1
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Li CD, Junaid M, Shan X, Wang Y, Wang X, Khan A, Wei DQ. Effect of Cholesterol on C99 Dimerization: Revealed by Molecular Dynamics Simulations. Front Mol Biosci 2022; 9:872385. [PMID: 35928227 PMCID: PMC9343951 DOI: 10.3389/fmolb.2022.872385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 03/18/2022] [Indexed: 11/28/2022] Open
Abstract
C99 is the immediate precursor for amyloid beta (Aβ) and therefore is a central intermediate in the pathway that is believed to result in Alzheimer’s disease (AD). It has been suggested that cholesterol is associated with C99, but the dynamic details of how cholesterol affects C99 assembly and the Aβ formation remain unclear. To investigate this question, we employed coarse-grained and all-atom molecular dynamics simulations to study the effect of cholesterol and membrane composition on C99 dimerization. We found that although the existence of cholesterol delays C99 dimerization, there is no direct competition between C99 dimerization and cholesterol association. In contrast, the existence of cholesterol makes the C99 dimer more stable, which presents a cholesterol binding C99 dimer model. Cholesterol and membrane composition change the dimerization rate and conformation distribution of C99, which will subsequently influence the production of Aβ. Our results provide insights into the potential influence of the physiological environment on the C99 dimerization, which will help us understand Aβ formation and AD’s etiology.
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Affiliation(s)
- Cheng-Dong Li
- State Key Laboratory of Microbial Metabolism, Joint Laboratory of International Cooperation in Metabolic and Developmental Sciences, Ministry of Education, Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Muhammad Junaid
- State Key Laboratory of Microbial Metabolism, Joint Laboratory of International Cooperation in Metabolic and Developmental Sciences, Ministry of Education, Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaoqi Shan
- State Key Laboratory of Microbial Metabolism, Joint Laboratory of International Cooperation in Metabolic and Developmental Sciences, Ministry of Education, Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yanjing Wang
- State Key Laboratory of Microbial Metabolism, Joint Laboratory of International Cooperation in Metabolic and Developmental Sciences, Ministry of Education, Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xiangeng Wang
- State Key Laboratory of Microbial Metabolism, Joint Laboratory of International Cooperation in Metabolic and Developmental Sciences, Ministry of Education, Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Abbas Khan
- State Key Laboratory of Microbial Metabolism, Joint Laboratory of International Cooperation in Metabolic and Developmental Sciences, Ministry of Education, Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Dong-Qing Wei
- State Key Laboratory of Microbial Metabolism, Joint Laboratory of International Cooperation in Metabolic and Developmental Sciences, Ministry of Education, Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Peng Cheng Laboratory, Shenzhen, China
- *Correspondence: Dong-Qing Wei,
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2
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Prescher M, Bonus M, Stindt J, Keitel-Anselmino V, Smits SHJ, Gohlke H, Schmitt L. Evidence for a credit-card-swipe mechanism in the human PC floppase ABCB4. Structure 2021; 29:1144-1155.e5. [PMID: 34107287 DOI: 10.1016/j.str.2021.05.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 04/27/2021] [Accepted: 05/17/2021] [Indexed: 10/21/2022]
Abstract
ABCB4 is described as an ATP-binding cassette (ABC) transporter that primarily transports lipids of the phosphatidylcholine (PC) family but is also capable of translocating a subset of typical multidrug-resistance-associated drugs. The high degree of amino acid identity of 76% for ABCB4 and ABCB1, which is a prototype multidrug-resistance-mediating protein, results in ABCB4's second subset of substrates, which overlap with ABCB1's substrates. This often leads to incomplete annotations of ABCB4, in which it was described as exclusively PC-lipid specific. When the hydrophilic amino acids from ABCB4 are changed to the analogous but hydrophobic ones from ABCB1, the stimulation of ATPase activity by 1,2-dioleoyl-sn-glycero-3-phosphocholine, as a prime example of PC lipids, is strongly diminished, whereas the modulation capability of ABCB1 substrates remains unchanged. This indicates two distinct and autonomous substrate binding sites in ABCB4.
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Affiliation(s)
- Martin Prescher
- Institute of Biochemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Michele Bonus
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Jan Stindt
- Clinic for Gastroenterology, Hepatology and Infectious Diseases University Hospital Düsseldorf, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Verena Keitel-Anselmino
- Clinic for Gastroenterology, Hepatology and Infectious Diseases University Hospital Düsseldorf, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Sander H J Smits
- Institute of Biochemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany; Center for Structural Studies, Heinrich Heine University Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Holger Gohlke
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany; John von Neumann Institute for Computing (NIC), Jülich Supercomputing Centre (JSC), Institute of Biological Information Processing (IBI-7: Structural Biochemistry) and Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Lutz Schmitt
- Institute of Biochemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.
