201
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Yasuda T, Kinoshita M, Murata M, Matsumori N. Detailed comparison of deuterium quadrupole profiles between sphingomyelin and phosphatidylcholine bilayers. Biophys J 2014; 106:631-8. [PMID: 24507603 DOI: 10.1016/j.bpj.2013.12.034] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Revised: 11/25/2013] [Accepted: 12/26/2013] [Indexed: 11/25/2022] Open
Abstract
Lipid rafts are microdomains rich in sphingomyelin (SM) and cholesterol (Chol). The essential question is why natural lipid rafts prefer SM rather than saturated diacyl glycerophosphocholine, although both form ordered membranes with Chol in model systems. Hence in this study, we synthesized site-specifically deuterated 1-palmitoyl-2-stearoyl-sn-glycero-3-phosphocholines that match the acyl chain length of stearoyl-SM (SSM), and compared their deuterium quadrupole coupling profiles in detail. The results suggest a deeper distribution of Chol in the SSM membranes, a lower entropic penalty upon accommodation of Chol in SSM membranes, and a higher thermal stability of acyl-chain orders in the SSM-Chol bilayers than in the 1-palmitoyl-2-stearoyl-sn-glycero-3-phosphocholine-Chol system at various Chol concentrations. The entropy effect and thermal stability should render SM a more preferred raft constituent than saturated diacyl glycerophosphocholine. Our data also demonstrate that the selective and comprehensive deuteration strategy is indispensable for accurate comparison of order profiles.
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Affiliation(s)
- Tomokazu Yasuda
- Department of Chemistry, Graduate School of Science, Osaka University, Toyonaka, Osaka, Japan; Japan Science and Technology Agency, ERATO, Lipid Active Structure Project, Toyonaka, Osaka, Japan
| | - Masanao Kinoshita
- Japan Science and Technology Agency, ERATO, Lipid Active Structure Project, Toyonaka, Osaka, Japan
| | - Michio Murata
- Department of Chemistry, Graduate School of Science, Osaka University, Toyonaka, Osaka, Japan; Japan Science and Technology Agency, ERATO, Lipid Active Structure Project, Toyonaka, Osaka, Japan
| | - Nobuaki Matsumori
- Department of Chemistry, Graduate School of Science, Osaka University, Toyonaka, Osaka, Japan.
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202
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Papadimitriou NI, Kainourgiakis ME, Karozis SN, Charalambopoulou GC. Studying the structure of single-component ceramide bilayers with molecular dynamics simulations using different force fields. MOLECULAR SIMULATION 2014. [DOI: 10.1080/08927022.2014.947483] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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203
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Pinto OA, Bouchet AM, Frías MA, Disalvo EA. Microthermodynamic Interpretation of Fluid States from FTIR Measurements in Lipid Membranes: A Monte Carlo Study. J Phys Chem B 2014; 118:10436-43. [DOI: 10.1021/jp5044078] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- O. A. Pinto
- Centro de Investigaciones y Transferencia
de Santiago del Estero
(CITSE) and ‡Laboratorio de Biointerfases y Sistemas Biomiméticos, Centro
de Investigación y Transferencia de Santiago del Estero (CITSE), Universidad Nacional de Santiago de Estero, CONICET RN 9 Km 1125 Villa el Zanjón, Santiago del Estero, CP 4206 Argentina
| | - A. M. Bouchet
- Centro de Investigaciones y Transferencia
de Santiago del Estero
(CITSE) and ‡Laboratorio de Biointerfases y Sistemas Biomiméticos, Centro
de Investigación y Transferencia de Santiago del Estero (CITSE), Universidad Nacional de Santiago de Estero, CONICET RN 9 Km 1125 Villa el Zanjón, Santiago del Estero, CP 4206 Argentina
| | - M. A. Frías
- Centro de Investigaciones y Transferencia
de Santiago del Estero
(CITSE) and ‡Laboratorio de Biointerfases y Sistemas Biomiméticos, Centro
de Investigación y Transferencia de Santiago del Estero (CITSE), Universidad Nacional de Santiago de Estero, CONICET RN 9 Km 1125 Villa el Zanjón, Santiago del Estero, CP 4206 Argentina
| | - E. A. Disalvo
- Centro de Investigaciones y Transferencia
de Santiago del Estero
(CITSE) and ‡Laboratorio de Biointerfases y Sistemas Biomiméticos, Centro
de Investigación y Transferencia de Santiago del Estero (CITSE), Universidad Nacional de Santiago de Estero, CONICET RN 9 Km 1125 Villa el Zanjón, Santiago del Estero, CP 4206 Argentina
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204
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Lim GS, Zidar J, Cheong DW, Jaenicke S, Klähn M. Impact of Ionic Liquids in Aqueous Solution on Bacterial Plasma Membranes Studied with Molecular Dynamics Simulations. J Phys Chem B 2014; 118:10444-59. [DOI: 10.1021/jp5060952] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Geraldine S. Lim
- Institute of High Performance Computing, Agency for Science, Technology and Research, 1 Fusionopolis
Way, #16-16, Connexis, Singapore 138632, Republic of Singapore
| | - Jernej Zidar
- Institute of High Performance Computing, Agency for Science, Technology and Research, 1 Fusionopolis
Way, #16-16, Connexis, Singapore 138632, Republic of Singapore
| | - Daniel W. Cheong
- Institute of High Performance Computing, Agency for Science, Technology and Research, 1 Fusionopolis
Way, #16-16, Connexis, Singapore 138632, Republic of Singapore
| | - Stephan Jaenicke
- National University of Singapore, Department of Chemistry, 3 Science Drive 3, Singapore 117543, Republic of Singapore
| | - Marco Klähn
- Institute of Chemical and Engineering Sciences, Agency for Science, Technology and Research, 1 Pesek
Road, Jurong Island, Singapore 627833, Republic of Singapore
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205
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Wu EL, Cheng X, Jo S, Rui H, Song KC, Dávila-Contreras EM, Qi Y, Lee J, Monje-Galvan V, Venable RM, Klauda JB, Im W. CHARMM-GUI Membrane Builder toward realistic biological membrane simulations. J Comput Chem 2014; 35:1997-2004. [PMID: 25130509 DOI: 10.1002/jcc.23702] [Citation(s) in RCA: 1542] [Impact Index Per Article: 154.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Revised: 07/16/2014] [Accepted: 07/18/2014] [Indexed: 01/12/2023]
Abstract
CHARMM-GUI Membrane Builder, http://www.charmm-gui.org/input/membrane, is a web-based user interface designed to interactively build all-atom protein/membrane or membrane-only systems for molecular dynamics simulations through an automated optimized process. In this work, we describe the new features and major improvements in Membrane Builder that allow users to robustly build realistic biological membrane systems, including (1) addition of new lipid types, such as phosphoinositides, cardiolipin (CL), sphingolipids, bacterial lipids, and ergosterol, yielding more than 180 lipid types, (2) enhanced building procedure for lipid packing around protein, (3) reliable algorithm to detect lipid tail penetration to ring structures and protein surface, (4) distance-based algorithm for faster initial ion displacement, (5) CHARMM inputs for P21 image transformation, and (6) NAMD equilibration and production inputs. The robustness of these new features is illustrated by building and simulating a membrane model of the polar and septal regions of E. coli membrane, which contains five lipid types: CL lipids with two types of acyl chains and phosphatidylethanolamine lipids with three types of acyl chains. It is our hope that CHARMM-GUI Membrane Builder becomes a useful tool for simulation studies to better understand the structure and dynamics of proteins and lipids in realistic biological membrane environments.
