151
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Bolmatov D, Soloviov D, Zhernenkov M, Zav'yalov D, Mamontov E, Suvorov A, Cai YQ, Katsaras J. Molecular Picture of the Transient Nature of Lipid Rafts. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:4887-4896. [PMID: 32259453 DOI: 10.1021/acs.langmuir.0c00125] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
In biological membranes, lipid rafts are now thought to be transient and nanoscopic. However, the mechanism responsible for these nanoscopic assemblies remains poorly understood, even in the case of model membranes. As a result, it has proven extremely challenging to probe the physicochemical properties of lipid rafts at the molecular level. Here, we use all-atom molecular dynamics (MD) simulations and inelastic X-ray scattering (IXS), an intrinsically nanoscale technique, to directly probe the energy transfer and collective short-wavelength dynamics (phonons) of biologically relevant model membranes. We show that the nanoscale propagation of stress in lipid rafts takes place in the form of collective motions made up of longitudinal (compression waves) and transverse (shear waves) molecular vibrations. Importantly, we provide a molecular picture for the so-called van der Waals mediated "force from lipid" [Anishkin, A. et al. Proc. Natl. Acad. Sci. U.S.A. 2014, 111, 7898], a key parameter for the ionic channel mechano-transduction and the mechanism for the lipid transfer of molecular level stress [Aponte-Santamarı́a, C. et al. J. Am. Chem. Soc. 2017, 139, 13588]. Specifically, we describe how lipid rafts are formed and maintained through the propagation of molecular stress, lipid raft rattling dynamics, and a relaxation process. Eventually, the rafts dissipate through the self-diffusion of lipids making up the rafts. We also show that the molecular stress and viscoelastic properties of transient lipid rafts can be modulated through the use of hydrophobic biomolecules such as melatonin and tryptophan. Ultimately, the herein proposed mechanism describing the molecular interactions for the formation and dissolution of lipid rafts may offer insights as to how lipid rafts enable biological function.
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Affiliation(s)
- Dima Bolmatov
- Large Scale Structures Group, Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
- Department of Physics and Astronomy, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Dmytro Soloviov
- Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
- Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, Dubna 141980, Russia
- Institute for Safety Problems of Nuclear Power Plants, NAS of Ukraine, Kyiv 03680, Ukraine
| | - Mikhail Zhernenkov
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, New York 11973, United States
| | | | - Eugene Mamontov
- Spectroscopy Group, Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Alexey Suvorov
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, New York 11973, United States
| | - Yong Q Cai
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, New York 11973, United States
| | - John Katsaras
- Large Scale Structures Group, Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
- Department of Physics and Astronomy, University of Tennessee, Knoxville, Tennessee 37996, United States
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152
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Krämer A, Hudson PS, Jones MR, Brooks BR. Multi-phase Boltzmann weighting: accounting for local inhomogeneity in molecular simulations of water-octanol partition coefficients in the SAMPL6 challenge. J Comput Aided Mol Des 2020; 34:471-483. [PMID: 32060677 PMCID: PMC8750956 DOI: 10.1007/s10822-020-00285-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 01/08/2020] [Indexed: 02/08/2023]
Abstract
Accurately computing partition coefficients is a pivotal part of drug discovery. Specifically, octanol-water partition coefficients can provide information into hydrophobicity of drug-like molecules, as well as a de facto representation of membrane permeability. However, one challenge facing the computation of partition coefficients is the need to encapsulate various microscopic environments. These include areas of largely bulk solvent (i.e., either water or octanol) or regions where octanol is saturated with water or areas of higher salt concentration. Also, tautomeric effects require consideration. Thus, we present a Boltzmann weighting approach that incorporates transfer free energies across varying microscopic media, as well as varying tautomeric state, to compute partition coefficients in the SAMPL6 challenge.
