1
|
Filipecka-Szymczyk K, Makowska-Janusik M, Marczak W. Molecular Dynamics Simulation of Hydrogels Based on Phosphorylcholine-Containing Copolymers for Soft Contact Lens Applications. Molecules 2023; 28:6562. [PMID: 37764338 PMCID: PMC10535866 DOI: 10.3390/molecules28186562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 09/04/2023] [Accepted: 09/06/2023] [Indexed: 09/29/2023] Open
Abstract
The structure and dynamics of copolymers of 2-hydroxyethyl methacrylate (HEMA) with 2-methacryloyloxyethyl phosphorylcholine (MPC) were studied by molecular dynamics simulations. In total, 20 systems were analyzed. They differed in numerical fractions of the MPC in the copolymer chain, equal to 0.26 and 0.74, in the sequence of mers, block and random, and the water content, from 0 to 60% by mass. HEMA side chains proved relatively rigid and stable in all considered configurations. MPC side chains, in contrast, were mobile and flexible. Water substantially influenced their dynamics. The copolymer swelling caused by water resulted in diffusion channels, pronounced in highly hydrated systems. Water in the hydrates existed in two states: those that bond to the polymer chain and the free one; the latter was similar to bulk water but with a lower self-diffusion coefficient. The results proved that molecular dynamics simulations could facilitate the preliminary selection of the polymer materials for specific purposes before their synthesis.
Collapse
Affiliation(s)
| | | | - Wojciech Marczak
- Faculty of Science and Technology, Jan Dlugosz University, Al. Armii Krajowej 13/15, 42-200 Częstochowa, Poland; (K.F.-S.); (M.M.-J.)
| |
Collapse
|
2
|
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.
Collapse
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
| |
Collapse
|
3
|
Ivanova KA, Bashkirov PV. Noise in Ultrashort Elastic Membrane Nanotube. BIOCHEMISTRY (MOSCOW), SUPPLEMENT SERIES A: MEMBRANE AND CELL BIOLOGY 2022. [DOI: 10.1134/s1990747822050063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
|
4
|
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.
Collapse
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
| |
Collapse
|
5
|
Asamoto DK, Kozachenko IA, López-Peña I, Kim JE. Bimolecular quenching of tryptophan fluorescence in a membrane protein: Evolution of local solvation and environment during folding into a bilayer. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 260:119919. [PMID: 34004426 DOI: 10.1016/j.saa.2021.119919] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Revised: 04/29/2021] [Accepted: 05/02/2021] [Indexed: 06/12/2023]
Abstract
Fluorescence spectroscopy, including Stern-Volmer quenching, is a valuable tool for the study of protein dynamics. Changes in protein solvation during the folding reaction of a membrane protein, Outer membrane protein A (OmpA), into lipid bilayers was probed with bimolecular fluorescence quenching with acrylamide quencher. Six single-tryptophan OmpA mutants (W7, W15, W57, W102, W129, and W143) allowed for site-specific investigations at varying locations within the transmembrane β-barrel domain. A sphere-of-action quenching model that combines both static and dynamic components gave rise to Stern-Volmer quenching constants, KD, for OmpA denatured in 8.0 M urea, aggregated in 0.5 M urea, adsorbed onto small unilamellar vesicles (SUVs), and folded in SUVs (t = 6 hrs). The average KD values were KDdenatured(6.4M-1)>KDaggregated5.9M-1>KDadsorbed(1.9M-1)>KDfolded(0.6M-1). With knowledge of the fluorescence lifetimes in the absence of quencher, the bimolecular quenching constants, kq, were derived; the evolution of kq (and therefore KD)during the folding reaction into SUVs (t = 0 hr to t = 6 hrs) revealed desolvation timescales, τdesolv of 41-46 min (W7, W15, W57, W102), 27 min (W129), and 15 min (W143). The evolution of λmax during folding revealed fast and slow components, τenvironmentfast and τenvironmentslow of 7-13 min and 25-84 min, respectively, for all mutants. For the five lipid- facing mutants (W7, W15, W57, W129, and W143), the general trend was τenvironmentfast7-13min<τdesolv15-46min≤τenvironmentslow(25-84min). These results suggest that there is an initial fast step in which there is a large change in polarity to a hydrophobic environment, followed by a slower desolvation process during evolution within the hydrophobic environment. These results complement previous mechanisms of concerted folding and provide insights into site-specific changes in solvation during formation of native β-barrel structure.
