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Miyajima A, Nakao H, Ikeda K, Nakano M. The Nanometer-Scale Proximity of Bilayers Facilitates Intermembrane Lipid Transfer. J Phys Chem Lett 2023; 14:4172-4178. [PMID: 37114850 DOI: 10.1021/acs.jpclett.3c00154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Biological membranes approach one another in various biological phenomena, such as lipid transport at membrane contact sites and membrane fusion. The proximity of two bilayers may cause environmental changes in the interbilayer space and alter the dynamics of lipid molecules. Here, we investigate the structure and dynamics of vesicles aggregated due to the depletion attraction caused by polyethylene glycol (PEG) through static and dynamic small-angle neutron scattering. Manipulation of the interbilayer distance using PEG-conjugated lipids reveals that lipid molecules rapidly transfer between vesicles when the opposing bilayers are within ∼2 nm of each other. This distance corresponds to a region in which water molecules are more structured than in bulk water. Kinetic analysis suggests that the decrease in water entropy is responsible for the progression of lipid transfer. These results provide a basis for understanding the dynamic function of biomembranes in confined regions.
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Affiliation(s)
- Ayari Miyajima
- Department of Biointerface Chemistry, Faculty of Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan
| | - Hiroyuki Nakao
- Department of Biointerface Chemistry, Faculty of Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan
| | - Keisuke Ikeda
- Department of Biointerface Chemistry, Faculty of Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan
| | - Minoru Nakano
- Department of Biointerface Chemistry, Faculty of Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan
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2
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Franco LR, Park P, Chaimovich H, Coutinho K, Cuccovia IM, Lima FS. Simulations reveal that antimicrobial BP100 induces local membrane thinning, slows lipid dynamics and favors water penetration. RSC Adv 2022; 12:4573-4588. [PMID: 35425494 PMCID: PMC8981376 DOI: 10.1039/d1ra06267k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 01/26/2022] [Indexed: 11/21/2022] Open
Abstract
MD simulations reveal that BP100 peptide induces local membrane thinning and negative curvature, slows lipid dynamics and increases the water life time in the lipid hydrophobic core and transmembrane water transport in the direction of the peptide.
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Affiliation(s)
| | - Peter Park
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Hernan Chaimovich
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Kaline Coutinho
- Instituto de Física, Universidade de São Paulo, São Paulo, Brazil
| | - Iolanda M. Cuccovia
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Filipe S. Lima
- Departamento de Química Fundamental, Centro de Ciências Exatas e da Natureza, Universidade Federal de Pernambuco, Recife, Brazil
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3
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Borocci S, Bozzuto G, Bombelli C, Ceccacci F, Formisano G, Stringaro A, Molinari A, Mancini G. How stereochemistry of lipid components can affect lipid organization and the route of liposome internalization into cells. NANOSCALE 2021; 13:11976-11993. [PMID: 34212969 DOI: 10.1039/d1nr02175c] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Though liposome-based drugs are in clinical use, the mechanism of cell internalization of liposomes is yet an object of controversy. The present experimental investigation, carried out on human glioblastoma cells, indicated different internalization routes for two diastereomeric liposomes. Molecular dynamics simulations of the lipid bilayers of the two formulations indicated that the different stereochemistry of a lipid component controls some parameters such as area per lipid molecule and fluidity of lipid membranes, surface potential and water organization at the lipid/water interface, all of which affect the interaction with biomolecules and cell components.
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Affiliation(s)
- Stefano Borocci
- Dipartimento per la Innovazione nei sistemi Biologici, Agroalimentari e Forestali (DIBAF), Università degli Studi della Tuscia, L.go dell'Università, s.n.c., 01100 Viterbo, Italy.