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Affiliation(s)
- Emilia L Wu
- Department of Molecular Biosciences and Center for Bioinformatics, University of Kansas, Lawrence, Kansas, 66047
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206
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Mouret L, Da Costa G, Bondon A. Sterols associated with small unilamellar vesicles (SUVs): intrinsic mobility role for 1H NMR detection. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2014; 52:339-344. [PMID: 24691941 DOI: 10.1002/mrc.4069] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Revised: 02/27/2014] [Accepted: 03/11/2014] [Indexed: 06/03/2023]
Abstract
Small unilamellar vesicles (SUVs) of phospholipids are often used as a membrane model system for studying the interaction of molecules. When using NMR under the standard liquid-state conditions, SUV phospholipid proton spectra can be recorded, exhibiting sharp signals. This is not only because of the fast vesicular tumbling but also because of the combination of this tumbling with the individual motion of the lipids inside the bilayer. This appears evident because addition of cholesterol is responsible of broader resonances because of the slowing down of the lipid motion. On the other hand, no (1)H signal is detected for cholesterol in the bilayer. This lack of detection of the inserted molecules explains why generally SUVs are not considered as a good model for NMR studies under the standard liquid-state conditions. Here, we use two other sterols in order to demonstrate that an increase of the molecular mobility inside the bilayer could allow the detection of their proton resonances. For desmosterol and lanosterol, which show higher mobility inside the bilayer, with increasing lateral diffusion rates, (1)H sterol signals are detected in contrast to cholesterol. For the fast diffusing lanosterol, no significant improvement in detection is observed using deuterated lipids, demonstrating that homonuclear dipolar coupling is fully averaged out. Furthermore, in the case of low mobility such as for cholesterol, the use of a fast magic angle spinning probe is shown to be efficient to recover the full proton spectrum.
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Affiliation(s)
- Liza Mouret
- Université de Rennes 1, UMR CNRS 6226, ICMV, PRISM Biosit, Campus de Villejean, 35043, Rennes Cedex, France
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207
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Liu W, Zhang S, Meng F, Tang L. Molecular simulation of ibuprofen passing across POPC membrane. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2014. [DOI: 10.1142/s0219633614500333] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Permeability assessment is an important procedure in the drug development process, and drug partitioning in membrane bilayer is related to permeability. To investigate the pH dependence on drug partitioning, the process of different ionization state of ibuprofen passing across POPC bilayer was studied using molecular dynamics simulation. The results show that both atomic charge scheme and ionization state of the drug affect the value and shape of energy profile when passing across the POPC bilayer. The neutral ibuprofen (ibuprofen under acidic condition) has a much lower energy barrier as compared with the anionic ibuprofen (ibuprofen under basic condition). Meantime, hydrogen bond analysis also certifies that it is easy for neutral ibuprofen to pass from bulk water to bilayer center. Our calculation suggests that the ionization state of ibuprofen may be changed between neutral and anionic state when passing across membrane: it may be ionized outside the membrane and neutralized inside the membrane.
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Affiliation(s)
- Wei Liu
- Tianjin Key Laboratory of Molecular Design and Drug Discovery, Tianjin Institute of Pharmaceutical Research, Tianjin, 300193, P. R. China
| | - Shijun Zhang
- Tianjin Key Laboratory of Molecular Design and Drug Discovery, Tianjin Institute of Pharmaceutical Research, Tianjin, 300193, P. R. China
| | - Fancui Meng
- Tianjin Key Laboratory of Molecular Design and Drug Discovery, Tianjin Institute of Pharmaceutical Research, Tianjin, 300193, P. R. China
| | - Lida Tang
- Tianjin Key Laboratory of Molecular Design and Drug Discovery, Tianjin Institute of Pharmaceutical Research, Tianjin, 300193, P. R. China
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208
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A systematic molecular dynamics simulation study of temperature dependent bilayer structural properties. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2014; 1838:2520-9. [PMID: 24953542 DOI: 10.1016/j.bbamem.2014.06.010] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Revised: 06/07/2014] [Accepted: 06/11/2014] [Indexed: 11/21/2022]
Abstract
Although lipid force fields (FFs) used in molecular dynamics (MD) simulations have proved to be accurate, there has not been a systematic study on their accuracy over a range of temperatures. Motivated by the X-ray and neutron scattering measurements of common phosphatidylcholine (PC) bilayers (Kučerka et al. BBA. 1808: 2761, 2011), the CHARMM36 (C36) FF accuracy is tested in this work with MD simulations of six common PC lipid bilayers over a wide range of temperatures. The calculated scattering form factors and deuterium order parameters from the C36 MD simulations agree well with the X-ray, neutron, and NMR experimental data. There is excellent agreement between MD simulations and experimental estimates for the surface area per lipid, bilayer thickness (DB), hydrophobic thickness (DC), and lipid volume (VL). The only minor discrepancy between simulation and experiment is a measure of (DB-DHH)/2 where DHH is the distance between the maxima in the electron density profile along the bilayer normal. Additional MD simulations with pure water and heptane over a range of temperatures provide explanations of possible reasons causing the minor deviation. Overall, the C36 FF is accurate for use with liquid crystalline PC bilayers of varying chain types and over biologically relevant temperatures.
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209
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Guixà-González R, Ramírez-Anguita JM, Kaczor AA, Selent J. Simulating G protein-coupled receptors in native-like membranes: from monomers to oligomers. Methods Cell Biol 2014; 117:63-90. [PMID: 24143972 DOI: 10.1016/b978-0-12-408143-7.00004-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2023]
Abstract
G protein-coupled receptors (GPCRs) are one of the most relevant superfamilies of transmembrane proteins as they participate in an important variety of biological events. Recently, the scientific community is witnessing an advent of a GPCR crystallization age along with impressive improvements achieved in the field of computer simulations during the last two decades. Computer simulation techniques such as molecular dynamics (MD) simulations are now frequent tools to study the dynamic behavior of GPCRs and, more importantly, to model the complex membrane environment where these proteins spend their lifetime. Thanks to these tools, GPCRs can be simulated not only longer but also in a more "physiological" fashion. In this scenario, scientists are taking advantage of such advances to approach certain phenomena such as GPCR oligomerization occurring only at timescales not reachable until now. Thus, despite current MD simulations having important limitations today, they have become an essential tool to study key biophysical properties of GPCRs and GPCR oligomers.
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Affiliation(s)
- Ramon Guixà-González
- Research Programme on Biomedical Informatics (GRIB), Department of Experimental and Health Sciences, Universitat Pompeu Fabra/IMIM (Hospital del Mar Medical Research Institute), Dr. Aiguader, Barcelona, Spain
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210
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Wu EL, Fleming PJ, Yeom MS, Widmalm G, Klauda JB, Fleming KG, Im W. E. coli outer membrane and interactions with OmpLA. Biophys J 2014; 106:2493-502. [PMID: 24896129 PMCID: PMC4052237 DOI: 10.1016/j.bpj.2014.04.024] [Citation(s) in RCA: 109] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2014] [Revised: 04/17/2014] [Accepted: 04/21/2014] [Indexed: 10/25/2022] Open
Abstract
The outer membrane of Gram-negative bacteria is a unique asymmetric lipid bilayer composed of phospholipids (PLs) in the inner leaflet and lipopolysaccharides (LPSs) in the outer leaflet. Its function as a selective barrier is crucial for the survival of bacteria in many distinct environments, and it also renders Gram-negative bacteria more resistant to antibiotics than their Gram-positive counterparts. Here, we report the structural properties of a model of the Escherichia coli outer membrane and its interaction with outer membrane phospholipase A (OmpLA) utilizing molecular dynamics simulations. Our results reveal that given the lipid composition used here, the hydrophobic thickness of the outer membrane is ∼3 Å thinner than the corresponding PL bilayer, mainly because of the thinner LPS leaflet. Further thinning in the vicinity of OmpLA is observed due to hydrophobic matching. The particular shape of the OmpLA barrel induces various interactions between LPS and PL leaflets, resulting in asymmetric thinning around the protein. The interaction between OmpLA extracellular loops and LPS (headgroups and core oligosaccharides) stabilizes the loop conformation with reduced dynamics, which leads to secondary structure variation and loop displacement compared to that in a DLPC bilayer. In addition, we demonstrate that the LPS/PL ratios in asymmetric bilayers can be reliably estimated by the per-lipid surface area of each lipid type, and there is no statistical difference in the overall membrane structure for the outer membranes with one more or less LPS in the outer leaflet, although individual lipid properties vary slightly.
