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Das D, Bharadwaz P, Mattaparthi VSK. Computational investigation on the effect of the peptidomimetic inhibitors (NPT100-18A and NPT200-11) on the α-synuclein and lipid membrane interactions. J Biomol Struct Dyn 2023:1-12. [PMID: 37768058 DOI: 10.1080/07391102.2023.2262599] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 09/18/2023] [Indexed: 09/29/2023]
Abstract
Parkinson's disease (PD) is associated with α-synuclein (α-Syn), a presynaptic protein that binds to cell membranes. The molecular pathophysiology of PD most likely begins with the binding of α-Syn to membranes. Recently, two peptidomimetic inhibitors (NPT100-18A and NPT200-11) were identified to potentially interact with α-Syn and affect the interaction of α-Syn with the membrane. In this study, the effect of the two peptidomimetic inhibitors on the α-Syn-membrane interaction was demonstrated. DFT calculations were performed for optimization of the two inhibitors, and the nucleophilicity (N) and electrophilicity (ω) of NPT100-18A and NPT200-11 were calculated to be 3.90 and 3.86 (N); 1.06 and 1.04 (ω), respectively. Using the docking tool (CB-dock2), the two α-Syn-peptidomimetic inhibitor complexes (α-Syn-NPT100-18A and α-Syn-NPT200-11) have been prepared. Then all-atom molecular dynamics (MD) simulation was carried out on the α-Syn (control), α-Syn-NPT100-18A and α-Syn-NPT200-11 complex systems in presence of DOPE: DOPS: DOPC (5:3:2) lipid bilayer. From the conformational dynamics analysis, the 3-D structure of α-Syn was found to be stable, and the helices present in the regions (1-37) and (45-95) of α-Syn were found to be retained in the presence of the two peptidomimetic inhibitors. The electron density profile analysis revealed the binding modes of NAC and C-terminal region of α-Syn (in the presence of NPT200-11 inhibitor) with lipid membrane are in the close vicinity from the lipid bilayer centre. Our findings in this study on α-Syn-membrane interactions may be useful for developing a new therapeutic approach for treating PD and other neurodegenerative disorders.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Dorothy Das
- Molecular Modelling and Simulation Laboratory, Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur, Assam, India
| | - Priyam Bharadwaz
- J. Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Prague, Czech Republic
| | - Venkata Satish Kumar Mattaparthi
- Molecular Modelling and Simulation Laboratory, Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur, Assam, India
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2
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Das D, Mattaparthi VSK. Conformational dynamics of A30G α-synuclein that causes familial Parkinson disease. J Biomol Struct Dyn 2023; 41:14702-14714. [PMID: 36961209 DOI: 10.1080/07391102.2023.2193997] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Accepted: 02/25/2023] [Indexed: 03/25/2023]
Abstract
The first gene shown to be responsible for autosomal-dominant Parkinson's disease (PD) is the SNCA gene, which encodes for alpha synuclein (α-Syn). Recently, a novel heterozygous A30G mutation of the SNCA gene associated with familial PD has been reported. However, little research has been done on how the A30G mutation affects the structure of α-Syn. So, using atomistic molecular dynamics (MD) simulation, we demonstrate here the key structural characteristics of A30G α-Syn in the free monomer form and membrane associated state. From the MD trajectory analysis, the structure of A30G α-Syn was noticed to exhibit rapid conformational change, increase in backbone flexibility near the site of mutation and decrease in α-helical propensity. The typical torsion angles in residues (Val26 and Glu28) near the mutation site were observed to deviate significantly in A30G α-Syn. In the case of membrane bound A30G α-Syn, the regions that were submerged in the lipid bilayer (N-helix (3-37) and turn region (38-44)) found to contain higher helical content than the elevated region above the lipid surface. The bending angle in the helix-N and helix-C regions were noticed to be relatively higher in the free form of A30G α-Syn (38.50) than in the membrane bound form (370). The A30G mutation in α-Syn was predicted to have an impact on the stability and function of the protein based on ΔΔG values obtained from the online servers. Our results demonstrate that the A30G mutation in α-Syn altered the protein's α-helical structure and slightly altered the membrane binding.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Dorothy Das
- Molecular Modelling and Simulation Laboratory, Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur, Assam, India
| | - Venkata Satish Kumar Mattaparthi
- Molecular Modelling and Simulation Laboratory, Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur, Assam, India
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3
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Oliveira NF, Machuqueiro M. Novel US-CpHMD Protocol to Study the Protonation-Dependent Mechanism of the ATP/ADP Carrier. J Chem Inf Model 2022; 62:2550-2560. [PMID: 35442654 PMCID: PMC9775199 DOI: 10.1021/acs.jcim.2c00233] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
We have designed a protocol combining constant-pH molecular dynamics (CpHMD) simulations with an umbrella sampling (US) scheme (US-CpHMD) to study the mechanism of ADP/ATP transport (import and export) by their inner mitochondrial membrane carrier protein [ADP/ATP carrier (AAC)]. The US scheme helped overcome the limitations of sampling the slow kinetics involved in these substrates' transport, while CpHMD simulations provided an unprecedented realism by correctly capturing the associated protonation changes. The import of anionic substrates along the mitochondrial membrane has a strong energetic disadvantage due to a smaller substrate concentration and an unfavorable membrane potential. These limitations may have created an evolutionary pressure on AAC to develop specific features benefiting the import of ADP. In our work, the potential of mean force profiles showed a clear selectivity in the import of ADP compared to ATP, while in the export, no selectivity was observed. We also observed that AAC sequestered both substrates at longer distances in the import compared to the export process. Furthermore, only in the import process do we observe transient protonation of both substrates when going through the AAC cavity, which is an important advantage to counteract the unfavorable mitochondrial membrane potential. Finally, we observed a substrate-induced disruption of the matrix salt-bridge network, which can promote the conformational transition (from the C- to M-state) required to complete the import process. This work unraveled several important structural features where the complex electrostatic interactions were pivotal to interpreting the protein function and illustrated the potential of applying the US-CpHMD protocol to other transport processes involving membrane proteins.
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pK a Calculations in Membrane Proteins from Molecular Dynamics Simulations. Methods Mol Biol 2021. [PMID: 34302677 DOI: 10.1007/978-1-0716-1468-6_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/01/2023]
Abstract
The conformational changes of membrane proteins are crucial to their function and usually lead to fluctuations in the electrostatic environment of the protein surface. A very effective way to quantify these changes is by calculating the pK a values of the protein's titratable residues, which can be regarded as electrostatic probes. To achieve this, we need to take advantage of the fast and reliable pK a calculators developed for globular proteins and adapt them to include the explicit effects of membranes. Here, we provide a detailed linear response approximation protocol that uses our own software (PypKa) to calculate reliable pK a values from short MD simulations of membrane proteins.
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Reflectometry and molecular dynamics study of the impact of cholesterol and melatonin on model lipid membranes. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2021; 50:1025-1035. [PMID: 34357445 DOI: 10.1007/s00249-021-01564-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 03/12/2021] [Accepted: 07/30/2021] [Indexed: 10/20/2022]
Abstract
The effect of melatonin and/or cholesterol on the structural properties of a model lipid bilayer prepared from 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) has been investigated both experimentally and via molecular dynamics (MD) simulations. Neutron reflectometry experiments performed with single supported membranes revealed changes in lipid bilayer thickness upon the introduction of additional components. While the presence of cholesterol led to an increase in membrane thickness, the opposite effect was observed in the case of melatonin. The results obtained are in a good agreement with MD simulations which provided further information on the organization of components within the systems examined, indicating a mechanism underlying the membranes' thickness changes due to cholesterol and melatonin that had been observed experimentally. Cholesterol and melatonin preferentially accumulate in different membrane regions, presumably affecting the conformation of lipid hydrophobic moieties differently, and in turn having distinct impacts on the structure of the entire membrane. Our findings may be relevant for understanding the effects of age-related changes in cholesterol and melatonin concentrations, including those in the brains of individuals with Alzheimer's disease.
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Borocci S, Bozzuto G, Bombelli C, Ceccacci F, Formisano G, Stringaro A, Molinari A, Mancini G. How stereochemistry of lipid components can affect lipid organization and the route of liposome internalization into cells. NANOSCALE 2021; 13:11976-11993. [PMID: 34212969 DOI: 10.1039/d1nr02175c] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Though liposome-based drugs are in clinical use, the mechanism of cell internalization of liposomes is yet an object of controversy. The present experimental investigation, carried out on human glioblastoma cells, indicated different internalization routes for two diastereomeric liposomes. Molecular dynamics simulations of the lipid bilayers of the two formulations indicated that the different stereochemistry of a lipid component controls some parameters such as area per lipid molecule and fluidity of lipid membranes, surface potential and water organization at the lipid/water interface, all of which affect the interaction with biomolecules and cell components.
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Affiliation(s)
- Stefano Borocci
- Dipartimento per la Innovazione nei sistemi Biologici, Agroalimentari e Forestali (DIBAF), Università degli Studi della Tuscia, L.go dell'Università, s.n.c., 01100 Viterbo, Italy.
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Kondela T, Dushanov E, Vorobyeva M, Mamatkulov K, Drolle E, Soloviov D, Hrubovčák P, Kholmurodov K, Arzumanyan G, Leonenko Z, Kučerka N. Investigating the competitive effects of cholesterol and melatonin in model lipid membranes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2021; 1863:183651. [PMID: 34023300 DOI: 10.1016/j.bbamem.2021.183651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 05/11/2021] [Accepted: 05/14/2021] [Indexed: 10/21/2022]
Abstract
We have studied the impact of cholesterol and/or melatonin on the static and dynamical properties of bilayers made of DPPC or DOPC utilizing neutron scattering techniques, Raman spectroscopy and molecular dynamics simulations. While differing in the amplitude of the effect due to cholesterol or melatonin when comparing their interactions with the two lipids, their addition ensued recognizable changes to both types of bilayers. As expected, based on the two-component systems of lipid/cholesterol or lipid/melatonin studied previously, we show the impact of cholesterol and melatonin being opposite and competitive in the case of three-component systems of lipid/cholesterol/melatonin. The effect of cholesterol appears to prevail over that of melatonin in the case of structural properties of DPPC-based bilayers, which can be explained by its interactions targeting primarily the saturated lipid chains. The dynamics of hydrocarbon chains represented by the ratio of trans/gauche conformers reveals the competitive effect of cholesterol and melatonin being somewhat more balanced. The additive yet opposing effects of cholesterol and melatonin have been observed also in the case of structural properties of DOPC-based bilayers. We report that cholesterol induced an increase in bilayer thickness, while melatonin induced a decrease in bilayer thickness in the three-component systems of DOPC/cholesterol/melatonin. Commensurately, by evaluating the projected area of DOPC, we demonstrate a lipid area decrease with an increasing concentration of cholesterol, and a lipid area increase with an increasing concentration of melatonin. The demonstrated condensing effect of cholesterol and the fluidizing effect of melatonin appear in an additive manner upon their mutual presence.