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4
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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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5
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Deplazes E, Sarrami F, Poger D. Effect of H3O+ on the Structure and Dynamics of Water at the Interface with Phospholipid Bilayers. J Phys Chem B 2020; 124:1361-1373. [DOI: 10.1021/acs.jpcb.9b10169] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Evelyne Deplazes
- School of Life Sciences, University of Technology Sydney, Ultimo, New South Wales 2007, Australia
- School of Pharmacy and Biomedical Sciences, Curtin Institute for Computation, Curtin University, Perth, Western Australia 6845, Australia
| | - Farzaneh Sarrami
- School of Chemistry and Biochemistry, The University of Western Australia, Perth, Western Australia 6009, Australia
| | - David Poger
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland 4072, Australia
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6
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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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7
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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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8
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Cui F, Chen W, Kong X, Liu L, Shi C, Li Y. Anomalous Dynamics of Water in Polyamide Matrix. J Phys Chem B 2019; 123:3086-3095. [PMID: 30879304 DOI: 10.1021/acs.jpcb.9b01491] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Water in polymer matrixes is likely to show anomalous dynamics, a problem that has not been well understood yet. Here, we performed atomistic molecular dynamics simulations to study the water dynamics in a polyamide (PA) matrix, the bulk phase of well-known reverse osmosis membranes. For time-dependent ensemble average, water molecules experienced ballistic diffusion at a shorter time scale, followed by a crossover from subdiffusion to Brownian diffusion at a time scale ∼10 ns, and non-Gaussian diffusion, an indication of anomalous dynamics, sticks on even in the Brownian diffusion region. The anomalous dynamics mainly originates from two distinct motions including small-step continuous diffusion and jumping diffusion. The jumping motion has a mean length of 3.08 ± 0.31 Å and characteristic relaxation time of 0.218 ± 0.040 ns, which dominates the water diffusion in a fully hydrated PA matrix. It comprised low- and high-frequency jumps; the former is almost unchanged, and the latter remarkably increases with the increase of the hydration level. Surrounding neighbors of water strongly affect the jumping frequency, which exponentially or linearly decays with the increase in the number of atoms from the PA matrix. Although the PA matrix is flexible, associated with the water dynamics, the translocation of water is mainly through either tracing the position of neighboring water or jumping into the adjacent accommodation space.
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Affiliation(s)
- Fengchao Cui
- Key Laboratory of High-Performance Synthetic Rubber and Its Composite Materials , Changchun Institute of Applied Chemistry (CIAC), Chinese Academy of Sciences , Changchun 130022 , P. R. China
| | - Wenduo Chen
- Key Laboratory of High-Performance Synthetic Rubber and Its Composite Materials , Changchun Institute of Applied Chemistry (CIAC), Chinese Academy of Sciences , Changchun 130022 , P. R. China.,School of Materials , Sun Yat-Sen University , 135 Xingang West , Guangzhou 510275 , P. R. China
| | - Xiangxin Kong
- Key Laboratory of High-Performance Synthetic Rubber and Its Composite Materials , Changchun Institute of Applied Chemistry (CIAC), Chinese Academy of Sciences , Changchun 130022 , P. R. China
| | - Lunyang Liu
- Key Laboratory of High-Performance Synthetic Rubber and Its Composite Materials , Changchun Institute of Applied Chemistry (CIAC), Chinese Academy of Sciences , Changchun 130022 , P. R. China
| | - Ce Shi
- Key Laboratory of High-Performance Synthetic Rubber and Its Composite Materials , Changchun Institute of Applied Chemistry (CIAC), Chinese Academy of Sciences , Changchun 130022 , P. R. China
| | - Yunqi Li
- Key Laboratory of High-Performance Synthetic Rubber and Its Composite Materials , Changchun Institute of Applied Chemistry (CIAC), Chinese Academy of Sciences , Changchun 130022 , P. R. China
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9
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Site-Specific Peptide Probes Detect Buried Water in a Lipid Membrane. Biophys J 2019; 116:1692-1700. [PMID: 31000156 DOI: 10.1016/j.bpj.2019.03.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Revised: 03/05/2019] [Accepted: 03/06/2019] [Indexed: 01/08/2023] Open
Abstract
Transmembrane peptides contain polar residues in the interior of the membrane, which may alter the electrostatic environment and favor hydration in the otherwise nonpolar environment of the membrane core. Here, we demonstrate a general, nonperturbative strategy to probe hydration of the peptide backbone at specific depths within the bilayer using a combination of site-specific isotope labels, ultrafast two-dimensional infrared spectroscopy, and spectral modeling based on molecular dynamics simulations. Our results show that the amphiphilic pH-low insertion peptide supports a highly heterogeneous environment, with significant backbone hydration of nonpolar residues neighboring charged residues. For example, a leucine residue located as far as 1 nm into the hydrophobic bulk reports hydrogen-bonded populations as high as ∼20%. These findings indicate that the polar nature of these residues may facilitate the transport of water molecules into the hydrophobic core of the membrane.