Collapse
Affiliation(s)
- DeeAnn K Asamoto
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, United States
| | - Ivan A Kozachenko
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, United States
| | - Ignacio López-Peña
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, United States
| | - Judy E Kim
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, United States.
| |
Collapse
|
6
|
Wang D, Tian Y, Jiang L. Abnormal Properties of Low-Dimensional Confined Water. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2021; 17:e2100788. [PMID: 34176214 DOI: 10.1002/smll.202100788] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Revised: 03/25/2021] [Indexed: 06/13/2023]
Abstract
Water molecules confined to low-dimensional spaces exhibit unusual properties compared to bulk water. For example, the alternating hydrophilic and hydrophobic nanodomains on flat silicon wafer can induce the abnormal spreading of water (contact angles near 0°) which is caused by the 2D capillary effect. Hence, exploring the physicochemical properties of confined water from the nanoscale is of great value for understanding the challenges in material science and promoting the applications of nanomaterials in the fields of mass transport, nanofluidic designing, and fuel cell. The knowledge framework of confined water can also help to better understand the complex functions of the hydration layer of biomolecules, and even trace the origin of life. In this review, the physical properties, abnormal behaviors, and functions of the confined water are mainly summarized through several common low-dimensional water formats in the fields of solid/air-water interface, nanochannel confinement, and biological hydration layer. These researches indicate that the unusual behaviors of the confined water depend strongly on the confinement size and the interaction between the molecules and confining surface. These diverse properties of confined water open a new door to materials science and may play an important role in the future development of biology.
Collapse
Affiliation(s)
- Dianyu Wang
- Key Laboratory of Bio-Inspired Smart Interfacial Science and Technology of Ministry of Education, School of Chemistry, Beihang University, Beijing, 100191, P. R. China
| | - Ye Tian
- Key Laboratory of Bioinspired Smart Interfacial Science, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Lei Jiang
- Key Laboratory of Bio-Inspired Smart Interfacial Science and Technology of Ministry of Education, School of Chemistry, Beihang University, Beijing, 100191, P. R. China
- Key Laboratory of Bioinspired Smart Interfacial Science, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| |
Collapse
|
7
|
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
| |
Collapse
|
8
|
Trofimov YA, Krylov NA, Efremov RG. Confined Dynamics of Water in Transmembrane Pore of TRPV1 Ion Channel. Int J Mol Sci 2019; 20:ijms20174285. [PMID: 31480555 PMCID: PMC6747475 DOI: 10.3390/ijms20174285] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 08/28/2019] [Accepted: 08/29/2019] [Indexed: 11/23/2022] Open
Abstract
Solvation effects play a key role in chemical and biological processes. The microscopic properties of water near molecular surfaces are radically different from those in the bulk. Furthermore, the behavior of water in confined volumes of a nanometer scale, including transmembrane pores of ion channels, is especially nontrivial. Knowledge at the molecular level of structural and dynamic parameters of water in such systems is necessary to understand the mechanisms of ion channels functioning. In this work, the results of molecular dynamics (MD) simulations of water in the pore and selectivity filter domains of TRPV1 (Transient Receptor Potential Vanilloid type 1) membrane channel are considered. These domains represent nanoscale volumes with strongly amphiphilic walls, where physical behavior of water radically differs from that of free hydration (e.g., at protein interfaces) or in the bulk. Inside the pore and filter domains, water reveals a very heterogeneous spatial distribution and unusual dynamics: It forms compact areas localized near polar groups of particular residues. Residence time of water molecules in such areas is at least 1.5 to 3 times larger than that observed for similar groups at the protein surface. Presumably, these water “blobs” play an important role in the functional activity of TRPV1. In particular, they take part in hydration of the hydrophobic TRPV1 pore by localizing up to six waters near the so-called “lower gate” of the channel and reducing by this way the free energy barrier for ion and water transport. Although the channel is formed by four identical protein subunits, which are symmetrically packed in the initial experimental 3D structure, in the course of MD simulations, hydration of the same amino acid residues of individual subunits may differ significantly. This greatly affects the microscopic picture of the distribution of water in the channel and, potentially, the mechanism of its functioning. Therefore, reconstruction of the full picture of TRPV1 channel solvation requires thorough atomistic simulations and analysis. It is important that the naturally occurring porous volumes, like ion-conducting protein domains, reveal much more sophisticated and fine-tuned regulation of solvation than, e.g., artificially designed carbon nanotubes.
Collapse
Affiliation(s)
- Yury A Trofimov
- M.M. Shemyakin & Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Street, 16/10, 117997 Moscow, Russia
- National Research University Higher School of Economics, Myasnitskaya ul. 20, 101000 Moscow, Russia
- National Research Nuclear University Moscow Engineering Physics Institute, Kashirskoe Shosse, 31, 115409 Moscow, Russia
| | - Nikolay A Krylov
- M.M. Shemyakin & Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Street, 16/10, 117997 Moscow, Russia
- National Research University Higher School of Economics, Myasnitskaya ul. 20, 101000 Moscow, Russia
| | - Roman G Efremov
- M.M. Shemyakin & Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Street, 16/10, 117997 Moscow, Russia.
- National Research University Higher School of Economics, Myasnitskaya ul. 20, 101000 Moscow, Russia.
