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Kasparyan G, Hub JS. Equivalence of Charge Imbalance and External Electric Fields during Free Energy Calculations of Membrane Electroporation. J Chem Theory Comput 2023; 19:2676-2683. [PMID: 37052575 DOI: 10.1021/acs.jctc.3c00065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/14/2023]
Abstract
Electric fields across lipid membranes play important roles in physiology, medicine, and biotechnology, rationalizing the wide interest in modeling transmembrane potentials in molecular dynamics simulations. Transmembrane potentials have been implemented with external electric fields or by imposing charge imbalance between the two water compartments of a stacked double-membrane system. We compare the two methods in the context of membrane electroporation, which involves a large change of membrane structure and capacitance. We show that, given that Ewald electrostatics are defined with tinfoil boundary conditions, the two methods lead to (i) identical potentials of mean force (PMFs) of pore formation and expansion at various potentials, demonstrating that the two methods impose equivalent driving forces for large-scale transitions at membranes, and (ii) to identical polarization of water within thin water wires or open pores, suggesting that the two methods furthermore impose equivalent local electric fields. Without tinfoil boundary conditions, effects from external fields on pore formation are spuriously suppressed or even removed. Together, our study shows that both methods, external fields and charge imbalance, are well suitable for studying large-scale transitions of lipid membranes that involve changes of membrane capacitance. However, using charge imbalance is technically more challenging for maintaining a constant transmembrane potential since it requires updating of the charge imbalance as the membrane capacitance changes.
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Affiliation(s)
- Gari Kasparyan
- Theoretical Physics and Center for Biophysics, Saarland University, 66123 Saarbrücken, Germany
| | - Jochen S Hub
- Theoretical Physics and Center for Biophysics, Saarland University, 66123 Saarbrücken, Germany
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2
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Kawaguchi K, Ito S, Saito H, Nagao H. Molecular dynamics study of lipid bilayer asymmetry induced by ion concentration gradient and electronic polarizability. MOLECULAR SIMULATION 2022. [DOI: 10.1080/08927022.2022.2025798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Kazutomo Kawaguchi
- Institute of Science and Engineering, Kanazawa University, Kanazawa, Japan
| | - Seiichiro Ito
- Institute of Science and Engineering, Kanazawa University, Kanazawa, Japan
| | - Hiroaki Saito
- Faculty of Pharmaceutical Sciences, Hokuriku University, Kanazawa, Japan
| | - Hidemi Nagao
- Institute of Science and Engineering, Kanazawa University, Kanazawa, Japan
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3
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Birdsall ER, Petti MK, Saraswat V, Ostrander JS, Arnold MS, Zanni MT. Structure Changes of a Membrane Polypeptide under an Applied Voltage Observed with Surface-Enhanced 2D IR Spectroscopy. J Phys Chem Lett 2021; 12:1786-1792. [PMID: 33576633 PMCID: PMC8162810 DOI: 10.1021/acs.jpclett.0c03706] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
The structures of many membrane-bound proteins and polypeptides depend on the membrane potential. However, spectroscopically studying their structures under an applied field is challenging, because a potential is difficult to generate across more than a few bilayers. We study the voltage-dependent structures of the membrane-bound polypeptide, alamethicin, using a spectroelectrochemical cell coated with a rough, gold film to create surface plasmons. The plasmons sufficiently enhance the 2D IR signal to measure a single bilayer. The film is also thick enough to conduct current and thereby apply a potential. The 2D IR spectra resolve features from both 310- and α-helical structures and cross-peaks connecting the two. We observe changes in the peak intensity, not their frequencies, upon applying a voltage. A similar change occurs with pH, which is known to alter the angle of alamethicin relative to the surface normal. The spectra are modeled using a vibrational exciton Hamiltonian, and the voltage-dependent spectra are consistent with a change in angle of the 310- and α-helices in the membrane from 55 to 44°and from 31 to 60°, respectively. The 310- and α-helices are coupled by approximately 10 cm-1. These experiments provide new structural information about alamethicin under a potential difference and demonstrate a technique that might be applied to voltage-gated membrane proteins and compared to molecular dynamics structures.
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Affiliation(s)
- Erin R Birdsall
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Megan K Petti
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Vivek Saraswat
- Department of Materials Science and Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Joshua S Ostrander
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Department of Chemistry, Indiana Wesleyan University, Marion, Indiana 46953, United States
| | - Michael S Arnold
- Department of Materials Science and Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Martin T Zanni
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
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4
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Prathyusha KR, Pagonabarraga I, Kumar PBS. Modification of lipid membrane compressibility induced by an electric field. Phys Rev E 2021; 102:062413. [PMID: 33466026 DOI: 10.1103/physreve.102.062413] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 10/20/2020] [Indexed: 11/07/2022]
Abstract
Changes in membrane deformation and compressibility, induced by an external electric field, are investigated using coarse-grained martini force field simulations in a salt-free environment. We observe changes in the area of the membrane above a critical electric field. Below this value, the membrane compressibility modulus is found to decrease monotonically. For higher electric fields, the membrane projected area remains constant while the net interfacial area increases, with the corresponding compressibility moduli, show the opposite behavior. We find that the mechanical parameters, surface tension and bending modulus, of a freely floating membrane in the absence of explicit ions, are unaffected by the presence of the electric field. We believe these results have a bearing on our understanding of the electroformation of uncharged lipids in a salt-free environment.
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Affiliation(s)
- K R Prathyusha
- Department of Physics, Indian Institute of Technology Madras, Chennai, India
| | - Ignacio Pagonabarraga
- CECAM, Centre Européen de Calcul Atomique et Moléculaire, École Polytechnique Fédérale de Laussane (EPFL), Batochime, Avenue Forel 2, 1015 Lausanne, Switzerland.,Departament de Física de la Matèria Condensada, Universitat de Barcelona, C. Martí Franquès 1, 08028 8 Barcelona, Spain.,University of Barcelona Institute of Complex Systems (UBICS), Universitat de Barcelona, 08028 10 Barcelona, Spain
| | - P B Sunil Kumar
- Department of Physics, Indian Institute of Technology Madras, Chennai, India.,Indian Institute of Technology Palakkad, Ahalia Integrated Campus, Kozhippara, Palakkad - 678557, Kerala, India
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5
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Effect of membrane potential on pore formation by the antimicrobial peptide magainin 2 in lipid bilayers. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183381. [DOI: 10.1016/j.bbamem.2020.183381] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 05/28/2020] [Accepted: 05/31/2020] [Indexed: 11/19/2022]
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6
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Forbrig E, Staffa JK, Salewski J, Mroginski MA, Hildebrandt P, Kozuch J. Monitoring the Orientational Changes of Alamethicin during Incorporation into Bilayer Lipid Membranes. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:2373-2385. [PMID: 29353482 DOI: 10.1021/acs.langmuir.7b04265] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Antimicrobial peptides (AMPs) are the first line of defense after contact of an infectious invader, for example, bacterium or virus, with a host and an integral part of the innate immune system of humans. Their broad spectrum of biological functions ranges from cell membrane disruption over facilitation of chemotaxis to interaction with membrane-bound or intracellular receptors, thus providing novel strategies to overcome bacterial resistances. Especially, the clarification of the mechanisms and dynamics of AMP incorporation into bacterial membranes is of high interest, and different mechanistic models are still under discussion. In this work, we studied the incorporation of the peptaibol alamethicin (ALM) into tethered bilayer lipid membranes on electrodes in combination with surface-enhanced infrared absorption (SEIRA) spectroscopy. This approach allows monitoring the spontaneous and potential-induced ion channel formation of ALM in situ. The complex incorporation kinetics revealed a multistep mechanism that points to peptide-peptide interactions prior to penetrating the membrane and adopting the transmembrane configuration. On the basis of the anisotropy of the backbone amide I and II infrared absorptions determined by density functional theory calculations, we employed a mathematical model to evaluate ALM reorientations monitored by SEIRA spectroscopy. Accordingly, ALM was found to adopt inclination angles of ca. 69°-78° and 21° in its interfacially adsorbed and transmembrane incorporated states, respectively. These orientations can be stabilized efficiently by the dipolar interaction with lipid head groups or by the application of a potential gradient. The presented potential-controlled mechanistic study suggests an N-terminal integration of ALM into membranes as monomers or parallel oligomers to form ion channels composed of parallel-oriented helices, whereas antiparallel oligomers are barred from intrusion.