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10
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11
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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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12
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Elola MD, Rodriguez J. Influence of Cholesterol on the Dynamics of Hydration in Phospholipid Bilayers. J Phys Chem B 2018; 122:5897-5907. [PMID: 29742895 DOI: 10.1021/acs.jpcb.8b00360] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We investigate the dynamics of interfacial waters in dipalmitoylphosphatidylcholine (DPPC) bilayers upon the addition of cholesterol, by molecular dynamics simulations. Our data reveal that the inclusion of cholesterol modifies the membrane aqueous interfacial dynamics: waters diffuse faster, their rotational decay time is shorter, and the DPPC/water hydrogen bond dynamics relaxes faster than in the pure DPPC membrane. The observed acceleration of the translational water dynamics agrees with recent experimental results, in which, by means of NMR techniques, an increment of the surface water diffusivity is measured upon the addition of cholesterol. A microscopic analysis of the lipid/water hydrogen bond network at the interfacial region suggests that the mechanism underlying the observed water mobility enhancement is given by the rupture of a fraction of interlipid water bridge hydrogen bonds connecting two different DPPC molecules, concomitant to the formation of new lipid/solvent bonds, whose dynamics is faster than that of the former. The consideration of a simple two-state model for the decay of the hydrogen bond correlation function yielded excellent results, obtaining two well-separated characteristic time scales: a slow one (∼250 ps) associated with bonds linking two DPPC molecules, and a fast one (∼15 ps), related to DPPC/solvent bonds.
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Affiliation(s)
- M Dolores Elola
- Departamento de Física , Comisión Nacional de Energía Atómica , Av Libertador 8250, 1429 Buenos Aires , Argentina
| | - Javier Rodriguez
- Departamento de Física , Comisión Nacional de Energía Atómica , Av Libertador 8250, 1429 Buenos Aires , Argentina.,ECyT , UNSAM , Martín de Irigoyen 3100, 1650 San Martín, Provincia de Buenos Aires , Argentina
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13
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Sharma S, Biswas P. Hydration water dynamics around a protein surface: a first passage time approach. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2018; 30:035101. [PMID: 29192889 DOI: 10.1088/1361-648x/aa9eab] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
A stochastic noise-driven dynamic model is proposed to study the diffusion of water molecules around a protein surface, under the effect of thermal fluctuations that arise due to the collision of water molecules with the surrounding environment. The underlying dynamics of such a system may be described in the framework of the generalized Langevin equation, where the thermal fluctuations are assumed to be algebraically correlated in time, which governs the non-Markovian behavior of the system. Results of the calculations of mean-square displacement and the velocity autocorrelation function reveal that the hydration water around the protein surface follows subdiffusive dynamics at long times. Analytical expressions for the first passage time distribution, survival probability, mean residence time and mean first passage time of water molecules are derived for different boundary conditions, to analyze hydration water dynamics under the effect of thermally correlated noise. The results depict a unimodal distribution of the first passage time unlike Brownian motion. The survival probability of hydration water follows a stretched exponential decay for both boundary conditions. The mean residence time of the hydration water molecule for different initial positions increases with increase in the complexity/heterogeneity of the surrounding environment for both boundary conditions. The mean first passage time of the water molecule to reach the absorbing/reflecting boundary follows an asymptotic power law with respect to the thickness of the hydration layer, and increases with increase in the complexity/heterogeneity of the environment.