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3
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Rogers JR, Geissler PL. Breakage of Hydrophobic Contacts Limits the Rate of Passive Lipid Exchange between Membranes. J Phys Chem B 2020; 124:5884-5898. [DOI: 10.1021/acs.jpcb.0c04139] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Julia R. Rogers
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Phillip L. Geissler
- Department of Chemistry, University of California, Berkeley, California 94720, United States
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
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4
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Nguyen MHL, DiPasquale M, Rickeard BW, Doktorova M, Heberle FA, Scott HL, Barrera FN, Taylor G, Collier CP, Stanley CB, Katsaras J, Marquardt D. Peptide-Induced Lipid Flip-Flop in Asymmetric Liposomes Measured by Small Angle Neutron Scattering. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:11735-11744. [PMID: 31408345 PMCID: PMC7393738 DOI: 10.1021/acs.langmuir.9b01625] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Despite the prevalence of lipid transbilayer asymmetry in natural plasma membranes, most biomimetic model membranes studied are symmetric. Recent advances have helped to overcome the difficulties in preparing asymmetric liposomes in vitro, allowing for the examination of a larger set of relevant biophysical questions. Here, we investigate the stability of asymmetric bilayers by measuring lipid flip-flop with time-resolved small-angle neutron scattering (SANS). Asymmetric large unilamellar vesicles with inner bilayer leaflets containing predominantly 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) and outer leaflets composed mainly of 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) displayed slow spontaneous flip-flop at 37 ◦C (half-time, t1/2 = 140 h). However, inclusion of peptides, namely, gramicidin, alamethicin, melittin, or pHLIP (i.e., pH-low insertion peptide), accelerated lipid flip-flop. For three of these peptides (i.e., pHLIP, alamethicin, and melittin), each of which was added externally to preformed asymmetric vesicles, we observed a completely scrambled bilayer in less than 2 h. Gramicidin, on the other hand, was preincorporated during the formation of the asymmetric liposomes and showed a time resolvable 8-fold increase in the rate of lipid asymmetry loss. These results point to a membrane surface-related (e.g., adsorption/insertion) event as the primary driver of lipid scrambling in the asymmetric model membranes of this study. We discuss the implications of membrane peptide binding, conformation, and insertion on lipid asymmetry.
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Affiliation(s)
- Michael H. L. Nguyen
- Department of Chemistry and Biochemistry, University
of Windsor, Windsor, N9B 3P4 ON Canada
| | - Mitchell DiPasquale
- Department of Chemistry and Biochemistry, University
of Windsor, Windsor, N9B 3P4 ON Canada
| | - Brett W. Rickeard
- Department of Chemistry and Biochemistry, University
of Windsor, Windsor, N9B 3P4 ON Canada
| | - Milka Doktorova
- Department of Integrative Biology and Pharmacology,
University of Texas Health Science Center at Houston, Houston, Texas 77225, United
States
| | - Frederick A. Heberle
- Department of Integrative Biology and Pharmacology,
University of Texas Health Science Center at Houston, Houston, Texas 77225, United
States
- Center for Environmental Biotechnology, University
of Tennessee, Knoxville, Tennessee 37996, United States
| | - Haden L. Scott
- Center for Environmental Biotechnology, University
of Tennessee, Knoxville, Tennessee 37996, United States
- Department of Biochemistry & Cellular and
Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, United
States
| | - Francisco N. Barrera
- Department of Biochemistry & Cellular and
Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, United
States
| | - Graham Taylor
- The Bredesen Center, University of Tennessee,
Knoxville, Tennessee 37996, United States
| | - Charles P. Collier
- The Bredesen Center, University of Tennessee,
Knoxville, Tennessee 37996, United States
- Center for Nanophase Materials Sciences, Oak Ridge National
Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Christopher B. Stanley
- Neutron Scattering Division, Oak Ridge National
Laboratory, Oak Ridge, Tennessee 37831, United States
| | - John Katsaras
- Large Scale Structures Group, Oak Ridge National
Laboratory, Oak Ridge, Tennessee 37831, United States
- Shull Wollan Center, a Joint Institute for Neutron
Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United
States
- Department of Physics and Astronomy, University of
Tennessee, Knoxville, Tennessee 37996, United States
| | - Drew Marquardt
- Department of Chemistry and Biochemistry, University
of Windsor, Windsor, N9B 3P4 ON Canada
- Department of Physics, University of Windsor, Windsor, N9B
3P4 ON Canada
- Corresponding Author:
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5
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6
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Enkavi G, Javanainen M, Kulig W, Róg T, Vattulainen I. Multiscale Simulations of Biological Membranes: The Challenge To Understand Biological Phenomena in a Living Substance. Chem Rev 2019; 119:5607-5774. [PMID: 30859819 PMCID: PMC6727218 DOI: 10.1021/acs.chemrev.8b00538] [Citation(s) in RCA: 184] [Impact Index Per Article: 36.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Indexed: 12/23/2022]
Abstract
Biological membranes are tricky to investigate. They are complex in terms of molecular composition and structure, functional over a wide range of time scales, and characterized by nonequilibrium conditions. Because of all of these features, simulations are a great technique to study biomembrane behavior. A significant part of the functional processes in biological membranes takes place at the molecular level; thus computer simulations are the method of choice to explore how their properties emerge from specific molecular features and how the interplay among the numerous molecules gives rise to function over spatial and time scales larger than the molecular ones. In this review, we focus on this broad theme. We discuss the current state-of-the-art of biomembrane simulations that, until now, have largely focused on a rather narrow picture of the complexity of the membranes. Given this, we also discuss the challenges that we should unravel in the foreseeable future. Numerous features such as the actin-cytoskeleton network, the glycocalyx network, and nonequilibrium transport under ATP-driven conditions have so far received very little attention; however, the potential of simulations to solve them would be exceptionally high. A major milestone for this research would be that one day we could say that computer simulations genuinely research biological membranes, not just lipid bilayers.