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Affiliation(s)
- Tomáš Kondela
- Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, Joliot-Curie 6, Dubna, Moscow Region 141980, Russian Federation; Faculty of Mathematics, Physics and Informatics, Comenius University in Bratislava, Mlynska dolina, Bratislava 842 48, Slovakia
| | - Ermuhammad Dushanov
- Laboratory of Radiation Biology, Joint Institute for Nuclear Research, Joliot-Curie 6, Dubna, Moscow Region 141980, Russian Federation; Department of Biophysics, Dubna State University, Universitetskaya 19, Dubna, Moscow Region 141980, Russian Federation
| | - Maria Vorobyeva
- Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, Joliot-Curie 6, Dubna, Moscow Region 141980, Russian Federation
| | - Kahramon Mamatkulov
- Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, Joliot-Curie 6, Dubna, Moscow Region 141980, Russian Federation
| | - Elizabeth Drolle
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
| | - Dmytro Soloviov
- Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, Joliot-Curie 6, Dubna, Moscow Region 141980, Russian Federation; Faculty of Physics, Taras Shevchenko National University of Kyiv, Hlushkova Ave. 4, Kyiv 03127, Ukraine
| | - Pavol Hrubovčák
- Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, Joliot-Curie 6, Dubna, Moscow Region 141980, Russian Federation; Department of Condensed Matter Physics, P. J. Šafárik University, Park Angelinum 9, Košice 04154, Slovakia
| | - Kholmirzo Kholmurodov
- Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, Joliot-Curie 6, Dubna, Moscow Region 141980, Russian Federation; Department of Chemistry, New Technologies and Materials, Dubna State University, Universitetskaya 19, Dubna, Moscow Region 141980, Russian Federation
| | - Grigory Arzumanyan
- Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, Joliot-Curie 6, Dubna, Moscow Region 141980, Russian Federation
| | - Zoya Leonenko
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada; Department of Physics and Astronomy, University of Waterloo, Waterloo, Ontario, Canada
| | - Norbert Kučerka
- Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, Joliot-Curie 6, Dubna, Moscow Region 141980, Russian Federation; Department of Physical Chemistry of Drugs, Faculty of Pharmacy, Comenius University in Bratislava, Odbojárov 10, Bratislava 832 32, Slovakia.
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8
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Souza LM, Souza FR, Reynaud F, Pimentel AS. Tuning the hydrophobicity of a coarse grained model of 1,2-dipalmitoyl-sn-glycero-3-phosphatidylcholine using the experimental octanol-water partition coefficient. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2020.114132] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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9
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Out of Sight, Out of Mind: The Effect of the Equilibration Protocol on the Structural Ensembles of Charged Glycolipid Bilayers. Molecules 2020; 25:molecules25215120. [PMID: 33158044 PMCID: PMC7663769 DOI: 10.3390/molecules25215120] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 10/28/2020] [Accepted: 10/30/2020] [Indexed: 11/16/2022] Open
Abstract
Molecular dynamics (MD) simulations represent an essential tool in the toolbox of modern chemistry, enabling the prediction of experimental observables for a variety of chemical systems and processes and majorly impacting the study of biological membranes. However, the chemical diversity of complex lipids beyond phospholipids brings new challenges to well-established protocols used in MD simulations of soft matter and requires continuous assessment to ensure simulation reproducibility and minimize unphysical behavior. Lipopolysaccharides (LPS) are highly charged glycolipids whose aggregation in a lamellar arrangement requires the binding of numerous cations to oppositely charged groups deep inside the membrane. The delicate balance between the fully hydrated carbohydrate region and the smaller hydrophobic core makes LPS membranes very sensitive to the choice of equilibration protocol. In this work, we show that the protocol successfully used to equilibrate phospholipid bilayers when applied to complex lipopolysaccharide membranes occasionally leads to a small expansion of the simulation box very early in the equilibration phase. Although the use of a barostat algorithm controls the system dimension and particle distances according to the target pressure, fluctuation in the fleeting pressure occasionally enables a few water molecules to trickle into the hydrophobic region of the membrane, with spurious solvent buildup. We show that this effect stems from the initial steps of NPT equilibration, where initial pressure can be fairly high. This can be solved with the use of a stepwise-thermalization NVT/NPT protocol, as demonstrated for atomistic MD simulations of LPS/DPPE and lipid-A membranes in the presence of different salts using an extension of the GROMOS forcefield within the GROMACS software. This equilibration protocol should be standard procedure for the generation of consistent structural ensembles of charged glycolipids starting from atomic coordinates not previously pre-equilibrated. Although different ways to deal with this issue can be envisioned, we investigated one alternative that could be readily available in major MD engines with general users in mind.
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10
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Tavanti F, Pedone A, Menziani MC, Alexander-Katz A. Computational Insights into the Binding of Monolayer-Capped Gold Nanoparticles onto Amyloid-β Fibrils. ACS Chem Neurosci 2020; 11:3153-3160. [PMID: 32926781 DOI: 10.1021/acschemneuro.0c00497] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Amyloids-β (Aβ) fibrils are involved in several neurodegenerative diseases. In this study, atomistic molecular dynamics simulations have been used to investigate how monolayer-protected gold nanoparticles interact with Aβ(1-40) and Aβ(1-42) fibrils. Our results show that small gold nanoparticles bind with the external side of amyloid-β fibrils that is involved in the fibrillation process. The binding affinity, studied for both kinds of fibrils as a function of the monolayer composition and the nanoparticle diameter, is modulated by hydrophobic interactions and ligand monolayer conformation. Our findings thus show that monolayer-protected nanoparticles are good candidates to prevent fibril aggregation and secondary nucleation or to deliver drugs to specific fibril regions.
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Affiliation(s)
- Francesco Tavanti
- Department of Chemical and Geological Sciences, University of Modena and Reggio Emilia, Via G. Campi, 103, I-41125 Modena, Italy
- CNR-NANO Istituto Nanoscienze, Centro S3, Via Campi 213/A, I-41125 Modena, Italy
| | - Alfonso Pedone
- Department of Chemical and Geological Sciences, University of Modena and Reggio Emilia, Via G. Campi, 103, I-41125 Modena, Italy
| | - Maria Cristina Menziani
- Department of Chemical and Geological Sciences, University of Modena and Reggio Emilia, Via G. Campi, 103, I-41125 Modena, Italy
| | - Alfredo Alexander-Katz
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Massachusetts Avenue, 77, Cambridge, Massachusetts 02142, United States
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Deplazes E, Sarrami F, Poger D. Effect of H3O+ on the Structure and Dynamics of Water at the Interface with Phospholipid Bilayers. J Phys Chem B 2020; 124:1361-1373. [DOI: 10.1021/acs.jpcb.9b10169] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Evelyne Deplazes
- School of Life Sciences, University of Technology Sydney, Ultimo, New South Wales 2007, Australia
- School of Pharmacy and Biomedical Sciences, Curtin Institute for Computation, Curtin University, Perth, Western Australia 6845, Australia
| | - Farzaneh Sarrami
- School of Chemistry and Biochemistry, The University of Western Australia, Perth, Western Australia 6009, Australia
| | - David Poger
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland 4072, Australia
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12
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Wang L, Song Y. Molecular insights into the effect of an apoptotic raft-like bilayer on the conformation and dynamics of calreticulin. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2019; 1862:183146. [PMID: 31816323 DOI: 10.1016/j.bbamem.2019.183146] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 11/29/2019] [Accepted: 12/02/2019] [Indexed: 11/29/2022]
Abstract
Cell surface calreticulin (CRT) can mediate apoptotic cells removal by binding and activating LDL receptor-related protein (LRP1). Phosphatidylserine (PS) lipids in the inner leaflet of the cell membrane are externalized and become exposed in cholesterol (CHOL)-rich membrane raft-like microdomain during apoptosis and co-localized with cell surface CRT. How the apoptotic raft-like membrane microdomain affects the structure and dynamics of CRT, further affecting CRT binding with LRP1 to signal apoptotic-cell clearance, remains unknown. In this study, we investigate the interactions between CRT and raft-like bilayers with or without POPS lipids with molecular dynamics simulations. In addition, the effect of an apoptotic raft bilayer on the binding between CRT and thrombospondin-1 (TSP1), a ligand of CRT on the cell surface to signal focal adhesion disassembly, was also investigated. Results of single CRT interactions with raft-like bilayers show that PS lipids in apoptotic raft-like bilayer increased the interactions between CRT and lipid bilayer, which enhanced the conformational stability and increased dynamical motion of CRT. The microscopic and mesoscopic properties of apoptotic raft-like bilayer were altered by the binding of CRT with lipid bilayer. Results of CRT-TSP1 complex interactions with raft-like bilayers show that the binding free energy between TSP1 and CRT was reduced in apoptotic raft-like bilayer environment. This study provides molecular and structural insight into the effect of an apoptotic raft-like bilayer on the conformation and dynamics of CRT, which could enrich our understanding of CRT-mediated apoptotic-cell clearance and focal adhesion disassembly.
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Affiliation(s)
- Lingyun Wang
- Department of Biomedical Engineering, The University of Alabama at Birmingham, Birmingham, AL 35294, United States
| | - Yuhua Song
- Department of Biomedical Engineering, The University of Alabama at Birmingham, Birmingham, AL 35294, United States.
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13
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Wu X, Chantemargue B, Di Meo F, Bourgaux C, Chapron D, Trouillas P, Rosilio V. Deciphering the Peculiar Behavior of β-Lapachone in Lipid Monolayers and Bilayers. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:14603-14615. [PMID: 31619039 DOI: 10.1021/acs.langmuir.9b02886] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
β-Lapachone (β-Lap) is a promising anticancer drug whose applications have been limited so far because of its poor solubility and stability. Its encapsulation in liposomes has been proposed to overcome these issues. However, surface pressure measurements show that β-Lap exhibits atypical interfacial behavior when mixed with lipids. Although the drug does not seem to be retained in lipid monolayers as deduced from the π-A isotherms, small changes in compressibility moduli suggest that β-Lap actually interacts with lipids, either disorganizing or rigidifying their monolayers. Thermal and structural analyses of lipid bilayers confirm the existence of β-Lap/lipid interactions and show that the drug inserts between hydrophobic chains, close to the polar headgroup in DPPC bilayers and deeper in the acyl chains in POPC bilayers. Molecular dynamics simulations allow a comprehensive description of the drug position and orientation in DOPC and POPC bilayers in the presence or absence of cholesterol.
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Affiliation(s)
- Xiao Wu
- Institut Galien Paris Sud , Univ Paris-Sud, CNRS, Université Paris-Saclay , 92296 Châtenay-Malabry , France
| | - Benjamin Chantemargue
- INSERM U1248, Faculty of Pharmacy , Université de Limoges , 2 rue du Docteur Marcland , 87025 Limoges, Cedex France
- Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science , Palacký University , tr. 17 listopadu 12 , 771 46 Olomouc , Czech Republic
| | - Florent Di Meo
- INSERM U1248, Faculty of Pharmacy , Université de Limoges , 2 rue du Docteur Marcland , 87025 Limoges, Cedex France
| | - Claudie Bourgaux
- Institut Galien Paris Sud , Univ Paris-Sud, CNRS, Université Paris-Saclay , 92296 Châtenay-Malabry , France
| | - David Chapron
- Institut Galien Paris Sud , Univ Paris-Sud, CNRS, Université Paris-Saclay , 92296 Châtenay-Malabry , France
| | - Patrick Trouillas
- INSERM U1248, Faculty of Pharmacy , Université de Limoges , 2 rue du Docteur Marcland , 87025 Limoges, Cedex France
- Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science , Palacký University , tr. 17 listopadu 12 , 771 46 Olomouc , Czech Republic
| | - Véronique Rosilio
- Institut Galien Paris Sud , Univ Paris-Sud, CNRS, Université Paris-Saclay , 92296 Châtenay-Malabry , France
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14
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Shahane G, Ding W, Palaiokostas M, Azevedo HS, Orsi M. Interaction of Antimicrobial Lipopeptides with Bacterial Lipid Bilayers. J Membr Biol 2019; 252:317-329. [PMID: 31098677 PMCID: PMC6790193 DOI: 10.1007/s00232-019-00068-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 05/03/2019] [Indexed: 02/07/2023]
Abstract
The resistance of pathogens to traditional antibiotics is currently a global issue of enormous concern. As the discovery and development of new antibiotics become increasingly challenging, synthetic antimicrobial lipopeptides (AMLPs) are now receiving renewed attention as a new class of antimicrobial agents. In contrast to traditional antibiotics, AMLPs act by physically disrupting the cell membrane (rather than targeting specific proteins), thus reducing the risk of inducing bacterial resistance. In this study, we use microsecond-timescale atomistic molecular dynamics simulations to quantify the interaction of a short AMLP (C16-KKK) with model bacterial lipid bilayers. In particular, we investigate how fundamental transmembrane properties change in relation to a range of lipopeptide concentrations. A number of structural, mechanical, and dynamical features are found to be significantly altered in a non-linear fashion. At 10 mol% concentration, lipopeptides have a condensing effect on bacterial bilayers, characterized by a decrease in the area per lipid and an increase in the bilayer order. Higher AMLP concentrations of 25 and 40 mol% destabilize the membrane by disrupting the bilayer core structure, inducing membrane thinning and water leakage. Important transmembrane properties such as the lateral pressure and dipole potential profiles are also affected. Potential implications on membrane function and associated proteins are discussed.