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Affiliation(s)
- Shivangi Sharma
- Department of Chemistry, University of Delhi, Delhi 110007, India
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14
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McDaniel JG, Yethiraj A. Coupling between the Dynamics of Water and Surfactants in Lyotropic Liquid Crystals. J Phys Chem B 2017; 121:5048-5057. [DOI: 10.1021/acs.jpcb.7b02551] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jesse G. McDaniel
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, United States
| | - Arun Yethiraj
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, United States
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15
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Miskowiec A, Buck ZN, Hansen FY, Kaiser H, Taub H, Tyagi M, Diallo SO, Mamontov E, Herwig KW. On the structure and dynamics of water associated with single-supported zwitterionic and anionic membranes. J Chem Phys 2017; 146:125102. [DOI: 10.1063/1.4978677] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- A. Miskowiec
- Department of Physics and Astronomy and University of Missouri Research Reactor, University of Missouri, Columbia, Missouri 65211, USA
| | - Z. N. Buck
- Department of Physics and Astronomy and University of Missouri Research Reactor, University of Missouri, Columbia, Missouri 65211, USA
| | - F. Y. Hansen
- Department of Chemistry, Technical University of Denmark, IK 207 DTU, DK-2800 Lyngby, Denmark
| | - H. Kaiser
- Department of Physics and Astronomy and University of Missouri Research Reactor, University of Missouri, Columbia, Missouri 65211, USA
| | - H. Taub
- Department of Physics and Astronomy and University of Missouri Research Reactor, University of Missouri, Columbia, Missouri 65211, USA
| | - M. Tyagi
- Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland 20899-6102, USA
- Department of Materials Science and Engineering, University of Maryland, College Park, Maryland 20742, USA
| | - S. O. Diallo
- Spallation Neutron Source, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - E. Mamontov
- Spallation Neutron Source, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - K. W. Herwig
- Spallation Neutron Source, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
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16
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Fisette O, Päslack C, Barnes R, Isas JM, Langen R, Heyden M, Han S, Schäfer LV. Hydration Dynamics of a Peripheral Membrane Protein. J Am Chem Soc 2016; 138:11526-35. [PMID: 27548572 DOI: 10.1021/jacs.6b07005] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Water dynamics in the hydration shell of the peripheral membrane protein annexin B12 were studied using MD simulations and Overhauser DNP-enhanced NMR. We show that retardation of water motions near phospholipid bilayers is extended by the presence of a membrane-bound protein, up to around 10 Å above that protein. Near the membrane surface, electrostatic interactions with the lipid head groups strongly slow down water dynamics, whereas protein-induced water retardation is weaker and dominates only at distances beyond 10 Å from the membrane surface. The results can be understood from a simple model based on additive contributions from the membrane and the protein to the activation free energy barriers of water diffusion next to the biomolecular surfaces. Furthermore, analysis of the intermolecular vibrations of the water network reveals that retarded water motions near the membrane shift the vibrational modes to higher frequencies, which we used to identify an entropy gradient from the membrane surface toward the bulk water. Our results have implications for processes that take place at lipid membrane surfaces, including molecular recognition, binding, and protein-protein interactions.
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Affiliation(s)
- Olivier Fisette
- Center for Theoretical Chemistry, Faculty of Chemistry and Biochemistry, Ruhr-University , 44780 Bochum, Germany
| | - Christopher Päslack
- Center for Theoretical Chemistry, Faculty of Chemistry and Biochemistry, Ruhr-University , 44780 Bochum, Germany.,Max-Planck Institut für Kohlenforschung , 45470 Mülheim an der Ruhr, Germany
| | - Ryan Barnes
- Department of Chemistry and Biochemistry and Department of Chemical Engineering, University of California, Santa Barbara , Santa Barbara, California 93106, United States
| | - J Mario Isas
- Department of Biochemistry and Molecular Biology, Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California , Los Angeles, California 90089, United States
| | - Ralf Langen
- Department of Biochemistry and Molecular Biology, Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California , Los Angeles, California 90089, United States
| | - Matthias Heyden
- Max-Planck Institut für Kohlenforschung , 45470 Mülheim an der Ruhr, Germany
| | - Songi Han
- Department of Chemistry and Biochemistry and Department of Chemical Engineering, University of California, Santa Barbara , Santa Barbara, California 93106, United States
| | - Lars V Schäfer
- Center for Theoretical Chemistry, Faculty of Chemistry and Biochemistry, Ruhr-University , 44780 Bochum, Germany
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17
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Anomalous Dynamics of a Lipid Recognition Protein on a Membrane Surface. Sci Rep 2015; 5:18245. [PMID: 26657413 PMCID: PMC4677404 DOI: 10.1038/srep18245] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Accepted: 11/11/2015] [Indexed: 12/12/2022] Open
Abstract
Pleckstrin homology (PH) domains are lipid-binding modules present in peripheral membrane proteins which interact with phosphatidyl-inositol phosphates (PIPs) in cell membranes. We use multiscale molecular dynamics simulations to characterize the localization and anomalous dynamics of the DAPP1 PH domain on the surface of a PIP-containing lipid bilayer. Both translational and rotational diffusion of the PH domain on the lipid membrane surface exhibit transient subdiffusion, with an exponent α ≈ 0.5 for times of less than 10 ns. In addition to a PIP3 molecule at the canonical binding site of the PH domain, we observe additional PIP molecules in contact with the protein. Fluctuations in the number of PIPs associated with the PH domain exhibit 1/f noise. We suggest that the anomalous diffusion and long-term correlated interaction of the PH domain with the membrane may contribute to an enhanced probability of encounter with target complexes on cell membrane surfaces.