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Affiliation(s)
- Andreas Krämer
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
| | - Phillip S Hudson
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA
- Department of Chemistry, University of South Florida, Tampa, FL, 33620, USA
| | - Michael R Jones
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Bernard R Brooks
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA
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153
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Buten C, Kortekaas L, Ravoo BJ. Design of Active Interfaces Using Responsive Molecular Components. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2020; 32:e1904957. [PMID: 31573115 DOI: 10.1002/adma.201904957] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 09/07/2019] [Indexed: 06/10/2023]
Abstract
Responsive interfaces are interfaces that show a defined and reversible change in physical properties in response to external stimuli. Typically, responsive interfaces result from the immobilization of responsive molecular components at the interface that translate a nanoscale signal into a macroscopic effect. Responsive interfaces can also be obtained if the topology of the interface can be reversibly changed using an external stimulus. As the surface of any material is its connection to the environment, responsive interfaces provide opportunities for interactive materials which are not only able to change properties upon demand, but also sense their environment and act autonomously. The application of responsive molecular components at interfaces, however, requires chemical and physical compatibility with the material surface of interest, posing a challenge not least in the retention of the responsive functionality. The state of the art in "active" interfaces which display responsive wettability, permeability, or adhesion is discussed, with a particular emphasis on microscale and nanoscale patterning since patterned interfaces can give rise to unique material properties. Finally, perspectives in the development of responsive interfaces, as well as promising approaches for bypassing the most prominent challenges are discussed.
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Affiliation(s)
- Christoph Buten
- Center for Soft Nanoscience and Organisch-Chemisches Institut, Westfälische Wilhelms-Universität Münster, Busso-Peus-Straße 10, 48149, Münster, Germany
| | - Luuk Kortekaas
- Center for Soft Nanoscience and Organisch-Chemisches Institut, Westfälische Wilhelms-Universität Münster, Busso-Peus-Straße 10, 48149, Münster, Germany
| | - Bart Jan Ravoo
- Center for Soft Nanoscience and Organisch-Chemisches Institut, Westfälische Wilhelms-Universität Münster, Busso-Peus-Straße 10, 48149, Münster, Germany
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154
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Abstract
Computational modelling and simulation form a consolidated branch in the multidisciplinary field of membrane science and technology [...]
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155
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Tang PK, Chakraborty K, Hu W, Kang M, Loverde SM. Interaction of Camptothecin with Model Cellular Membranes. J Chem Theory Comput 2020; 16:3373-3384. [PMID: 32126167 DOI: 10.1021/acs.jctc.9b00541] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Accurate and efficient prediction of drug partitioning in model membranes is of significant interest to the pharmaceutical industry. Herein, we utilize advanced sampling methods, specifically, the adaptive biasing force methodology to calculate the potential of mean force for a model hydrophobic anticancer drug, camptothecin (CPT), across three model interfaces. We consider an octanol bilayer, a thick octanol/water interface, and a model 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC)/water interface. We characterize the enthalpic and entropic contributions of the drug to the potential of mean force. We show that the rotational entropy of the drug is inversely related to the probability of hydrogen bond formation of the drug with the POPC membrane. In addition, in long-time microsecond simulations of a high concentration of CPT above the POPC membrane, we show that strong drug-drug aromatic interactions shift the spatial orientation of the drug with the membrane. Stacks of hydrophobic drugs form, allowing penetration of the drug just under the POPC head groups. These results imply that inhomogeneous membrane models need to take into account the effect of drug aggregation on the membrane environment.