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Affiliation(s)
- Enrico Forbrig
- Technische Universität Berlin, Institut für Chemie , Sekr. PC14, Strasse des 17. Juni 135, D-10623 Berlin, Germany
| | - Jana K Staffa
- Technische Universität Berlin, Institut für Chemie , Sekr. PC14, Strasse des 17. Juni 135, D-10623 Berlin, Germany
| | - Johannes Salewski
- Technische Universität Berlin, Institut für Chemie , Sekr. PC14, Strasse des 17. Juni 135, D-10623 Berlin, Germany
| | - Maria Andrea Mroginski
- Technische Universität Berlin, Institut für Chemie , Sekr. PC14, Strasse des 17. Juni 135, D-10623 Berlin, Germany
| | - Peter Hildebrandt
- Technische Universität Berlin, Institut für Chemie , Sekr. PC14, Strasse des 17. Juni 135, D-10623 Berlin, Germany
| | - Jacek Kozuch
- Technische Universität Berlin, Institut für Chemie , Sekr. PC14, Strasse des 17. Juni 135, D-10623 Berlin, Germany
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Structural Behavior of the Peptaibol Harzianin HK VI in a DMPC Bilayer: Insights from MD Simulations. Biophys J 2017. [PMID: 28636916 DOI: 10.1016/j.bpj.2017.05.019] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Microsecond molecular dynamics simulations of harzianin HK VI (HZ) interacting with a dimyristoylphosphatidylcholine bilayer were performed at the condition of low peptide-to-lipid ratio. Two orientations of HZ molecule in the bilayer were found and characterized. In the orientation perpendicular to the bilayer surface, HZ induces a local thinning of the bilayer. When inserted into the bilayer parallel to its surface, HZ is located nearly completely within the hydrophobic region of the bilayer. A combination of solid-state NMR and circular dichroism experiments found the latter orientation to be dominant. An extended sampling simulation provided qualitative results and showed the same orientation to be a global minimum of free energy. The secondary structure of HZ was characterized, and it was found to be located in the 310-helical family. The specific challenges of computer simulation of nonpolar peptides are discussed briefly.
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Melcr J, Bonhenry D, Timr Š, Jungwirth P. Transmembrane Potential Modeling: Comparison between Methods of Constant Electric Field and Ion Imbalance. J Chem Theory Comput 2016; 12:2418-25. [DOI: 10.1021/acs.jctc.5b01202] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Josef Melcr
- Institute of Organic
Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo
nám. 2, 16610 Prague 6, Czech Republic
| | - Daniel Bonhenry
- Institute of Organic
Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo
nám. 2, 16610 Prague 6, Czech Republic
| | - Štěpán Timr
- Institute of Organic
Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo
nám. 2, 16610 Prague 6, Czech Republic
| | - Pavel Jungwirth
- Institute of Organic
Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo
nám. 2, 16610 Prague 6, Czech Republic
- Department of Physics, Tampere University of Technology, P.O. Box 692, FI-33101 Tampere, Finland
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9
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Casciola M, Tarek M. A molecular insight into the electro-transfer of small molecules through electropores driven by electric fields. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:2278-2289. [PMID: 27018309 DOI: 10.1016/j.bbamem.2016.03.022] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2016] [Revised: 03/21/2016] [Accepted: 03/21/2016] [Indexed: 11/26/2022]
Abstract
The transport of chemical compounds across the plasma membrane into the cell is relevant for several biological and medical applications. One of the most efficient techniques to enhance this uptake is reversible electroporation. Nevertheless, the detailed molecular mechanism of transport of chemical species (dyes, drugs, genetic materials, …) following the application of electric pulses is not yet fully elucidated. In the past decade, molecular dynamics (MD) simulations have been conducted to model the effect of pulsed electric fields on membranes, describing several aspects of this phenomenon. Here, we first present a comprehensive review of the results obtained so far modeling the electroporation of lipid membranes, then we extend these findings to study the electrotransfer across lipid bilayers subject to microsecond pulsed electric fields of Tat11, a small hydrophilic charged peptide, and of siRNA. We use in particular a MD simulation protocol that allows to characterize the transport of charged species through stable pores. Unexpectedly, our results show that for an electroporated bilayer subject to transmembrane voltages in the order of 500mV, i.e. consistent with experimental conditions, both Tat11 and siRNA can translocate through nanoelectropores within tens of ns. We discuss these results in comparison to experiments in order to rationalize the mechanism of drug uptake by cells. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg.
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Affiliation(s)
- Maura Casciola
- Université de Lorraine, UMR 7565, F-54506 Vandoeuvre les Nancy, France; Department of Information Engineering, Electronics and Telecommunications (D.I.E.T), Sapienza University of Rome, 00184 Rome, Italy; Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, 00161 Rome, Italy
| | - Mounir Tarek
- Université de Lorraine, UMR 7565, F-54506 Vandoeuvre les Nancy, France; CNRS, UMR 7565, F-54506 Vandoeuvre les Nancy, France.
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10
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Kutzner C, Köpfer DA, Machtens JP, de Groot BL, Song C, Zachariae U. Insights into the function of ion channels by computational electrophysiology simulations. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:1741-52. [PMID: 26874204 DOI: 10.1016/j.bbamem.2016.02.006] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Revised: 02/03/2016] [Accepted: 02/04/2016] [Indexed: 12/11/2022]
Abstract
Ion channels are of universal importance for all cell types and play key roles in cellular physiology and pathology. Increased insight into their functional mechanisms is crucial to enable drug design on this important class of membrane proteins, and to enhance our understanding of some of the fundamental features of cells. This review presents the concepts behind the recently developed simulation protocol Computational Electrophysiology (CompEL), which facilitates the atomistic simulation of ion channels in action. In addition, the review provides guidelines for its application in conjunction with the molecular dynamics software package GROMACS. We first lay out the rationale for designing CompEL as a method that models the driving force for ion permeation through channels the way it is established in cells, i.e., by electrochemical ion gradients across the membrane. This is followed by an outline of its implementation and a description of key settings and parameters helpful to users wishing to set up and conduct such simulations. In recent years, key mechanistic and biophysical insights have been obtained by employing the CompEL protocol to address a wide range of questions on ion channels and permeation. We summarize these recent findings on membrane proteins, which span a spectrum from highly ion-selective, narrow channels to wide diffusion pores. Finally we discuss the future potential of CompEL in light of its limitations and strengths. This article is part of a Special Issue entitled: Membrane Proteins edited by J.C. Gumbart and Sergei Noskov.
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Affiliation(s)
- Carsten Kutzner
- Department of Theoretical and Computational Biophysics, Computational Biomolecular Dynamics Group, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - David A Köpfer
- Department of Theoretical and Computational Biophysics, Computational Biomolecular Dynamics Group, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Jan-Philipp Machtens
- Institute of Complex Systems, Zelluläre Biophysik (ICS-4), Forschungszentrum Jülich, Jülich, Germany
| | - Bert L de Groot
- Department of Theoretical and Computational Biophysics, Computational Biomolecular Dynamics Group, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Chen Song
- Department of Biochemistry, University of Oxford, United Kingdom
| | - Ulrich Zachariae
- Physics, School of Science and Engineering, University of Dundee, United Kingdom; Computational Biology, School of Life Sciences, University of Dundee, United Kingdom.