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Affiliation(s)
- Emilia L Wu
- Department of Molecular Biosciences and Center for Bioinformatics, The University of Kansas, Lawrence, Kansas
| | - Patrick J Fleming
- T. C. Jenkins Department of Biophysics, John Hopkins University, Baltimore, Maryland
| | - Min Sun Yeom
- Korean Institute of Science and Technology Information, Daejeon, Korea
| | - Göran Widmalm
- Department of Organic Chemistry and Stockholm Center for Biomembrane Research, Arrhenius Laboratory, Stockholm University, Stockholm, Sweden
| | - Jeffery B Klauda
- Department of Chemical and Biomolecular Engineering, The University of Maryland, College Park, Maryland
| | - Karen G Fleming
- T. C. Jenkins Department of Biophysics, John Hopkins University, Baltimore, Maryland.
| | - Wonpil Im
- Department of Molecular Biosciences and Center for Bioinformatics, The University of Kansas, Lawrence, Kansas.
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211
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Islami M, Mehrnejad F, Doustdar F, Alimohammadi M, Khadem-Maaref M, Mir-Derikvand M, Taghdir M. Study of orientation and penetration of LAH4 into lipid bilayer membranes: pH and composition dependence. Chem Biol Drug Des 2014; 84:242-52. [PMID: 24581146 DOI: 10.1111/cbdd.12311] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2013] [Revised: 02/12/2014] [Accepted: 02/14/2014] [Indexed: 11/29/2022]
Abstract
LAH4 is an antimicrobial peptide that is believed to possess both antibiotic and DNA delivery capabilities. It is one of a number of membrane-active peptides that show increased affinity toward anionic lipids. Herein, we have performed molecular dynamics simulations to compare LAH4 effects on anionic palmitoyl-oleoyl-phosphatidylglycerol bilayer, which approximate a prokaryotic membrane environment and zwitterionic palmitoyl-oleoyl-phosphatidylcholine bilayer, which approximate a eukaryotic membrane environment. One particular interest in this work is to study how different kinds of lipid bilayers respond to the attraction of LAH4. Remarkably, our data have shown that the depth of peptide penetration strongly depends on membrane composition and pH. At acidic pH, LAH4 has exhibited a high tendency to interact strongly with and be adsorbed on anionic membrane. We have also shown that electrostatic interactions between His11 and the phosphor atoms of bilayers should have a significant impact on the penetration of LAH4. These results provide insights into the interactions of LAH4 and lipid bilayers at the atomic level, which is useful to understand cell selectivity and mechanism of the peptide action.
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Affiliation(s)
- Matin Islami
- Department of Cellular and Molecular Biology, Faculty of Science, Azarbaijan Shahid Madani University, Tabriz, 53714-161, Iran
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212
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Wu EL, Qi Y, Song KC, Klauda JB, Im W. Preferred orientations of phosphoinositides in bilayers and their implications in protein recognition mechanisms. J Phys Chem B 2014; 118:4315-25. [PMID: 24689790 DOI: 10.1021/jp500610t] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Phosphoinositides (PIPs), phosphorylated derivatives of phosphatidylinositol (PI), are essential regulatory lipids involved in various cellular processes, including signal transduction, membrane trafficking, and cytoskeletal remodeling. To gain insight into the protein-PIPs recognition process, it is necessary to study the inositol ring orientation (with respect to the membrane) of PIPs with different phosphorylation states. In this study, 8 PIPs (3 PIP, 2 PIP2, and 3 PIP3) with different phosphorylation and protonation sites have been separately simulated in two mixed bilayers (one with 20% phosphatidylserine (PS) lipids and another with PS lipids switched to phosphatidylcholine (PC) lipids), which roughly correspond to yeast membranes. Uniformity of the bilayer properties including hydrophobic thickness, acyl chain order parameters, and heavy atom density profiles is observed in both PS-contained and PC-enriched membranes due to the same hydrophobic core composition. The relationship between the inositol ring orientation (tilt and rotation angles) and its solvent-accessible surface area indicates that the orientation is mainly determined by its solvation energy. Different PIPs exhibit a clear preference in the inositol ring rotation angle. Surprisingly, a larger proportion of PIPs inositol rings stay closer to the surface of PS-contained membranes compared to PC-enriched ones. Such a difference is rationalized with the formation of more hydrogen bonds between the PS/PI headgroups and the PIPs inositol rings in PS-contained membranes. This hydrogen bond network could be functionally important; thus, the present results can potentially add important and detailed features into the existing protein-PIPs recognition mechanism.
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Affiliation(s)
- Emilia L Wu
- Department of Molecular Biosciences and Center for Bioinformatics, The University of Kansas , Lawrence, Kansas 66047, United States
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213
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Wu EL, Engström O, Jo S, Stuhlsatz D, Yeom MS, Klauda JB, Widmalm G, Im W. Molecular dynamics and NMR spectroscopy studies of E. coli lipopolysaccharide structure and dynamics. Biophys J 2014; 105:1444-55. [PMID: 24047996 DOI: 10.1016/j.bpj.2013.08.002] [Citation(s) in RCA: 134] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2013] [Revised: 07/31/2013] [Accepted: 08/01/2013] [Indexed: 01/18/2023] Open
Abstract
Lipopolysaccharide (LPS), a component of Gram-negative bacterial outer membranes, comprises three regions: lipid A, core oligosaccharide, and O-antigen polysaccharide. Using the CHARMM36 lipid and carbohydrate force fields, we have constructed a model of an Escherichia coli R1 (core) O6 (antigen) LPS molecule. Several all-atom bilayers are built and simulated with lipid A only (LIPA) and varying lengths of 0 (LPS0), 5 (LPS5), and 10 (LPS10) O6 antigen repeating units; a single unit of O6 antigen contains five sugar residues. From (1)H,(1)H-NOESY experiments, cross-relaxation rates are obtained from an O-antigen polysaccharide sample. Although some experimental deviations are due to spin-diffusion, the remaining effective proton-proton distances show generally very good agreement between NMR experiments and molecular dynamics simulations. The simulation results show that increasing the LPS molecular length has an impact on LPS structure and dynamics and also on LPS bilayer properties. Terminal residues in a LPS bilayer are more flexible and extended along the membrane normal. As the core and O-antigen are added, per-lipid area increases and lipid bilayer order decreases. In addition, results from mixed LPS0/5 and LPS0/10 bilayer simulations show that the LPS O-antigen conformations at a higher concentration of LPS5 and LPS10 are more orthogonal to the membrane and less flexible. The O-antigen concentration of mixed LPS bilayers does not have a significant effect on per-lipid area and hydrophobic thickness. Analysis of ion and water penetration shows that water molecules can penetrate inside the inner core region, and hydration is critical to maintain the integrity of the bilayer structure.