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Affiliation(s)
- Giray Enkavi
- Department
of Physics, University of
Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
| | - Matti Javanainen
- Department
of Physics, University of
Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy
of Sciences, Flemingovo naḿesti 542/2, 16610 Prague, Czech Republic
- Computational
Physics Laboratory, Tampere University, P.O. Box 692, FI-33014 Tampere, Finland
| | - Waldemar Kulig
- Department
of Physics, University of
Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
| | - Tomasz Róg
- Department
of Physics, University of
Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
- Computational
Physics Laboratory, Tampere University, P.O. Box 692, FI-33014 Tampere, Finland
| | - Ilpo Vattulainen
- Department
of Physics, University of
Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
- Computational
Physics Laboratory, Tampere University, P.O. Box 692, FI-33014 Tampere, Finland
- MEMPHYS-Center
for Biomembrane Physics
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7
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Muller MP, Jiang T, Sun C, Lihan M, Pant S, Mahinthichaichan P, Trifan A, Tajkhorshid E. Characterization of Lipid-Protein Interactions and Lipid-Mediated Modulation of Membrane Protein Function through Molecular Simulation. Chem Rev 2019; 119:6086-6161. [PMID: 30978005 PMCID: PMC6506392 DOI: 10.1021/acs.chemrev.8b00608] [Citation(s) in RCA: 153] [Impact Index Per Article: 30.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The cellular membrane constitutes one of the most fundamental compartments of a living cell, where key processes such as selective transport of material and exchange of information between the cell and its environment are mediated by proteins that are closely associated with the membrane. The heterogeneity of lipid composition of biological membranes and the effect of lipid molecules on the structure, dynamics, and function of membrane proteins are now widely recognized. Characterization of these functionally important lipid-protein interactions with experimental techniques is however still prohibitively challenging. Molecular dynamics (MD) simulations offer a powerful complementary approach with sufficient temporal and spatial resolutions to gain atomic-level structural information and energetics on lipid-protein interactions. In this review, we aim to provide a broad survey of MD simulations focusing on exploring lipid-protein interactions and characterizing lipid-modulated protein structure and dynamics that have been successful in providing novel insight into the mechanism of membrane protein function.
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Affiliation(s)
- Melanie P. Muller
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- College of Medicine
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Tao Jiang
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Chang Sun
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Muyun Lihan
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Shashank Pant
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Paween Mahinthichaichan
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Anda Trifan
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Emad Tajkhorshid
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- College of Medicine
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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8
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Manna M, Nieminen T, Vattulainen I. Understanding the Role of Lipids in Signaling Through Atomistic and Multiscale Simulations of Cell Membranes. Annu Rev Biophys 2019; 48:421-439. [DOI: 10.1146/annurev-biophys-052118-115553] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Cell signaling controls essentially all cellular processes. While it is often assumed that proteins are the key architects coordinating cell signaling, recent studies have shown more and more clearly that lipids are also involved in signaling processes in a number of ways. Lipids do, for instance, act as messengers, modulate membrane receptor conformation and dynamics, and control membrane receptor partitioning. Further, through structural modifications such as oxidation, the functions of lipids as part of signaling processes can be modified. In this context, in this article we discuss the understanding recently revealed by atomistic and coarse-grained computer simulations of nanoscale processes and underlying physicochemical principles related to lipids’ functions in cellular signaling.
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Affiliation(s)
- Moutusi Manna
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal, Madhya Pradesh 462 066, India
| | - Tuomo Nieminen
- Computational Physics Laboratory, Tampere University, FI-33014 Tampere, Finland
| | - Ilpo Vattulainen
- Computational Physics Laboratory, Tampere University, FI-33014 Tampere, Finland
- Department of Physics, University of Helsinki, FI-00014 Helsinki, Finland
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9
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Li CD, Junaid M, Chen H, Ali A, Wei DQ. Helix-Switch Enables C99 Dimer Transition between the Multiple Conformations. J Chem Inf Model 2019; 59:339-350. [PMID: 30570254 DOI: 10.1021/acs.jcim.8b00559] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
C99 is the immediate precursor of amyloid-β (Aβ) and therefore is a central intermediate in the pathway that is believed to result in Alzheimer's disease (AD). Recent studies have shown that C99 dimerization changes the Aβ ratio, but the mechanism remains unclear. Previous studies of the C99 dimer have produced controversial structure models. To address these questions, we investigated C99 dimerization using molecular dynamics (MD) simulations. A helix-switch model was revealed in the formation and transition of the C99 dimer, and six types of conformations were identified. The different conformations show differential exposures of γ-cleavage sites and insertion depths in the bilayer, which may modulate γ-cleavage of C99 and lead to different Aβ levels. Our results redefine C99 dimerization, provide a framework to mediate the current controversial results, and give insights into the understanding of the relationship between C99 dimerization and Aβ formation.
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Affiliation(s)
- Cheng-Dong Li
- State Key Laboratory of Microbial Metabolism and College of Life Sciences and Biotechnology , Shanghai Jiao Tong University , Minhang District, Shanghai 200240 , China.,Department of Mechanical Engineering and Material Science , Yale University , New Haven , Connecticut 06520-8286 , United States
| | - Muhammad Junaid
- State Key Laboratory of Microbial Metabolism and College of Life Sciences and Biotechnology , Shanghai Jiao Tong University , Minhang District, Shanghai 200240 , China
| | - Hui Chen
- State Key Laboratory of Microbial Metabolism and College of Life Sciences and Biotechnology , Shanghai Jiao Tong University , Minhang District, Shanghai 200240 , China
| | - Arif Ali
- State Key Laboratory of Microbial Metabolism and College of Life Sciences and Biotechnology , Shanghai Jiao Tong University , Minhang District, Shanghai 200240 , China
| | - Dong-Qing Wei
- State Key Laboratory of Microbial Metabolism and College of Life Sciences and Biotechnology , Shanghai Jiao Tong University , Minhang District, Shanghai 200240 , China
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10
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Inokuchi T, Arai N. Relationship between water permeation and flip-flop motion in a bilayer membrane. Phys Chem Chem Phys 2018; 20:28155-28161. [PMID: 30387788 DOI: 10.1039/c8cp04610g] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The lipid bilayer membrane facilitates various biological reactions and is thus an essential structure that sustains all higher forms of life. The unique local environment of the lipid bilayer plays critical roles for the diffusion of biomolecules as well as water molecules in biological reactions. Although fluctuation of the cell membrane is expected to allow for the transport of some water molecules, the flip-flop of lipid molecules corresponds to lipid transport between membrane leaflets, and is considered to be an important process to regulate the lipid composition of biological membranes. However, the relationship between these flip-flop phenomena and surrounding water molecules remains poorly understood. We hypothesized that the flip-flop is caused by water molecules permeating through the cell membrane. To test this hypothesis, we used millisecond-order coarse-grained molecular simulations (dissipative particle dynamics) to investigate the distance between water molecules and lipid molecules depending on the position of the lipid molecule. The results clearly showed that water molecules affect the flip-flop motion in the early stage, but have minimal contribution to the subsequent behavior. Moreover, based on the results of dissipative particle dynamics simulation, we computed several first-passage-time (FPT) quantities to describe the detailed dynamics of water permeation. We modeled arrangements in the middle of the flip-flop process, which were compared with the arrangement without lipid molecules. Overall, our results indicate that lipid molecules located both in perpendicular and parallel arrangements largely affect water permeation. These findings provide new insight into the detailed relationship between water permeation and the flip-flop motion.