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18
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Roy S, Gruenbaum SM, Skinner JL. Theoretical vibrational sum-frequency generation spectroscopy of water near lipid and surfactant monolayer interfaces. II. Two-dimensional spectra. J Chem Phys 2015; 141:22D505. [PMID: 25494776 DOI: 10.1063/1.4895968] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The structural stability and function of biomolecules is strongly influenced by the dynamics and hydrogen bonding of interfacial water. Understanding and characterizing the dynamics of these water molecules require a surface-sensitive technique such as two-dimensional vibrational sum-frequency generation (2DSFG) spectroscopy. We have combined theoretical 2DSFG calculations with molecular dynamics simulations in order to investigate the dynamics of water near different lipid and surfactant monolayer surfaces. We show that 2DSFG can distinguish the dynamics of interfacial water as a function of the lipid charge and headgroup chemistry. The dynamics of water is slow compared to the bulk near water-zwitterionic and water-anionic interfaces due to conformational constraints on interfacial water imposed by strong phosphate-water hydrogen bonding. The dynamics of water is somewhat faster near water-cationic lipid interfaces as no such constraint is present. Using hydrogen bonding and rotational correlation functions, we characterize the dynamics of water as a function of the distance from the interface between water and zwitterionic lipids. We find that there is a transition from bulk-like to interface-like dynamics approximately 7 Å away from a zwitterionic phosphatidylcholine monolayer surface.
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Affiliation(s)
- S Roy
- Theoretical Chemistry Institute and Department of Chemistry, 1101 University Ave., University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - S M Gruenbaum
- Theoretical Chemistry Institute and Department of Chemistry, 1101 University Ave., University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - J L Skinner
- Theoretical Chemistry Institute and Department of Chemistry, 1101 University Ave., University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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19
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Aoun B, Sharma VK, Pellegrini E, Mitra S, Johnson M, Mukhopadhyay R. Structure and dynamics of ionic micelles: MD simulation and neutron scattering study. J Phys Chem B 2015; 119:5079-86. [PMID: 25803564 DOI: 10.1021/acs.jpcb.5b00020] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Fully atomistic molecular dynamics (MD) simulations have been carried out on sodium dodecyl sulfate (SDS), an anionic micelle, and three cationic (CnTAB; n = 12, 14, 16) micelles, investigating the effects of size, the form of the headgroup, and chain length. They have been used to analyze neutron scattering data. MD simulations confirm the dynamical model of global motion of the whole micelle, segmental motion (headgroup and alkyl chain), and fast torsional motion associated with the surfactants that is used to analyze the experimental data. It is found that the solvent surrounding the headgroups results in their significant mobility, which exceeds that of the tails on the nanosecond time scale. The middle of the chain is found to be least mobile, consolidating the micellar configuration. This dynamical feature is similar for all the ionic micelles investigated and therefore independent of headgroup form and charge and chain length. Diffusion constants for global and segmental motion of the different micelles are consistent with experimentally obtained values as well as known structural features. This work provides a more realistic model of micelle dynamics and offers new insight into the strongly fluctuating surface of micelles which is important in understanding micelle dispersion and related functionality, like drug delivery.
