer simulation that will offer far richer interpretations of ODNP results in future studies.
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Affiliation(s)
- John M Franck
- Department of Chemistry, Syracuse University, Syracuse, NY, United States.
| | - Songi Han
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, CA, United States; Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, CA, United States
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