- Moscow Institute of Physics and Technology (State University), Dolgoprudny, 141701 Moscow, Russia.
| |
Collapse
|
9
|
Efremov RG. Dielectric-Dependent Strength of Interlipid Hydrogen Bonding in Biomembranes: Model Case Study. J Chem Inf Model 2019; 59:2765-2775. [PMID: 31135153 DOI: 10.1021/acs.jcim.9b00193] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Atomistic aspects of the structural organization, dynamics, and functioning of hydrated lipid bilayers-model cell membranes-are primarily governed by the fine balance of intermolecular interactions between all constituents of these systems. Besides the hydrophobic effect, which shapes the overall skeleton of lipid membranes, a very important contribution to their behavior is made by hydrogen bonds (H-bonds) between lipid head groups. The latter determine crucial phenomena in cell membranes, such as dynamic ultrananodomain organization, hydration, and fine-tuning of microscopic physicochemical properties that allow the membrane to adapt quickly when binding/insertion external agents (proteins, etc.). The characteristics of such H-bonds (strength, spatial localization, etc.) dramatically depend on the local polarity properties of the lipid-water environment. In this work, we calculated free energies of H-bonded complexes between typical donor (NH3+, NH, OH) and acceptor (C═O, OH, COO-, COOH) groups of lipids in vacuo and in a set of explicit solvents with dielectric constants (ε) from 1 to 78.3, which mimic membrane environment at different depths. This was done using Monte Carlo simulations and an assessment of the corresponding potential of mean force profiles. The strongest H-bonded complexes were observed in the nonpolar environment, and their strength increased sharply with decreasing ε below 17. When ε changed, the largest free energy gain (>10.8 kcal/mol) was observed for pairs of acceptors C═O and O(H) with donor NH3+. The complexation of the same acceptors with NH donor in this range of ε values was rather less sensitive to the environmental polarity, by ∼1.5 kcal/mol. Dielectric-dependent interactions of polar lipid groups with water were evaluated as well. The results explain the delicate balance that determines the unique pattern of H-bonds for a particular lipid bilayer. Understanding the factors that regulate the propensity for H-bonding in lipid bilayers provides a fundamental basis for the rational design of new membrane nano objects with predefined properties.
Collapse
Affiliation(s)
- R G Efremov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry , Russian Academy of Sciences , 16/10, Miklukho-Maklaya Str. , Moscow , 117997 Russia.,Higher School of Economics , 20, Myasnitskaya Str. , Moscow , 101000 Russia.,Moscow Institute of Physics and Technology (State University) , 9 Institutskiy per. , Dolgoprudny , Moscow Region , 141700 Russia
| |
Collapse
|
10
|
Issack BB, Peslherbe GH. Accuracy and precision of simulated free energies: water permeation of hydrated DPPC bilayers as a paradigm. MOLECULAR SIMULATION 2019. [DOI: 10.1080/08927022.2019.1572141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Bilkiss B. Issack
- Centre for Research in Molecular Modeling, and Department of Chemistry and Biochemistry, Concordia University, Montreal, Canada
- Département des sciences expérimentales, Université de Saint-Boniface, Winnipeg, Canada
| | - Gilles H. Peslherbe
- Centre for Research in Molecular Modeling, and Department of Chemistry and Biochemistry, Concordia University, Montreal, Canada
| |
Collapse
|
11
|
Bolmatov D, Cai YQ, Zav'yalov D, Zhernenkov M. Crossover from picosecond collective to single particle dynamics defines the mechanism of lateral lipid diffusion. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2018; 1860:2446-2455. [PMID: 30031781 DOI: 10.1016/j.bbamem.2018.07.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Revised: 07/04/2018] [Accepted: 07/13/2018] [Indexed: 10/28/2022]
Abstract
It has been widely accepted that the thermally excited motions of the molecules in a cell membrane is the prerequisite for a cell to carry its biological functions. On the other hand, the detailed mapping of the ultrafast picosecond single-molecule and the collective lipid dynamics in a cell membrane remains rather elusive. Here, we report all-atom molecular dynamics simulations of a 1,2-dipalmitoyl-sn-glycero-3-phosphocholine bilayer over a wide range of temperature. We elucidate a molecular mechanism underlying the lateral lipid diffusion in a cell membrane across the gel, rippled, and liquid phases using an analysis of the longitudinal and transverse current correlation spectra, the velocity auto-correlation functions, and the molecules mean square displacements. The molecular mechanism is based on the anomalous ultrafast vibrational properties of lipid molecules at the viscous-to-elastic crossover. The macroscopic lipid diffusion coefficients predicted by the proposed diffusion model are in a good agreement with experimentally observed values. Furthermore, we unveil the role of water confined at the water-lipid interface in triggering collective vibrations in a lipid bilayer.