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Affiliation(s)
- Takuya Inokuchi
- Department of Mechanical Engineering, Kindai University, 3-4-1 Kowakae, Higashiosaka, Osaka 577-8502, Japan
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11
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Wan M, Gao L, Fang W. Implicit-solvent dissipative particle dynamics force field based on a four-to-one coarse-grained mapping scheme. PLoS One 2018; 13:e0198049. [PMID: 29795682 PMCID: PMC5967728 DOI: 10.1371/journal.pone.0198049] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 05/12/2018] [Indexed: 11/30/2022] Open
Abstract
A new set of efficient solvent-free dissipative particle dynamics (DPD) force fields was developed for phospholipids and peptides. To enhance transferability, this model maps around four heavy atoms and their connected hydrogen atoms into a coarse-grained elementary bead based on functional group. The effective hybrid potential between any pair of beads is composed of a short-range repulsive soft-core potential that directly adopts the form of an explicit-solvent DPD model and a long-range attractive hydrophobic potential. The parameters of the attractive potentials for lipid molecules were obtained by fitting the explicit-solvent DPD simulation of one bead of any type in a water box, then finely tuning it until the bilayer membrane properties obtained in the explicit-solvent model were matched. These parameters were further extended to amino acids according to bead type. The structural and elastic properties of bilayer membranes, free energy profiles for a lipid flip-flop and amino acid analogues translocating across the membrane, and membrane pore formation induced by antimicrobial peptides obtained from this solvent-free DPD force field considerably agreed with the explicit-solvent DPD results. Importantly, the efficiency of this method is guaranteed to accelerate the assembly of vesicles composed of several thousand lipids by up to 50-fold, rendering the experimental liposome dynamics as well as membrane-peptide interactions feasible at accessible computational expense.
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Affiliation(s)
- Mingwei Wan
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, China
| | - Lianghui Gao
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, China
- * E-mail:
| | - Weihai Fang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, China
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12
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Bygd HC, Ma L, Bratlie KM. Physicochemical properties of liposomal modifiers that shift macrophage phenotype. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2017. [DOI: 10.1016/j.msec.2017.05.032] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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13
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Van Lehn RC, Alexander-Katz A. Grafting Charged Species to Membrane-Embedded Scaffolds Dramatically Increases the Rate of Bilayer Flipping. ACS CENTRAL SCIENCE 2017; 3:186-195. [PMID: 28386596 PMCID: PMC5364453 DOI: 10.1021/acscentsci.6b00365] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Indexed: 05/07/2023]
Abstract
The cell membrane is a barrier to the passive diffusion of charged molecules due to the chemical properties of the lipid bilayer. Surprisingly, recent experiments have identified processes in which synthetic and biological charged species directly transfer across lipid bilayers on biologically relevant time scales. In particular, amphiphilic nanoparticles have been shown to insert into lipid bilayers, requiring the transport of charged species across the bilayer. The molecular factors facilitating this rapid insertion process remain unknown. In this work, we use atomistic molecular dynamics simulations to calculate the free energy barrier associated with "flipping" charged species across a lipid bilayer for species that are grafted to a membrane-embedded scaffold, such as a membrane-embedded nanoparticle. We find that the free energy barrier for flipping a grafted ligand can be over 7 kcal/mol lower than the barrier for translocating an isolated, equivalent ion, yielding a 5 order of magnitude decrease in the corresponding flipping time scale. Similar results are found for flipping charged species grafted to either nanoparticle or protein scaffolds. These results reveal new mechanistic insight into the flipping of charged macromolecular components that might play an important, yet overlooked, role in signaling and charge transport in biological settings. Furthermore, our results suggest guidelines for the design of synthetic materials capable of rapidly flipping charged moieties across the cell membrane.