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Affiliation(s)
- Phu K Tang
- Department of Chemistry, College of Staten Island, City University of New York, 2800 Victory Boulevard, 6S-238, Staten Island, New York 10314, United States.,Ph.D. Program in Chemistry, Biochemistry, and Physics, The Graduate Center of the City University of New York, New York, New York 10016, United States
| | - Kaushik Chakraborty
- Department of Chemistry, College of Staten Island, City University of New York, 2800 Victory Boulevard, 6S-238, Staten Island, New York 10314, United States
| | - William Hu
- Hunter College High School, New York, New York, 10128, United States
| | - Myungshim Kang
- Department of Chemistry, College of Staten Island, City University of New York, 2800 Victory Boulevard, 6S-238, Staten Island, New York 10314, United States
| | - Sharon M Loverde
- Department of Chemistry, College of Staten Island, City University of New York, 2800 Victory Boulevard, 6S-238, Staten Island, New York 10314, United States.,Department of Physics, Graduate Center, City University of New York, 365 Fifth Avenue, New York, New York 10016, United States.,Ph.D. Program in Chemistry, Biochemistry, and Physics, The Graduate Center of the City University of New York, New York, New York 10016, United States
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156
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Prasad K, Nikzad M, Sbarski I. Modeling Permeability in Multi-Phase Polymer Composites: A Critical Review of Semi-Empirical Approaches. POLYM REV 2020. [DOI: 10.1080/15583724.2020.1743306] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- K. Prasad
- Faculty of Science, Engineering and Technology, Swinburne University of Technology, Melbourne, Australia
| | - M. Nikzad
- Faculty of Science, Engineering and Technology, Swinburne University of Technology, Melbourne, Australia
| | - I. Sbarski
- Faculty of Science, Engineering and Technology, Swinburne University of Technology, Melbourne, Australia
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157
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Chen CH, Melo MC, Berglund N, Khan A, de la Fuente-Nunez C, Ulmschneider JP, Ulmschneider MB. Understanding and modelling the interactions of peptides with membranes: from partitioning to self-assembly. Curr Opin Struct Biol 2020; 61:160-166. [PMID: 32006812 DOI: 10.1016/j.sbi.2019.12.021] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 12/27/2019] [Accepted: 12/28/2019] [Indexed: 12/14/2022]
Abstract
Atomic detail simulations are starting to reveal how flexible polypeptides interact with fluid lipid bilayers. These insights are transforming our understanding of one of the fundamental processes in biology: membrane protein folding and assembly. Advanced molecular dynamics (MD) simulation techniques enable accurate prediction of protein structure, folding pathways and assembly in microsecond-timescales. Such simulations show how membrane-active peptides self-assemble in cell membranes, revealing their binding, folding, insertion, and aggregation, while at the same time providing atomic resolution details of peptide-lipid interactions. Essential to the impact of simulations are experimental approaches that enable calibration and validation of the computational models and techniques. In this review, we summarize the current development of applying unbiased atomic detail MD simulations and the relation to experimental techniques, to study peptide folding and provide our perspective of the field.
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Affiliation(s)
- Charles H Chen
- Department of Chemistry, King's College London, London, UK
| | - Marcelo Cr Melo
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, Penn Institute for Computational Science, and Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Nils Berglund
- Department of Chemistry, Aarhus University, Aarhus, Denmark
| | - Ayesha Khan
- College of Medicine and Health, University of Exeter, Exeter, UK
| | - Cesar de la Fuente-Nunez
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, Penn Institute for Computational Science, and Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania, USA.
| | - Jakob P Ulmschneider
- Institute of Natural Sciences and School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai, China.
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158
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Levental KR, Malmberg E, Symons JL, Fan YY, Chapkin RS, Ernst R, Levental I. Lipidomic and biophysical homeostasis of mammalian membranes counteracts dietary lipid perturbations to maintain cellular fitness. Nat Commun 2020; 11:1339. [PMID: 32165635 PMCID: PMC7067841 DOI: 10.1038/s41467-020-15203-1] [Citation(s) in RCA: 84] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 02/21/2020] [Indexed: 11/29/2022] Open
Abstract
Proper membrane physiology requires maintenance of biophysical properties, which must be buffered from external perturbations. While homeostatic adaptation of membrane fluidity to temperature variation is a ubiquitous feature of ectothermic organisms, such responsive membrane adaptation to external inputs has not been directly observed in mammals. Here, we report that challenging mammalian membranes by dietary lipids leads to robust lipidomic remodeling to preserve membrane physical properties. Specifically, exogenous polyunsaturated fatty acids are rapidly incorporated into membrane lipids, inducing a reduction in membrane packing. These effects are rapidly compensated both in culture and in vivo by lipidome-wide remodeling, most notably upregulation of saturated lipids and cholesterol, resulting in recovery of membrane packing and permeability. Abrogation of this response results in cytotoxicity when membrane homeostasis is challenged by dietary lipids. These results reveal an essential mammalian mechanism for membrane homeostasis wherein lipidome remodeling in response to dietary lipid inputs preserves functional membrane phenotypes. Proper membrane physiology requires maintenance of a narrow range of physicochemical properties, which must be buffered from external perturbations. Here, authors report lipidomic remodeling to preserve membrane physical properties upon exogenous polyunsaturated fatty acids exposure.