Collapse
Affiliation(s)
- Dima Bolmatov
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; Department of Physics and Astronomy, University of Tennessee, Knoxville, TN 37996, USA.
| | - Yong Q Cai
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY 11973, USA
| | | | - Mikhail Zhernenkov
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY 11973, USA.
| |
Collapse
|
12
|
Bocharov EV, Lesovoy DM, Bocharova OV, Urban AS, Pavlov KV, Volynsky PE, Efremov RG, Arseniev AS. Structural basis of the signal transduction via transmembrane domain of the human growth hormone receptor. Biochim Biophys Acta Gen Subj 2018; 1862:1410-1420. [DOI: 10.1016/j.bbagen.2018.03.022] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2017] [Revised: 03/13/2018] [Accepted: 03/19/2018] [Indexed: 12/18/2022]
|
13
|
Stereospecific Interactions of Cholesterol in a Model Cell Membrane: Implications for the Membrane Dipole Potential. J Membr Biol 2018; 251:507-519. [DOI: 10.1007/s00232-018-0016-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 01/25/2018] [Indexed: 12/11/2022]
|
14
|
Torchi A, Simonelli F, Ferrando R, Rossi G. Local Enhancement of Lipid Membrane Permeability Induced by Irradiated Gold Nanoparticles. ACS NANO 2017; 11:12553-12561. [PMID: 29161019 DOI: 10.1021/acsnano.7b06690] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Photothermal therapies are based on the optical excitation of plasmonic nanoparticles in the biological environment. The effects of the irradiation on the biological medium depend critically on the heat transfer process at the nanoparticle interface, on the temperature reached by the tissues, as well as on the spatial extent of temperature gradients. Unfortunately, both the temperature and its biological effects are difficult to be probed experimentally at the molecular scale. Here, we approach this problem using nonequilibrium molecular dynamics simulations. We focus on photoporation, a photothermal application based on the irradiation of gold nanoparticles by single, short-duration laser pulses. The nanoparticles, stably bound to cell membranes, convert the radiation into heat, inducing transient changes of membrane permeability. We make a quantitative prediction of the temperature gradient around the nanoparticle upon irradiation by typical experimental laser fluences. Water permeability is locally enhanced around the nanoparticle, in an annular region that extends only a few nanometers from the nanoparticle interface. We correlate the local enhancement of permeability at the nanoparticle-lipid interface to the temperature inhomogeneities of the membrane and to the consequent availability of free volume pockets within the membrane core.
Collapse
Affiliation(s)
- Andrea Torchi
- Physics Department, University of Genoa , via Dodecaneso 33, 16146 Genoa, Italy
| | - Federica Simonelli
- Physics Department, University of Genoa , via Dodecaneso 33, 16146 Genoa, Italy
| | - Riccardo Ferrando
- Chemistry Department, University of Genoa , via Dodecaneso 31, 16146 Genoa, Italy
| | - Giulia Rossi
- Physics Department, University of Genoa , via Dodecaneso 33, 16146 Genoa, Italy
| |
Collapse
|
15
|
Su J, Zhao Y, Fang C, Shi Y. Asymmetric osmotic water permeation through a vesicle membrane. J Chem Phys 2017; 146:204902. [PMID: 28571349 PMCID: PMC5440233 DOI: 10.1063/1.4983749] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 05/08/2017] [Indexed: 11/14/2022] Open
Abstract
Understanding the water permeation through a cell membrane is of primary importance for biological activities and a key step to capture its shape transformation in salt solution. In this work, we reveal the dynamical behaviors of osmotically driven transport of water molecules across a vesicle membrane by molecular dynamics simulations. Of particular interest is that the water transport in and out of vesicles is highly distinguishable given the osmotic force are the same, suggesting an asymmetric osmotic transportation. This asymmetric phenomenon exists in a broad range of parameter space such as the salt concentration, temperature, and vesicle size and can be ascribed to the similar asymmetric potential energy of lipid-ion, lipid-water, lipid-solution, lipid-lipid, and the lipid-lipid energy fluctuation. Specifically, the water flux has a linear increase with the salt concentration, similar to the prediction by Nernst-Planck equation or Fick's first law. Furthermore, due to the Arrhenius relation between the membrane permeability and temperature, the water flux also exhibits excellent Arrhenius dependence on the temperature. Meanwhile, the water flux shows a linear increase with the vesicle surface area since the flux amount across a unit membrane area should be a constant. Finally, we also present the anonymous diffusion behaviors for the vesicle itself, where transitions from normal diffusion at short times to subdiffusion at long times are identified. Our results provide significant new physical insights for the osmotic water permeation through a vesicle membrane and are helpful for future experimental studies.