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Affiliation(s)
- Ganesh Shahane
- Institute of Bioengineering, Queen Mary University of London, Mile End Road, London, E1 4NS, UK
| | - Wei Ding
- School of Engineering & Materials Science, Queen Mary University of London, Mile End Road, London, E1 4NS, UK
| | - Michail Palaiokostas
- School of Engineering & Materials Science, Queen Mary University of London, Mile End Road, London, E1 4NS, UK
| | - Helena S Azevedo
- School of Engineering & Materials Science, Queen Mary University of London, Mile End Road, London, E1 4NS, UK
| | - Mario Orsi
- Department of Applied Sciences, University of the West of England, Coldharbour Lane, Bristol, BS16 1QY, UK.
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Marzuoli I, Margreitter C, Fraternali F. Lipid Head Group Parameterization for GROMOS 54A8: A Consistent Approach with Protein Force Field Description. J Chem Theory Comput 2019; 15:5175-5193. [PMID: 31433640 PMCID: PMC7377650 DOI: 10.1021/acs.jctc.9b00509] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
![]()
Membranes
are a crucial component of both bacterial and mammalian
cells, being involved in signaling, transport, and compartmentalization.
This versatility requires a variety of lipid species to tailor the
membrane’s behavior as needed, increasing the complexity of
the system. Molecular dynamics simulations have been successfully
applied to study model membranes and their interactions with proteins,
elucidating some crucial mechanisms at the atomistic detail and thus
complementing experimental techniques. An accurate description of
the functional interplay of the diverse membrane components crucially
depends on the selected parameters that define the adopted force field.
A coherent parameterization for lipids and proteins is therefore needed.
In this work, we propose and validate new lipid head group parameters
for the GROMOS 54A8 force field, making use of recently published
parametrizations for key chemical moieties present in lipids. We make
use additionally of a new canonical set of partial charges for lipids,
chosen to be consistent with the parameterization of soluble molecules
such as proteins. We test the derived parameters on five phosphocholine
model bilayers, composed of lipid patches four times larger than the
ones used in previous studies, and run 500 ns long simulations of
each system. Reproduction of experimental data like area per lipid
and deuterium order parameters is good and comparable with previous
parameterizations, as well as the description of liquid crystal to
gel-phase transition. On the other hand, the orientational behavior
of the head groups is more realistic for this new parameter set, and
this can be crucial in the description of interactions with other
polar molecules. For that reason, we tested the interaction of the
antimicrobial peptide lactoferricin with two model membranes showing
that the new parameters lead to a weaker peptide–membrane binding
and give a more realistic outcome in comparing binding to antimicrobial
versus mammal membranes.
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Affiliation(s)
- Irene Marzuoli
- Randall Centre for Cell and Molecular Biology , King's College London , London SE1 1UL , U.K
| | - Christian Margreitter
- Randall Centre for Cell and Molecular Biology , King's College London , London SE1 1UL , U.K
| | - Franca Fraternali
- Randall Centre for Cell and Molecular Biology , King's College London , London SE1 1UL , U.K
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16
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Balusek C, Hwang H, Lau CH, Lundquist K, Hazel A, Pavlova A, Lynch DL, Reggio PH, Wang Y, Gumbart JC. Accelerating Membrane Simulations with Hydrogen Mass Repartitioning. J Chem Theory Comput 2019; 15:4673-4686. [PMID: 31265271 PMCID: PMC7271963 DOI: 10.1021/acs.jctc.9b00160] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The time step of atomistic molecular dynamics (MD) simulations is determined by the fastest motions in the system and is typically limited to 2 fs. An increasingly popular approach is to increase the mass of the hydrogen atoms to ∼3 amu and decrease the mass of the parent atom by an equivalent amount. This approach, known as hydrogen-mass repartitioning (HMR), permits time steps up to 4 fs with reasonable simulation stability. While HMR has been applied in many published studies to date, it has not been extensively tested for membrane-containing systems. Here, we compare the results of simulations of a variety of membranes and membrane-protein systems run using a 2 fs time step and a 4 fs time step with HMR. For pure membrane systems, we find almost no difference in structural properties, such as area-per-lipid, electron density profiles, and order parameters, although there are differences in kinetic properties such as the diffusion constant. Conductance through a porin in an applied field, partitioning of a small peptide, hydrogen-bond dynamics, and membrane mixing show very little dependence on HMR and the time step. We also tested a 9 Å cutoff as compared to the standard CHARMM cutoff of 12 Å, finding significant deviations in many properties tested. We conclude that HMR is a valid approach for membrane systems, but a 9 Å cutoff is not.
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Affiliation(s)
| | | | - Chun Hon Lau
- Department of Physics , The Chinese University of Hong Kong , Shatin, NT, Hong Kong , People's Republic of China
| | | | | | | | - Diane L Lynch
- Department of Chemistry and Biochemistry , University of North Carolina , Greensboro , North Carolina 27402 , United States
| | - Patricia H Reggio
- Department of Chemistry and Biochemistry , University of North Carolina , Greensboro , North Carolina 27402 , United States
| | - Yi Wang
- Department of Physics , The Chinese University of Hong Kong , Shatin, NT, Hong Kong , People's Republic of China
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17
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Abstract
Triclosan and chloroxylenol are broad-spectrum biocides used extensively in healthcare and consumer products. They have been suggested to perturb the structure of bacterial membranes, but studies so far have not considered that most bacterial membranes contain large amounts of branched-chain lipids. Here, molecular dynamics simulation is used to examine the effect of the two biocides on membranes consisting of lipids with methyl-branched chains, cyclopropanated chains, and nonbranched chains. It is shown that triclosan and chloroxylenol induced a phase transition in membranes from a liquid-crystalline to a liquid-ordered phase irrespective of the presence and nature of branching groups. At high concentration, chloroxylenol promoted chain interdigitation. Our results suggest that triclosan and chloroxylenol decrease the degree of fluidity of membranes and that this effect is more pronounced in bacterial membranes. As a result, their biocidal activity could be associated with a change in the function of membrane proteins.
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Affiliation(s)
- David Poger
- School of Chemistry & Molecular Biosciences , The University of Queensland , Brisbane QLD 4072 , Australia
| | - Alan E Mark
- School of Chemistry & Molecular Biosciences , The University of Queensland , Brisbane QLD 4072 , Australia
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18
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Van Lehn RC, Alexander-Katz A. Energy landscape for the insertion of amphiphilic nanoparticles into lipid membranes: A computational study. PLoS One 2019; 14:e0209492. [PMID: 30625163 PMCID: PMC6326551 DOI: 10.1371/journal.pone.0209492] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 11/30/2018] [Indexed: 11/19/2022] Open
Abstract
Amphiphilic, monolayer-protected gold nanoparticles (NPs) have been shown to enter cells via a non-endocytic, non-disruptive pathway that could be valuable for biomedical applications. The same NPs were also found to insert into a series of model cell membranes as a precursor to cellular uptake, but the insertion mechanism remains unclear. Previous simulations have demonstrated that an amphiphilic NP can insert into a single leaflet of a planar lipid bilayer, but in this configuration all charged end groups are localized to one side of the bilayer and it is unknown if further insertion is thermodynamically favorable. Here, we use atomistic molecular dynamics simulations to show that an amphiphilic NP can reach the bilayer midplane non-disruptively if charged ligands iteratively "flip" across the bilayer. Ligand flipping is a favorable process that relaxes bilayer curvature, decreases the nonpolar solvent-accessible surface area of the NP monolayer, and increases attractive ligand-lipid electrostatic interactions. Analysis of end group hydration further indicates that iterative ligand flipping can occur on experimentally relevant timescales. Supported by these results, we present a complete energy landscape for the non-disruptive insertion of amphiphilic NPs into lipid bilayers. These findings will help guide the design of NPs to enhance bilayer insertion and non-endocytic cellular uptake, and also provide physical insight into a possible pathway for the translocation of charged biomacromolecules.
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Affiliation(s)
- Reid C. Van Lehn
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Alfredo Alexander-Katz
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States of America
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19
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Silva TFD, Vila-Viçosa D, Reis PBPS, Victor BL, Diem M, Oostenbrink C, Machuqueiro M. The Impact of Using Single Atomistic Long-Range Cutoff Schemes with the GROMOS 54A7 Force Field. J Chem Theory Comput 2018; 14:5823-5833. [DOI: 10.1021/acs.jctc.8b00758] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Tomás F. D. Silva
- Centro de Química e Bioquímica, Departamento de Química e Bioquímica, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
- BioISI - Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Campo Grande, C8 bdg, 1749-016 Lisboa, Portugal
| | - Diogo Vila-Viçosa
- Centro de Química e Bioquímica, Departamento de Química e Bioquímica, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
- BioISI - Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Campo Grande, C8 bdg, 1749-016 Lisboa, Portugal
| | - Pedro B. P. S. Reis
- Centro de Química e Bioquímica, Departamento de Química e Bioquímica, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
- BioISI - Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Campo Grande, C8 bdg, 1749-016 Lisboa, Portugal
| | - Bruno L. Victor
- Centro de Química e Bioquímica, Departamento de Química e Bioquímica, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
| | - Matthias Diem
- Department of Material Sciences and Process Engineering, Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences Vienna, Muthgasse 18, A-1190 Vienna, Austria
| | - Chris Oostenbrink
- Department of Material Sciences and Process Engineering, Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences Vienna, Muthgasse 18, A-1190 Vienna, Austria
| | - Miguel Machuqueiro
- Centro de Química e Bioquímica, Departamento de Química e Bioquímica, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
- BioISI - Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Campo Grande, C8 bdg, 1749-016 Lisboa, Portugal
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20
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The effect of H 3O + on the membrane morphology and hydrogen bonding of a phospholipid bilayer. Biophys Rev 2018; 10:1371-1376. [PMID: 30219992 DOI: 10.1007/s12551-018-0454-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 09/06/2018] [Indexed: 12/30/2022] Open
Abstract
At the 2017 meeting of the Australian Society for Biophysics, we presented the combined results from two recent studies showing how hydronium ions (H3O+) modulate the structure and ion permeability of phospholipid bilayers. In the first study, the impact of H3O+ on lipid packing had been identified using tethered bilayer lipid membranes in conjunction with electrical impedance spectroscopy and neutron reflectometry. The increased presence of H3O+ (i.e. lower pH) led to a significant reduction in membrane conductivity and increased membrane thickness. A first-order explanation for the effect was assigned to alterations in the steric packing of the membrane lipids. Changes in packing were described by a critical packing parameter (CPP) related to the interfacial area and volume and shape of the membrane lipids. We proposed that increasing the concentraton of H3O+ resulted in stronger hydrogen bonding between the phosphate oxygens at the water-lipid interface leading to a reduced area per lipid and slightly increased membrane thickness. At the meeting, a molecular model for these pH effects based on the result of our second study was presented. Multiple μs-long, unrestrained molecular dynamic (MD) simulations of a phosphatidylcholine lipid bilayer were carried out and showed a concentration dependent reduction in the area per lipid and an increase in bilayer thickness, in agreement with experimental data. Further, H3O+ preferentially accumulated at the water-lipid interface, suggesting the localised pH at the membrane surface is much lower than the bulk bathing solution. Another significant finding was that the hydrogen bonds formed by H3O+ ions with lipid headgroup oxygens are, on average, shorter in length and longer-lived than the ones formed in bulk water. In addition, the H3O+ ions resided for longer periods in association with the carbonyl oxygens than with either phosphate oxygen in lipids. In summary, the MD simulations support a model where the hydrogen bonding capacity of H3O+ for carbonyl and phosphate oxygens is the origin of the pH-induced changes in lipid packing in phospholipid membranes. These molecular-level studies are an important step towards a better understanding of the effect of pH on biological membranes.