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Affiliation(s)
- Emilia L Wu
- Department of Molecular Biosciences and Center for Bioinformatics, The University of Kansas, Lawrence, Kansas
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214
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Nadvorny D, da Silva JBP, Lins RD. Anionic Form of Usnic Acid Promotes Lamellar to Nonlamellar Transition in DPPC and DOPC Membranes. J Phys Chem B 2014; 118:3881-6. [DOI: 10.1021/jp412176f] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Daniela Nadvorny
- Fundamental
Chemistry Department, Federal University of Pernambuco, Recife PE 50.740-540, Brazil
| | - João Bosco P. da Silva
- Fundamental
Chemistry Department, Federal University of Pernambuco, Recife PE 50.740-540, Brazil
| | - Roberto D. Lins
- Fundamental
Chemistry Department, Federal University of Pernambuco, Recife PE 50.740-540, Brazil
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215
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Guixà-González R, Rodriguez-Espigares I, Ramírez-Anguita JM, Carrió-Gaspar P, Martinez-Seara H, Giorgino T, Selent J. MEMBPLUGIN: studying membrane complexity in VMD. ACTA ACUST UNITED AC 2014; 30:1478-80. [PMID: 24451625 DOI: 10.1093/bioinformatics/btu037] [Citation(s) in RCA: 154] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
SUMMARY Computer simulations are giving way to more complex and accurate studies of biological membranes by molecular dynamics (MD) simulations. The analysis of MD trajectories comprises the biophysical characterization of membrane properties or the study of protein-lipid interactions and dynamics. However, there is a lack of automated tools to analyse MD simulations of complex membrane or membrane-protein systems. Here we present MEMBPLUGIN, a plugin for the Visual Molecular Dynamics package that provides algorithms to measure a host of essential biophysical properties in simulated membranes. MEMBPLUGIN features are accessible both through a user-friendly graphical interface and as command-line procedures to be invoked in analysis scripts. AVAILABILITY AND IMPLEMENTATION MEMBPLUGIN is a VMD extension written in Tcl. Multi-platform source code, documentation and tutorials are freely available at http://membplugin.sourceforge.net. CONTACT toni.giorgino@isib.cnr.it or jana.selent@upf.edu SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Ramon Guixà-González
- Pharmacoinformatics group, Research Programme on Biomedical Informatics (GRIB), Universitat Pompeu Fabra (UPF)-Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain, Department of Physics, Tampere University of Technology, Tampere, Finland and Institute of Biomedical Engineering, National Research Council of Italy (ISIB-CNR), Padua, Italy
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216
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Huster D. Solid-state NMR spectroscopy to study protein-lipid interactions. Biochim Biophys Acta Mol Cell Biol Lipids 2013; 1841:1146-60. [PMID: 24333800 DOI: 10.1016/j.bbalip.2013.12.002] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Accepted: 12/04/2013] [Indexed: 12/22/2022]
Abstract
The appropriate lipid environment is crucial for the proper function of membrane proteins. There is a tremendous variety of lipid molecules in the membrane and so far it is often unclear which component of the lipid matrix is essential for the function of a respective protein. Lipid molecules and proteins mutually influence each other; parameters such as acyl chain order, membrane thickness, membrane elasticity, permeability, lipid-domain and annulus formation are strongly modulated by proteins. More recent data also indicates that the influence of proteins goes beyond a single annulus of next-neighbor boundary lipids. Therefore, a mesoscopic approach to membrane lipid-protein interactions in terms of elastic membrane deformations has been developed. Solid-state NMR has greatly contributed to the understanding of lipid-protein interactions and the modern view of biological membranes. Methods that detect the influence of proteins on the membrane as well as direct lipid-protein interactions have been developed and are reviewed here. Examples for solid-state NMR studies on the interaction of Ras proteins, the antimicrobial peptide protegrin-1, the G protein-coupled receptor rhodopsin, and the K(+) channel KcsA are discussed. This article is part of a Special Issue entitled Tools to study lipid functions.
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Affiliation(s)
- Daniel Huster
- Institute of Medical Physics and Biophysics, University of Leipzig, Härtelstr. 16-18, D-04107 Leipzig, Germany.
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217
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Lukat G, Krüger J, Sommer B. APL@Voro: a Voronoi-based membrane analysis tool for GROMACS trajectories. J Chem Inf Model 2013; 53:2908-25. [PMID: 24175728 DOI: 10.1021/ci400172g] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
APL@Voro is a new program developed to aid in the analysis of GROMACS trajectories of lipid bilayer simulations. It can read a GROMACS trajectory file, a PDB coordinate file, and a GROMACS index file to create a two-dimensional geometric representation of a bilayer. Voronoi diagrams and Delaunay triangulations--generated for different selection models of lipids--support the analysis of the bilayer. The values calculated on the geometric structures can be visualized in a user-friendly interactive environment and, then, plotted and exported to different file types. APL@Voro supports complex bilayers with a mix of various lipids and proteins. For the calculation of the projected area per lipid, a modification of the well-known Voronoi approach is presented as well as the presentation of a new approach for including atoms into an existing triangulation. The application of the developed software is discussed for three example systems simulated with GROMACS. The program is written in C++, is open source, and is available free of charge.
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Affiliation(s)
- Gunther Lukat
- Bio-/Medical Informatics Department, University of Bielefeld , Universitätsstr. 25, 33615 Bielefeld, Germany
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218
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Schäfer B, Orbán E, Borics A, Huszár K, Nyeste A, Welker E, Tömböly C. Preparation of semisynthetic lipoproteins with fluorescent cholesterol anchor and their introduction to the cell membrane with minimal disruption of the membrane. Bioconjug Chem 2013; 24:1684-97. [PMID: 24020959 DOI: 10.1021/bc4002135] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The exogenous introduction of fluorescent lipoproteins into cell membranes is a method for visualizing the cellular traffic of membrane associated proteins, and also for altering the cell surface in a controlled manner. In order to achieve the cell membrane anchoring of proteins and their subsequent fluorescence based detection, a cholesterol derivative was designed. The headgroup of the novel cholesterol anchor contains a fluorescent reporter and a thiol reactive maleimide for protein conjugation. Protein conjugation was demonstrated by the addition of a green fluorescent maleimido anchor to the C-terminus of a Cys extended red fluorescent protein, mCherry. The resulting dual fluorescent cholesteryl lipoprotein was successfully separated from the micellar associates of the surplus fluorescent lipid anchor without denaturing the protein, and the lipoprotein containing only the covalently linked, stoichiometric fluorescent lipid was efficiently delivered to the plasma membrane of live cells. It was demonstrated that the membrane fluorescence could be directly assigned to the protein-anchor conjugate, because no excess of fluorescent lipid species were present during the imaging experiment and the protein and anchor fluorescence colocalized in the cell membrane. Molecular dynamics simulations and subsequent trajectory analysis suggest also the spontaneous and stable membrane association of the cholesterol anchor. Thus, the method could be beneficially applied for studying membrane associated proteins and for preparing mimetics of glycosylphosphatidylinositol (GPI)-anchored proteins to target cholesterol-rich membrane microdomains.
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Affiliation(s)
- Balázs Schäfer
- Laboratory of Chemical Biology and §Laboratory of Conformational Diseases, Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences , Temesvári krt. 62., 6726 Szeged, Hungary
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219
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Effect of acetone accumulation on structure and dynamics of lipid membranes studied by molecular dynamics simulations. Comput Biol Chem 2013; 46:23-31. [DOI: 10.1016/j.compbiolchem.2013.04.005] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2013] [Revised: 04/27/2013] [Accepted: 04/29/2013] [Indexed: 12/30/2022]
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220
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Cord factor (trehalose 6,6′-dimycolate) forms fully stable and non-permeable lipid bilayers required for a functional outer membrane. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2013; 1828:2173-81. [DOI: 10.1016/j.bbamem.2013.04.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Revised: 04/22/2013] [Accepted: 04/23/2013] [Indexed: 11/22/2022]
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221
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Motegi T, Nabika H, Murakoshi K. Single-molecule observations for determining the orientation and diffusivity of dye molecules in lipid bilayers. Phys Chem Chem Phys 2013; 15:12895-902. [PMID: 23812281 DOI: 10.1039/c3cp51585k] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The molecular orientation and diffusion of dye molecules in artificial lipid bilayers were observed using total internal reflection fluorescence microscopy. An artificial lipid bilayer composed of a ternary lipid mixture of 1,2-dilauroyl-sn-glycero-3-phosphocholine (DLPC), 1,2-dipalmitoyl-sn-glycero-3-phosphatidylcholine (DPPC), and cholesterol was used. The molecular orientation, which was obtained through defocused imaging, clarified the microscopic features, including cholesterol-induced changes in the local packing structure. Diffusion analysis gave insights into the macroscopic aspects of phase distribution in the heterogeneous bilayer system. Combining these two independent investigations, we revealed the effect of cholesterol addition on microscopic local packing and macroscopic phase structures. Our observations showed a transition from a DLPC-network-like structure to a DPPC-network-like structure upon the addition of cholesterol, which was not evident from previous domain shape observations. The present single-molecule observations yielded the actual phase structure that controls the motion of molecules in the membrane. The results imply that the orientation and diffusivity of molecules offer useful information regarding the phase distribution, which may be hindered by the apparent phase structure in a heterogeneous lipid bilayer that contains cholesterol.