Collapse
Affiliation(s)
- Jiaye Su
- Department of Applied Physics, Nanjing University of Science and Technology, Nanjing, Jiangsu 210094, China
| | - Yunzhen Zhao
- Department of Applied Physics, Nanjing University of Science and Technology, Nanjing, Jiangsu 210094, China
| | - Chang Fang
- Department of Applied Physics, Nanjing University of Science and Technology, Nanjing, Jiangsu 210094, China
| | - Yue Shi
- Department of Applied Physics, Nanjing University of Science and Technology, Nanjing, Jiangsu 210094, China
| |
Collapse
|
16
|
Pearlstein RA, Dickson CJ, Hornak V. Contributions of the membrane dipole potential to the function of voltage-gated cation channels and modulation by small molecule potentiators. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1859:177-194. [PMID: 27836643 DOI: 10.1016/j.bbamem.2016.11.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Revised: 10/28/2016] [Accepted: 11/06/2016] [Indexed: 01/27/2023]
Abstract
The membrane dipole potential (Ψd) constitutes one of three electrical potentials generated by cell membranes. Ψd arises from the unfavorable parallel alignment of phospholipid and water dipoles, and varies in magnitude both longitudinally and laterally across the bilayer according to membrane composition and phospholipid packing density. In this work, we propose that dynamic counter-balancing between Ψd and the transmembrane potential (ΔΨm) governs the conformational state transitions of voltage-gated ion channels. Ψd consists of 1) static outer, and dynamic inner leaflet components (Ψd(extra) and Ψd(intra), respectively); and 2) a transmembrane component (ΔΨd(inner-outer)), ariing from differences in intra- and extracellular leaflet composition. Ψd(intra), which transitions between high and low energy states (Ψd(intra, high) and Ψd(intra, low)) as a function of channel conformation, is transduced by the pore domain. ΔΨd(inner-outer) is transduced by the voltage-sensing (VS) domain in summation with ΔΨm. Potentiation of voltage-gated ion channels is of interest for the treatment of cardiac, neuronal, and other disorders arising from inherited/acquired ion channel dysfunction. Potentiators are widely believed to alter the rates and voltage-dependencies of channel gating transitions by binding to pockets in the membrane-facing and other regions of ion channel targets. Here, we propose that potentiators alter Ψd(intra) and/or Ψd(extra), thereby increasing or decreasing the energy barriers governing channel gating transitions. We used quantum mechanical and molecular dynamics (MD) simulations to predict the overall Ψd-modulating effects of a series of published positive hERG potentiators partitioned into model DOPC bilayers. Our findings suggest a strong correlation between the magnitude of Ψd-lowering and positive hERG potentiation across the series.
Collapse
Affiliation(s)
- Robert A Pearlstein
- Global Discovery Chemistry, Computer-Aided Drug Discovery, Novartis Institutes for BioMedical Research, 181 Mass Ave., Cambridge, MA 02139, USA.
| | - Callum J Dickson
- Global Discovery Chemistry, Computer-Aided Drug Discovery, Novartis Institutes for BioMedical Research, 181 Mass Ave., Cambridge, MA 02139, USA
| | - Viktor Hornak
- Global Discovery Chemistry, Computer-Aided Drug Discovery, Novartis Institutes for BioMedical Research, 181 Mass Ave., Cambridge, MA 02139, USA
| |
Collapse
|
17
|
Schroeder TBH, Leriche G, Koyanagi T, Johnson MA, Haengel KN, Eggenberger OM, Wang CL, Kim YH, Diraviyam K, Sept D, Yang J, Mayer M. Effects of Lipid Tethering in Extremophile-Inspired Membranes on H(+)/OH(-) Flux at Room Temperature. Biophys J 2016; 110:2430-2440. [PMID: 27276261 PMCID: PMC4906265 DOI: 10.1016/j.bpj.2016.04.044] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Revised: 04/08/2016] [Accepted: 04/12/2016] [Indexed: 01/22/2023] Open
Abstract
This work explores the proton/hydroxide permeability (PH+/OH-) of membranes that were made of synthetic extremophile-inspired phospholipids with systematically varied structural elements. A fluorescence-based permeability assay was optimized to determine the effects on the PH+/OH- through liposome membranes with variations in the following lipid attributes: transmembrane tethering, tether length, and the presence of isoprenoid methyl groups on one or both lipid tails. All permeability assays were performed in the presence of a low concentration of valinomycin (10 nM) to prevent buildup of a membrane potential without artificially increasing the measured PH+/OH-. Surprisingly, the presence of a transmembrane tether did not impact PH+/OH- at room temperature. Among tethered lipid monolayers, PH+/OH- increased with increasing tether length if the number of carbons in the untethered acyl tail was constant. Untethered lipids with two isoprenoid methyl tails led to lower PH+/OH- values than lipids with only one or no isoprenoid tails. Molecular dynamics simulations revealed a strong positive correlation between the probability of observing water molecules in the hydrophobic core of these lipid membranes and their proton permeability. We propose that water penetration as revealed by molecular dynamics may provide a general strategy for predicting proton permeability through various lipid membranes without the need for experimentation.
Collapse
Affiliation(s)
- Thomas B H Schroeder
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan; Adolphe Merkle Institute, University of Fribourg, Fribourg, Switzerland
| | - Geoffray Leriche
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California
| | - Takaoki Koyanagi
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California
| | - Mitchell A Johnson
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan
| | - Kathryn N Haengel
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan
| | - Olivia M Eggenberger
- Adolphe Merkle Institute, University of Fribourg, Fribourg, Switzerland; Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan
| | - Claire L Wang
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan
| | - Young Hun Kim
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California
| | - Karthik Diraviyam
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan
| | - David Sept
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan
| | - Jerry Yang
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California
| | - Michael Mayer
- Adolphe Merkle Institute, University of Fribourg, Fribourg, Switzerland; Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan.