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Affiliation(s)
- B Aoun
- †Institut Laue-Langevin, BP 156, 6, rue Jules Horowitz, 38042 Grenoble Cedex 9, France
| | - V K Sharma
- ‡Solid State Physics Division, Bhabha Atomic Research Centre, Mumbai 400 085, India
| | - E Pellegrini
- †Institut Laue-Langevin, BP 156, 6, rue Jules Horowitz, 38042 Grenoble Cedex 9, France
| | - S Mitra
- ‡Solid State Physics Division, Bhabha Atomic Research Centre, Mumbai 400 085, India
| | - M Johnson
- †Institut Laue-Langevin, BP 156, 6, rue Jules Horowitz, 38042 Grenoble Cedex 9, France
| | - R Mukhopadhyay
- ‡Solid State Physics Division, Bhabha Atomic Research Centre, Mumbai 400 085, India
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20
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Yamamoto E, Akimoto T, Yasui M, Yasuoka K. Origin of 1/f noise in hydration dynamics on lipid membrane surfaces. Sci Rep 2015; 5:8876. [PMID: 25743377 PMCID: PMC4351557 DOI: 10.1038/srep08876] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Accepted: 02/09/2015] [Indexed: 12/15/2022] Open
Abstract
Water molecules on lipid membrane surfaces are known to contribute to membrane stability by connecting lipid molecules and acting as a water bridge. Although water structures and diffusivities near the membrane surfaces have been extensively studied, hydration dynamics on the surfaces has remained an open question. Here we investigate residence time statistics of water molecules on the surface of lipid membranes using all-atom molecular dynamics simulations. We show that hydration dynamics on the lipid membranes exhibits 1/f noise. Constructing a dichotomous process for the hydration dynamics, we find that residence times in each state follow a power-law with exponential cutoff and that the process can be regarded as a correlated renewal process where interoccurrence times are correlated. The results imply that the origin of the 1/f noise in hydration dynamics on the membrane surfaces is a combination of a power-law distribution with cutoff of interoccurrence times of switching events and a long-term correlation between the interoccurrence times. These results suggest that the 1/f noise attributed to the correlated renewal process may contribute to the stability of the hydration layers and lipid membranes.
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Affiliation(s)
- Eiji Yamamoto
- Department of Mechanical Engineering, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan
| | - Takuma Akimoto
- Department of Mechanical Engineering, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan
| | - Masato Yasui
- Department of Pharmacology, School of Medicine, Keio University, 35 Shinanomachi, Shinju-ku, Tokyo 160-8582, Japan
| | - Kenji Yasuoka
- Department of Mechanical Engineering, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan
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21
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Fogarty JC, Arjunwadkar M, Pandit SA, Pan J. Atomically detailed lipid bilayer models for the interpretation of small angle neutron and X-ray scattering data. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2014; 1848:662-72. [PMID: 25448879 DOI: 10.1016/j.bbamem.2014.10.041] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Revised: 10/11/2014] [Accepted: 10/29/2014] [Indexed: 10/24/2022]
Abstract
We present a new atom density profile (ADP) model and a statistical approach for extracting structural characteristics of lipid bilayers from X-ray and neutron scattering data. Models for five lipids with varying head and tail chemical composition in the fluid phase, 1,2-dioleoyl-sn-glycero-3-phosphatidylcholine (DOPC), 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylcholine (POPC), 1,2-dipalmitoyl-sn-glycero-3-phosphatidylcholine (DPPC), 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylserine (POPS), and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylglycerol (POPG), are optimized using a simplex based method to simultaneously reproduce both neutron and X-ray scattering data. Structural properties are determined using statistical analysis of multiple optimal model structures. The method and models presented make minimal assumptions regarding the atomic configuration, while taking into account the underlying physical properties of the system. The more general model and statistical approach yield data with well defined uncertainties, indicating the precision in determining density profiles, atomic locations, and bilayer structural characteristics. Resulting bilayer structures include regions exhibiting large conformational variation. Due to the increased detail in the model, the results demonstrate the possibility of a distinct hydration layer within the interfacial (backbone) region.