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21
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Furlan AL, Buchoux S, Miao Y, Banchet V, Létévé M, Lambertyn V, Michel J, Sarazin C, Bonnet V. Nanoparticles based on lipidyl-β-cyclodextrins: synthesis, characterization, and experimental and computational biophysical studies for encapsulation of atazanavir. NEW J CHEM 2018. [DOI: 10.1039/c8nj03237h] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
After showing tensioactive properties of the compounds, the formation, stability and morphology of nanoparticles were demonstrated.
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Affiliation(s)
- Aurélien L. Furlan
- Génie Enzymatique et Cellulaire (GEC)
- UMR 7025 CNRS/Université de Picardie Jules Verne
- 80039 Cedex 1 Amiens
- France
| | - Sébastien Buchoux
- Génie Enzymatique et Cellulaire (GEC)
- UMR 7025 CNRS/Université de Picardie Jules Verne
- 80039 Cedex 1 Amiens
- France
| | - Yong Miao
- Laboratoire de Glycochimie des Antimicrobiens et des Agroressources (LG2A)
- UMR 7378 CNRS/Université de Picardie Jules Verne
- ICP FR3085 CNRS
- 80039 Cedex 1 Amiens
- France
| | - Vincent Banchet
- Laboratoire de Recherche en Nanosciences (LRN)
- EA 4682 Université de Reims Champagne-Ardenne
- 51685 Reims Cedex 2
- France
| | - Mathieu Létévé
- Laboratoire de Glycochimie des Antimicrobiens et des Agroressources (LG2A)
- UMR 7378 CNRS/Université de Picardie Jules Verne
- ICP FR3085 CNRS
- 80039 Cedex 1 Amiens
- France
| | - Virginie Lambertyn
- Génie Enzymatique et Cellulaire (GEC)
- UMR 7025 CNRS/Université de Picardie Jules Verne
- 80039 Cedex 1 Amiens
- France
| | - Jean Michel
- Laboratoire de Recherche en Nanosciences (LRN)
- EA 4682 Université de Reims Champagne-Ardenne
- 51685 Reims Cedex 2
- France
- Plate-forme d’Imagerie Cellulaire et Tissulaire (PICT)
| | - Catherine Sarazin
- Génie Enzymatique et Cellulaire (GEC)
- UMR 7025 CNRS/Université de Picardie Jules Verne
- 80039 Cedex 1 Amiens
- France
| | - Véronique Bonnet
- Laboratoire de Glycochimie des Antimicrobiens et des Agroressources (LG2A)
- UMR 7378 CNRS/Université de Picardie Jules Verne
- ICP FR3085 CNRS
- 80039 Cedex 1 Amiens
- France
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22
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Deplazes E, Poger D, Cornell B, Cranfield CG. The effect of hydronium ions on the structure of phospholipid membranes. Phys Chem Chem Phys 2018; 20:357-366. [DOI: 10.1039/c7cp06776c] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
This work studies the mechanisms by which hydronium ions modulate the structure of phospholipid bilayers.
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Affiliation(s)
- Evelyne Deplazes
- School of Biomedical Sciences
- Curtin Health Innovation Research Institute and Curtin Institute for Computation
- Curtin University
- Perth
- Australia
| | - David Poger
- School of Chemistry and Molecular Biosciences
- The University of Queensland
- Brisbane
- Australia
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23
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Piggot TJ, Allison JR, Sessions RB, Essex JW. On the Calculation of Acyl Chain Order Parameters from Lipid Simulations. J Chem Theory Comput 2017; 13:5683-5696. [PMID: 28876925 DOI: 10.1021/acs.jctc.7b00643] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
For molecular dynamics simulations of biological membrane systems to live up to the potential of providing accurate atomic level detail into membrane properties and functions, it is essential that the force fields used to model such systems are as accurate as possible. One membrane property that is often used to assess force field accuracy is the carbon-hydrogen (or carbon-deuterium) order parameters of the lipid tails, which can be accurately measured using experimental NMR techniques. There are a variety of analysis tools available to calculate these order parameters from simulations and it is essential that these computational tools work correctly to ensure the accurate assessment of the simulation force fields. In this work we compare many of these computational tools for calculating the order parameters of POPC membranes. While tools that work on all-atom systems and tools that work on saturated lipid tails in general work extremely well, we demonstrate that the majority of the tested tools that calculate the order parameters for unsaturated united-atom lipid tails do so incorrectly. We identify tools that do perform accurate calculations and include one such program with this work, enabling rapid and accurate calculation of united-atom lipid order parameters. Furthermore, we discuss cases in which it is nontrivial to appropriately predict the unsaturated carbon order parameters in united-atom systems. Finally, we examine order parameter splitting for carbon 2 in sn-2 lipid chains, demonstrating substantial deviations from experimental values in several all-atom and united-atom lipid force fields.
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Affiliation(s)
- Thomas J Piggot
- Chemical, Biological and Radiological Sciences, Defence Science and Technology Laboratory , Porton Down, Salisbury, Wiltshire SP4 0JQ, U.K.,Chemistry, University of Southampton , Highfield, Southampton SO17 1BJ, U.K
| | - Jane R Allison
- Centre for Theoretical Chemistry and Physics, Institute of Natural and Mathematical Sciences, Massey University , Auckland 0632, New Zealand
| | - Richard B Sessions
- School of Biochemistry, University of Bristol , University Walk, Bristol BS8 1TD, U.K
| | - Jonathan W Essex
- Chemistry, University of Southampton , Highfield, Southampton SO17 1BJ, U.K
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24
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da Cunha AR, Duarte EL, Stassen H, Lamy MT, Coutinho K. Experimental and theoretical studies of emodin interacting with a lipid bilayer of DMPC. Biophys Rev 2017; 9:729-745. [PMID: 28940105 DOI: 10.1007/s12551-017-0323-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 08/29/2017] [Indexed: 12/23/2022] Open
Abstract
Emodin is one of the most abundant anthraquinone derivatives found in nature. It is the active principle of some traditional herbal medicines with known biological activities. In this work, we combined experimental and theoretical studies to reveal information about location, orientation, interaction and perturbing effects of Emodin on lipid bilayers, where we have taken into account the neutral form of the Emodin (EMH) and its anionic/deprotonated form (EM-). Using both UV/Visible spectrophotometric techniques and molecular dynamics (MD) simulations, we showed that both EMH and EM- are located in a lipid membrane. Additionally, using MD simulations, we revealed that both forms of Emodin are very close to glycerol groups of the lipid molecules, with the EMH inserted more deeply into the bilayer and more disoriented relative to the normal of the membrane when compared with the EM-, which is more exposed to interfacial water. Analysis of several structural properties of acyl chains of the lipids in a hydrated pure DMPC bilayer and in the presence of Emodin revealed that both EMH and EM- affect the lipid bilayer, resulting in a remarkable disorder of the bilayer in the vicinity of the Emodin. However, the disorder caused by EMH is weaker than that caused by EM-. Our results suggest that these disorders caused by Emodin might lead to distinct effects on lipid bilayers including its disruption which are reported in the literature.
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Affiliation(s)
- Antonio R da Cunha
- Universidade Federal do Maranhão, UFMA, Campus Balsas, Maranhão, 06500-000, Brazil.,Instituto de Física da Universidade de São Paulo, 05508-090, Cidade Universitária, São Paulo, Brazil
| | - Evandro L Duarte
- Instituto de Física da Universidade de São Paulo, 05508-090, Cidade Universitária, São Paulo, Brazil
| | - Hubert Stassen
- Grupo de Química Teórica, Instituto de Química, UFRGS, Av. Bento Gonçalves 9500, Porto Alegre, 91540-000, Brazil
| | - M Teresa Lamy
- Instituto de Física da Universidade de São Paulo, 05508-090, Cidade Universitária, São Paulo, Brazil
| | - Kaline Coutinho
- Instituto de Física da Universidade de São Paulo, 05508-090, Cidade Universitária, São Paulo, Brazil.
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25
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Isabettini S, Massabni S, Kohlbrecher J, Schuler LD, Walde P, Sturm M, Windhab EJ, Fischer P, Kuster S. Understanding the Enhanced Magnetic Response of Aminocholesterol Doped Lanthanide-Ion-Chelating Phospholipid Bicelles. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:8533-8544. [PMID: 28759249 DOI: 10.1021/acs.langmuir.7b01370] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Cholesterol (Chol-OH) and its conjugates are powerful molecules for engineering the physicochemical and magnetic properties of phospholipid bilayers in bicelles. Introduction of aminocholesterol (3β-amino-5-cholestene, Chol-NH2) in bicelles composed of 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) and the thulium-ion-chelating phospholipid 1,2-dimyristoyl-sn-glycero-3-phospho-ethanolamine-diethylene triaminepentaacetate (DMPE-DTPA/Tm3+) results in unprecedented high magnetic alignments by selectively tuning the magnetic susceptibility Δχ of the bilayer. However, little is known on the underlying mechanisms behind the magnetic response and, more generally, on the physicochemical forces governing a Chol-NH2 doped DMPC bilayer. We tackled this shortcoming with a multiscale bottom-up comparative investigation of Chol-OH and Chol-NH2 mixed with DMPC. First, simplified monolayer models on a Langmuir trough were employed to compare the two steroid molecules at various contents in DMPC. In a second step, a molecular dynamics (MD) simulation allowed for a more representative model of the bicelle bilayer while monitoring the amphiphiles and their interactions on the molecular level. In a final step, we moved away from the models and investigated the effect of temperature on the structure and magnetic alignment of Chol-NH2 doped bicelles by SANS. The DMPC/steroid monolayer studies showed that Chol-OH induces a larger condensation effect than Chol-NH2 at steroid contents of 16 and 20 mol %. However, this tendency was inversed at steroid contents of 10, 30, and 40 mol %. Although the MD simulation with 16 mol % steroid revealed that both compounds induce a liquid-ordered state in DMPC, the bilayer containing Chol-NH2 was much less ordered than the analogous system containing Chol-OH. Chol-NH2 underwent significantly more hydrogen bonding interactions with neighboring DMPC lipids than Chol-OH. It seems that, by altering the dynamics of the hydrophilic environment of the bicelle, Chol-NH2 changes the crystal field and angle of the phospholipid-lanthanide DMPE-DTPA/Tm3+ complex. These parameters largely determine the magnetic susceptibility Δχ of the complex, explaining the SANS results, which show significant differences in magnetic alignment of the steroid doped bicelles. Highly magnetically alignable DMPC/Chol-NH2/DMPE-DTPA/Tm3+ (molar ratio 16:4:5:5) bicelles were achieved up to temperatures of 35 °C before a thermoreversible rearrangement into nonalignable vesicles occurred. The results confirm the potential of Chol-NH2 doped bicelles to act as building blocks for the development of the magnetically responsive soft materials of tomorrow.