| |
Collapse
|
18
|
Zhernenkov M, Bolmatov D, Soloviov D, Zhernenkov K, Toperverg BP, Cunsolo A, Bosak A, Cai YQ. Revealing the mechanism of passive transport in lipid bilayers via phonon-mediated nanometre-scale density fluctuations. Nat Commun 2016; 7:11575. [PMID: 27175859 PMCID: PMC4865866 DOI: 10.1038/ncomms11575] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 04/10/2016] [Indexed: 12/21/2022] Open
Abstract
The passive transport of molecules through a cell membrane relies on thermal motions of the lipids. However, the nature of transmembrane transport and the precise mechanism remain elusive and call for a comprehensive study of phonon excitations. Here we report a high resolution inelastic X-ray scattering study of the in-plane phonon excitations in 1,2-dipalmitoyl-sn-glycero-3-phosphocholine above and below the main transition temperature. In the gel phase, for the first time, we observe low-frequency transverse modes, which exhibit a phonon gap when the lipid transitions into the fluid phase. We argue that the phonon gap signifies the formation of short-lived nanometre-scale lipid clusters and transient pores, which facilitate the passive molecular transport across the bilayer plane. Our findings suggest that the phononic motion of the hydrocarbon tails provides an effective mechanism of passive transport, and illustrate the importance of the collective dynamics of biomembranes. The molecular transport through bio-membranes of cells heavily relies on the dynamics of lipids, but the related mechanism remains unknown. Here, Zhernenkov et al. observe the propagating transverse phonon mode with a finite band gap and suggest its connection to short-lived local lipid clustering.
Collapse
Affiliation(s)
- Mikhail Zhernenkov
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, New York 11973, USA
| | - Dima Bolmatov
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, New York 11973, USA
| | - Dmitry Soloviov
- Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, Dubna 141980, Russia.,Moscow Institute of Physics and Technology, Dolgoprudny 141700, Russia
| | - Kirill Zhernenkov
- Institut Nanosciences et Cryogénie, Commissariat à l'Energie Atomique, Grenoble 38054, France
| | - Boris P Toperverg
- Petersburg Nuclear Physics Institute, Gatchina 188300, Russia.,Institut Laue Langevin, 6, rue Jules Horowitz, Grenoble 38042, France
| | - Alessandro Cunsolo
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, New York 11973, USA
| | - Alexey Bosak
- European Synchrotron Radiation Facility, Grenoble 38000, France
| | - Yong Q Cai
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, New York 11973, USA
| |
Collapse
|
19
|
Casalegno M, Raos G, Sello G. From dioxin to dioxin congeners: understanding the differences in hydrophobic aggregation in water and absorption into lipid membranes by means of atomistic simulations. Phys Chem Chem Phys 2016; 18:17731-9. [DOI: 10.1039/c6cp01728b] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Molecular dynamics simulations indicate that dioxin likely accumulates in cell membranes more than its congeners (anthracene, tetrahydrodioxin, 3,3′,5,5′-tetrachlorobiphenyl, and 1,2-dihydroxytetrahydrodibenzo-p-dioxin).
Collapse
Affiliation(s)
- Mosé Casalegno
- Dipartimento di Chimica
- Materiali e Ingegneria Chimica “G. Natta”
- Politecnico di Milano
- 20131 Milano
- Italy
| | - Guido Raos
- Dipartimento di Chimica
- Materiali e Ingegneria Chimica “G. Natta”
- Politecnico di Milano
- 20131 Milano
- Italy
| | - Guido Sello
- Dipartimento di Chimica
- Università degli Studi di Milano
- I-20133 Milano
- Italy
| |
Collapse
|
20
|
Awoonor-Williams E, Rowley CN. Molecular simulation of nonfacilitated membrane permeation. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1858:1672-87. [PMID: 26706099 DOI: 10.1016/j.bbamem.2015.12.014] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Revised: 12/05/2015] [Accepted: 12/09/2015] [Indexed: 12/29/2022]
Abstract
This is a review. Non-electrolytic compounds typically cross cell membranes by passive diffusion. The rate of permeation is dependent on the chemical properties of the solute and the composition of the lipid bilayer membrane. Predicting the permeability coefficient of a solute is important in pharmaceutical chemistry and toxicology. Molecular simulation has proven to be a valuable tool for modeling permeation of solutes through a lipid bilayer. In particular, the solubility-diffusion model has allowed for the quantitative calculation of permeability coefficients. The underlying theory and computational methods used to calculate membrane permeability are reviewed. We also discuss applications of these methods to examine the permeability of solutes and the effect of membrane composition on permeability. The application of coarse grain and polarizable models is discussed. This article is part of a Special Issue entitled: Membrane Proteins edited by J.C. Gumbart and Sergei Noskov.
