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Chandra A, Kayal A, Das B, Chandra A. Dynamical Crossover of Interfacial Water upon Melting of a Lipid Bilayer: Influence of Different Parts of the Headgroups. J Phys Chem B 2023. [PMID: 38032152 DOI: 10.1021/acs.jpcb.3c04792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2023]
Abstract
All-atom molecular dynamics simulations of a 1,2-dimyristoyl-sn-glycero-3-phosphocholine bilayer in contact with liquid water were performed at different temperatures ranging from 285 to 320 K. We have investigated the heterogeneity and dynamical transitions in interfacial water as the lipid bilayer undergoes a melting transition. Results are obtained for water at the outer surface of the bilayer and for those buried more deeply in the lipid chains of the bilayer. It is found that lipid bilayer melting influences both the structure and dynamics of interfacial water. The number of interfacial water molecules shows a jump in the melting of the bilayer. The temperature dependence of the diffusivity and orientational relaxation of interfacial water molecules exhibits a dynamical crossover upon melting of the bilayer. The extent of dynamical crossover is found to be rather strong with significant changes in activation barriers for interfacial water around the carbonyl groups, which are deeply buried toward the lipid chains of the bilayer. The dynamical crossover gradually decreases as one moves further away from the outer surface, and it essentially vanishes for water in the region of 5-10 Å from the outer surface. It is found that the lipid melting-induced dynamical crossover of interfacial water is significant only for water that is in close proximity to the bilayer surface or deeply buried into it. The current results reveal that water molecules in different parts of the interface respond differently on melting of the bilayer. The current study also shows that the carbonyl-bound water molecules can play an important role in the phase transition of the bilayer as the temperature is raised through its melting point.
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Affiliation(s)
- Abhilash Chandra
- Department of Chemistry, Indian Institute of Technology Kanpur, Uttar Pradesh 208016, India
| | - Abhijit Kayal
- Department of Chemistry, Indian Institute of Technology Kanpur, Uttar Pradesh 208016, India
| | - Banshi Das
- Department of Chemistry, Indian Institute of Technology Kanpur, Uttar Pradesh 208016, India
| | - Amalendu Chandra
- Department of Chemistry, Indian Institute of Technology Kanpur, Uttar Pradesh 208016, India
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Yamaguchi YY, Kaneko K. Collective 1/f fluctuation by pseudo-Casimir-invariants. Phys Rev E 2018; 98:020201. [PMID: 30253593 DOI: 10.1103/physreve.98.020201] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Indexed: 11/07/2022]
Abstract
In this study, we propose a universal scenario explaining the 1/f fluctuation, including pink noises, in Hamiltonian dynamical systems with many degrees of freedom under long-range interaction. In the thermodynamic limit, the dynamics of such systems can be described by the Vlasov equation, which has an infinite number of Casimir invariants. In a finite system, they become pseudoinvariants, which yield quasistationary states. The dynamics then exhibit slow motion over them, up to the timescale where the pseudo-Casimir-invariants are effective. Such long-time correlation leads to 1/f fluctuations of collective variables, as is confirmed by direct numerical simulations. The universality of this collective 1/f fluctuation is demonstrated by taking a variety of Hamiltonians and changing the range of interaction and number of particles.
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Affiliation(s)
- Yoshiyuki Y Yamaguchi
- Department of Applied Mathematics and Physics, Graduate School of Informatics, Kyoto University, Kyoto 606-8501, Japan
| | - Kunihiko Kaneko
- Department of Basic Science, University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan
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Mestre ALG, Cerquido M, Inácio PMC, Asgarifar S, Lourenço AS, Cristiano MLS, Aguiar P, Medeiros MCR, Araújo IM, Ventura J, Gomes HL. Ultrasensitive gold micro-structured electrodes enabling the detection of extra-cellular long-lasting potentials in astrocytes populations. Sci Rep 2017; 7:14284. [PMID: 29079771 PMCID: PMC5660243 DOI: 10.1038/s41598-017-14697-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 10/17/2017] [Indexed: 12/13/2022] Open
Abstract
Ultra-sensitive electrodes for extracellular recordings were fabricated and electrically characterized. A signal detection limit defined by a noise level of 0.3-0.4 μV for a bandwidth of 12.5 Hz was achieved. To obtain this high sensitivity, large area (4 mm2) electrodes were used. The electrode surface is also micro-structured with an array of gold mushroom-like shapes to further enhance the active area. In comparison with a flat gold surface, the micro-structured surface increases the capacitance of the electrode/electrolyte interface by 54%. The electrode low impedance and low noise enable the detection of weak and low frequency quasi-periodic signals produced by astrocytes populations that thus far had remained inaccessible using conventional extracellular electrodes. Signals with 5 μV in amplitude and lasting for 5-10 s were measured, with a peak-to-peak signal-to-noise ratio of 16. The electrodes and the methodology developed here can be used as an ultrasensitive electrophysiological tool to reveal the synchronization dynamics of ultra-slow ionic signalling between non-electrogenic cells.