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Affiliation(s)
- Reid C. Van Lehn
- Department
of Chemical and Biological Engineering, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
- E-mail:
| | - Alfredo Alexander-Katz
- Department
of Materials Science and Engineering, Massachusetts
Institute of Technology, Cambridge, Massachusetts 02139, United States
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14
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Bennett WFD, Hong CK, Wang Y, Tieleman DP. Antimicrobial Peptide Simulations and the Influence of Force Field on the Free Energy for Pore Formation in Lipid Bilayers. J Chem Theory Comput 2016; 12:4524-33. [DOI: 10.1021/acs.jctc.6b00265] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- W. F. Drew Bennett
- Department
of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
| | - Chun Kit Hong
- Shenzhen
Research Institute, Chinese University of Hong Kong, Nanshan District, Shenzhen 518057, P. R. China
- Department
of Physics, Chinese University of Hong Kong, Shatin, N.T., Hong Kong
| | - Yi Wang
- Shenzhen
Research Institute, Chinese University of Hong Kong, Nanshan District, Shenzhen 518057, P. R. China
- Department
of Physics, Chinese University of Hong Kong, Shatin, N.T., Hong Kong
| | - D. Peter Tieleman
- Centre
for Molecular Simulation and Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N1N4, Canada
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15
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LeBarron J, London E. Effect of lipid composition and amino acid sequence upon transmembrane peptide-accelerated lipid transleaflet diffusion (flip-flop). BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:1812-20. [PMID: 27131444 DOI: 10.1016/j.bbamem.2016.04.011] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Revised: 03/21/2016] [Accepted: 04/21/2016] [Indexed: 12/15/2022]
Abstract
We examined how hydrophobic peptide-accelerated transleaflet lipid movement (flip-flop) was affected by peptide sequence and vesicle composition and properties. A peptide with a completely hydrophobic sequence had little if any effect upon flip-flop. While peptides with a somewhat less hydrophobic sequence accelerated flip-flop, the half-time remained slow (hours) with substantial (0.5mol%) peptide in the membranes. It appears that peptide-accelerated lipid flip-flop involves a rare event that may reflect a rare state of the peptide or lipid bilayer. There was no simple relationship between peptide overall hydrophobicity and flip-flop. In addition, flip-flop was not closely linked to whether the peptides were in a transmembrane or non-transmembrane (interfacial) inserted state. Flip-flop was also not associated with peptide-induced pore formation. We found that peptide-accelerated flip-flop is initially faster in small (highly curved) unilamellar vesicles relative to that in large unilamellar vesicles. Peptide-accelerated flip-flop was also affected by lipid composition, being slowed in vesicles with thick bilayers or those containing 30% cholesterol. Interestingly, these factors also slow spontaneous lipid flip-flop in the absence of peptide. Combined with previous studies, the results are most consistent with acceleration of lipid flip-flop by peptide-induced thinning of bilayer width.
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Affiliation(s)
- Jamie LeBarron
- Dept. of Biochemistry and Cell Biology, Stony Brook, NY 11794-5215, United States
| | - Erwin London
- Dept. of Biochemistry and Cell Biology, Stony Brook, NY 11794-5215, United States
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16
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Brown KL, Conboy JC. Phosphatidylglycerol Flip-Flop Suppression due to Headgroup Charge Repulsion. J Phys Chem B 2015. [DOI: 10.1021/acs.jpcb.5b05523] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Krystal L. Brown
- Department
of Chemistry, University of Utah, 315 South 1400 East, RM 2020, Salt Lake City, Utah 84103, United States
| | - John C. Conboy
- Department
of Chemistry, University of Utah, 315 South 1400 East, RM 2020, Salt Lake City, Utah 84103, United States
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17
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Bennett WFD, Sapay N, Tieleman DP. Atomistic simulations of pore formation and closure in lipid bilayers. Biophys J 2014; 106:210-9. [PMID: 24411253 DOI: 10.1016/j.bpj.2013.11.4486] [Citation(s) in RCA: 121] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Revised: 11/13/2013] [Accepted: 11/25/2013] [Indexed: 10/25/2022] Open
Abstract
Cellular membranes separate distinct aqueous compartments, but can be breached by transient hydrophilic pores. A large energetic cost prevents pore formation, which is largely dependent on the composition and structure of the lipid bilayer. The softness of bilayers and the disordered structure of pores make their characterization difficult. We use molecular-dynamics simulations with atomistic detail to study the thermodynamics, kinetics, and mechanism of pore formation and closure in DLPC, DMPC, and DPPC bilayers, with pore formation free energies of 17, 45, and 78 kJ/mol, respectively. By using atomistic computer simulations, we are able to determine not only the free energy for pore formation, but also the enthalpy and entropy, which yields what is believed to be significant new insights in the molecular driving forces behind membrane defects. The free energy cost for pore formation is due to a large unfavorable entropic contribution and a favorable change in enthalpy. Changes in hydrogen bonding patterns occur, with increased lipid-water interactions, and fewer water-water hydrogen bonds, but the total number of overall hydrogen bonds is constant. Equilibrium pore formation is directly observed in the thin DLPC lipid bilayer. Multiple long timescale simulations of pore closure are used to predict pore lifetimes. Our results are important for biological applications, including the activity of antimicrobial peptides and a better understanding of membrane protein folding, and improve our understanding of the fundamental physicochemical nature of membranes.
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Affiliation(s)
- W F Drew Bennett
- University of Calgary, Department of Biological Sciences and Centre for Molecular Simulation, Calgary, Alberta, Canada
| | - Nicolas Sapay
- University of Calgary, Department of Biological Sciences and Centre for Molecular Simulation, Calgary, Alberta, Canada
| | - D Peter Tieleman
- University of Calgary, Department of Biological Sciences and Centre for Molecular Simulation, Calgary, Alberta, Canada.
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18
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Grafmüller A, Knecht V. The free energy of nanopores in tense membranes. Phys Chem Chem Phys 2014; 16:11270-8. [PMID: 24780914 DOI: 10.1039/c3cp54685c] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Membrane nanopores are central players for a range of important cellular membrane remodeling processes as well as membrane rupture. Understanding pore formation in tense membranes requires comprehension of the molecular mechanism of pore formation and the associated free energy change as a function of the membrane tension. Here we propose a scheme to calculate the free energy change associated with the formation of a nanometer sized pore in molecular dynamics simulations as a function of membrane tension, which requires the calculation of only one computationally expensive potential of mean force. We show that membrane elastic theory can be used to estimate the pore formation free energy at different tension values from the free energy change in a relaxed membrane and the area expansion curves of the membranes. We have computed the pore formation free energy for a dipalmitoyl-phosphatidylcholine (DPPC) membrane at two different lateral pressure values, 1 bar and -40 bar, by calculating the potential of mean force acting on the head group of a single lipid molecule. Unrestrained simulations of the closing process confirm that the intermediate states along this reaction coordinate are reasonable and show that hydrophilic indentations spanning half the bilayer connected by a hydrophobic pore segment represent the corresponding high energy transition state. A comparison of the stability of simulated membranes to experiment at high loading rates show that, contrary to expectation, pores form too easily in small simulated membrane patches. This discrepancy originates from a combination of the absence of ions in the simulations and the small membrane size.