Collapse
Affiliation(s)
- Ernest Awoonor-Williams
- Department of Chemistry, Memorial University of Newfoundland, St. John's, NL, A1B 3X7 Canada
| | - Christopher N Rowley
- Department of Chemistry, Memorial University of Newfoundland, St. John's, NL, A1B 3X7 Canada.
| |
Collapse
|
21
|
Basu I, Manna M, Mukhopadhyay C. Insights into the behavioral difference of water in the presence of GM1. FEBS Lett 2015; 589:3887-92. [DOI: 10.1016/j.febslet.2015.11.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Revised: 11/16/2015] [Accepted: 11/16/2015] [Indexed: 11/26/2022]
|
22
|
Artificial biomembrane based on DPPC — Investigation into phase transition and thermal behavior through ellipsometric techniques. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1848:2295-307. [DOI: 10.1016/j.bbamem.2015.07.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Revised: 07/01/2015] [Accepted: 07/02/2015] [Indexed: 12/12/2022]
|
23
|
Kuznetsov AS, Polyansky AA, Fleck M, Volynsky PE, Efremov RG. Adaptable Lipid Matrix Promotes Protein–Protein Association in Membranes. J Chem Theory Comput 2015; 11:4415-26. [DOI: 10.1021/acs.jctc.5b00206] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Andrey S. Kuznetsov
- M.
M. Shemyakin and Yu. A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str., 16/10, Moscow 117997, Russia
| | - Anton A. Polyansky
- M.
M. Shemyakin and Yu. A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str., 16/10, Moscow 117997, Russia
- Department
of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, Vienna AT-1030, Austria
| | - Markus Fleck
- Department
of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, Vienna AT-1030, Austria
| | - Pavel E. Volynsky
- M.
M. Shemyakin and Yu. A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str., 16/10, Moscow 117997, Russia
| | - Roman G. Efremov
- M.
M. Shemyakin and Yu. A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str., 16/10, Moscow 117997, Russia
- Higher School of Economics, Myasnitskaya Str., 20, Moscow 101000, Russia
| |
Collapse
|
24
|
Moskovitz Y, Yang H. Modelling of noble anaesthetic gases and high hydrostatic pressure effects in lipid bilayers. SOFT MATTER 2015; 11:2125-2138. [PMID: 25612767 DOI: 10.1039/c4sm02667e] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Our objective was to study molecular processes that might be responsible for inert gas narcosis and high-pressure nervous syndrome. The classical molecular dynamics trajectories (200 ns) of dioleoylphosphatidylcholine (DOPC) bilayers simulated by the Berger force field were evaluated for water and the atomic distribution of noble gases around DOPC molecules in the pressure range of 1-1000 bar and at a temperature of 310 K. Xenon and argon have been tested as model gases for general anaesthetics, and neon has been investigated for distortions that are potentially responsible for neurological tremors in hyperbaric conditions. The analysis of stacked radial pair distribution functions of DOPC headgroup atoms revealed the explicit solvation potential of the gas molecules, which correlates with their dimensions. The orientational dynamics of water molecules at the biomolecular interface should be considered as an influential factor, while excessive solvation effects appearing in the lumen of membrane-embedded ion channels could be a possible cause of inert gas narcosis. All the noble gases tested exhibit similar order parameter patterns for both DOPC acyl chains, which are opposite of the patterns found for the order parameter curve at high hydrostatic pressures in intact bilayers. This finding supports the 'critical volume' hypothesis of anaesthesia pressure reversal. The irregular lipid headgroup-water boundary observed in DOPC bilayers saturated with neon in the pressure range of 1-100 bar could be associated with the possible manifestation of neurological tremors at the atomic scale. The non-immobiliser neon also demonstrated the highest momentum impact on the normal component of the DOPC diffusion coefficient representing the monolayer undulation rate, which indicates that enhanced diffusivity rather than atomic size is the key factor.
Collapse
Affiliation(s)
- Yevgeny Moskovitz
- Department of Chemistry, Middle Tennessee State University, Murfreesboro, TN 37130, USA
| | | |
Collapse
|
25
|
Goda T, Ishihara K, Miyahara Y. Critical update on 2-methacryloyloxyethyl phosphorylcholine (MPC) polymer science. J Appl Polym Sci 2015. [DOI: 10.1002/app.41766] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Tatsuro Goda
- Institute of Biomaterials and Bioengineering; Tokyo Medical and Dental University; 2-3-10 Kanda-Surugadai Chiyoda Tokyo 101-0062 Japan
| | - Kazuhiko Ishihara
- Department of Materials Engineering; The University of Tokyo; 7-3-1 Hongo Bunkyo Tokyo 113-8656 Japan
- Department of Bioengineering; The University of Tokyo; 7-3-1 Hongo Bunkyo Tokyo 113-8656 Japan
| | - Yuji Miyahara
- Institute of Biomaterials and Bioengineering; Tokyo Medical and Dental University; 2-3-10 Kanda-Surugadai Chiyoda Tokyo 101-0062 Japan
| |
Collapse
|
26
|
Chugunov AO, Volynsky PE, Krylov NA, Boldyrev IA, Efremov RG. Liquid but durable: molecular dynamics simulations explain the unique properties of archaeal-like membranes. Sci Rep 2014; 4:7462. [PMID: 25501042 PMCID: PMC4264030 DOI: 10.1038/srep07462] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Accepted: 11/24/2014] [Indexed: 12/12/2022] Open
Abstract
Archaeal plasma membranes appear to be extremely durable and almost impermeable to water and ions, in contrast to the membranes of Bacteria and Eucaryota. Additionally, they remain liquid within a temperature range of 0-100°C. These are the properties that have most likely determined the evolutionary fate of Archaea, and it may be possible for bionanotechnology to adopt these from nature. In this work, we use molecular dynamics simulations to assess at the atomistic level the structure and dynamics of a series of model archaeal membranes with lipids that have tetraether chemical nature and "branched" hydrophobic tails. We conclude that the branched structure defines dense packing and low water permeability of archaeal-like membranes, while at the same time ensuring a liquid-crystalline state, which is vital for living cells. This makes tetraether lipid systems promising in bionanotechnology and material science, namely for design of new and unique membrane nanosystems.