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Affiliation(s)
- Stéphane Isabettini
- Laboratory of Food Process Engineering, ETH Zürich , Schmelzbergstrasse 9, 8092 Zürich, Switzerland
| | - Sarah Massabni
- Laboratory of Food Process Engineering, ETH Zürich , Schmelzbergstrasse 9, 8092 Zürich, Switzerland
| | - Joachim Kohlbrecher
- Laboratory for Neutron Scattering and Imaging, Paul Scherrer Institute , 5232 Villigen PSI, Switzerland
| | | | - Peter Walde
- Department of Materials, ETH Zürich , Vladimir-Prelog-Weg 5, 8093 Zürich, Switzerland
| | - Marina Sturm
- Max Planck Institute of Colloids and Interfaces , Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Erich J Windhab
- Laboratory of Food Process Engineering, ETH Zürich , Schmelzbergstrasse 9, 8092 Zürich, Switzerland
| | - Peter Fischer
- Laboratory of Food Process Engineering, ETH Zürich , Schmelzbergstrasse 9, 8092 Zürich, Switzerland
| | - Simon Kuster
- Laboratory of Food Process Engineering, ETH Zürich , Schmelzbergstrasse 9, 8092 Zürich, Switzerland
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26
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Li H, Chowdhary J, Huang L, He X, MacKerell AD, Roux B. Drude Polarizable Force Field for Molecular Dynamics Simulations of Saturated and Unsaturated Zwitterionic Lipids. J Chem Theory Comput 2017; 13:4535-4552. [PMID: 28731702 DOI: 10.1021/acs.jctc.7b00262] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Additive force fields are designed to account for induced electronic polarization in a mean-field average way, using effective empirical fixed charges. The limitation of this approximation is cause for serious concerns, particularly in the case of lipid membranes, where the molecular environment undergoes dramatic variations over microscopic length scales. A polarizable force field based on the classical Drude oscillator offers a practical and computationally efficient framework for an improved representation of electrostatic interactions in molecular simulations. Building on the first-generation Drude polarizable force field for the dipalmitoylphosphatidylcholine 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) molecule, the present effort was undertaken to improve this initial model and expand the force field to a wider range of phospholipid molecules. New lipids parametrized include dimyristoylphosphatidylcholine (DMPC), dilauroylphosphatidylcholine (DLPC), 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC), 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC), dipalmitoylphosphatidylethanolamine (DPPE), 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine (POPE), and 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine (DOPE). The iterative optimization protocol employed in this effort led to lipid models that achieve a good balance between reproducing quantum mechanical data on model compound representative of phospholipids and reproducing a range of experimental condensed phase properties of bilayers. A parametrization strategy based on a restrained ensemble-maximum entropy methodology was used to help accurately match the experimental NMR order parameters in the polar headgroup region. All the parameters were developed to be compatible with the remainder of the Drude polarizable force field, which includes water, ions, proteins, DNA, and selected carbohydrates.
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Affiliation(s)
- Hui Li
- Department of Biochemistry and Molecular Biology, Gordon Center for Integrative Science, University of Chicago , Chicago, Illinois 60637, United States
| | - Janamejaya Chowdhary
- Department of Biochemistry and Molecular Biology, Gordon Center for Integrative Science, University of Chicago , Chicago, Illinois 60637, United States
| | - Lei Huang
- Department of Biochemistry and Molecular Biology, Gordon Center for Integrative Science, University of Chicago , Chicago, Illinois 60637, United States
| | - Xibing He
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore , Baltimore, Maryland 21201, United States
| | - Alexander D MacKerell
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore , Baltimore, Maryland 21201, United States
| | - Benoît Roux
- Department of Biochemistry and Molecular Biology, Gordon Center for Integrative Science, University of Chicago , Chicago, Illinois 60637, United States
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27
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Reißer S, Poger D, Stroet M, Mark AE. Real Cost of Speed: The Effect of a Time-Saving Multiple-Time-Stepping Algorithm on the Accuracy of Molecular Dynamics Simulations. J Chem Theory Comput 2017; 13:2367-2372. [DOI: 10.1021/acs.jctc.7b00178] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Sabine Reißer
- Institute
of Biological Interfaces (IBG-2) and ‡Department of Theoretical Chemical
Biology, Institute of Physical Chemistry, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
- School of Chemistry and Molecular Biosciences and §Institute for Molecular
Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - David Poger
- Institute
of Biological Interfaces (IBG-2) and ‡Department of Theoretical Chemical
Biology, Institute of Physical Chemistry, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
- School of Chemistry and Molecular Biosciences and §Institute for Molecular
Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Martin Stroet
- Institute
of Biological Interfaces (IBG-2) and ‡Department of Theoretical Chemical
Biology, Institute of Physical Chemistry, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
- School of Chemistry and Molecular Biosciences and §Institute for Molecular
Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Alan E. Mark
- Institute
of Biological Interfaces (IBG-2) and ‡Department of Theoretical Chemical
Biology, Institute of Physical Chemistry, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
- School of Chemistry and Molecular Biosciences and §Institute for Molecular
Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
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28
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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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29
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Jia Z, Whitaker SK, Tomich JM, Chen J. Organization and Structure of Branched Amphipathic Oligopeptide Bilayers. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:9883-91. [PMID: 27584835 PMCID: PMC5039110 DOI: 10.1021/acs.langmuir.6b02421] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
A class of self-assembling branched amphiphilic peptide capsules (BAPCs) was recently developed that could serve as a new drug delivery vehicle. BAPCs can encapsulate solutes up to ∼12 kDa during assembly, are unusually stable, and are readily taken up by cells with low cytotoxicity. Coarse-grained simulations have supported that BAPCs are defined by bilayers that resemble those formed by diacyl phospholipids. Here, atomistic simulations were performed to characterize the structure and organization of bilayers formed by three branched amphiphilic peptides (BAPs): bis(Ac-FLIVIGSII)-K-K4-CO-NH2, bis(Ac-CHA-LIVIGSII)-K-K4-CO-NH2, and bis(Ac-FLIVI)-K-K4-CO-NH2. The results show BAPs form a network of intra- and intermolecular backbone hydrogen bonds within the same leaflet in addition to hydrophobic side-chain interactions. The terminal residues of two leaflets form an interdigitation region locking two leaflets together. The phenyl groups in bis(Ac-FLIVIGSII)-K-K4-CO-NH2 and bis(Ac-FLIVI)-K-K4-CO-NH2 are tightly packed near the bilayer center but do not formed ordered structures with specific π-π stacking. Replacing phenyl groups with the cyclohexane side chain only slightly increases the level of disorder in bilayer structures and thus should not significantly affect the stability, consistent with experimental results on bis(Ac-CHA-LIVIGSII)-K-K4-CO-NH2 BAPCs. Self-assembly simulations further suggest that leaflet interdigitation likely occurs at early stages of BAPC formation. Atomistic simulations also reveal that the BAPC bilayers are highly permeable to water. This prediction was validated using fluorescence measurements of encapsulated self-quenching dye upon transferring BAPCs to buffers with different salt concentrations. Improved understanding of the organization and structure of BAPC bilayers at the atomic level will provide a basis for future rational modifications of BAP sequence to improve BAPC properties as a new class of delivery vehicle.
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Affiliation(s)
| | | | | | - Jianhan Chen
- Corresponding Author: Phone: (785) 532-2518; Fax: (785) 532-7278;
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30
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Poger D, Caron B, Mark AE. Validating lipid force fields against experimental data: Progress, challenges and perspectives. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:1556-65. [DOI: 10.1016/j.bbamem.2016.01.029] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Revised: 01/07/2016] [Accepted: 01/27/2016] [Indexed: 01/16/2023]
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31
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Henriques ST, Deplazes E, Lawrence N, Cheneval O, Chaousis S, Inserra M, Thongyoo P, King GF, Mark AE, Vetter I, Craik DJ, Schroeder CI. Interaction of Tarantula Venom Peptide ProTx-II with Lipid Membranes Is a Prerequisite for Its Inhibition of Human Voltage-gated Sodium Channel NaV1.7. J Biol Chem 2016; 291:17049-65. [PMID: 27311819 DOI: 10.1074/jbc.m116.729095] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Indexed: 12/11/2022] Open
Abstract
ProTx-II is a disulfide-rich peptide toxin from tarantula venom able to inhibit the human voltage-gated sodium channel 1.7 (hNaV1.7), a channel reported to be involved in nociception, and thus it might have potential as a pain therapeutic. ProTx-II acts by binding to the membrane-embedded voltage sensor domain of hNaV1.7, but the precise peptide channel-binding site and the importance of membrane binding on the inhibitory activity of ProTx-II remain unknown. In this study, we examined the structure and membrane-binding properties of ProTx-II and several analogues using NMR spectroscopy, surface plasmon resonance, fluorescence spectroscopy, and molecular dynamics simulations. Our results show a direct correlation between ProTx-II membrane binding affinity and its potency as an hNaV1.7 channel inhibitor. The data support a model whereby a hydrophobic patch on the ProTx-II surface anchors the molecule at the cell surface in a position that optimizes interaction of the peptide with the binding site on the voltage sensor domain. This is the first study to demonstrate that binding of ProTx-II to the lipid membrane is directly linked to its potency as an hNaV1.7 channel inhibitor.
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Affiliation(s)
| | - Evelyne Deplazes
- From the Institute for Molecular Bioscience and School of Chemistry and Molecular Biosciences, University of Queensland, Queensland 4072 and
| | | | | | | | | | | | | | - Alan E Mark
- From the Institute for Molecular Bioscience and School of Chemistry and Molecular Biosciences, University of Queensland, Queensland 4072 and
| | - Irina Vetter
- From the Institute for Molecular Bioscience and the School of Pharmacy, University of Queensland, Queensland 4102, Australia
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32
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Eleftheriou K, Sideratou Z, Thanassoulas A, Papakyriakou A, Tsiourvas D. Comparative Experimental and Computational Study of Monoalkyl Chain Phosphatidylcholine-Containing Thermoresponsive Liposomes. J Phys Chem B 2016; 120:5417-28. [PMID: 27280363 DOI: 10.1021/acs.jpcb.6b02783] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Liposomes containing lysophospholipids are intensively studied as drug delivery systems that are stable at normal body temperature but exhibit fast release of their drug load at slightly elevated temperatures. In this study, the stability and release properties of dipalmitoylglycerophosphocholine (DPPC)-based liposomes incorporating the commonly used lysophosphatidylocholine (lyso-PC), and a series of monoalkyl chain ether-linked phosphatidylcholine, i.e., the biologically relevant monoalkyl chain platelet activating factor (PAF) and its derivatives lyso-PAF and methyl-PAF, were investigated. To this end a series of PEGylated small unilamellar liposomes with DPPC:monoalkyl lipid compositions of 5% and 10% molar ratio were prepared and compared with regard to stability (37 °C) and release properties at elevated temperatures (38-43 °C). All systems were characterized with respect to size distribution, ζ-potential, and phase transition characteristics. The presence of ether-lipids endows liposomes with superior (∼10% increase) release properties at 5% incorporation compared to lyso-PC, while at 10% molar ratio the formulations do not differ significantly, the release being close to 90%. The findings are supported by atomistic molecular dynamics simulations that suggest a correlation between the enhanced permeability and increased penetration of water molecules within the bilayers with density fluctuations resulting from the increased area-per-lipid and the disorder of the lysolipids alkyl chains.