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Affiliation(s)
- Kandice R Levental
- Department of Integrative Biology & Pharmacology, University of Texas Health Science Center at Houston, Houston, TX, USA.
| | - Eric Malmberg
- Department of Integrative Biology & Pharmacology, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Jessica L Symons
- Department of Integrative Biology & Pharmacology, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Yang-Yi Fan
- Program in Integrative Nutrition & Complex Diseases and Department of Nutrition, Texas A&M University, College Station, TX, USA
| | - Robert S Chapkin
- Program in Integrative Nutrition & Complex Diseases and Department of Nutrition, Texas A&M University, College Station, TX, USA
| | - Robert Ernst
- Department of Medical Biochemistry & Molecular Biology, Medical Faculty, Saarland University, Homburg, Germany
| | - Ilya Levental
- Department of Integrative Biology & Pharmacology, University of Texas Health Science Center at Houston, Houston, TX, USA.
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159
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Lin X, Lin X, Gu N. Optimization of hydrophobic nanoparticles to better target lipid rafts with molecular dynamics simulations. NANOSCALE 2020; 12:4101-4109. [PMID: 32022059 DOI: 10.1039/c9nr09226a] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Due to different interactions between lipids and proteins, a plasma membrane can segregate into different membrane domains. Among them, ordered functional membrane domains are defined as "lipid rafts", which play key roles in many biological processes (e.g., signal transduction, endocytosis, etc.) in the cell. Hence, it will be of much biological significance to monitor and even regulate the dynamics of lipid rafts. In this work, we designed a ligand-modified spherical nanoparticle with coarse-grained molecular dynamics simulations, which can be encapsulated into the hydrophobic region of the lipid membrane and specifically target either raft or non-raft membrane domains. The preferred localization of the nanoparticle can be tuned by adjusting ligand hydrophobicity, length and density. Generally, more hydrophobic nanoparticles tend to target the raft domain, while less hydrophobic nanoparticles prefer the non-raft domain. Besides, ligand length and density jointly determine the exposure of nanoparticle cores and thus affect the roles of ligands in nanoparticles' final localization. Our results may provide insights into the experimental design of functional nanoparticles, targeting the lipid raft and regulating its dynamics.
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Affiliation(s)
- Xiaoqian Lin
- Institute of Nanotechnology for Single Cell Analysis (INSCA), Beijing Advanced Innovation Center for Biomedical Engineering, Beihang University, Beijing 100191, China. and School of Biological Science and Medical Engineering, Beihang University, Beijing 100191, China
| | - Xubo Lin
- Institute of Nanotechnology for Single Cell Analysis (INSCA), Beijing Advanced Innovation Center for Biomedical Engineering, Beihang University, Beijing 100191, China. and School of Biological Science and Medical Engineering, Beihang University, Beijing 100191, China
| | - Ning Gu
- State Key Laboratory of Bioelectronics, Jiangsu Key Laboratory for Biomaterials and Devices, School of Biological Sciences & Medical Engineering, Southeast University, Nanjing 210096, China.