Collapse
Affiliation(s)
- Anton O Chugunov
- M.M. Shemyakin &Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya, 16/10, Moscow 117997
| | - Pavel E Volynsky
- M.M. Shemyakin &Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya, 16/10, Moscow 117997
| | - Nikolay A Krylov
- 1] M.M. Shemyakin &Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya, 16/10, Moscow 117997 [2] Joint Supercomputer Center, Russian Academy of Sciences, Leninsky prospect, 32a, Moscow 119991, Russia
| | - Ivan A Boldyrev
- M.M. Shemyakin &Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya, 16/10, Moscow 117997
| | - Roman G Efremov
- 1] M.M. Shemyakin &Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya, 16/10, Moscow 117997 [2] Moscow Institute of Physics and Technology (State University), Dolgoprudny, Moscow Region, 141700, Russia [3] Higher School of Economics, Myasnitskaya ul. 20, 101000 Moscow, Russia
| |
Collapse
|
27
|
Yang J, Calero C, Martí J. Diffusion and spectroscopy of water and lipids in fully hydrated dimyristoylphosphatidylcholine bilayer membranes. J Chem Phys 2014; 140:104901. [PMID: 24628199 DOI: 10.1063/1.4867385] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Microscopic structure and dynamics of water and lipids in a fully hydrated dimyristoylphosphatidylcholine phospholipid lipid bilayer membrane in the liquid-crystalline phase have been analyzed with all-atom molecular dynamics simulations based on the recently parameterized CHARMM36 force field. The diffusive dynamics of the membrane lipids and of its hydration water, their reorientational motions as well as their corresponding spectral densities, related to the absorption of radiation, have been considered for the first time using the present force field. In addition, structural properties such as density and pressure profiles, a deuterium-order parameter, surface tension, and the extent of water penetration in the membrane have been analyzed. Molecular self-diffusion, reorientational motions, and spectral densities of atomic species reveal a variety of time scales playing a role in membrane dynamics. The mechanisms of lipid motion strongly depend on the time scale considered, from fast ballistic translation at the scale of picoseconds (effective diffusion coefficients of the order of 10(-5) cm(2)/s) to diffusive flow of a few lipids forming nanodomains at the scale of hundreds of nanoseconds (diffusion coefficients of the order of 10(-8) cm(2)/s). In the intermediate regime of sub-diffusion, collisions with nearest neighbors prevent the lipids to achieve full diffusion. Lipid reorientations along selected directions agree well with reported nuclear magnetic resonance data and indicate two different time scales, one about 1 ns and a second one in the range of 2-8 ns. We associated the two time scales of reorientational motions with angular distributions of selected vectors. Calculated spectral densities corresponding to lipid and water reveal an overall good qualitative agreement with Fourier transform infrared spectroscopy experiments. Our simulations indicate a blue-shift of the low frequency spectral bands of hydration water as a result of its interaction with lipids. We have thoroughly analyzed the physical meaning of all spectral features from lipid atomic sites and correlated them with experimental data. Our findings include a "wagging of the tails" frequency around 30 cm(-1), which essentially corresponds to motions of the tail-group along the instantaneous plane formed by the two lipid tails, i.e., in-plane oscillations are clearly of bigger importance than those along the normal-to-the plane direction.
Collapse
Affiliation(s)
- J Yang
- Department of Physics and Nuclear Engineering, Technical University of Catalonia-Barcelona Tech, B4-B5 Northern Campus, Jordi Girona 1-3, 08034 Barcelona, Catalonia, Spain
| | - C Calero
- Department of Physics and Nuclear Engineering, Technical University of Catalonia-Barcelona Tech, B4-B5 Northern Campus, Jordi Girona 1-3, 08034 Barcelona, Catalonia, Spain
| | - J Martí
- Department of Physics and Nuclear Engineering, Technical University of Catalonia-Barcelona Tech, B4-B5 Northern Campus, Jordi Girona 1-3, 08034 Barcelona, Catalonia, Spain
| |
Collapse
|
28
|
Feng JW, Ding HM, Ma YQ. Controlling water flow inside carbon nanotube with lipid membranes. J Chem Phys 2014; 141:094901. [DOI: 10.1063/1.4893964] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|