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11
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Pothula KR, Solano CJF, Kleinekathöfer U. Simulations of outer membrane channels and their permeability. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1858:1760-71. [PMID: 26721326 DOI: 10.1016/j.bbamem.2015.12.020] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Revised: 12/15/2015] [Accepted: 12/17/2015] [Indexed: 12/25/2022]
Abstract
Channels in the outer membrane of Gram-negative bacteria provide essential pathways for the controlled and unidirectional transport of ions, nutrients and metabolites into the cell. At the same time the outer membrane serves as a physical barrier for the penetration of noxious substances such as antibiotics into the bacteria. Most antibiotics have to pass through these membrane channels to either reach cytoplasmic bound targets or to further cross the hydrophobic inner membrane. Considering the pharmaceutical significance of antibiotics, understanding the functional role and mechanism of these channels is of fundamental importance in developing strategies to design new drugs with enhanced permeation abilities. Due to the biological complexity of membrane channels and experimental limitations, computer simulations have proven to be a powerful tool to investigate the structure, dynamics and interactions of membrane channels. Considerable progress has been made in computer simulations of membrane channels during the last decade. The goal of this review is to provide an overview of the computational techniques and their roles in modeling the transport across outer membrane channels. A special emphasis is put on all-atom molecular dynamics simulations employed to better understand the transport of molecules. Moreover, recent molecular simulations of ion, substrate and antibiotics translocation through membrane pores are briefly summarized. This article is part of a Special Issue entitled: Membrane Proteins edited by J.C. Gumbart and Sergei Noskov.
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Affiliation(s)
- Karunakar R Pothula
- Department of Physics and Earth Sciences, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
| | - Carlos J F Solano
- Department of Physics and Earth Sciences, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
| | - Ulrich Kleinekathöfer
- Department of Physics and Earth Sciences, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
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12
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Sternberg U, Witter R. Molecular dynamics simulations on PGLa using NMR orientational constraints. JOURNAL OF BIOMOLECULAR NMR 2015; 63:265-274. [PMID: 26358333 DOI: 10.1007/s10858-015-9983-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 09/01/2015] [Indexed: 06/05/2023]
Abstract
NMR data obtained by solid state NMR from anisotropic samples are used as orientational constraints in molecular dynamics simulations for determining the structure and dynamics of the PGLa peptide within a membrane environment. For the simulation the recently developed molecular dynamics with orientational constraints technique (MDOC) is used. This method introduces orientation dependent pseudo-forces into the COSMOS-NMR force field. Acting during a molecular dynamics simulation these forces drive molecular rotations, re-orientations and folding in such a way that the motional time-averages of the tensorial NMR properties are consistent with the experimentally measured NMR parameters. This MDOC strategy does not depend on the initial choice of atomic coordinates, and is in principle suitable for any flexible and mobile kind of molecule; and it is of course possible to account for flexible parts of peptides or their side-chains. MDOC has been applied to the antimicrobial peptide PGLa and a related dimer model. With these simulations it was possible to reproduce most NMR parameters within the experimental error bounds. The alignment, conformation and order parameters of the membrane-bound molecule and its dimer were directly derived with MDOC from the NMR data. Furthermore, this new approach yielded for the first time the distribution of segmental orientations with respect to the membrane and the order parameter tensors of the dimer systems. It was demonstrated the deuterium splittings measured at the peptide to lipid ratio of 1/50 are consistent with a membrane spanning orientation of the peptide.
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Affiliation(s)
- Ulrich Sternberg
- Technomedicum, Tallinn University of Technology, Ehitajate tee 5, 19086, Tallinn, Estonia.
| | - Raiker Witter
- Technomedicum, Tallinn University of Technology, Ehitajate tee 5, 19086, Tallinn, Estonia
- Institute of Nanotechnology, Karlsruhe Institute of Technology (KIT), POB 3640, 76021, Karlsruhe, Germany
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13
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Freeman EC, Farimani AB, Aluru NR, Philen MK. Multiscale modeling of droplet interface bilayer membrane networks. BIOMICROFLUIDICS 2015; 9:064101. [PMID: 26594262 PMCID: PMC4644148 DOI: 10.1063/1.4935382] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 10/28/2015] [Indexed: 05/17/2023]
Abstract
Droplet interface bilayer (DIB) networks are considered for the development of stimuli-responsive membrane-based materials inspired by cellular mechanics. These DIB networks are often modeled as combinations of electrical circuit analogues, creating complex networks of capacitors and resistors that mimic the biomolecular structures. These empirical models are capable of replicating data from electrophysiology experiments, but these models do not accurately capture the underlying physical phenomena and consequently do not allow for simulations of material functionalities beyond the voltage-clamp or current-clamp conditions. The work presented here provides a more robust description of DIB network behavior through the development of a hierarchical multiscale model, recognizing that the macroscopic network properties are functions of their underlying molecular structure. The result of this research is a modeling methodology based on controlled exchanges across the interfaces of neighboring droplets. This methodology is validated against experimental data, and an extension case is provided to demonstrate possible future applications of droplet interface bilayer networks.
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Affiliation(s)
- Eric C Freeman
- College of Engineering, University of Georgia , Athens, Georgia 30602, USA
| | - Amir B Farimani
- Department of Mechanical Science and Engineering, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, USA
| | - Narayana R Aluru
- Department of Mechanical Science and Engineering, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, USA
| | - Michael K Philen
- Department of Aerospace and Ocean Engineering, Virginia Tech , Blacksburg, Virginia 24061, USA
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14
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Nagao T, Mishima D, Javkhlantugs N, Wang J, Ishioka D, Yokota K, Norisada K, Kawamura I, Ueda K, Naito A. Structure and orientation of antibiotic peptide alamethicin in phospholipid bilayers as revealed by chemical shift oscillation analysis of solid state nuclear magnetic resonance and molecular dynamics simulation. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1848:2789-98. [PMID: 26248014 DOI: 10.1016/j.bbamem.2015.07.019] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Revised: 07/01/2015] [Accepted: 07/31/2015] [Indexed: 11/26/2022]
Abstract
The structure, topology and orientation of membrane-bound antibiotic alamethicin were studied using solid state nuclear magnetic resonance (NMR) spectroscopy. (13)C chemical shift interaction was observed in [1-(13)C]-labeled alamethicin. The isotropic chemical shift values indicated that alamethicin forms a helical structure in the entire region. The chemical shift anisotropy of the carbonyl carbon of isotopically labeled alamethicin was also analyzed with the assumption that alamethicin molecules rotate rapidly about the bilayer normal of the phospholipid bilayers. It is considered that the adjacent peptide planes form an angle of 100° or 120° when it forms α-helix or 310-helix, respectively. These properties lead to an oscillation of the chemical shift anisotropy with respect to the phase angle of the peptide plane. Anisotropic data were acquired for the 4 and 7 sites of the N- and C-termini, respectively. The results indicated that the helical axes for the N- and C-termini were tilted 17° and 32° to the bilayer normal, respectively. The chemical shift oscillation curves indicate that the N- and C-termini form the α-helix and 310-helix, respectively. The C-terminal 310-helix of alamethicin in the bilayer was experimentally observed and the unique bending structure of alamethicin was further confirmed by measuring the internuclear distances of [1-(13)C] and [(15)N] doubly-labeled alamethicin. Molecular dynamics simulation of alamethicin embedded into dimyristoyl phophatidylcholine (DMPC) bilayers indicates that the helical axes for α-helical N- and 310-helical C-termini are tilted 12° and 32° to the bilayer normal, respectively, which is in good agreement with the solid state NMR results.
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Affiliation(s)
- Takashi Nagao
- Graduate School of Engineering, Yokohama National University, Tokiwadai 79-5 Hodogaya-ku, Yokohama 240-8501, Japan
| | - Daisuke Mishima
- Graduate School of Engineering, Yokohama National University, Tokiwadai 79-5 Hodogaya-ku, Yokohama 240-8501, Japan
| | - Namsrai Javkhlantugs
- Graduate School of Engineering, Yokohama National University, Tokiwadai 79-5 Hodogaya-ku, Yokohama 240-8501, Japan; Center for Nanoscience and Nanotechnology, School of Engineering and Applied Sciences, National University of Mongolia, Ulaanbaatar 14201, Mongolia
| | - Jun Wang
- Graduate School of Engineering, Yokohama National University, Tokiwadai 79-5 Hodogaya-ku, Yokohama 240-8501, Japan
| | - Daisuke Ishioka
- Graduate School of Engineering, Yokohama National University, Tokiwadai 79-5 Hodogaya-ku, Yokohama 240-8501, Japan
| | - Kiyonobu Yokota
- Graduate School of Engineering, Yokohama National University, Tokiwadai 79-5 Hodogaya-ku, Yokohama 240-8501, Japan
| | - Kazushi Norisada
- Graduate School of Engineering, Yokohama National University, Tokiwadai 79-5 Hodogaya-ku, Yokohama 240-8501, Japan
| | - Izuru Kawamura
- Graduate School of Engineering, Yokohama National University, Tokiwadai 79-5 Hodogaya-ku, Yokohama 240-8501, Japan
| | - Kazuyoshi Ueda
- Graduate School of Engineering, Yokohama National University, Tokiwadai 79-5 Hodogaya-ku, Yokohama 240-8501, Japan
| | - Akira Naito
- Graduate School of Engineering, Yokohama National University, Tokiwadai 79-5 Hodogaya-ku, Yokohama 240-8501, Japan.