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160
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Multifunctional conjugated 1,6-heptadiynes and its derivatives stimulated molecular electronics: Future moletronics. Eur Polym J 2020. [DOI: 10.1016/j.eurpolymj.2019.109467] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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161
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Fukunishi Y, Mashimo T, Kurosawa T, Wakabayashi Y, Nakamura HK, Takeuchi K. Prediction of Passive Membrane Permeability by Semi-Empirical Method Considering Viscous and Inertial Resistances and Different Rates of Conformational Change and Diffusion. Mol Inform 2020; 39:e1900071. [PMID: 31609549 PMCID: PMC7050510 DOI: 10.1002/minf.201900071] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 09/22/2019] [Indexed: 12/24/2022]
Abstract
Membrane permeability is an important property of drugs in adsorption. Many prediction methods work well for small molecules, but the prediction of middle-molecule permeability is still difficult. In the present study, we modified a classical permeability model based on Fick's law to study passive membrane permeability. The model consisted of the distribution of solute from water to membrane and the diffusion of solute in each solvent. The diffusion coefficient is the inverse of the resistance, and we examined the inertial resistance in addition to the viscous resistance, the latter of which has been widely used in permeability prediction. Also, we examined three models changing the balance between the diffusion of solute in membrane and the conformational change of solute. The inertial resistance improved the prediction results in addition to the viscous resistance. The models worked well not only for small molecules but also for middle molecules, whose structures have more conformational freedom.
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Affiliation(s)
- Yoshifumi Fukunishi
- Molecular Profiling Research Center for Drug Discovery (molprof)National Institute of Advanced Industrial Science and Technology (AIST)2-3-26, Aomi, Koto-kuTokyo135-0064Japan
| | - Tadaaki Mashimo
- Technology Research Association for Next-Generation Natural Products Chemistry2-3-26, Aomi, Koto-kuTokyo135-0064Japan
- IMSBIO Co., Ltd.Owl Tower, 4–21-1, Higashi-Ikebukuro, Toshima-kuTokyo170-0013Japan
| | - Takashi Kurosawa
- Technology Research Association for Next-Generation Natural Products Chemistry2-3-26, Aomi, Koto-kuTokyo135-0064Japan
- Hitachi Solutions East Japan, 12–1 Ekimaehoncho, Kawasaki-ku, KawasakiKanagawa210-0007Japan
| | | | - Hironori K. Nakamura
- Biomodeling Research Co., Ltd.1-704-2 Uedanishi, Tenpaku-ku, NagoyaAichi468-0058Japan
| | - Koh Takeuchi
- Molecular Profiling Research Center for Drug Discovery (molprof)National Institute of Advanced Industrial Science and Technology (AIST)2-3-26, Aomi, Koto-kuTokyo135-0064Japan
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162
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Fuoco A, Satilmis B, Uyar T, Monteleone M, Esposito E, Muzzi C, Tocci E, Longo M, De Santo MP, Lanč M, Friess K, Vopička O, Izák P, Jansen JC. Comparison of pure and mixed gas permeation of the highly fluorinated polymer of intrinsic microporosity PIM-2 under dry and humid conditions: Experiment and modelling. J Memb Sci 2020. [DOI: 10.1016/j.memsci.2019.117460] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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163
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Ghysels A, Krämer A, Venable RM, Teague WE, Lyman E, Gawrisch K, Pastor RW. Permeability of membranes in the liquid ordered and liquid disordered phases. Nat Commun 2019; 10:5616. [PMID: 31819053 PMCID: PMC6901538 DOI: 10.1038/s41467-019-13432-7] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 11/06/2019] [Indexed: 11/09/2022] Open
Abstract
The functional significance of ordered nanodomains (or rafts) in cholesterol rich eukaryotic cell membranes has only begun to be explored. This study exploits the correspondence of cellular rafts and liquid ordered (Lo) phases of three-component lipid bilayers to examine permeability. Molecular dynamics simulations of Lo phase dipalmitoylphosphatidylcholine (DPPC), dioleoylphosphatidylcholine (DOPC), and cholesterol show that oxygen and water transit a leaflet through the DOPC and cholesterol rich boundaries of hexagonally packed DPPC microdomains, freely diffuse along the bilayer midplane, and escape the membrane along the boundary regions. Electron paramagnetic resonance experiments provide critical validation: the measured ratio of oxygen concentrations near the midplanes of liquid disordered (Ld) and Lo bilayers of DPPC/DOPC/cholesterol is 1.75 ± 0.35, in very good agreement with 1.3 ± 0.3 obtained from simulation. The results show how cellular rafts can be structurally rigid signaling platforms while remaining nearly as permeable to small molecules as the Ld phase.