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Affiliation(s)
- Toshinori Motegi
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
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222
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Bhatnagar N, Kamath G, Potoff JJ. Biomolecular Simulations with the Transferable Potentials for Phase Equilibria: Extension to Phospholipids. J Phys Chem B 2013; 117:9910-21. [DOI: 10.1021/jp404314k] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Navendu Bhatnagar
- Department of Chemical Engineering
and Materials Science, Wayne State University, Detroit, Michigan 48202, United States
| | - Ganesh Kamath
- Department of Chemistry, University of Missouri−Columbia, Columbia, Missouri
65211-7600, United States
| | - Jeffrey J. Potoff
- Department of Chemical Engineering
and Materials Science, Wayne State University, Detroit, Michigan 48202, United States
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223
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Rabinovich AL, Lyubartsev AP. Computer simulation of lipid membranes: Methodology and achievements. POLYMER SCIENCE SERIES C 2013. [DOI: 10.1134/s1811238213070060] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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224
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Deng Y, Qian Z, Luo Y, Zhang Y, Mu Y, Wei G. Membrane binding and insertion of a pHLIP peptide studied by all-atom molecular dynamics simulations. Int J Mol Sci 2013; 14:14532-49. [PMID: 23857053 PMCID: PMC3742258 DOI: 10.3390/ijms140714532] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Revised: 06/24/2013] [Accepted: 06/25/2013] [Indexed: 11/16/2022] Open
Abstract
Recent experiments in function mechanism study reported that a pH low-insertion peptide (pHLIP) can insert into a zwitterionic palmitoyloleoylphosphatidylcholine (POPC) lipid bilayer at acidic pH while binding to the bilayer surface at basic pH. However, the atomic details of the pH-dependent interaction of pHLIP with a POPC bilayer are not well understood. In this study, we investigate the detailed interactions of pHLIP with a POPC bilayer at acidic and basic pH conditions as those used in function mechanism study, using all-atom molecular dynamics (MD) simulations. Simulations have been performed by employing the initial configurations, where pHLIP is placed in aqueous solution, parallel to bilayer surface (system S), partially-inserted (system P), or fully-inserted (system F) in POPC bilayers. On the basis of multiple 200-ns MD simulations, we found (1) pHLIP in system S can spontaneously insert into a POPC bilayer at acidic pH, while binding to the membrane surface at basic pH; (2) pHLIP in system P can insert deep into a POPC bilayer at acidic pH, while it has a tendency to exit, and stays at bilayer surface at basic pH; (3) pHLIP in system F keeps in an α-helical structure at acidic pH while partially unfolding at basic pH. This study provides at atomic-level the pH-induced insertion of pHLIP into POPC bilayer.
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Affiliation(s)
- Yonghua Deng
- State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (Ministry of Education), and Department of Physics, Fudan University, 220 Handan Road, Shanghai 200433, China; E-Mails: (Y.D.); (Z.Q.); (Y.L.); (Y.Z.)
| | - Zhenyu Qian
- State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (Ministry of Education), and Department of Physics, Fudan University, 220 Handan Road, Shanghai 200433, China; E-Mails: (Y.D.); (Z.Q.); (Y.L.); (Y.Z.)
| | - Yin Luo
- State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (Ministry of Education), and Department of Physics, Fudan University, 220 Handan Road, Shanghai 200433, China; E-Mails: (Y.D.); (Z.Q.); (Y.L.); (Y.Z.)
| | - Yun Zhang
- State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (Ministry of Education), and Department of Physics, Fudan University, 220 Handan Road, Shanghai 200433, China; E-Mails: (Y.D.); (Z.Q.); (Y.L.); (Y.Z.)
| | - Yuguang Mu
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore; E-Mail:
| | - Guanghong Wei
- State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (Ministry of Education), and Department of Physics, Fudan University, 220 Handan Road, Shanghai 200433, China; E-Mails: (Y.D.); (Z.Q.); (Y.L.); (Y.Z.)
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +86-21-5566-5231; Fax: +86-21-6510-4949
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225
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Jarerattanachat V, Karttunen M, Wong-ekkabut J. Molecular Dynamics Study of Oxidized Lipid Bilayers in NaCl Solution. J Phys Chem B 2013; 117:8490-501. [DOI: 10.1021/jp4040612] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Viwan Jarerattanachat
- Department of Physics, Faculty
of Science, Kasetsart University, 50 Phahon
Yothin Rd, Chatuchak, Bangkok, Thailand
| | - Mikko Karttunen
- Department of Chemistry and
Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Avenue West, Waterloo, Ontario,
Canada
| | - Jirasak Wong-ekkabut
- Department of Physics, Faculty
of Science, Kasetsart University, 50 Phahon
Yothin Rd, Chatuchak, Bangkok, Thailand
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226
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Coimbra JT, Sousa SF, Fernandes PA, Rangel M, Ramos MJ. Biomembrane simulations of 12 lipid types using the general amber force field in a tensionless ensemble. J Biomol Struct Dyn 2013; 32:88-103. [DOI: 10.1080/07391102.2012.750250] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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227
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Adsorption and Orientation of Human Islet Amyloid Polypeptide (hIAPP) Monomer at Anionic Lipid Bilayers: Implications for Membrane-Mediated Aggregation. Int J Mol Sci 2013; 14:6241-58. [PMID: 23519103 PMCID: PMC3634446 DOI: 10.3390/ijms14036241] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Revised: 03/11/2013] [Accepted: 03/12/2013] [Indexed: 01/05/2023] Open
Abstract
Protein misfolding and aggregation cause serious degenerative diseases, such as Alzheimer's and type II diabetes. Human islet amyloid polypeptide (hIAPP) is the major component of amyloid deposits found in the pancreas of type II diabetic patients. Increasing evidence suggests that β-cell death is related to the interaction of hIAPP with the cellular membrane, which accelerates peptide aggregation. In this study, as a first step towards understanding the membrane-mediated hIAPP aggregation, we investigate the atomic details of the initial step of hIAPP-membrane interaction, including the adsorption orientation and conformation of hIAPP monomer at an anionic POPG lipid bilayer by performing all-atom molecular dynamics simulations. We found that hIAPP monomer is quickly adsorbed to bilayer surface, and the adsorption is initiated from the N-terminal residues driven by strong electrostatic interactions of the positively-charged residues K1 and R11 with negatively-charged lipid headgroups. hIAPP binds parallel to the lipid bilayer surface as a stable helix through residues 7-22, consistent with previous experimental study. Remarkably, different simulations lead to the same binding orientation stabilized by electrostatic and H-bonding interactions, with residues R11, F15 and S19 oriented towards membrane and hydrophobic residues L12, A13, L16 and V17 exposed to solvent. Implications for membrane-mediated hIAPP aggregation are discussed.