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15
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Casciola M, Bonhenry D, Liberti M, Apollonio F, Tarek M. A molecular dynamic study of cholesterol rich lipid membranes: comparison of electroporation protocols. Bioelectrochemistry 2014; 100:11-7. [DOI: 10.1016/j.bioelechem.2014.03.009] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2013] [Revised: 03/20/2014] [Accepted: 03/20/2014] [Indexed: 01/25/2023]
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16
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Yu H, Yzeiri I, Hou B, Chen CH, Bu W, Vanysek P, Chen YS, Lin B, Král P, Schlossman ML. Electric Field Effect on Phospholipid Monolayers at an Aqueous-Organic Liquid-Liquid Interface. J Phys Chem B 2014; 119:9319-34. [PMID: 25289837 DOI: 10.1021/jp5098525] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The electric potential difference across cell membranes, known as the membrane potential, plays an important role in the activation of many biological processes. To investigate the effect of the membrane potential on the molecular ordering of lipids within a biomimetic membrane, a self-assembled monolayer of 1-stearoyl-2-oleoyl-sn-glycero-3-phosphocholine (SOPC) lipids at an electrified 1,2-dichloroethane/water interface is studied with X-ray reflectivity and interfacial tension. Measurements over a range of electric potential differences, -150 to +130 mV, that encompass the range of typical biomembrane potentials demonstrate a nearly constant and stable structure whose lipid interfacial density is comparable to that found in other biomimetic membrane systems. Measurements at higher positive potentials, up to 330 mV, illustrate a monotonic decrease in the lipid interfacial density and accompanying variations in the interfacial configuration of the lipid. Molecular dynamics simulations, designed to mimic the experimental conditions, show that the measured changes in lipid configuration are due primarily to the variation in area per lipid with increasing applied electric field. Rotation of the SOPC dipole moment by the torque from the applied electric field appears to be negligible, except at the highest measured potentials. The simulations confirm in atomistic detail the measured potential-dependent characteristics of SOPC monolayers. Our hybrid study sheds light on phospholipid monolayer stability under different membrane potentials, which is important for understanding membrane processes. This study also illustrates the use of X-ray surface scattering to probe the ordering of surfactant monolayers at an electrified aqueous-organic liquid-liquid interface.
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Affiliation(s)
- Hao Yu
- †Department of Physics, University of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Irena Yzeiri
- ‡Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Binyang Hou
- †Department of Physics, University of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Chiu-Hao Chen
- †Department of Physics, University of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Wei Bu
- †Department of Physics, University of Illinois at Chicago, Chicago, Illinois 60607, United States
| | | | - Yu-Sheng Chen
- ∥The Center for Advanced Radiation Sources, University of Chicago, Chicago, Illinois 60637, United States
| | - Binhua Lin
- ∥The Center for Advanced Radiation Sources, University of Chicago, Chicago, Illinois 60637, United States
| | - Petr Král
- †Department of Physics, University of Illinois at Chicago, Chicago, Illinois 60607, United States.,‡Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Mark L Schlossman
- †Department of Physics, University of Illinois at Chicago, Chicago, Illinois 60607, United States
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17
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Rahaman A, Lazaridis T. A thermodynamic approach to alamethicin pore formation. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2014. [DOI: 10.1016/j.bbamem.2014.01.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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18
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Wang S, Larson RG. Water channel formation and ion transport in linear and branched lipid bilayers. Phys Chem Chem Phys 2014; 16:7251-62. [DOI: 10.1039/c3cp55116d] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The lipid bilayer stability and water channel morphologies are affected by the presence of methyl branches on lipid tails.
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Affiliation(s)
- Shihu Wang
- Department of Chemical Engineering
- University of Michigan
- Ann Arbor, USA
| | - Ronald G. Larson
- Department of Chemical Engineering
- University of Michigan
- Ann Arbor, USA
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19
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Rahaman A, Lazaridis T. A thermodynamic approach to alamethicin pore formation. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2013; 1838:98-105. [PMID: 24071593 DOI: 10.1016/j.bbamem.2013.09.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2013] [Revised: 09/10/2013] [Accepted: 09/17/2013] [Indexed: 12/15/2022]
Abstract
The structure and energetics of alamethicin Rf30 monomer to nonamer in cylindrical pores of 5 to 11Å radius are investigated using molecular dynamics simulations in an implicit membrane model that includes the free energy cost of acyl chain hydrophobic area exposure. Stable, low energy pores are obtained for certain combinations of radius and oligomeric number. The trimer and the tetramer formed 6Å pores that appear closed while the larger oligomers formed open pores at their optimal radius. The hexamer in an 8Å pore and the octamer in an 11Å pore give the lowest effective energy per monomer. However, all oligomers beyond the pentamer have comparable energies, consistent with the observation of multiple conductance levels. The results are consistent with the widely accepted "barrel-stave" model. The N terminal portion of the molecule exhibits smaller tilt with respect to the membrane normal than the C terminal portion, resulting in a pore shape that is a hybrid between a funnel and an hourglass. Transmembrane voltage has little effect on the structure of the oligomers but enhances or decreases their stability depending on its orientation. Antiparallel bundles are lower in energy than the commonly accepted parallel ones and could be present under certain experimental conditions. Dry aggregates (without an aqueous pore) have lower average effective energy than the corresponding aggregates in a pore, suggesting that alamethicin pores may be excited states that are stabilized in part by voltage and in part by the ion flow itself.
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Affiliation(s)
- Asif Rahaman
- Department of Chemistry, City College of New York, 160 Convent Avenue, New York, NY 10031, USA
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20
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Breton M, Delemotte L, Silve A, Mir LM, Tarek M. Transport of siRNA through Lipid Membranes Driven by Nanosecond Electric Pulses: An Experimental and Computational Study. J Am Chem Soc 2012; 134:13938-41. [DOI: 10.1021/ja3052365] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Marie Breton
- Université Paris-Sud, Laboratoire de Vectorologie et Thérapeutiques
Anticancéreuses, UMR 8203, Orsay F-91405, France
- CNRS,
Laboratoire de Vectorologie et Thérapeutiques Anticancéreuses,
UMR 8203, Orsay F-91405, France
- Institut Gustave Roussy, Laboratoire de Vectorologie et Thérapeutiques
Anticancéreuses, UMR 8203, Villejuif F-94805, France
| | - Lucie Delemotte
- Université de Lorraine, UMR Structure et Réactivité
des Systèmes Moléculaires Complexes, CNRS, Nancy 54003,
France
| | - Aude Silve
- Université Paris-Sud, Laboratoire de Vectorologie et Thérapeutiques
Anticancéreuses, UMR 8203, Orsay F-91405, France
- CNRS,
Laboratoire de Vectorologie et Thérapeutiques Anticancéreuses,
UMR 8203, Orsay F-91405, France
- Institut Gustave Roussy, Laboratoire de Vectorologie et Thérapeutiques
Anticancéreuses, UMR 8203, Villejuif F-94805, France
| | - Lluis M. Mir
- Université Paris-Sud, Laboratoire de Vectorologie et Thérapeutiques
Anticancéreuses, UMR 8203, Orsay F-91405, France
- CNRS,
Laboratoire de Vectorologie et Thérapeutiques Anticancéreuses,
UMR 8203, Orsay F-91405, France
- Institut Gustave Roussy, Laboratoire de Vectorologie et Thérapeutiques
Anticancéreuses, UMR 8203, Villejuif F-94805, France
| | - Mounir Tarek
- Université de Lorraine, UMR Structure et Réactivité
des Systèmes Moléculaires Complexes, CNRS, Nancy 54003,
France
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21
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Molecular Dynamics Simulations of Lipid Membrane Electroporation. J Membr Biol 2012; 245:531-43. [DOI: 10.1007/s00232-012-9434-6] [Citation(s) in RCA: 101] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2011] [Accepted: 04/30/2012] [Indexed: 10/28/2022]
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22
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Gumbart J, Khalili-Araghi F, Sotomayor M, Roux B. Constant electric field simulations of the membrane potential illustrated with simple systems. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2011; 1818:294-302. [PMID: 22001851 DOI: 10.1016/j.bbamem.2011.09.030] [Citation(s) in RCA: 133] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2011] [Revised: 08/28/2011] [Accepted: 09/26/2011] [Indexed: 01/29/2023]
Abstract
Advances in modern computational methods and technology make it possible to carry out extensive molecular dynamics simulations of complex membrane proteins based on detailed atomic models. The ultimate goal of such detailed simulations is to produce trajectories in which the behavior of the system is as realistic as possible. A critical aspect that requires consideration in the case of biological membrane systems is the existence of a net electric potential difference across the membrane. For meaningful computations, it is important to have well validated methodologies for incorporating the latter in molecular dynamics simulations. A widely used treatment of the membrane potential in molecular dynamics consists of applying an external uniform electric field E perpendicular to the membrane. The field acts on all charged particles throughout the simulated system, and the resulting applied membrane potential V is equal to the applied electric field times the length of the periodic cell in the direction perpendicular to the membrane. A series of test simulations based on simple membrane-slab models are carried out to clarify the consequences of the applied field. These illustrative tests demonstrate that the constant-field method is a simple and valid approach for accounting for the membrane potential in molecular dynamics studies of biomolecular systems. This article is part of a Special Issue entitled: Membrane protein structure and function.