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Affiliation(s)
- Ana L G Mestre
- Universidade do Algarve, Faculdade de Ciências e Tecnologia, 8005-139, Faro, Portugal
- Instituto de Telecomunicações, Avenida Rovisco Pais 1, 1049-001, Lisboa, Portugal
| | - Mónica Cerquido
- Instituto de Física dos Materiais da Universidade do Porto, Instituto de Nanociências e Nanotecnologia, Departamento de Física e Astronomia, Universidade do Porto, Rua do Campo Alegre 687, 4169-007, Porto, Portugal
| | - Pedro M C Inácio
- Universidade do Algarve, Faculdade de Ciências e Tecnologia, 8005-139, Faro, Portugal
- Instituto de Telecomunicações, Avenida Rovisco Pais 1, 1049-001, Lisboa, Portugal
| | - Sanaz Asgarifar
- Universidade do Algarve, Faculdade de Ciências e Tecnologia, 8005-139, Faro, Portugal
- Instituto de Telecomunicações, Avenida Rovisco Pais 1, 1049-001, Lisboa, Portugal
| | - Ana S Lourenço
- Departamento de Ciências Biomédicas e Medicina, Universidade do Algarve, 8005-139, Faro, Portugal
- Centro de Investigação em Biomedicina, Universidade do Algarve, 8005-139, Faro, Portugal
| | - Maria L S Cristiano
- Universidade do Algarve, Faculdade de Ciências e Tecnologia, 8005-139, Faro, Portugal
- Centro de Ciências do Mar, Universidade do Algarve, 8005-139, Faro, Portugal
| | - Paulo Aguiar
- Instituto de Engenharia Biomédica, Universidade do Porto, Rua Alfredo Allen 208, 4200-135, Porto, Portugal
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, 4200-135, Porto, Portugal
| | - Maria C R Medeiros
- Instituto de Telecomunicações, Departamento de Engenharia Electrotécnica e Computadores, Universidade de Coimbra, 3030-290, Coimbra, Portugal
| | - Inês M Araújo
- Departamento de Ciências Biomédicas e Medicina, Universidade do Algarve, 8005-139, Faro, Portugal
- Centro de Investigação em Biomedicina, Universidade do Algarve, 8005-139, Faro, Portugal
| | - João Ventura
- Instituto de Física dos Materiais da Universidade do Porto, Instituto de Nanociências e Nanotecnologia, Departamento de Física e Astronomia, Universidade do Porto, Rua do Campo Alegre 687, 4169-007, Porto, Portugal
| | - Henrique L Gomes
- Universidade do Algarve, Faculdade de Ciências e Tecnologia, 8005-139, Faro, Portugal.
- Instituto de Telecomunicações, Avenida Rovisco Pais 1, 1049-001, Lisboa, Portugal.
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Yadav AC, Ramaswamy R, Dhar D. General mechanism for the 1/f noise. Phys Rev E 2017; 96:022215. [PMID: 28950591 DOI: 10.1103/physreve.96.022215] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Indexed: 11/07/2022]
Abstract
We consider the response of a memoryless nonlinear device that acts instantaneously, converting an input signal ξ(t) into an output η(t) at the same time t. For input Gaussian noise with power-spectrum 1/f^{α}, the nonlinearity can modify the spectral index of the output to give a spectrum that varies as 1/f^{α^{'}} with α^{'}≠α. We show that the value of α^{'} depends on the nonlinear transformation and can be tuned continuously. This provides a general mechanism for the ubiquitous 1/f noise found in nature.
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Affiliation(s)
- Avinash Chand Yadav
- Department of Physics and Astronomical Sciences, Central University of Jammu, Samba 181 143, India
| | | | - Deepak Dhar
- Department of Physics, Indian Institute of Science, Education and Research, Dr. Homi Bhabha Road, Pashan, Pune 411 008, India
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Yamamoto E, Akimoto T, Kalli AC, Yasuoka K, Sansom MSP. Dynamic interactions between a membrane binding protein and lipids induce fluctuating diffusivity. SCIENCE ADVANCES 2017; 3:e1601871. [PMID: 28116358 PMCID: PMC5249258 DOI: 10.1126/sciadv.1601871] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 12/07/2016] [Indexed: 05/08/2023]
Abstract
Pleckstrin homology (PH) domains are membrane-binding lipid recognition proteins that interact with phosphatidylinositol phosphate (PIP) molecules in eukaryotic cell membranes. Diffusion of PH domains plays a critical role in biological reactions on membrane surfaces. Although diffusivity can be estimated by long-time measurements, it lacks information on the short-time diffusive nature. We reveal two diffusive properties of a PH domain bound to the surface of a PIP-containing membrane using molecular dynamics simulations. One is fractional Brownian motion, attributed to the motion of the lipids with which the PH domain interacts. The other is temporally fluctuating diffusivity; that is, the short-time diffusivity of the bound protein changes substantially with time. Moreover, the diffusivity for short-time measurements is intrinsically different from that for long-time measurements. This fluctuating diffusivity results from dynamic changes in interactions between the PH domain and PIP molecules. Our results provide evidence that the complexity of protein-lipid interactions plays a crucial role in the diffusion of proteins on biological membrane surfaces. Changes in the diffusivity of PH domains and related membrane-bound proteins may in turn contribute to the formation/dissolution of protein complexes in membranes.
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Affiliation(s)
- Eiji Yamamoto
- Graduate School of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan
| | - Takuma Akimoto
- Graduate School of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan
| | - Antreas C. Kalli
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
- Leeds Institute of Cancer and Pathology, School of Medicine, St. James’s University Hospital, University of Leeds, Leeds LS9 7TF, UK
| | - Kenji Yasuoka
- Department of Mechanical Engineering, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan
| | - Mark S. P. Sansom
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
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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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