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228
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Choi HG, Kim C. A 2H solid-state NMR study on the lipid phase change in the presence of an antimicrobial peptide. ANALYTICAL SCIENCE AND TECHNOLOGY 2013. [DOI: 10.5806/ast.2013.26.1.061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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229
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Mao Y, Du Y, Cang X, Wang J, Chen Z, Yang H, Jiang H. Binding Competition to the POPG Lipid Bilayer of Ca2+, Mg2+, Na+, and K+ in Different Ion Mixtures and Biological Implication. J Phys Chem B 2013; 117:850-8. [DOI: 10.1021/jp310163z] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Yanyan Mao
- Drug Discovery and Design Center, State Key Laboratory
of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai
201203, China
| | - Yun Du
- Drug Discovery and Design Center, State Key Laboratory
of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai
201203, China
| | - Xiaohui Cang
- Drug Discovery and Design Center, State Key Laboratory
of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai
201203, China
| | - Jinan Wang
- Drug Discovery and Design Center, State Key Laboratory
of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai
201203, China
| | - Zhuxi Chen
- Drug Discovery and Design Center, State Key Laboratory
of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai
201203, China
| | - Huaiyu Yang
- Drug Discovery and Design Center, State Key Laboratory
of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai
201203, China
| | - Hualiang Jiang
- Drug Discovery and Design Center, State Key Laboratory
of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai
201203, China
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230
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Lemmin T, Bovigny C, Lançon D, Dal Peraro M. Cardiolipin Models for Molecular Simulations of Bacterial and Mitochondrial Membranes. J Chem Theory Comput 2012; 9:670-8. [PMID: 26589063 DOI: 10.1021/ct300590v] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Present in bacterial and mitochondrial membranes, cardiolipins have a unique dimeric structure, which carries up to two charges (i.e., one per phosphate group) and, under physiological conditions, can be unprotonated or singly protonated. Exhaustive models and characterization of cardiolipins are to date scarce; therefore we propose an ab initio parametrization of cardiolipin species for molecular simulation consistent with commonly used force fields. Molecular dynamics simulations using these models indicate a protonation dependent lipid packing. A peculiar interaction with solvating mono- and divalent cations is also observed. The proposed models will contribute to the study of the assembly of more realistic bacterial and mitochondrial membranes and the investigation of the role of cardiolipins for the biophysical and biochemical properties of membranes and membrane-embedded proteins.
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Affiliation(s)
- Thomas Lemmin
- Laboratory for Biomolecular Modeling, Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Switzerland
| | - Christophe Bovigny
- Laboratory for Biomolecular Modeling, Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Switzerland
| | - Diane Lançon
- Laboratory for Biomolecular Modeling, Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Switzerland
| | - Matteo Dal Peraro
- Laboratory for Biomolecular Modeling, Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Switzerland
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231
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Jämbeck JPM, Lyubartsev AP. Another Piece of the Membrane Puzzle: Extending Slipids Further. J Chem Theory Comput 2012; 9:774-84. [PMID: 26589070 DOI: 10.1021/ct300777p] [Citation(s) in RCA: 207] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
To be able to model complex biological membranes in a more realistic manner, the force field Slipids (Stockholm lipids) has been extended to include parameters for sphingomyelin (SM), phosphatidylglycerol (PG), phosphatidylserine (PS) lipids, and cholesterol. Since the parametrization scheme was faithful to the scheme used in previous editions of Slipids, all parameters are consistent and fully compatible. The results of careful validation of a number of key structural properties for one and two component lipid bilayers are in excellent agreement with experiments. Potentials of mean force for transferring water across binary mixtures of lipids and cholesterol were also computed in order to compare water permeability rates to experiments. In agreement with experimental and simulation studies, it was found that the permeability and partitioning of water is affected by cholesterol in lipid bilayers made of saturated lipids to the largest extent. With the extensions of Slipids presented here, it is now possible to study complex systems containing many different lipids and proteins in a fully atomistic resolution in the isothermic-isobaric (NPT) ensemble, which is the proper ensemble for membrane simulations.
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Affiliation(s)
- Joakim P M Jämbeck
- Division of Physical Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm, SE-10691, Sweden
| | - Alexander P Lyubartsev
- Division of Physical Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm, SE-10691, Sweden
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232
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Design of peptide-membrane interactions to modulate single-file water transport through modified gramicidin channels. Biophys J 2012; 103:1698-705. [PMID: 23083713 DOI: 10.1016/j.bpj.2012.08.059] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2012] [Revised: 08/22/2012] [Accepted: 08/23/2012] [Indexed: 11/22/2022] Open
Abstract
Water permeability through single-file channels is affected by intrinsic factors such as their size and polarity and by external determinants like their lipid environment in the membrane. Previous computational studies revealed that the obstruction of the channel by lipid headgroups can be long-lived, in the range of nanoseconds, and that pore-length-matching membrane mimetics could speed up water permeability. To test the hypothesis of lipid-channel interactions modulating channel permeability, we designed different gramicidin A derivatives with attached acyl chains. By combining extensive molecular-dynamics simulations and single-channel water permeation measurements, we show that by tuning lipid-channel interactions, these modifications reduce the presence of lipid headgroups in the pore, which leads to a clear and selective increase in their water permeability.
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233
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Parthasarathi R, Tummala NR, Striolo A. Embedded Single-Walled Carbon Nanotubes Locally Perturb DOPC Phospholipid Bilayers. J Phys Chem B 2012; 116:12769-82. [DOI: 10.1021/jp306299x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- R. Parthasarathi
- The School of Chemical, Biological
and Materials Engineering, The University of Oklahoma, Norman, Oklahoma 73019, United States
| | - N. R. Tummala
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332,
United States
| | - A. Striolo
- The School of Chemical, Biological
and Materials Engineering, The University of Oklahoma, Norman, Oklahoma 73019, United States
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234
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Jämbeck JPM, Lyubartsev AP. An Extension and Further Validation of an All-Atomistic Force Field for Biological Membranes. J Chem Theory Comput 2012; 8:2938-48. [PMID: 26592132 DOI: 10.1021/ct300342n] [Citation(s) in RCA: 346] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Biological membranes are versatile in composition and host intriguing molecular processes. In order to be able to study these systems, an accurate model Hamiltonian or force field (FF) is a necessity. Here, we report the results of our extension of earlier developed all-atomistic FF parameters for fully saturated phospholipids that complements an earlier parameter set for saturated phosphatidylcholine lipids (J. Phys. Chem. B, 2012, 116, 3164-3179). The FF, coined Slipids (Stockholm lipids), now also includes parameters for unsaturated phosphatidylcholine and phosphatidylethanolamine lipids, e.g., POPC, DOPC, SOPC, POPE, and DOPE. As the extended set of parameters is derived with the same philosophy as previously applied, the resulting FF has been developed in a fully consistent manner. The capabilities of Slipids are demonstrated by performing long simulations without applying any surface tension and using the correct isothermal-isobaric (NPT) ensemble for a range of temperatures and carefully comparing a number of properties with experimental findings. Results show that several structural properties are very well reproduced, such as scattering form factors, NMR order parameters, thicknesses, and area per lipid. Thermal dependencies of different thicknesses and area per lipid are reproduced as well. Lipid diffusion is systematically slightly underestimated, whereas the normalized lipid diffusion follows the experimental trends. This is believed to be due to the lack of collective movement in the relatively small bilayer patches used. Furthermore, the compatibility with amino acid FFs from the AMBER family is tested in explicit transmembrane complexes of the WALP23 peptide with DLPC and DOPC bilayers, and this shows that Slipids can be used to study more complex and biologically relevant systems.