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Affiliation(s)
- James Gumbart
- Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA
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23
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Parthasarathi R, Tian J, Redondo A, Gnanakaran S. Quantum Chemical Study of Carbohydrate–Phospholipid Interactions. J Phys Chem A 2011; 115:12826-40. [DOI: 10.1021/jp204015j] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- R. Parthasarathi
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Jianhui Tian
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Antonio Redondo
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - S. Gnanakaran
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
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24
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Dryga A, Chakrabarty S, Vicatos S, Warshel A. Coarse grained model for exploring voltage dependent ion channels. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2011; 1818:303-17. [PMID: 21843502 DOI: 10.1016/j.bbamem.2011.07.043] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2011] [Revised: 07/28/2011] [Accepted: 07/29/2011] [Indexed: 11/18/2022]
Abstract
The relationship between the membrane voltage and the gating of voltage activated ion channels and other systems have been a problem of great current interest. Unfortunately, reliable molecular simulations of external voltage effects present a major challenge, since meaningful converging microscopic simulations are not yet available and macroscopic treatments involve major uncertainties in terms of the dielectric used and other key features. This work extends our coarse grained (CG) model to simulations of membrane/protein systems under external potential. Special attention is devoted to a consistent modeling of the effect of external potential due to the electrodes, emphasizing semimacroscopic description of the electrolytes in the solution regions between the membranes and the electrodes, as well as the coupling between the combined potential from the electrodes plus the electrolytes and the protein ionized groups. We also provide a clear connection to microscopic treatment of the electrolytes and thus can explore possible conceptual problems that are hard to resolve by other current approaches. For example, we obtain a clear description of the charge distribution in the entire electrolyte system, including near the electrodes in membrane/electrodes systems (where continuum models do not seem to provide the relevant results). Furthermore, the present treatment provides an insight on the distribution of the electrolyte charges before and after equilibration across the membrane, and thus on the nature of the gating charge. The different aspects of the model have been carefully validated by considering problems ranging for the simple Debye-Huckel, and the Gouy-Chapman models to the evaluation of the electrolyte distribution between two electrodes, as well as the effect of extending the simulation system by periodic replicas. Overall the clear connection to microscopic descriptions combined with the power of the CG modeling seems to offer a powerful tool for exploring the balance between the protein conformational energy and the interaction with the external potential in voltage activated channels. To illustrate these features we present a preliminary study of the gating charge in the voltage activated Kv1.2 channel, using the actual change in the electrolyte charge distribution rather than the conventional macroscopic estimate. We also discuss other special features of the model, which include the ability to capture the effect of changes in the protonation states of the protein residues during the close to open voltage induced transition. This article is part of a Special Issue entitled: Membrane protein structure and function.
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Affiliation(s)
- Anatoly Dryga
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089-1062, USA
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25
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Balleza D. Toward understanding protocell mechanosensation. ORIGINS LIFE EVOL B 2011; 41:281-304. [PMID: 21080073 DOI: 10.1007/s11084-010-9225-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2010] [Accepted: 10/20/2010] [Indexed: 01/11/2023]
Abstract
Mechanosensitive (MS) channels can prevent bacterial bursting during hypo-osmotic shocks by responding to increases in lateral tension at the membrane level through an integrated and coordinated opening mechanism. Mechanical regulation in protocells could have been one of the first mechanisms to evolve in order to preserve their integrity against changing environmental conditions. How has the rich functional diversity found in present cells been created throughout evolution, and what did the primordial MS channels look like? This review has been written with the aim of identifying which factors may have been important for the appearance of the first osmotic valve in a prebiotic context, and what this valve may have been like. It highlights the mechanical properties of lipid bilayers, the association of peptides as aggregates in membranes, and the conservation of sequence motifs as central aspects to understand the evolution of proteins that gate below the tension required for spontaneous pore formation and membrane rupture. The arguments developed here apply to both MscL and MscS homologs, but could be valid to mechano-susceptible proteins in general.
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Affiliation(s)
- Daniel Balleza
- Unidad de Biofísica, CSIC-UPV/EHU, Universidad del País Vasco, Barrio Sarriena s/n, Leioa, Spain.
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26
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Venturini A, Zerbetto F. Dynamics of a lipid bilayer induced by electric fields. Phys Chem Chem Phys 2011; 13:9216-22. [DOI: 10.1039/c1cp20322c] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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27
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Bechinger B, Resende JM, Aisenbrey C. The structural and topological analysis of membrane-associated polypeptides by oriented solid-state NMR spectroscopy: established concepts and novel developments. Biophys Chem 2010; 153:115-25. [PMID: 21145159 DOI: 10.1016/j.bpc.2010.11.002] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2010] [Revised: 11/05/2010] [Accepted: 11/05/2010] [Indexed: 10/18/2022]
Abstract
Solid-state NMR spectroscopy is a powerful technique for the investigation of membrane-associated peptides and proteins as well as their interactions with lipids, and a variety of conceptually different approaches have been developed for their study. The technique is unique in allowing for the high-resolution investigation of liquid disordered lipid bilayers representing well the characteristics of natural membranes. Whereas magic angle solid-state NMR spectroscopy follows approaches that are related to those developed for solution NMR spectroscopy the use of static uniaxially oriented samples results in angular constraints which also provide information for the detailed analysis of polypeptide structures. This review introduces this latter concept theoretically and provides a number of examples. Furthermore, ongoing developments combining solid-state NMR spectroscopy with information from solution NMR spectroscopy and molecular modelling as well as exploratory studies using dynamic nuclear polarization solid-state NMR will be presented.
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Affiliation(s)
- Burkhard Bechinger
- Université de Strasbourg/CNRS, UMR7177, Institut de Chimie, 4 Rue Blaise Pascal, 67070 Strasbourg, France.