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Affiliation(s)
- Kleopatra Eleftheriou
- Institute of Nanoscience and Nanotechology, NCSR ''Demokritos" , 15310 Aghia Paraskevi, Attiki, Greece
| | - Zili Sideratou
- Institute of Nanoscience and Nanotechology, NCSR ''Demokritos" , 15310 Aghia Paraskevi, Attiki, Greece
| | - Angelos Thanassoulas
- Institute of Nuclear & Radiological Sciences and Technology, Energy & Safety, NCSR ''Demokritos" , 15310 Aghia Paraskevi, Attiki, Greece
| | - Athanasios Papakyriakou
- Institute of Nanoscience and Nanotechology, NCSR ''Demokritos" , 15310 Aghia Paraskevi, Attiki, Greece
| | - Dimitris Tsiourvas
- Institute of Nanoscience and Nanotechology, NCSR ''Demokritos" , 15310 Aghia Paraskevi, Attiki, Greece
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33
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Pineda De Castro LF, Dopson M, Friedman R. Biological Membranes in Extreme Conditions: Simulations of Anionic Archaeal Tetraether Lipid Membranes. PLoS One 2016; 11:e0155287. [PMID: 27167213 PMCID: PMC4864297 DOI: 10.1371/journal.pone.0155287] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Accepted: 03/29/2016] [Indexed: 01/25/2023] Open
Abstract
In contrast to the majority of organisms that have cells bound by di-ester phospholipids, archaeal membranes consist of di- and tetraether phospholipids. Originating from organisms that withstand harsh conditions (e.g., low pH and a wide range of temperatures) such membranes have physical properties that make them attractive materials for biological research and biotechnological applications. We developed force-field parameters based on the widely used Generalized Amber Force Field (GAFF) to enable the study of anionic tetraether membranes of the model archaean Sulfolobus acidocaldarius by computer simulations. The simulations reveal that the physical properties of these unique membranes depend on the number of cyclopentane rings included in each lipid unit, and on the size of cations that are used to ensure charge neutrality. This suggests that the biophysical properties of Sulfolobus acidocaldarius cells depend not only on the compositions of their membranes but also on the media in which they grow.
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Affiliation(s)
- Luis Felipe Pineda De Castro
- Computational Chemistry and Biochemistry research Group (CCBG), Department of Chemistry and Biomedical Sciences, Linnæus University, 391 82 Kalmar, Sweden
- Centre of Excellence “Biomaterials Chemistry”, Linnæus University, 391 82 Kalmar, Sweden
| | - Mark Dopson
- Systems Biology of Microorganisms Research Group (SBMR), Centre for Ecology and Evolution in Microbial model Systems (EEMiS), Linnæus University, 391 82 Kalmar, Sweden
| | - Ran Friedman
- Computational Chemistry and Biochemistry research Group (CCBG), Department of Chemistry and Biomedical Sciences, Linnæus University, 391 82 Kalmar, Sweden
- Centre of Excellence “Biomaterials Chemistry”, Linnæus University, 391 82 Kalmar, Sweden
- * E-mail:
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34
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Identification of novel natural compound inhibitors for human complement component 5a receptor by homology modeling and virtual screening. Med Chem Res 2016; 25:1564-1573. [PMID: 27499603 PMCID: PMC4958400 DOI: 10.1007/s00044-016-1591-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Accepted: 04/25/2016] [Indexed: 01/09/2023]
Abstract
Abstract Neuropathic pain and inflammatory pain are two common types of pathological pain in human health problems. To date, normal painkillers are only partially effective in treating such pain, leading to a tremendous demand to develop new chemical entities to combat pain and inflammation. A promising pharmacological treatment is to control signal transduction via the inflammatory mediator-coupled receptor protein C5aR by finding antagonists to inhibit C5aR activation. Here, we report the first computational study on the identification of non-peptide natural compound inhibitors for C5aR by homology modeling and virtual screening. Our study revealed a novel natural compound inhibitor Acteoside with better docking scores than all four existing non-peptidic natural compounds. The MM-GBSA binding free energy calculations confirmed that Acteoside has a decrease of ~39 kcal/mol in the free energy of binding compared to the strongest binding reference compound. Main contributions to the higher affinity of Acteoside to C5aR are the exceptionally strong lipophilic interaction, enhanced electrostatics and hydrogen bond interactions. Detailed analysis on the physiochemical properties of Acteoside suggests further directions in lead optimization. Taken together, our study proposes that Acteoside is a potential lead molecule targeting the C5aR allosteric site and provides helpful information for further experimental studies. Graphical Abstract ![]()
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35
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Pluhackova K, Kirsch SA, Han J, Sun L, Jiang Z, Unruh T, Böckmann RA. A Critical Comparison of Biomembrane Force Fields: Structure and Dynamics of Model DMPC, POPC, and POPE Bilayers. J Phys Chem B 2016; 120:3888-903. [DOI: 10.1021/acs.jpcb.6b01870] [Citation(s) in RCA: 107] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Kristyna Pluhackova
- Computational
Biology, Department of Biology, Friedrich-Alexander-University of Erlangen-Nürnberg, Staudtstr. 5, 91058 Erlangen, Germany
| | - Sonja A. Kirsch
- Computational
Biology, Department of Biology, Friedrich-Alexander-University of Erlangen-Nürnberg, Staudtstr. 5, 91058 Erlangen, Germany
| | - Jing Han
- Computational
Biology, Department of Biology, Friedrich-Alexander-University of Erlangen-Nürnberg, Staudtstr. 5, 91058 Erlangen, Germany
| | - Liping Sun
- Computational
Biology, Department of Biology, Friedrich-Alexander-University of Erlangen-Nürnberg, Staudtstr. 5, 91058 Erlangen, Germany
| | - Zhenyan Jiang
- Computational
Biology, Department of Biology, Friedrich-Alexander-University of Erlangen-Nürnberg, Staudtstr. 5, 91058 Erlangen, Germany
| | - Tobias Unruh
- Lehrstuhl
für Kristallografie und Strukturphysik, Department Physik, Friedrich-Alexander-University of Erlangen-Nürnberg, Staudtstr. 3, 91058 Erlangen, Germany
| | - Rainer A. Böckmann
- Computational
Biology, Department of Biology, Friedrich-Alexander-University of Erlangen-Nürnberg, Staudtstr. 5, 91058 Erlangen, Germany
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36
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Deplazes E, Henriques ST, Smith JJ, King GF, Craik DJ, Mark AE, Schroeder CI. Membrane-binding properties of gating modifier and pore-blocking toxins: Membrane interaction is not a prerequisite for modification of channel gating. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:872-82. [DOI: 10.1016/j.bbamem.2016.02.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Revised: 01/21/2016] [Accepted: 02/01/2016] [Indexed: 12/30/2022]
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37
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Subramanian N, Schumann-Gillett A, Mark AE, O'Mara ML. Understanding the accumulation of P-glycoprotein substrates within cells: The effect of cholesterol on membrane partitioning. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:776-82. [DOI: 10.1016/j.bbamem.2015.12.025] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Revised: 11/18/2015] [Accepted: 12/21/2015] [Indexed: 11/25/2022]
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38
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Tahir MA, Van Lehn RC, Choi SH, Alexander-Katz A. Solvent-exposed lipid tail protrusions depend on lipid membrane composition and curvature. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:1207-15. [PMID: 26828121 DOI: 10.1016/j.bbamem.2016.01.026] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Revised: 01/20/2016] [Accepted: 01/27/2016] [Indexed: 10/22/2022]
Abstract
The stochastic protrusion of hydrophobic lipid tails into solution, a subclass of hydrophobic membrane defects, has recently been shown to be a critical step in a number of biological processes like membrane fusion. Understanding the factors that govern the appearance of lipid tail protrusions is critical for identifying membrane features that affect the rate of fusion or other processes that depend on contact with solvent-exposed lipid tails. In this work, we utilize atomistic molecular dynamics simulations to characterize the likelihood of tail protrusions in phosphotidylcholine lipid bilayers of varying composition, curvature, and hydration. We distinguish two protrusion modes corresponding to atoms near the end of the lipid tail or near the glycerol group. Through potential of mean force calculations, we demonstrate that the thermodynamic cost for inducing a protrusion depends on tail saturation but is insensitive to other bilayer structural properties or hydration above a threshold value. Similarly, highly curved vesicles or micelles increase both the overall frequency of lipid tail protrusions as well as the preference for splay protrusions, both of which play an important role in driving membrane fusion. In multi-component bilayers, however, the incidence of protrusion events does not clearly depend on the mismatch between tail length or tail saturation of the constituent lipids. Together, these results provide significant physical insight into how system components might affect the appearance of protrusions in biological membranes, and help explain the roles of composition or curvature-modifying proteins in membrane fusion.
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Affiliation(s)
- Mukarram A Tahir
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Reid C Van Lehn
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - S H Choi
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Alfredo Alexander-Katz
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
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39
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Maximally asymmetric transbilayer distribution of anionic lipids alters the structure and interaction with lipids of an amyloidogenic protein dimer bound to the membrane surface. Chem Phys Lipids 2016; 196:33-51. [PMID: 26827904 DOI: 10.1016/j.chemphyslip.2016.01.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2015] [Revised: 01/13/2016] [Accepted: 01/14/2016] [Indexed: 12/23/2022]
Abstract
We used molecular dynamics simulations to explore the effects of asymmetric transbilayer distribution of anionic phosphatidylserine (PS) lipids on the structure of a protein on the membrane surface and subsequent protein-lipid interactions. Our simulation systems consisted of an amyloidogenic, beta-sheet rich dimeric protein (D42) absorbed to the phosphatidylcholine (PC) leaflet, or protein-contact PC leaflet, of two membrane systems: a single-component PC bilayer and double PC/PS bilayers. The latter comprised of a stable but asymmetric transbilayer distribution of PS in the presence of counterions, with a 1-component PC leaflet coupled to a 1-component PS leaflet in each bilayer. The maximally asymmetric PC/PS bilayer had a non-zero transmembrane potential (TMP) difference and higher lipid order packing, whereas the symmetric PC bilayer had a zero TMP difference and lower lipid order packing under physiologically relevant conditions. Analysis of the adsorbed protein structures revealed weaker protein binding, more folding in the N-terminal domain, more aggregation of the N- and C-terminal domains and larger tilt angle of D42 on the PC leaflet surface of the PC/PS bilayer versus the PC bilayer. Also, analysis of protein-induced membrane structural disruption revealed more localized bilayer thinning in the PC/PS versus PC bilayer. Although the electric field profile in the non-protein-contact PS leaflet of the PC/PS bilayer differed significantly from that in the non-protein-contact PC leaflet of the PC bilayer, no significant difference in the electric field profile in the protein-contact PC leaflet of either bilayer was evident. We speculate that lipid packing has a larger effect on the surface adsorbed protein structure than the electric field for a maximally asymmetric PC/PS bilayer. Our results support the mechanism that the higher lipid packing in a lipid leaflet promotes stronger protein-protein but weaker protein-lipid interactions for a dimeric protein on membrane surfaces.