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Affiliation(s)
- Joakim P M Jämbeck
- Division of Physical Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm, SE-10691, Sweden
| | - Alexander P Lyubartsev
- Division of Physical Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm, SE-10691, Sweden
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235
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Darré L, Tek A, Baaden M, Pantano S. Mixing Atomistic and Coarse Grain Solvation Models for MD Simulations: Let WT4 Handle the Bulk. J Chem Theory Comput 2012; 8:3880-94. [DOI: 10.1021/ct3001816] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Leonardo Darré
- Institut Pasteur de Montevideo,
Mataojo 2020, CP 11400, Uruguay
| | - Alex Tek
- Laboratoire de Biochimie Théorique,
CNRS, UPR9080, Univ Paris Diderot, Sorbonne Paris Cité. 13
rue Pierre et Marie Curie, 75005, Paris, France
- Université Pierre et Marie
Curie, UPMC Sorbonne Universités, 4 place Jussieu 75005 Paris,
France
| | - Marc Baaden
- Laboratoire de Biochimie Théorique,
CNRS, UPR9080, Univ Paris Diderot, Sorbonne Paris Cité. 13
rue Pierre et Marie Curie, 75005, Paris, France
| | - Sergio Pantano
- Institut Pasteur de Montevideo,
Mataojo 2020, CP 11400, Uruguay
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236
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Lipid interaction and membrane perturbation of human islet amyloid polypeptide monomer and dimer by molecular dynamics simulations. PLoS One 2012; 7:e38191. [PMID: 22693597 PMCID: PMC3364971 DOI: 10.1371/journal.pone.0038191] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2012] [Accepted: 05/04/2012] [Indexed: 11/19/2022] Open
Abstract
The aggregation of human islet amyloid polypeptide (hIAPP or amylin) is associated with the pathogenesis of type 2 diabetes mellitus. Increasing evidence suggests that the interaction of hIAPP with β-cell membranes plays a crucial role in cytotoxicity. However, the hIAPP-lipid interaction and subsequent membrane perturbation is not well understood at atomic level. In this study, as a first step to gain insight into the mechanism of hIAPP-induced cytotoxicity, we have investigated the detailed interactions of hIAPP monomer and dimer with anionic palmitoyloleolyophosphatidylglycerol (POPG) bilayer using all-atom molecular dynamics (MD) simulations. Multiple MD simulations have been performed by employing the initial configurations where the N-terminal region of hIAPP is pre-inserted in POPG bilayer. Our simulations show that electrostatic interaction between hIAPP and POPG bilayer plays a major role in peptide-lipid interaction. In particular, the N-terminal positively-charged residues Lys1 and Arg11 make a dominant contribution to the interaction. During peptide-lipid interaction process, peptide dimerization occurs mostly through the C-terminal 20–37 region containing the amyloidogenic 20–29-residue segment. Membrane-bound hIAPP dimers display a pronounced ability of membrane perturbation than monomers. The higher bilayer perturbation propensity of hIAPP dimer likely results from the cooperativity of the peptide-peptide interaction (or peptide aggregation). This study provides insight into the hIAPP-membrane interaction and the molecular mechanism of membrane disruption by hIAPP oligomers.
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237
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Bechinger B, Salnikov ES. The membrane interactions of antimicrobial peptides revealed by solid-state NMR spectroscopy. Chem Phys Lipids 2012; 165:282-301. [DOI: 10.1016/j.chemphyslip.2012.01.009] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2011] [Revised: 01/25/2012] [Accepted: 01/27/2012] [Indexed: 01/29/2023]
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238
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Yeh IC, Ripoll DR, Wallqvist A. Free energy difference in indolicidin attraction to eukaryotic and prokaryotic model cell membranes. J Phys Chem B 2012; 116:3387-96. [PMID: 22376120 DOI: 10.1021/jp211883u] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
We analyzed the thermodynamic and structural determinants of indolicidin interactions with eukaryotic and prokaryotic cell membranes using a series of atomistically detailed molecular dynamics simulations. We used quartz-supported bilayers with two different compositions of zwitterionic and anionic phospholipids as model eukaryotic and prokaryotic cell membranes. Indolicidin was preferentially attracted to the model prokaryotic cell membrane in contrast to the weak adsorption on the eukaryotic membrane. The nature of the indolicidin surface adsorption depended on an electrostatic guiding component, an attractive enthalpic component derived from van der Waals interactions, and a balance between entropic factors related to peptide confinement at the interface and counterion release from the bilayer surface. Thus, whereas we attributed the specificity of the indolicidin/membrane interaction to electrostatics, these interactions were not the sole contributors to the free energy of adsorption. Instead, a balance between an attractive van der Waals enthalpic component and a repulsive entropic component determined the overall strength of indolicidin adsorption.
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Affiliation(s)
- In-Chul Yeh
- Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Materiel Command, Fort Detrick, Maryland, USA.
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239
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Shintani M, Matsuo Y, Sakuraba S, Matubayasi N. Interaction of naphthalene derivatives with lipids in membranes studied by the 1H-nuclear Overhauser effect and molecular dynamics simulation. Phys Chem Chem Phys 2012; 14:14049-60. [DOI: 10.1039/c2cp41984j] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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240
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Schubert T, Schneck E, Tanaka M. First order melting transitions of highly ordered dipalmitoyl phosphatidylcholine gel phase membranes in molecular dynamics simulations with atomistic detail. J Chem Phys 2011; 135:055105. [PMID: 21823736 DOI: 10.1063/1.3615937] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Molecular dynamics simulations with atomistic detail of the gel phase and melting transitions of dipalmitoyl phosphatidylcholine bilayers in water reveal the dependency of many thermodynamic and structural parameters on the initial system ordering. We quantitatively compare different methods to create a gel phase system and we observe that a very high ordering of the gel phase starting system is necessary to observe behavior which reproduces experimental data. We performed heating scans with speeds down to 0.5 K/ns and could observe sharp first order phase transitions. Also, we investigated the transition enthalpy as the natural intrinsic parameter of first order phase transitions, and obtained a quantitative match with experimental values. Furthermore, we performed systematic investigations of the statistical distribution and heating rate dependency of the microscopic phase transition temperature.
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Affiliation(s)
- Thomas Schubert
- Physical Chemistry of Biosystems, Institute of Physical Chemistry, University of Heidelberg, Heidelberg, Germany
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241
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von Deuster CIE, Knecht V. Competing interactions for antimicrobial selectivity based on charge complementarity. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2011; 1808:2867-76. [PMID: 21893025 DOI: 10.1016/j.bbamem.2011.08.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2011] [Revised: 07/29/2011] [Accepted: 08/01/2011] [Indexed: 11/24/2022]
Abstract
Antimicrobial peptides (AMPs) are an evolutionary conserved component of the innate immune system and possible templates for the development of new antibiotics. An important property of antimicrobial peptides is their ability to discriminate bacterial from eucaryotic cells which is attributed to the difference in lipid composition of the outer leaflet of the plasma membrane between the two types of cells. Whereas eucaryotic cells usually expose zwitterionic lipids, procaryotic cells expose also anionic lipids which bind the cationic antimicrobial peptides electrostatically. An example is the antimicrobial peptide NK-2 which is highly cationic and favors binding to anionic membranes. In the present study, the difference in binding affinity of NK-2 for palmitoyl-oleoyl-phosphatidyl-glycerol (POPG) and palmitoyl-oleoyl-phosphatidyl-choline (POPC) is studied using molecular dynamics simulations in conjunction with a coarse grained model and thermodynamic integration, by computing the change in free energy and its components upon the transfer of NK-2 from POPC to POPG. The transfer is indeed found to be highly favorable. Interestingly, the favorable contribution from the electrostatic interaction between the peptide and the anionic lipids is overcompensated by an unfavorable contribution from the change in lipid-cation interactions due to the release of counterions from the lipids. The increase in entropy due to the release of the cations is compensated by other entropic components. The largest favorable contribution arises from the solvation of the counterions. Overall the interaction between NK-2 and POPG is not determined by a single driving force but a subtle balance of competing interactions.