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28
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Nikolic A, Baud S, Rauscher S, Pomès R. Molecular mechanism of β-sheet self-organization at water-hydrophobic interfaces. Proteins 2010; 79:1-22. [DOI: 10.1002/prot.22854] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2010] [Revised: 07/21/2010] [Accepted: 07/24/2010] [Indexed: 12/20/2022]
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29
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Mihajlovic M, Lazaridis T. Antimicrobial peptides in toroidal and cylindrical pores. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2010; 1798:1485-93. [PMID: 20403332 DOI: 10.1016/j.bbamem.2010.04.004] [Citation(s) in RCA: 115] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Received: 09/23/2009] [Revised: 02/02/2010] [Accepted: 04/08/2010] [Indexed: 11/17/2022]
Abstract
Antimicrobial peptides (AMPs) are small, usually cationic peptides, which permeabilize biological membranes. Their mechanism of action is still not well understood. Here we investigate the preference of alamethicin and melittin for pores of different shapes, using molecular dynamics (MD) simulations of the peptides in pre-formed toroidal and cylindrical pores. When an alamethicin hexamer is initially embedded in a cylindrical pore, at the end of the simulation the pore remains cylindrical or closes if glutamines in the N-termini are not located within the pore. On the other hand, when a melittin tetramer is embedded in toroidal pore or in a cylindrical pore, at the end of the simulation the pore is lined both with peptides and lipid headgroups, and, thus, can be classified as a toroidal pore. These observations agree with the prevailing views that alamethicin forms barrel-stave pores whereas melittin forms toroidal pores. Both alamethicin and melittin form amphiphilic helices in the presence of membranes, but their net charge differs; at pH approximately 7, the net charge of alamethicin is -1 whereas that of melittin is +5. This gives rise to stronger electrostatic interactions of melittin with membranes than those of alamethicin. The melittin tetramer interacts more strongly with lipids in the toroidal pore than in the cylindrical one, due to more favorable electrostatic interactions.
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Affiliation(s)
- Maja Mihajlovic
- Department of Chemistry, The City College of New York, New York, NY 10031, USA
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30
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Oliveira Costa SD, Fernández Romero AJ, López Cascales JJ. Physicochemical study of the acetonitrile insertion into polypyrrole films. J Chem Phys 2010; 132:144702. [DOI: 10.1063/1.3378267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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31
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Bertelsen K, Paaske B, Thøgersen L, Tajkhorshid E, Schiøtt B, Skrydstrup T, Nielsen NC, Vosegaard T. Residue-specific information about the dynamics of antimicrobial peptides from (1)H-(15)N and (2)H solid-state NMR spectroscopy. J Am Chem Soc 2010; 131:18335-42. [PMID: 19929000 DOI: 10.1021/ja908604u] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We present a new method to obtain information about the conformational dynamics of membrane-proteins using solid-state NMR experiments of oriented samples. By measuring the orientation-dependent (1)H-(15)N dipole-dipole coupling, (15)N anisotropic chemical shift, and (2)H quadrupole coupling parameters for a single residue, it is possible to obtain information about the local dynamics of each residue in the protein. This may be interpreted on an individual basis or through models extended to study conformational motion of membrane-protein segments. The method is demonstrated for the antimicrobial peptaibol alamethicin for which combined analysis of anisotropic interactions for the Aib(8) residue provides detailed information about helix-tilt angle, wobbling, and oscillatory rotation around the helix axis in the membrane bound state. This information is in very good agreement with coarse-grained MD simulations of the peptide in lipid bilayers.
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Affiliation(s)
- Kresten Bertelsen
- Center for Insoluble Protein Structures (inSPIN), Interdisciplinary Nanoscience Center (iNANO), and Department of Chemistry, Bioinformatics Research Center, University of Aarhus, DK-8000 Aarhus C, Denmark
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32
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Mihajlovic M, Lazaridis T. Antimicrobial peptides bind more strongly to membrane pores. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2010; 1798:1494-502. [PMID: 20188066 DOI: 10.1016/j.bbamem.2010.02.023] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2009] [Revised: 12/22/2009] [Accepted: 02/17/2010] [Indexed: 11/16/2022]
Abstract
Antimicrobial peptides (AMPs) are small, usually cationic peptides, which permeabilize bacterial membranes. Understanding their mechanism of action might help design better antibiotics. Using an implicit membrane model, modified to include pores of different shapes, we show that four AMPs (alamethicin, melittin, a magainin analogue, MG-H2, and piscidin 1) bind more strongly to membrane pores, consistent with the idea that they stabilize them. The effective energy of alamethicin in cylindrical pores is similar to that in toroidal pores, whereas the effective energy of the other three peptides is lower in toroidal pores. Only alamethicin intercalates into the membrane core; MG-H2, melittin and piscidin are located exclusively at the hydrophobic/hydrophilic interface. In toroidal pores, the latter three peptides often bind at the edge of the pore, and are in an oblique orientation. The calculated binding energies of the peptides are correlated with their hemolytic activities. We hypothesize that one distinguishing feature of AMPs may be the fact that they are imperfectly amphipathic which allows them to bind more strongly to toroidal pores. An initial test on a melittin-based mutant seems to support this hypothesis.
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Affiliation(s)
- Maja Mihajlovic
- Department of Chemistry, The City College of New York, New York, NY 10031, USA
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33
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San-Miguel MA, Robinson C, Mark Rodger P. Secondary structure simulations of twin-arginine signal peptides in different environments. MOLECULAR SIMULATION 2009. [DOI: 10.1080/08927020902974063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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34
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Kouzayha A, Nasir MN, Buchet R, Wattraint O, Sarazin C, Besson F. Conformational and Interfacial Analyses of K3A18K3 and Alamethicin in Model Membranes. J Phys Chem B 2009; 113:7012-9. [DOI: 10.1021/jp810539b] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Achraf Kouzayha
- Université de Lyon, Université Lyon 1, INSA de Lyon, and ICBMS CNRS UMR 5246, Villeurbanne, F-69622, France, CPE Lyon, Villeurbanne, F-69616, France, and Unité de Génie Enzymatique et Cellulaire, UMR 6022 du CNRS—Université de Picardie Jules Verne, Amiens, France
| | - Mehmet N. Nasir
- Université de Lyon, Université Lyon 1, INSA de Lyon, and ICBMS CNRS UMR 5246, Villeurbanne, F-69622, France, CPE Lyon, Villeurbanne, F-69616, France, and Unité de Génie Enzymatique et Cellulaire, UMR 6022 du CNRS—Université de Picardie Jules Verne, Amiens, France
| | - René Buchet
- Université de Lyon, Université Lyon 1, INSA de Lyon, and ICBMS CNRS UMR 5246, Villeurbanne, F-69622, France, CPE Lyon, Villeurbanne, F-69616, France, and Unité de Génie Enzymatique et Cellulaire, UMR 6022 du CNRS—Université de Picardie Jules Verne, Amiens, France
| | - Olivier Wattraint
- Université de Lyon, Université Lyon 1, INSA de Lyon, and ICBMS CNRS UMR 5246, Villeurbanne, F-69622, France, CPE Lyon, Villeurbanne, F-69616, France, and Unité de Génie Enzymatique et Cellulaire, UMR 6022 du CNRS—Université de Picardie Jules Verne, Amiens, France
| | - Catherine Sarazin
- Université de Lyon, Université Lyon 1, INSA de Lyon, and ICBMS CNRS UMR 5246, Villeurbanne, F-69622, France, CPE Lyon, Villeurbanne, F-69616, France, and Unité de Génie Enzymatique et Cellulaire, UMR 6022 du CNRS—Université de Picardie Jules Verne, Amiens, France
| | - Françoise Besson
- Université de Lyon, Université Lyon 1, INSA de Lyon, and ICBMS CNRS UMR 5246, Villeurbanne, F-69622, France, CPE Lyon, Villeurbanne, F-69616, France, and Unité de Génie Enzymatique et Cellulaire, UMR 6022 du CNRS—Université de Picardie Jules Verne, Amiens, France
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35
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The effects of light-induced reduction of the photosystem II reaction center. J Mol Model 2009; 15:923-33. [DOI: 10.1007/s00894-008-0448-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2008] [Accepted: 12/15/2008] [Indexed: 11/25/2022]
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36
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Marrink SJ, de Vries AH, Tieleman DP. Lipids on the move: simulations of membrane pores, domains, stalks and curves. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2008; 1788:149-68. [PMID: 19013128 DOI: 10.1016/j.bbamem.2008.10.006] [Citation(s) in RCA: 369] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2008] [Revised: 10/13/2008] [Accepted: 10/14/2008] [Indexed: 11/16/2022]
Abstract
In this review we describe the state-of-the-art of computer simulation studies of lipid membranes. We focus on collective lipid-lipid and lipid-protein interactions that trigger deformations of the natural lamellar membrane state, showing that many important biological processes including self-aggregation of membrane components into domains, the formation of non-lamellar phases, and membrane poration and curving, are now amenable to detailed simulation studies.