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40
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Atomistic resolution structure and dynamics of lipid bilayers in simulations and experiments. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:2512-2528. [PMID: 26809025 DOI: 10.1016/j.bbamem.2016.01.019] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Revised: 01/15/2016] [Accepted: 01/19/2016] [Indexed: 01/18/2023]
Abstract
Accurate details on the sampled atomistic resolution structures of lipid bilayers can be experimentally obtained by measuring C-H bond order parameters, spin relaxation rates and scattering form factors. These parameters can be also directly calculated from the classical atomistic resolution molecular dynamics simulations (MD) and compared to the experimentally achieved results. This comparison measures the simulation model quality with respect to 'reality'. If agreement is sufficient, the simulation model gives an atomistic structural interpretation of the acquired experimental data. Significant advance of MD models is made by jointly interpreting different experiments using the same structural model. Here we focus on phosphatidylcholine lipid bilayers, which out of all model membranes have been studied mostly by experiments and simulations, leading to the largest available dataset. From the applied comparisons we conclude that the acyl chain region structure and rotational dynamics are generally well described in simulation models. Also changes with temperature, dehydration and cholesterol concentration are qualitatively correctly reproduced. However, the quality of the underlying atomistic resolution structural changes is uncertain. Even worse, when focusing on the lipid bilayer properties at the interfacial region, e.g. glycerol backbone and choline structures, and cation binding, many simulation models produce an inaccurate description of experimental data. Thus extreme care must be applied when simulations are applied to understand phenomena where the interfacial region plays a significant role. This work is done by the NMRlipids Open Collaboration project running at https://nmrlipids.blogspot.fi and https://github.com/NMRLipids. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg.
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41
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Botan A, Favela-Rosales F, Fuchs PFJ, Javanainen M, Kanduč M, Kulig W, Lamberg A, Loison C, Lyubartsev A, Miettinen MS, Monticelli L, Määttä J, Ollila OHS, Retegan M, Róg T, Santuz H, Tynkkynen J. Toward Atomistic Resolution Structure of Phosphatidylcholine Headgroup and Glycerol Backbone at Different Ambient Conditions. J Phys Chem B 2015; 119:15075-88. [PMID: 26509669 PMCID: PMC4677354 DOI: 10.1021/acs.jpcb.5b04878] [Citation(s) in RCA: 95] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Revised: 10/19/2015] [Indexed: 11/28/2022]
Abstract
Phospholipids are essential building blocks of biological membranes. Despite a vast amount of very accurate experimental data, the atomistic resolution structures sampled by the glycerol backbone and choline headgroup in phoshatidylcholine bilayers are not known. Atomistic resolution molecular dynamics simulations have the potential to resolve the structures, and to give an arrestingly intuitive interpretation of the experimental data, but only if the simulations reproduce the data within experimental accuracy. In the present work, we simulated phosphatidylcholine (PC) lipid bilayers with 13 different atomistic models, and compared simulations with NMR experiments in terms of the highly structurally sensitive C-H bond vector order parameters. Focusing on the glycerol backbone and choline headgroups, we showed that the order parameter comparison can be used to judge the atomistic resolution structural accuracy of the models. Accurate models, in turn, allow molecular dynamics simulations to be used as an interpretation tool that translates these NMR data into a dynamic three-dimensional representation of biomolecules in biologically relevant conditions. In addition to lipid bilayers in fully hydrated conditions, we reviewed previous experimental data for dehydrated bilayers and cholesterol-containing bilayers, and interpreted them with simulations. Although none of the existing models reached experimental accuracy, by critically comparing them we were able to distill relevant chemical information: (1) increase of choline order parameters indicates the P-N vector tilting more parallel to the membrane, and (2) cholesterol induces only minor changes to the PC (glycerol backbone) structure. This work has been done as a fully open collaboration, using nmrlipids.blogspot.fi as a communication platform; all the scientific contributions were made publicly on this blog. During the open research process, the repository holding our simulation trajectories and files ( https://zenodo.org/collection/user-nmrlipids ) has become the most extensive publicly available collection of molecular dynamics simulation trajectories of lipid bilayers.
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Affiliation(s)
- Alexandru Botan
- Institut
Lumière Matière, UMR5306 Université
Lyon 1-CNRS, Université de Lyon, 69622 Villeurbanne, France
| | - Fernando Favela-Rosales
- Departamento
de Física, Centro de Investigación
y de Estudios Avanzados del IPN, Apartado, Postal 14-740, Mexico City, 07000 México
D.F., México
| | - Patrick F. J. Fuchs
- Institut
Jacques Monod, UMR 7592 CNRS, Université Paris
Diderot, Sorbonne, Paris Cité, F-75205 Paris, France
| | - Matti Javanainen
- Department
of Physics, Tampere University of Technology, Tampere, 33101 Finland
| | - Matej Kanduč
- Fachbereich
Physik, Freie Universität Berlin, Berlin, 14195 Germany
| | - Waldemar Kulig
- Department
of Physics, Tampere University of Technology, Tampere, 33101 Finland
| | - Antti Lamberg
- Department
of Chemical Engineering, Kyoto University, 615-8510 Kyoto, Japan
| | - Claire Loison
- Institut
Lumière Matière, UMR5306 Université
Lyon 1-CNRS, Université de Lyon, 69622 Villeurbanne, France
| | - Alexander Lyubartsev
- Division
of Physical Chemistry, Department of Materials and Environmental Chemistry, Stockholm University, S-106 91 Stockholm, Sweden
| | | | - Luca Monticelli
- Institut
de Biologie et Chimie des Protéines (IBCP), CNRS UMR 5086, Lyon 69 367, France
| | - Jukka Määttä
- Department of Chemistry, Aalto University, 00076 Aalto, Finland
| | - O. H. Samuli Ollila
- Department of Neuroscience and Biomedical Engineering, Aalto University, 00076 Aalto, Finland
| | - Marius Retegan
- Max Planck Institute
for Chemical Energy Conversion, Stiftstr. 34-38, 45470 Mülheim an der Ruhr, Germany
| | - Tomasz Róg
- Department
of Physics, Tampere University of Technology, Tampere, 33101 Finland
| | - Hubert Santuz
- INSERM, UMR_S 1134, DSIMB, Paris 75739, France
- Université
Paris Diderot, Sorbonne Paris Cité, UMR_S 1134, Paris, France
- Institut
National de la Transfusion Sanguine (INTS), Paris 75739, France
- Laboratoire d’Excellence GR-Ex, Paris 75015, France
| | - Joona Tynkkynen
- Department
of Physics, Tampere University of Technology, Tampere, 33101 Finland
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42
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Huang K, García AE. Effects of truncating van der Waals interactions in lipid bilayer simulations. J Chem Phys 2015; 141:105101. [PMID: 25217953 DOI: 10.1063/1.4893965] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
In membrane simulations, it is known that truncating electrostatic interactions results in artificial ordering of lipids at the truncation distance. However, less attention has been paid to the effect of truncating van der Waals (VDW) interactions. Since the VDW potential decays as r(-6), it is frequently neglected beyond a cutoff of around 1 nm. In some cases, analytical dispersion corrections appropriate for isotropic systems are applied to the pressure and the potential energy. In this work, we systematically study the effect of truncating VDW interactions at different cutoffs in 1,2-Dipalmitoyl-sn-glycero-3-phosphocholine bilayers with the Berger force field. We show that the area per lipid decreases systematically when the VDW cutoff (r(c)) increases. This dependence persists even when dispersion corrections are applied. Since the analytical form of the dispersion correction is only appropriate for isotropic systems, we suggest that a long VDW cutoff should be used in preference over a short VDW cutoff. To determine the appropriate cutoff, we simulate liquid pentadecane with the Berger parameters and find that r(c) ≥ 1.4 nm is sufficient to reproduce the density and the heat of vaporization of pentadecane. Bilayers simulated with r(c) ≥ 1.4 nm show an improved agreement with experiments in both the form factors and the deuterium order parameters. Finally, we report that the VDW cutoff has a significant impact on the lipid flip-flop energetics and an inappropriate short VDW cutoff results in a bilayer that is prone to form water defects across the bilayer.
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Affiliation(s)
- Kun Huang
- Department of Physics, Applied Physics and Astronomy, Rensselaer Polytechnic Institute, Troy, New York 12180, USA
| | - Angel E García
- Department of Physics, Applied Physics and Astronomy, and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, USA
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Poger D, Mark AE. Effect of Ring Size in ω-Alicyclic Fatty Acids on the Structural and Dynamical Properties Associated with Fluidity in Lipid Bilayers. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2015; 31:11574-11582. [PMID: 26444798 DOI: 10.1021/acs.langmuir.5b02635] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Fatty acids containing a terminal cyclic group such as cyclohexyl and cycloheptyl are commonly found in prokaryotic membranes, especially in those of thermo-acidophilic bacteria. These so-called ω-alicyclic fatty acids have been proposed to stabilize the membranes of bacteria by reducing the fluidity in membranes and increasing lipid packing and lipid chain order. In this article, molecular dynamics simulations are used to examine the effect of 3- to 7-membered cycloalkyl saturated and unsaturated (cyclopent-2-enyl and phenyl) rings in ω-alicyclic fatty acyl chains on the structure (lipid packing, lipid chain order, and fraction of gauche defects in the chains) and dynamics (lateral lipid diffusion) of a model lipid bilayer. It was found that ω-alicyclic chains in which the ring was saturated reduced lipid condensation and lowered chain order which would be associated with enhanced fluidity. However, this effect was limited. The lateral diffusion of the lipids diminished as the ring size increased. In particular, ω-cyclohexyl and ω-cycloheptyl acyl tails led to a decrease in lipid diffusion. In contrast, ω-alicyclic acyl chains that contain an unsaturated ring promoted membrane fluidity both in terms of changes in membrane structure and lipid diffusion. This may indicate that saturated and unsaturated terminal rings in ω-alicyclic fatty acids fulfill alternative functions within membranes. Overall, the simulations suggest that ω-alicyclic fatty acids in which the terminal ring is saturated might protect the membrane of thermo-acidophilic bacteria from high-temperature and low-pH conditions through a "dynamical barrier" that would limit lipid diffusion and transmembrane diffusion of undesired ions and molecules.
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Affiliation(s)
- David Poger
- School of Chemistry and Molecular Biosciences, The University of Queensland , Brisbane QLD 4072, Australia
| | - Alan E Mark
- School of Chemistry and Molecular Biosciences, The University of Queensland , Brisbane QLD 4072, Australia
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Lipid insertion domain unfolding regulates protein orientational transition behavior in a lipid bilayer. Biophys Chem 2015; 206:22-39. [PMID: 26164502 DOI: 10.1016/j.bpc.2015.06.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Revised: 06/24/2015] [Accepted: 06/25/2015] [Indexed: 01/02/2023]
Abstract
We have used coarse-grained (CG) and united atom (UA) molecular dynamics simulations to explore the mechanisms of protein orientational transition of a model peptide (Aβ42) in a phosphatidylcholine/cholesterol (PC/CHO) lipid bilayer. We started with an inserted state of Aβ42 containing a folded (I) or unfolded (II) K28-A42 lipid insertion domain (LID), which was stabilized by the K28-snorkeling and A42-anchoring to the PC polar groups in the lipid bilayer. After a UA-to-CG transformation and a 1000ns-CG simulation for enhancing the sampling of protein orientations, we discovered two transitions: I-to-"deep inserted" state with disrupted K28-snorkeling and II-to-"deep surface" state with disrupted A42-anchoring. The new states remained stable after a CG-to-UA transformation and a 200ns-UA simulation relaxation. Significant changes in the cholesterol-binding domain of Aβ42 and protein-induced membrane disruptions were evident after the transitions. We propose that the conformation of the LID regulates protein orientational transitions in the lipid membrane.