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Affiliation(s)
- Carola I E von Deuster
- Theory and Bio-Systems, Max Planck Institute of Colloids and Interfaces, Potsdam, Germany
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242
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Yeh IC, Wallqvist A. On the proper calculation of electrostatic interactions in solid-supported bilayer systems. J Chem Phys 2011; 134:055109. [DOI: 10.1063/1.3548836] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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243
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Chen R, Poger D, Mark AE. Effect of High Pressure on Fully Hydrated DPPC and POPC Bilayers. J Phys Chem B 2010; 115:1038-44. [DOI: 10.1021/jp110002q] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Rong Chen
- School of Chemistry and Molecular Biosciences and ‡Institute for Molecular Bioscience, The University of Queensland, Brisbane QLD 4072, Australia
| | - David Poger
- School of Chemistry and Molecular Biosciences and ‡Institute for Molecular Bioscience, The University of Queensland, Brisbane QLD 4072, Australia
| | - Alan E. Mark
- School of Chemistry and Molecular Biosciences and ‡Institute for Molecular Bioscience, The University of Queensland, Brisbane QLD 4072, Australia
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244
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Chang Z, Luo Y, Zhang Y, Wei G. Interactions of Aβ25−35 β-Barrel-like Oligomers with Anionic Lipid Bilayer and Resulting Membrane Leakage: An All-Atom Molecular Dynamics Study. J Phys Chem B 2010; 115:1165-74. [DOI: 10.1021/jp107558e] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Zhongwen Chang
- State Key Laboratory of Surface Physics and Department of Physics, Fudan University, 220 Handan Road, Shanghai, 200433, China
| | - Yin Luo
- State Key Laboratory of Surface Physics and Department of Physics, Fudan University, 220 Handan Road, Shanghai, 200433, China
| | - Yun Zhang
- State Key Laboratory of Surface Physics and Department of Physics, Fudan University, 220 Handan Road, Shanghai, 200433, China
| | - Guanghong Wei
- State Key Laboratory of Surface Physics and Department of Physics, Fudan University, 220 Handan Road, Shanghai, 200433, China
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245
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Leftin A, Brown MF. An NMR database for simulations of membrane dynamics. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2010; 1808:818-39. [PMID: 21134351 DOI: 10.1016/j.bbamem.2010.11.027] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2010] [Revised: 11/18/2010] [Accepted: 11/22/2010] [Indexed: 10/18/2022]
Abstract
Computational methods are powerful in capturing the results of experimental studies in terms of force fields that both explain and predict biological structures. Validation of molecular simulations requires comparison with experimental data to test and confirm computational predictions. Here we report a comprehensive database of NMR results for membrane phospholipids with interpretations intended to be accessible by non-NMR specialists. Experimental ¹³C-¹H and ²H NMR segmental order parameters (S(CH) or S(CD)) and spin-lattice (Zeeman) relaxation times (T(1Z)) are summarized in convenient tabular form for various saturated, unsaturated, and biological membrane phospholipids. Segmental order parameters give direct information about bilayer structural properties, including the area per lipid and volumetric hydrocarbon thickness. In addition, relaxation rates provide complementary information about molecular dynamics. Particular attention is paid to the magnetic field dependence (frequency dispersion) of the NMR relaxation rates in terms of various simplified power laws. Model-free reduction of the T(1Z) studies in terms of a power-law formalism shows that the relaxation rates for saturated phosphatidylcholines follow a single frequency-dispersive trend within the MHz regime. We show how analytical models can guide the continued development of atomistic and coarse-grained force fields. Our interpretation suggests that lipid diffusion and collective order fluctuations are implicitly governed by the viscoelastic nature of the liquid-crystalline ensemble. Collective bilayer excitations are emergent over mesoscopic length scales that fall between the molecular and bilayer dimensions, and are important for lipid organization and lipid-protein interactions. Future conceptual advances and theoretical reductions will foster understanding of biomembrane structural dynamics through a synergy of NMR measurements and molecular simulations.
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Affiliation(s)
- Avigdor Leftin
- Department of Chemistry, University of Arizona, Tucson, AZ 85721, USA
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246
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Mojumdar EH, Lyubartsev AP. Molecular dynamics simulations of local anesthetic articaine in a lipid bilayer. Biophys Chem 2010; 153:27-35. [DOI: 10.1016/j.bpc.2010.10.001] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2010] [Revised: 09/30/2010] [Accepted: 10/03/2010] [Indexed: 10/24/2022]
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247
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Fuchs PFJ. Molecular dynamics of membrane peptides and proteins: principles and comparison to experimental data. Methods Mol Biol 2010; 654:403-21. [PMID: 20665278 DOI: 10.1007/978-1-60761-762-4_21] [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] [Indexed: 03/07/2023]
Abstract
Molecular dynamics (MD) simulation is a standard tool used to assess the motion of biomolecules at atomic resolution. It requires a so-called "force field" that allows the evaluation of an empirical energy from the 3D coordinates of the atoms in the system. In this chapter, the application of MD simulations to membrane proteins and peptides is described with a particular emphasis on the comparison of MD results to experimental data. Such a comparison can be used either for (1) validating the results of a simulation, (2) interpreting an experiment at the atomic level, or (3) calibrating the force field. This last step is particularly important for the use of MD as a predictive tool. As an illustration, a comparison of (2)H NMR experiments to MD simulations of a transmembrane peptide is presented and discussed.
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Affiliation(s)
- Patrick F J Fuchs
- Equipe de Bioinformatique Génomique et Moléculaire, INSERM UMR-S726, Institut National de Transfusion Sanguine, Université Paris Diderot - Paris 7, Paris, France.
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248
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249
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Basso LGM, Rodrigues RZ, Naal RMZG, Costa-Filho AJ. Effects of the antimalarial drug primaquine on the dynamic structure of lipid model membranes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2010; 1808:55-64. [PMID: 20713019 DOI: 10.1016/j.bbamem.2010.08.009] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2010] [Revised: 07/28/2010] [Accepted: 08/10/2010] [Indexed: 01/28/2023]
Abstract
Primaquine (PQ) is a potent therapeutic agent used in the treatment of malaria and its mechanism of action still lacks a more detailed understanding at a molecular level. In this context, we used differential scanning calorimetry (DSC), pressure perturbation calorimetry (PPC), and electron spin resonance (ESR) to investigate the effects of PQ on the lipid phase transition, acyl chain dynamics, and on volumetric properties of lipid model membranes. DSC thermograms revealed that PQ stabilizes the fluid phase of the lipid model membranes and interacts mainly with the lipid headgroups. This result was revealed by the great effect on the pretransition of phosphatidylcholines and the destabilization of the inverted hexagonal phase of a phosphatidylethanolamine bilayer. Spin probes located at different positions along the lipid chain were used to monitor different membrane regions. ESR results indicated that PQ is effective in changing the acyl chain ordering and dynamics of the whole chain of dimyristoylphosphatidylcholine (DMPC) phospholipid in the rippled gel phase. The combined ESR and PPC results revealed that the slight DMPC volume changes at the main phase transition induced by the presence of PQ is probably due to a less dense lipid gel phase. At physiological pH, the cationic amphiphilic PQ strongly interacts with the lipid headgroup region of the bilayers, causing considerable disorganization in the hydrophobic core. These results shed light on the molecular mechanism of primaquine-lipid interaction, which may be useful in the understanding of the complex mechanism of action and/or the adverse effects of this antimalarial drug.
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Affiliation(s)
- Luis G M Basso
- Grupo de Biofísica Molecular Sérgio Mascarenhas, Departamento de Física e Informática, Instituto de Física de São Carlos, Universidade de São Paulo, Av. Trabalhador São-carlense 400, C.P. 369, CEP 13560-970, São Carlos, SP, Brazil
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250
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Prakash P, Sankararamakrishnan R. Force field dependence of phospholipid headgroup and acyl chain properties: comparative molecular dynamics simulations of DMPC bilayers. J Comput Chem 2010; 31:266-77. [PMID: 19475632 DOI: 10.1002/jcc.21313] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The reliability of molecular simulations largely depends on the quality of the empirical force field parameters. Force fields used in lipid simulations continue to be improved to enhance the agreement with experiments for a number of different properties. In this work, we have carried out molecular dynamics simulations of neat DMPC bilayers using united-atom Berger force field and three versions of all-atom CHARMM force fields. Three different systems consisting of 48, 72, and 96 lipids were studied. Both particle mesh Ewald (PME) and spherical cut-off schemes were used to evaluate the long-range electrostatic interactions. In total, 21 simulations were carried out and analyzed to find out the dependence of lipid properties on force fields, system size, and schemes to calculate long-range interactions. The acyl chain order parameters calculated from Berger and the recent versions of CHARMM simulations have shown generally good agreement with the experimental results. However, both sets of force fields deviate significantly from the experimentally observed P-C dipolar coupling values for the carbon atoms that link the choline and glycerol groups with the phosphate groups. Significant differences are also observed in several headgroup parameters between CHARMM and Berger simulations. Our results demonstrate that when changes were introduced to improve CHARMM force field using PME scheme, all the headgroup parameters have not been reoptimized. The headgroup properties are likely to play a significant role in lipid-lipid, protein-lipid, and ligand-lipid interactions and hence headgroup parameters in phospholipids require refinement for both Berger and CHARMM force fields.
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Affiliation(s)
- Priyanka Prakash
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh 208016, India
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