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Affiliation(s)
- Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands.
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Abstract
We investigate the mode of action of Cateslytin, an antimicrobial peptide, on zwitterionic biomembranes by performing numerical simulations and electrophysiological measurements on membrane vesicles. Using this natural beta-sheet antimicrobial peptide secreted during stress as a model we show that a single peptide is able to form a stable membrane pore of 1 nm diameter of 0.25 nS conductance found both from calculation and electrical measurements. The resulting structure does not resemble the barrel-stave or carpet models earlier predicted, but is very close to that found in the simulation of alpha-helical peptides. Based on the simulation of a mutated peptide and the effects of small external electric fields, we conclude that electrostatic forces play a crucial role in the process of pore formation.
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38
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Fortunelli A, Monti S. Simulations of lipid adsorption on TiO2 surfaces in solution. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2008; 24:10145-10154. [PMID: 18712891 DOI: 10.1021/la801787s] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Molecular dynamics simulations are carried out to study the adsorption of three lipids, namely, DOPC, DOPS, and DMTAP, on TiO2(110) rutile surfaces and the influence of the interface on their conformational properties. Three types of rutile (110) surfaces, characterized by a different degree of hydroxylation (the neutral nonhydroxylated and hydroxylated surfaces and a partially hydroxylated surface with charge density corresponding to physiological pH) are investigated using force fields derived from ab initio calculations and experimental data. It is found that the stability of the adsorbate and the strength of the attachment are strictly connected with the nature of both the lipid and the surface. Direct coordination of the phosphate or carbonyl oxygens of the lipids with available titanium sites, observed in the case of partially or nonhydroxylated layers, determines stronger adsorption and, as a consequence, reduced dynamics. For a given hydration state of the surface, the adsorption strengths are in the order DOPS > DOPC >> DMTAP, in agreement with experimental data according to which the presence of DOPS units inside lipid bilayers favors stronger adsorption and lower mobility. The adsorption geometry, the hydration state of the lipid headgroups, and the dynamical processes (detachment, diffusion, etc.) occurring at the lipid/oxide interface are analyzed in detail, putting on a roughly quantitative basis time scales and energy barriers of the latter processes.
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Affiliation(s)
- Alessandro Fortunelli
- Molecular Modeling Laboratory, Istituto per i Processi Chimico-Fisici of the Italian Consiglio Nazionale delle Ricerche (IPCF-CNR), via G. Moruzzi 1, Pisa, Italy
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39
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Jørgensen AM, Tagmose L, Jørgensen AMM, Bøgesø KP, Peters GH. Molecular dynamics simulations of Na+/Cl(-)-dependent neurotransmitter transporters in a membrane-aqueous system. ChemMedChem 2008; 2:827-40. [PMID: 17436258 DOI: 10.1002/cmdc.200600243] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
We have performed molecular dynamics simulations of a homology model of the human serotonin transporter (hSERT) in a membrane environment and in complex with either the natural substrate 5-HT or the selective serotonin reuptake inhibitor escitalopram. We have also included a transporter homologue, the Aquifex aeolicus leucine transporter (LeuT), in our study to evaluate the applicability of a simple and computationally attractive membrane system. Fluctuations in LeuT extracted from simulations are in good agreement with crystallographic B factors. Furthermore, key interactions identified in the X-ray structure of LeuT are maintained throughout the simulations indicating that our simple membrane system is suitable for studying the transmembrane protein hSERT in complex with 5-HT or escitalopram. For these transporter complexes, only relatively small fluctuations are observed in the ligand-binding cleft. Specific interactions responsible for ligand recognition, are identified in the hSERT-5HT and hSERT-escitalopram complexes. Our findings are in good agreement with predictions from mutagenesis studies.
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Affiliation(s)
- Anne Marie Jørgensen
- MEMPHYS-Center for Biomembrane Physics, Department of Chemistry, Technical University of Denmark, Building 206, 2800 Kgs. Lyngby, Denmark
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40
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Peptide aggregation and pore formation in a lipid bilayer: a combined coarse-grained and all atom molecular dynamics study. Biophys J 2008; 95:4337-47. [PMID: 18676652 DOI: 10.1529/biophysj.108.133330] [Citation(s) in RCA: 114] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We present a simulation study where different resolutions, namely coarse-grained (CG) and all-atom (AA) molecular dynamics simulations, are used sequentially to combine the long timescale reachable by CG simulations with the high resolution of AA simulations, to describe the complete processes of peptide aggregation and pore formation by alamethicin peptides in a hydrated lipid bilayer. In the 1-micros CG simulations the peptides spontaneously aggregate in the lipid bilayer and exhibit occasional transitions between the membrane-spanning and the surface-bound configurations. One of the CG systems at t = 1 micros is reverted to an AA representation and subjected to AA simulation for 50 ns, during which water molecules penetrate the lipid bilayer through interactions with the peptide aggregates, and the membrane starts leaking water. During the AA simulation significant deviations from the alpha-helical structure of the peptides are observed, however, the size and arrangement of the clusters are not affected within the studied time frame. Solid-state NMR experiments designed to match closely the setup used in the molecular dynamics simulations provide strong support for our finding that alamethicin peptides adopt a diverse set of configurations in a lipid bilayer, which is in sharp contrast to the prevailing view of alamethicin oligomers formed by perfectly aligned helical alamethicin peptides in a lipid bilayer.
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41
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Tang J, Gai F. Dissecting the Membrane Binding and Insertion Kinetics of a pHLIP Peptide. Biochemistry 2008; 47:8250-2. [DOI: 10.1021/bi801103x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jia Tang
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Feng Gai
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104
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42
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The membrane potential and its representation by a constant electric field in computer simulations. Biophys J 2008; 95:4205-16. [PMID: 18641071 DOI: 10.1529/biophysj.108.136499] [Citation(s) in RCA: 144] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A theoretical framework is elaborated to account for the effect of a transmembrane potential in computer simulations. It is shown that a simulation with a constant external electric field applied in the direction normal to the membrane is equivalent to the influence of surrounding infinite baths maintained to a voltage difference via ion-exchanging electrodes connected to an electromotive force. It is also shown that the linearly-weighted displacement charge within the simulation system tracks the net flow of charge through the external circuit comprising the electromotive force and the electrodes. Using a statistical mechanical reduction of the degrees of freedom of the external system, three distinct theoretical routes are formulated and examined for the purpose of characterizing the free energy of a protein embedded in a membrane that is submitted to a voltage difference. The W-route is constructed from the variations in the voltage-dependent potential of mean force along a reaction path connecting two conformations of the protein. The Q-route is based on the average displacement charge as a function of the conformation of the protein. Finally, the G-route considers the relative charging free energy of specific residues, with and without applied membrane potentials. The theoretical formulation is illustrated with a simple model of an ion crossing a vacuum slab surrounded by two aqueous bulk phases and with a fragment of the voltage-sensor of the KvAP potassium channel.
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43
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Delemotte L, Dehez F, Treptow W, Tarek M. Modeling Membranes under a Transmembrane Potential. J Phys Chem B 2008; 112:5547-50. [DOI: 10.1021/jp710846y] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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44
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Banerjee M, Meyerowitz E, Huang C, Mohanty S. Probing the conformation and dynamics of allatostatin neuropeptides: a structural model for functional differences. Peptides 2008; 29:375-85. [PMID: 18191874 DOI: 10.1016/j.peptides.2007.11.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/23/2007] [Revised: 11/06/2007] [Accepted: 11/09/2007] [Indexed: 11/17/2022]
Abstract
Allatostatins are a family of related neuropeptides that play an important role in development, reproduction, and digestion in insects. The cockroach Diploptera punctata has 13 allatostatin neuropeptides, with pleiotropic functions, two of which are: inhibition of juvenile hormone (JH) production and inhibition of gut muscle contraction. In this study, the conformation and dynamics of D. punctata allatostatin 5 (Dippu-AST 5) and allatostatin 8 (Dippu-AST 8) are investigated by CD, NMR, and molecular dynamics simulations. These peptides contain eight and nine residues, respectively, and the identical six-residue C-terminal motif. Yet Dippu-AST 5 and Dippu-AST 8 affect juvenile hormone production and hindgut contraction with different potencies. Dippu-AST 5 is one of the most potent inhibitors of juvenile hormone production and one of the least potent inhibitors of gut contraction, whereas Dippu-AST 8 has the opposite potencies with respect to these tissues. From the NMR structure, it is clear that Dippu-AST 5 has a 3(10) helix involving three of its residues and a "gamma" turn at the end of its C-terminal motif. In contrast Dippu-AST 8 has an open "pi" turn among five of its central residues. In addition, the orientation preferences within the membrane of the two peptides were simulated. Our simulation results show that the C-terminal segment of Dippu-AST 5 orients in the membrane surface with an average angle of 17.5 degrees, whereas Dippu-AST 8 orients with an average angle of 5.1 degrees. Taken together, from the structures and orientation preferences of these peptides within the membrane, it appears that these peptides may interact with the receptor very differently.