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Affiliation(s)
- Andrea Grafmüller
- Max Planck Institute for Colloids and Interfaces, 14424 Potsdam, Germany.
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19
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Wang Y, Hu D, Wei D. Transmembrane Permeation Mechanism of Charged Methyl Guanidine. J Chem Theory Comput 2014; 10:1717-26. [DOI: 10.1021/ct400738r] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Yukun Wang
- State Key Laboratory of Microbial Metabolism
and College of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, People’s Republic of China
| | - Dan Hu
- Department
of Mathematics, Institute of Natural Sciences, and MOE-LSC, Shanghai Jiao Tong University, Shanghai 200240, People’s Republic of China
| | - Dongqing Wei
- State Key Laboratory of Microbial Metabolism
and College of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, People’s Republic of China
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20
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Filipe HAL, Moreno MJ, Róg T, Vattulainen I, Loura LMS. How to tackle the issues in free energy simulations of long amphiphiles interacting with lipid membranes: convergence and local membrane deformations. J Phys Chem B 2014; 118:3572-81. [PMID: 24635540 DOI: 10.1021/jp501622d] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
One of the great challenges in membrane biophysics is to find a means to foster the transport of drugs across complex membrane structures. In this spirit, we elucidate methodological challenges associated with free energy computations of complex chainlike molecules across lipid membranes. As an appropriate standard molecule to this end, we consider 7-nitrobenz-2-oxa-1,3-diazol-4-yl-labeled fatty amine, NBD-Cn, which is here dealt with as a homologous series with varying chain lengths. We found the membrane-water interface region to be highly sensitive to details in free energy computations. Despite considerable simulation times, we observed substantial hysteresis, the cause being the small frequency of insertion/desorption events of the amphiphile's alkyl chain in the membrane interface. The hysteresis was most pronounced when the amphiphile was pulled from water to the membrane and compromised the data that were not in line with experiments. The subtleties in umbrella sampling for computing distance along the transition path were also observed to be potential causes of artifacts. With the PGD (pull geometry distance) scheme, in which the distance from the molecule was computed to a reference plane determined by an average over all lipids in the membrane, we found marked deformations in membrane structure when the amphiphile was close to the membrane. The deformations were weaker with the PGC (pull geometry cylinder) method, where the reference plane is chosen based on lipids that are within a cylinder of radius 1.7 nm from the amphiphile. Importantly, the free energy results given by PGC were found to be qualitatively consistent with experimental data, while the PGD results were not. We conclude that with long amphiphiles there is reason for concern with regard to computations of their free energy profiles. The membrane-water interface is the region where the greatest care is warranted.
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Affiliation(s)
- Hugo A L Filipe
- Centro de Química de Coimbra, Largo D. Dinis, Rua Larga, 3004-535 Coimbra, Portugal
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21
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Langer M, Sah R, Veser A, Gütlich M, Langosch D. Structural properties of model phosphatidylcholine flippases. ACTA ACUST UNITED AC 2013; 20:63-72. [PMID: 23352140 DOI: 10.1016/j.chembiol.2012.11.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2011] [Revised: 11/13/2012] [Accepted: 11/20/2012] [Indexed: 11/28/2022]
Abstract
Lipid translocation from one lipid bilayer leaflet to the other, termed flip-flop, is required for the distribution of newly synthesized phospholipids during membrane biogenesis. However, a dedicated biogenic lipid flippase has not yet been identified. Here, we show that the efficiency by which model transmembrane peptides facilitate flip of reporter lipids with different headgroups critically depends on their content of helix-destabilizing residues, the charge state of polar flanking residues, and the composition of the host membrane. In particular, increased backbone dynamics of the transmembrane helix relates to its increased ability to flip lipids with phosphatidylcholine and phosphatidylserine headgroups, whereas a more rigid helix favors phosphatidylethanolamine flip. Further, the transmembrane domains of many SNARE protein subtypes share essential features with the dynamic model peptides. Indeed, recombinant SNAREs possess significant lipid flippase activity.
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Affiliation(s)
- Marcella Langer
- Lehrstuhl für Chemie der Biopolymere, Department für biowissenschaftliche Grundlagen, Technische Universität München, Weihenstephaner Berg 3, 85354 Freising and Munich Center For Integrated Protein Science (CIPS(M)), Germany
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22
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Grafmüller A, Lipowsky R, Knecht V. Effect of tension and curvature on the chemical potential of lipids in lipid aggregates. Phys Chem Chem Phys 2013. [PMID: 23201829 DOI: 10.1039/c2cp43018e] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Understanding the factors that influence the free energy of lipids in bilayer membranes is an essential step toward understanding exchange processes of lipids between membranes. In general, both lipid composition and membrane geometry can affect lipid exchange rates between bilayer membranes. Here, the free energy change ΔG(des) for the desorption of dipalmitoyl-phosphatidylcholine (DPPC) lipids from different lipid aggregates has been computed using molecular dynamics simulations and umbrella sampling. The value of ΔG(des) is found to depend strongly on the local properties of the aggregate, in that both tension and curvature lead to an increase in ΔG(des). A detailed analysis shows that the increased desorption free energy for tense bilayers arises from the increased conformational entropy of the lipid tails, which reduces the favorable component -TΔS(L) of the desorption free energy.