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Van Lehn RC, Alexander-Katz A. Pathway for insertion of amphiphilic nanoparticles into defect-free lipid bilayers from atomistic molecular dynamics simulations. SOFT MATTER 2015; 11:3165-75. [PMID: 25757187 DOI: 10.1039/c5sm00287g] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Gold nanoparticles (NPs) have been increasingly used in biological applications that involve potential contact with cellular membranes. As a result, it is essential to gain a physical understanding of NP-membrane interactions to guide the design of next-generation bioactive nanoparticles. In previous work, we showed that charged, amphiphilic NPs can fuse with lipid bilayers after contact between protruding solvent-exposed lipid tails and the NP monolayer. Fusion was only observed at the high-curvature edges of large bilayer defects, but not in low-curvature regions where protrusions are rarely observed. Here, we use atomistic molecular dynamics simulations to show that the same NPs can also fuse with low-curvature bilayers in the absence of defects if NP-protrusion contact occurs, generalizing the results of our previous work. Insertion proceeds without applying biasing forces to the NP, driven by the hydrophobic effect, and involves the transient generation of bilayer curvature. We further find that NPs with long hydrophobic ligands can insert a single ligand into the bilayer core in a manner similar to the binding of peripheral proteins. Such anchoring may precede insertion, revealing potential methods for engineering NP monolayers to enhance NP-bilayer fusion in systems with a low likelihood of lipid tail protrusions. These results reveal new pathways for NP-bilayer fusion and provide fundamental insight into behavior at the nano-bio interface.
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Affiliation(s)
- Reid C Van Lehn
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
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46
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Poger D, Mark AE. A ring to rule them all: the effect of cyclopropane Fatty acids on the fluidity of lipid bilayers. J Phys Chem B 2015; 119:5487-95. [PMID: 25804677 DOI: 10.1021/acs.jpcb.5b00958] [Citation(s) in RCA: 90] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cyclopropane fatty acids are widespread in bacteria. As their concentration increases on exposure to hostile environments, they have been proposed to protect membranes. Here, the effect of cyclopropane and unsaturated fatty acids, both in cis and trans configurations, on the packing, order, and fluidity of lipid bilayers is explored using molecular dynamics simulations. It is shown that cyclopropane fatty acids disrupt lipid packing, favor the occurrence of gauche defects in the chains, and increase the lipid lateral diffusion, suggesting that they enhance fluidity. At the same time, they generally induce a greater degree of order than unsaturated fatty acids of the same configuration and limit the rotation about the bonds surrounding the cyclopropane ring. This indicates that cyclopropane fatty acids may fulfill a dual function: stabilizing membranes against adverse conditions while simultaneously promoting their fluidity. Marked differences in the effect of cis- and trans-monocyclopropanated fatty acids were also observed, suggesting that they may play alternative roles in membranes.
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Affiliation(s)
- 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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Hughes ZE, Mancera RL. Molecular mechanism of the synergistic effects of vitrification solutions on the stability of phospholipid bilayers. Biophys J 2015; 106:2617-24. [PMID: 24940779 DOI: 10.1016/j.bpj.2014.05.012] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Revised: 05/03/2014] [Accepted: 05/09/2014] [Indexed: 11/15/2022] Open
Abstract
The vitrification solutions used in the cryopreservation of biological samples aim to minimize the deleterious formation of ice by dehydrating cells and promoting the formation of the glassy state of water. They contain a mixture of different cryoprotective agents (CPAs) in water, typically polyhydroxylated alcohols and/or dimethyl sulfoxide (DMSO), which can damage cell membranes. Molecular dynamics simulations have been used to investigate the behavior of pure DPPC, pure DOPC, and mixed DOPC-β-sitosterol bilayers solvated in a vitrification solution containing glycerol, ethylene glycol, and DMSO at concentrations that approximate the widely used plant vitrification solution 2. As in the case of solutions containing a single CPA, the vitrification solution causes the bilayer to thin and become disordered, and pores form in the case of some bilayers. Importantly, the degree of thinning is, however, substantially reduced compared to solutions of DMSO containing the same total CPA concentration. The reduction in the damage done to the bilayers is a result of the ability of the polyhydroxylated species (especially glycerol) to form hydrogen bonds to the lipid and sterol molecules of the bilayer. A decrease in the amount of DMSO in the vitrification solution with a corresponding increase in the amount of glycerol or ethylene glycol diminishes further its damaging effect due to increased hydrogen bonding of the polyol species to the bilayer headgroups. These findings rationalize, to our knowledge for the first time, the synergistic effects of combining different CPAs, and form the basis for the optimization of vitrification solutions.
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Affiliation(s)
- Zak E Hughes
- Institute for Frontier Materials, Deakin University, Waurn Ponds, Australia
| | - Ricardo L Mancera
- School of Biomedical Sciences, CHIRI Biosciences, Curtin University, Perth, Australia.
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Hughes ZE, Walsh TR. Tristearin bilayers: structure of the aqueous interface and stability in the presence of surfactants. RSC Adv 2015. [DOI: 10.1039/c5ra09192f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Molecular dynamics simulations predict that sodium dodecylbenzene sulphonate surfactant molecules embed themselves in a tristearin bilayer, packing commensurate with the hexagonally packed lattice formed by the acyl tails of tristearin.
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Affiliation(s)
- Zak E. Hughes
- Institute for Frontier Materials
- Deakin University
- Geelong
- Australia
| | - Tiffany R. Walsh
- Institute for Frontier Materials
- Deakin University
- Geelong
- Australia
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Qiu L, Buie C, Cheng KH, Vaughn MW. Scaling and alpha-helix regulation of protein relaxation in a lipid bilayer. J Chem Phys 2014; 141:225101. [PMID: 25494768 PMCID: PMC4265037 DOI: 10.1063/1.4902229] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Accepted: 11/10/2014] [Indexed: 11/15/2022] Open
Abstract
Protein conformation and orientation in the lipid membrane plays a key role in many cellular processes. Here we use molecular dynamics simulation to investigate the relaxation and C-terminus diffusion of a model helical peptide: beta-amyloid (Aβ) in a lipid membrane. We observed that after the helical peptide was initially half-embedded in the extracelluar leaflet of phosphatidylcholine (PC) or PC/cholesterol (PC/CHOL) membrane, the C-terminus diffused across the membrane and anchored to PC headgroups of the cytofacial lipid leaflet. In some cases, the membrane insertion domain of the Aβ was observed to partially unfold. Applying a sigmoidal fit to the process, we found that the characteristic velocity of the C-terminus, as it moved to its anchor site, scaled with θu (-4/3), where θu is the fraction of the original helix that was lost during a helix to coil transition. Comparing this scaling with that of bead-spring models of polymer relaxation suggests that the C-terminus velocity is highly regulated by the peptide helical content, but that it is independent of the amino acid type. The Aβ was stabilized by the attachment of the positive Lys28 side chain to the negative phosphate of PC or 3β oxygen of CHOL in the extracellular lipid leaflet and of the C-terminus to its anchor site in the cytofacial lipid leaflet.
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Affiliation(s)
- Liming Qiu
- Department of Physics, Texas Tech University, Lubbock, Texas 79409, USA
| | - Creighton Buie
- Department of Chemical Engineering, Texas Tech University, Lubbock, Texas 79409, USA
| | - Kwan Hon Cheng
- Department of Physics, Texas Tech University, Lubbock, Texas 79409, USA
| | - Mark W Vaughn
- Department of Chemical Engineering, Texas Tech University, Lubbock, Texas 79409, USA
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Oliveira ASF, Damas JM, Baptista AM, Soares CM. Exploring O2 diffusion in A-type cytochrome c oxidases: molecular dynamics simulations uncover two alternative channels towards the binuclear site. PLoS Comput Biol 2014; 10:e1004010. [PMID: 25474152 PMCID: PMC4256069 DOI: 10.1371/journal.pcbi.1004010] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Accepted: 10/29/2014] [Indexed: 12/04/2022] Open
Abstract
Cytochrome c oxidases (Ccoxs) are the terminal enzymes of the respiratory chain in mitochondria and most bacteria. These enzymes couple dioxygen (O2) reduction to the generation of a transmembrane electrochemical proton gradient. Despite decades of research and the availability of a large amount of structural and biochemical data available for the A-type Ccox family, little is known about the channel(s) used by O2 to travel from the solvent/membrane to the heme a3-CuB binuclear center (BNC). Moreover, the identification of all possible O2 channels as well as the atomic details of O2 diffusion is essential for the understanding of the working mechanisms of the A-type Ccox. In this work, we determined the O2 distribution within Ccox from Rhodobacter sphaeroides, in the fully reduced state, in order to identify and characterize all the putative O2 channels leading towards the BNC. For that, we use an integrated strategy combining atomistic molecular dynamics (MD) simulations (with and without explicit O2 molecules) and implicit ligand sampling (ILS) calculations. Based on the 3D free energy map for O2 inside Ccox, three channels were identified, all starting in the membrane hydrophobic region and connecting the surface of the protein to the BNC. One of these channels corresponds to the pathway inferred from the X-ray data available, whereas the other two are alternative routes for O2 to reach the BNC. Both alternative O2 channels start in the membrane spanning region and terminate close to Y288I. These channels are a combination of multiple transiently interconnected hydrophobic cavities, whose opening and closure is regulated by the thermal fluctuations of the lining residues. Furthermore, our results show that, in this Ccox, the most likely (energetically preferred) routes for O2 to reach the BNC are the alternative channels, rather than the X-ray inferred pathway. Cytochrome c oxidases (Ccoxs), the terminal enzymes of the respiratory electron transport chain in eukaryotes and many prokaryotes, are key enzymes in aerobic respiration. These proteins couple the reduction of molecular dioxygen to water with the creation of a transmembrane electrochemical proton gradient. Over the last decades, most of the Ccoxs research focused on the mechanisms and energetics of reduction and/or proton pumping, and little emphasis has been given to the pathways used by dioxygen to reach the binuclear center, where dioxygen reduction takes place. In particular, the existence and the characteristics of the channel(s) used by O2 to travel from the solvent/membrane to the binuclear site are still unclear. In this work, we combine all-atom molecular dynamics simulations and implicit ligand sampling calculations in order to identify and characterize the O2 delivery channels in the Ccox from Rhodobacter sphaeroides. Altogether, our results suggest that, in this Ccox, O2 can diffuse via three well-defined channels that start in membrane region (where O2 solubility is higher than in the water). One of these channels corresponds to the pathway inferred from the X-ray data available, whereas the other two are alternative routes for O2 to reach the binuclear center.
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Affiliation(s)
- A. Sofia F. Oliveira
- ITQB - Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - João M. Damas
- ITQB - Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - António M. Baptista
- ITQB - Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Cláudio M. Soares
- ITQB - Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
- * E-mail:
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