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Affiliation(s)
- Monimoy Banerjee
- Department of Chemistry and Biochemistry, Auburn University, Auburn, AL 36849-5312, USA
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45
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Molecular dynamics simulations suggest a mechanism for translocation of the HIV-1 TAT peptide across lipid membranes. Proc Natl Acad Sci U S A 2007; 104:20805-10. [PMID: 18093956 DOI: 10.1073/pnas.0706574105] [Citation(s) in RCA: 334] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The recombinant HIV-1 Tat protein contains a small region corresponding to residues (47)YGRKKRRQRR(57)R, which is capable of translocating cargoes of different molecular sizes, such as proteins, DNA, RNA, or drugs, across the cell membrane in an apparently energy-independent manner. The pathway that these peptides follow for entry into the cell has been the subject of strong controversy for the last decade. This peptide is highly basic and hydrophilic. Therefore, a central question that any candidate mechanism has to answer is how this highly hydrophilic peptide is able to cross the hydrophobic barrier imposed by the cell membrane. We propose a mechanism for the spontaneous translocation of the Tat peptides across a lipid membrane. This mechanism involves strong interactions between the Tat peptides and the phosphate groups on both sides of the lipid bilayer, the insertion of charged side chains that nucleate the formation of a transient pore, followed by the translocation of the Tat peptides by diffusing on the pore surface. This mechanism explains how key ingredients, such as the cooperativity among the peptides, the large positive charge, and specifically the arginine amino acids, contribute to the uptake. The proposed mechanism also illustrates the importance of membrane fluctuations. Indeed, mechanisms that involve large fluctuations of the membrane structure, such as transient pores and the insertion of charged amino acid side chains, may be common and perhaps central to the functions of many membrane protein functions.
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46
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Vernier PT, Ziegler MJ. Nanosecond field alignment of head group and water dipoles in electroporating phospholipid bilayers. J Phys Chem B 2007; 111:12993-6. [PMID: 17949035 DOI: 10.1021/jp077148q] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
To investigate the mechanism of biological cell membrane electroporation at the nanosecond and nanometer scale, we tracked pore-forming lipids and water in molecular dynamics simulations of a palmitoyloleoylphosphatidylcholine bilayer in a minimum porating electric field. Although the field-generated torque tilts the mean head group dipole a few degrees away from its equilibrium, zero-field position relative to the bilayer plane, this change in conformation does not appear to contribute directly to the development of the pore-initiating aggregation of lipid head groups and water that leads to the formation of a membrane-spanning hydrophilic pore. Field-directed rotation of the head group dipoles in the plane of the incipient pore wall, in combination with water dipole and solvation interactions at the aqueous-lipid interface, is one component in the coordinated ensemble of electroporation events.
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Affiliation(s)
- P Thomas Vernier
- Ming Hsieh Department of Electrical Engineering, Viterbi School of Engineering, University of Southern California, Los Angeles, California 90089-0271, USA.
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47
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Widge AS, Matsuoka Y, Kurnikova M. Computational modeling of poly(alkylthiophene) conductive polymer insertion into phospholipid bilayers. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2007; 23:10672-81. [PMID: 17867709 PMCID: PMC2872182 DOI: 10.1021/la070214v] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
We have previously demonstrated that some poly(alkylthiophenes) (PATs) are able to increase the electrical conductance of unsupported phospholipid bilayers and have hypothesized that this effect is due to the ability of some PAT side chains to permit stable insertion into the bilayer. We have further proposed the development of long-term intracellular electrodes based on that phenomenon. In this article, we apply molecular dynamics techniques to study the insertion of two model PATs into a patch of a lipid bilayer. Steered molecular dynamics is used to obtain potential trajectories of insertion, followed by umbrella sampling to determine the free-energy change upon insertion. Our results indicate that both branched-side-chain poly(3-(2-ethylhexyl)thiophene) (EHPT) and straight-side-chain poly(3-hexylthiophene) (HPT) are able to enter the bilayer but only EHPT can cross the center of the membrane and establish an electrical bridge. HPT penetrates the head groups but is not able to enter the alkyl tail phase. These findings support the feasibility of our electrode concept and raise questions regarding the mechanisms by which branched side chains grant PATs greater solubility in a lipid bilayer environment. The parameters and methods used in this study establish a novel framework for studying these and similar systems, and the results hold promise for the use of EHPT in biosensing and neural interfacing.
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48
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Kandasamy SK, Larson RG. Binding modes of protegrin-1, a beta-strand antimicrobial peptide, in lipid bilayers. MOLECULAR SIMULATION 2007. [DOI: 10.1080/08927020701313737] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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49
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Leitgeb B, Szekeres A, Manczinger L, Vágvölgyi C, Kredics L. The history of alamethicin: a review of the most extensively studied peptaibol. Chem Biodivers 2007; 4:1027-51. [PMID: 17589875 DOI: 10.1002/cbdv.200790095] [Citation(s) in RCA: 180] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Balázs Leitgeb
- Institute of Biophysics, Biological Research Center of the Hungarian Academy of Sciences, Temesvári krt. 62, Szeged, Hungary
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50
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Sternberg U, Witter R, Ulrich AS. All-atom molecular dynamics simulations using orientational constraints from anisotropic NMR samples. JOURNAL OF BIOMOLECULAR NMR 2007; 38:23-39. [PMID: 17334824 PMCID: PMC1892527 DOI: 10.1007/s10858-007-9142-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2006] [Accepted: 12/14/2006] [Indexed: 05/13/2023]
Abstract
Orientational constraints obtained from solid state NMR experiments on anisotropic samples are used here in molecular dynamics (MD) simulations for determining the structure and dynamics of several different membrane-bound molecules. The new MD technique is based on the inclusion of orientation dependent pseudo-forces in the COSMOS-NMR force field. These forces drive molecular rotations and re-orientations in the simulation, such that the motional time-averages of the tensorial NMR properties approach the experimentally measured parameters. The orientational-constraint-driven MD simulations are universally applicable to all NMR interaction tensors, such as chemical shifts, dipolar couplings and quadrupolar interactions. The strategy does not depend on the initial choice of coordinates, and is in principle suitable for any flexible molecule. To test the method on three systems of increasing complexity, we used as constraints some deuterium quadrupolar couplings from the literature on pyrene, cholesterol and an antimicrobial peptide embedded in oriented lipid bilayers. The MD simulations were able to reproduce the NMR parameters within experimental error. The alignment of the three membrane-bound molecules and some aspects of their conformation were thus derived from the NMR data, in good agreement with previous analyses. Furthermore, the new approach yielded for the first time the distribution of segmental orientations with respect to the membrane and the order parameter tensors of all three systems.
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Affiliation(s)
- Ulrich Sternberg
- Institute of Biological Interfaces, Forschungszentrum Karlsruhe, Hermann-von-Helmholtz-Platz 1, POB 3640, 76021 Karlsruhe, Germany
| | - Raiker Witter
- Institute of Biological Interfaces, Forschungszentrum Karlsruhe, Hermann-von-Helmholtz-Platz 1, POB 3640, 76021 Karlsruhe, Germany
| | - Anne S. Ulrich
- Institute of Biological Interfaces, Forschungszentrum Karlsruhe, Hermann-von-Helmholtz-Platz 1, POB 3640, 76021 Karlsruhe, Germany
- Institute of Organic Chemistry, University of Karlsruhe, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
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