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Affiliation(s)
- Andrea Grafmüller
- Max Planck Institute for Colloids and Interfaces, 14424 Potsdam, Germany.
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23
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Vazdar M, Jurkiewicz P, Hof M, Jungwirth P, Cwiklik L. Behavior of 4-hydroxynonenal in phospholipid membranes. J Phys Chem B 2012; 116:6411-5. [PMID: 22577896 DOI: 10.1021/jp3044219] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Under conditions of oxidative stress, 4-hydroxy-2-nonenal (4-HNE) is commonly present in vivo. This highly reactive and cytotoxic compound is generated by oxidation of lipids in membranes and can be easily transferred from a membrane to both cytosol and the extracellular space. Employing time-dependent fluorescence shift (TDFS) method and molecular dynamics simulations, we found that 4-HNE is stabilized in the carbonyl region of a 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) bilayer. 4-HNE is thus able to react with cell membrane proteins and lipids. Stabilization in the membrane is, however, moderate and a transfer of 4-HNE to either extra- or intracellular space occurs on a microsecond time scale. These molecular-level details of 4-HNE behavior in the lipid membrane rationalize the experimentally observed reactivity of 4-HNE with proteins inside and outside the cell. Furthermore, these results support the view that 4-HNE may play an active role in cell signaling pathways.
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Affiliation(s)
- Mario Vazdar
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic and Center for Biomolecules and Complex Molecular Systems, 16610 Prague 6, Czech Republic
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24
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Sanderson JM. Resolving the kinetics of lipid, protein and peptide diffusion in membranes. Mol Membr Biol 2012; 29:118-43. [DOI: 10.3109/09687688.2012.678018] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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25
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Khabiri M, Roeselova M, Cwiklik L. Properties of oxidized phospholipid monolayers: An atomistic molecular dynamics study. Chem Phys Lett 2012. [DOI: 10.1016/j.cplett.2011.11.016] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
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26
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MacCallum JL, Bennett WFD, Tieleman DP. Transfer of arginine into lipid bilayers is nonadditive. Biophys J 2011; 101:110-7. [PMID: 21723820 DOI: 10.1016/j.bpj.2011.05.038] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2011] [Revised: 04/29/2011] [Accepted: 05/17/2011] [Indexed: 01/21/2023] Open
Abstract
Computer simulations suggest that the translocation of arginine through the hydrocarbon core of a lipid membrane proceeds by the formation of a water-filled defect that keeps the arginine molecule hydrated even at the center of the bilayer. We show here that adding additional arginine molecules into one of these water defects causes only a small change in free energy. The barrier for transferring multiple arginines through the membrane is approximately the same as for a single arginine and may even be lower depending on the exact geometry of the system. We discuss these results in the context of arginine-rich peptides such as antimicrobial and cell-penetrating peptides.
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Affiliation(s)
- Justin L MacCallum
- Department of Biological Sciences, Institute for Biocomplexity and Informatics, University of Calgary, Calgary, Alberta, Canada
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27
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Bennett WFD, Tieleman DP. Water Defect and Pore Formation in Atomistic and Coarse-Grained Lipid Membranes: Pushing the Limits of Coarse Graining. J Chem Theory Comput 2011; 7:2981-8. [PMID: 26605486 DOI: 10.1021/ct200291v] [Citation(s) in RCA: 99] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Defects in lipid bilayers are important in a range of biological processes, including interactions between antimicrobial peptides and membranes, transport of polar molecules (including drugs) across membranes, and lipid flip-flop from one monolayer to the other. Passive lipid flip-flop and the translocation of polar molecules across lipid membranes occur on a slow time scale because of high-energy intermediates involving water defects and pores in the membrane. Such defects are an interesting test case for coarse-grained models because of their relatively small characteristic size at the level of water molecules and the complex environment of water and polar head groups in a low-dielectric membrane interior. Here we compare coarse-grained simulations with the MARTINI model with the standard MARTINI water and two recently developed coarse-grained polarizable water models to atomistic simulations. Although in several cases the MARTINI model reproduces the correct free energies, there are structural differences between the atomistic and coarse-grained models. The polarizable water model improves the free energies but only moderately improves the structures. Atomistic test simulations in which water molecules are artificially tethered to each other in groups of four, the resolution of MARTINI, suggest that the limiting factor is not the size of the coarse-grained particles but rather the simple interaction potential and/or the entropy lost in coarse graining the system. By increasing the attractive interaction between the lipids' headgroup and water, we did observe pore formation but at the expense of the correct equilibrium properties of the bilayers.
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Affiliation(s)
- W F Drew Bennett
- Department of Biological Sciences and Institute for Biocomplexity and Informatics, University of Calgary , 2500 University Drive N.W., Calgary, Alberta T2N 1N4, Canada
| | - D Peter Tieleman
- Department of Biological Sciences and Institute for Biocomplexity and Informatics, University of Calgary , 2500 University Drive N.W., Calgary, Alberta T2N 1N4, Canada
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28
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Qian S, Heller WT. Peptide-induced asymmetric distribution of charged lipids in a vesicle bilayer revealed by small-angle neutron scattering. J Phys Chem B 2011; 115:9831-7. [PMID: 21751797 DOI: 10.1021/jp204045t] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Cellular membranes are complex mixtures of lipids, proteins, and other small molecules that provide functional, dynamic barriers between the cell and its environment, as well as between environments within the cell. The lipid composition of the membrane is highly specific and controlled in terms of both content and lipid localization. The membrane structure results from the complex interplay between the wide varieties of molecules present. Here, small-angle neutron scattering and selective deuterium labeling were used to probe the impact of the membrane-active peptides melittin and alamethicin on the structure of lipid bilayers composed of a mixture of the lipids dimyristoyl phosphatidylglycerol (DMPG) and chain-perdeuterated dimyristoyl phosphatidylcholine (DMPC). We found that both peptides enriched the outer leaflet of the bilayer with the negatively charged DMPG, creating an asymmetric distribution of lipids. The level of enrichment is peptide concentration-dependent and is stronger for melittin than it is for alamethicin. The enrichment between the inner and outer bilayer leaflets occurs at very low peptide concentrations and increases with peptide concentration, including when the peptide adopts a membrane-spanning, pore-forming state. The results suggest that these membrane-active peptides may have a secondary stressful effect on target cells at low concentrations that results from a disruption of the lipid distribution between the inner and outer leaflets of the bilayer that is independent of the formation of transmembrane pores.