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Affiliation(s)
- Joseph C Fogarty
- Department of Physics, University of South Florida, Tampa, FL 33620, USA
| | - Mihir Arjunwadkar
- Centre for Modeling and Simulation, University of Pune, Pune 411007, India
| | - Sagar A Pandit
- Department of Physics, University of South Florida, Tampa, FL 33620, USA.
| | - Jianjun Pan
- Department of Physics, University of South Florida, Tampa, FL 33620, USA
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22
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Disalvo EA, Martini MF, Bouchet AM, Hollmann A, Frías MA. Structural and thermodynamic properties of water-membrane interphases: significance for peptide/membrane interactions. Adv Colloid Interface Sci 2014; 211:17-33. [PMID: 25085854 DOI: 10.1016/j.cis.2014.05.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Revised: 05/16/2014] [Accepted: 05/16/2014] [Indexed: 12/28/2022]
Abstract
Water appears as a common intermediary in the mechanisms of interaction of proteins and polypeptides with membranes of different lipid composition. In this review, how water modulates the interaction of peptides and proteins with lipid membranes is discussed by correlating the thermodynamic response and the structural changes of water at the membrane interphases. The thermodynamic properties of the lipid-protein interaction are governed by changes in the water activity of monolayers of different lipid composition according to the lateral surface pressure. In this context, different water populations can be characterized below and above the phase transition temperature in relation to the CH₂ conformers' states in the acyl chains. According to water species present at the interphase, lipid membrane acts as a water state regulator, which determines the interfacial water domains in the surface. It is proposed that those domains are formed by the contact between lipids themselves and between lipids and the water phase, which are needed to trigger adsorption-insertion processes. The water domains are essential to maintain functional dynamical properties and are formed by water beyond the hydration shell of the lipid head groups. These confined water domains probably carries information in local units in relation to the lipid composition thus accounting for the link between lipidomics and aquaomics. The analysis of these results contributes to a new insight of the lipid bilayer as a non-autonomous, responsive (reactive) structure that correlates with the dynamical properties of a living system.
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Affiliation(s)
- E A Disalvo
- Centro de Investigaciones y Transferencia Santiago del Estero (CITSE), (CONICET-UNSE), Laboratorio de Biointerfases y Sistemas Biomiméticos, Laboratorios Centrales - Ala Norte, Ruta Nacional 9, Km 1125 - Villa El Zanjón, CP 4206 Santiago del Estero, Argentina.
| | - M F Martini
- Department of Pharmaceutical Technology, Universidad de Buenos Aires, Buenos Aires, Argentina and CONICET
| | - A M Bouchet
- Centro de Investigaciones y Transferencia Santiago del Estero (CITSE), (CONICET-UNSE), Laboratorio de Biointerfases y Sistemas Biomiméticos, Laboratorios Centrales - Ala Norte, Ruta Nacional 9, Km 1125 - Villa El Zanjón, CP 4206 Santiago del Estero, Argentina
| | - A Hollmann
- Centro de Investigaciones y Transferencia Santiago del Estero (CITSE), (CONICET-UNSE), Laboratorio de Biointerfases y Sistemas Biomiméticos, Laboratorios Centrales - Ala Norte, Ruta Nacional 9, Km 1125 - Villa El Zanjón, CP 4206 Santiago del Estero, Argentina
| | - M A Frías
- Centro de Investigaciones y Transferencia Santiago del Estero (CITSE), (CONICET-UNSE), Laboratorio de Biointerfases y Sistemas Biomiméticos, Laboratorios Centrales - Ala Norte, Ruta Nacional 9, Km 1125 - Villa El Zanjón, CP 4206 Santiago del Estero, Argentina
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23
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Origin of subdiffusion of water molecules on cell membrane surfaces. Sci Rep 2014; 4:4720. [PMID: 24739933 PMCID: PMC5380161 DOI: 10.1038/srep04720] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Accepted: 03/31/2014] [Indexed: 12/22/2022] Open
Abstract
Water molecules play an important role in providing unique environments for biological reactions on cell membranes. It is widely believed that water molecules form bridges that connect lipid molecules and stabilize cell membranes. Using all-atom molecular dynamics simulations, we show that translational and rotational diffusion of water molecules on lipid membrane surfaces exhibit subdiffusion and aging. Moreover, we provide evidence that both divergent mean trapping time (continuous-time random walk) and long-correlated noise (fractional Brownian motion) contribute to this subdiffusion. These results suggest that subdiffusion on cell membranes causes the water retardation, an enhancement of cell membrane stability, and a higher reaction efficiency.
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