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Affiliation(s)
- Shuo Qian
- Center for Structural Molecular Biology, Chemical Sciences and Neutron Scattering Science Divisions, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
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29
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Bocchinfuso G, Bobone S, Mazzuca C, Palleschi A, Stella L. Fluorescence spectroscopy and molecular dynamics simulations in studies on the mechanism of membrane destabilization by antimicrobial peptides. Cell Mol Life Sci 2011; 68:2281-301. [PMID: 21584808 PMCID: PMC11114703 DOI: 10.1007/s00018-011-0719-1] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2011] [Revised: 04/26/2011] [Accepted: 04/26/2011] [Indexed: 10/18/2022]
Abstract
Since their initial discovery, 30 years ago, antimicrobial peptides (AMPs) have been intensely investigated as a possible solution to the increasing problem of drug-resistant bacteria. The interaction of antimicrobial peptides with the cellular membrane of bacteria is the key step of their mechanism of action. Fluorescence spectroscopy can provide several structural details on peptide-membrane systems, such as partition free energy, aggregation state, peptide position and orientation in the bilayer, and the effects of the peptides on the membrane order. However, these "low-resolution" structural data are hardly sufficient to define the structural requirements for the pore formation process. Molecular dynamics simulations, on the other hand, provide atomic-level information on the structure and dynamics of the peptide-membrane system, but they need to be validated experimentally. In this review we summarize the information that can be obtained by both approaches, highlighting their versatility and complementarity, suggesting that their synergistic application could lead to a new level of insight into the mechanism of membrane destabilization by AMPs.
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Affiliation(s)
- Gianfranco Bocchinfuso
- Dipartimento di Scienze e Tecnologie Chimiche, Università di Roma Tor Vergata, Via della Ricerca Scientifica 1, 00133 Rome, Italy
| | - Sara Bobone
- Dipartimento di Scienze e Tecnologie Chimiche, Università di Roma Tor Vergata, Via della Ricerca Scientifica 1, 00133 Rome, Italy
| | - Claudia Mazzuca
- Dipartimento di Scienze e Tecnologie Chimiche, Università di Roma Tor Vergata, Via della Ricerca Scientifica 1, 00133 Rome, Italy
| | - Antonio Palleschi
- Dipartimento di Scienze e Tecnologie Chimiche, Università di Roma Tor Vergata, Via della Ricerca Scientifica 1, 00133 Rome, Italy
- IRCCS Neuromed, 86077 Pozzilli, IS Italy
| | - Lorenzo Stella
- Dipartimento di Scienze e Tecnologie Chimiche, Università di Roma Tor Vergata, Via della Ricerca Scientifica 1, 00133 Rome, Italy
- IRCCS Neuromed, 86077 Pozzilli, IS Italy
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30
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Menger FM. Remembrances of self-assemblies past. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2011; 27:5176-5183. [PMID: 20945842 DOI: 10.1021/la103268d] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Research on four types of self-assemblies (micelles, coacervates, gels, and vesicles) is discussed via a particular investigative methodology (in order of appearance): kinetics, dynamic NMR, PGSE-NMR, double-(13)C labeling, molecular dynamics computations, phase diagrams, cryo-HRSEM, rheology, light/electron microscopy, electrophoretic mobility, electroformation, confocal microscopy, and calorimetry. The emphasis here is on how a given method, each in its own special way, illuminates a complex system.
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Affiliation(s)
- Fredric M Menger
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, Georgia 30322, United States
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31
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A lipocentric view of peptide-induced pores. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2011; 40:399-415. [PMID: 21442255 PMCID: PMC3070086 DOI: 10.1007/s00249-011-0693-4] [Citation(s) in RCA: 88] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2010] [Accepted: 03/03/2011] [Indexed: 01/26/2023]
Abstract
Although lipid membranes serve as effective sealing barriers for the passage of most polar solutes, nonmediated leakage is not completely improbable. A high activation energy normally keeps unassisted bilayer permeation at a very low frequency, but lipids are able to self-organize as pores even in peptide-free and protein-free membranes. The probability of leakage phenomena increases under conditions such as phase coexistence, external stress or perturbation associated to binding of nonlipidic molecules. Here, we argue that pore formation can be viewed as an intrinsic property of lipid bilayers, with strong similarities in the structure and mechanism between pores formed with participation of peptides, lipidic pores induced by different types of stress, and spontaneous transient bilayer defects driven by thermal fluctuations. Within such a lipocentric framework, amphipathic peptides are best described as pore-inducing rather than pore-forming elements. Active peptides bound to membranes can be understood as a source of internal surface tension which facilitates pore formation by diminishing the high activation energy barrier. This first or immediate action of the peptide has some resemblance to catalysis. However, the presence of membrane-active peptides has the additional effect of displacing the equilibrium towards the pore-open state, which is then maintained over long times, and reducing the size of initial individual pores. Thus, pore-inducing peptides, regardless of their sequence and oligomeric organization, can be assigned a double role of increasing the probability of pore formation in membranes to high levels as well as stabilizing these pores after they appear.
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