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Affiliation(s)
- An Ghysels
- Center for Molecular Modeling, Ghent University, Technologiepark 46, 9052, Gent, Belgium.
| | - Andreas Krämer
- Laboratory of Computational Biology, National Heart Lung Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Richard M Venable
- Laboratory of Computational Biology, National Heart Lung Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Walter E Teague
- Laboratory of Membrane Biochemistry and Biophysics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Edward Lyman
- Department of Physics and Astronomy and Department of Chemistry and Biochemistry, University of Delaware, Newark, 19716, DE, USA
| | - Klaus Gawrisch
- Laboratory of Membrane Biochemistry and Biophysics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Richard W Pastor
- Laboratory of Computational Biology, National Heart Lung Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
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164
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Melcr J, Piquemal JP. Accurate Biomolecular Simulations Account for Electronic Polarization. Front Mol Biosci 2019; 6:143. [PMID: 31867342 PMCID: PMC6904368 DOI: 10.3389/fmolb.2019.00143] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 11/20/2019] [Indexed: 11/29/2022] Open
Abstract
In this perspective, we discuss where and how accounting for electronic many-body polarization affects the accuracy of classical molecular dynamics simulations of biomolecules. While the effects of electronic polarization are highly pronounced for molecules with an opposite total charge, they are also non-negligible for interactions with overall neutral molecules. For instance, neglecting these effects in important biomolecules like amino acids and phospholipids affects the structure of proteins and membranes having a large impact on interpreting experimental data as well as building coarse grained models. With the combined advances in theory, algorithms and computational power it is currently realistic to perform simulations with explicit polarizable dipoles on systems with relevant sizes and complexity. Alternatively, the effects of electronic polarization can also be included at zero additional computational cost compared to standard fixed-charge force fields using the electronic continuum correction, as was recently demonstrated for several classes of biomolecules.
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Affiliation(s)
- Josef Melcr
- Groningen Biomolecular Sciences and Biotechnology Institute and the Zernike Institute for Advanced Materials, University of Groningen, Groningen, Netherlands
| | - Jean-Philip Piquemal
- Laboratoire de Chimie Théorique, Sorbonne Université, UMR7616 CNRS, Paris, France
- Institut Universitaire de France, Paris, France
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX, United States
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165
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Wood I, Fabian L, Moglioni A, Cabeça LF, de Paula E, Pickholz M. Combining nuclear magnetic resonance with molecular dynamics simulations to address sumatriptan interaction with model membranes. Chem Phys Lipids 2019; 225:104792. [DOI: 10.1016/j.chemphyslip.2019.104792] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 06/21/2019] [Accepted: 07/17/2019] [Indexed: 02/07/2023]
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166
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Park S, Yeom MS, Andersen OS, Pastor RW, Im W. Quantitative Characterization of Protein-Lipid Interactions by Free Energy Simulation between Binary Bilayers. J Chem Theory Comput 2019; 15:6491-6503. [PMID: 31560853 PMCID: PMC7076909 DOI: 10.1021/acs.jctc.9b00815] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Using a recently developed binary bilayer system (BBS) consisting of two patches of laterally contacting bilayers, umbrella sampling molecular dynamics (MD) simulations were performed for quantitative characterization of protein-lipid interactions. The BBS is composed of 1,2-dilauroyl-sn-glycero-3-phosphocholine (DLPC) and 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) with an embedded model membrane protein, a gramicidin A (gA) channel. The calculated free energy difference for the transfer of a gA channel from DLPC (hydrophobic thickness ≈ 21.5 Å) to DMPC (hydrophobic thickness ≈ 25.5 Å) bilayers, ΔG(DLPC → DMPC), is -2.2 ± 0.7 kcal/mol. This value appears at odds with the traditional view that the hydrophobic length of the gA channel is ∼22 Å. To understand this discrepancy, we first note that recent MD simulations by different groups have shown that lipid bilayer thickness profiles in the vicinity of a gA channel differ qualitatively from the deformation profile predicted from continuum elastic bilayer models. Our MD simulations at low and high gA:lipid molar ratios and different membrane compositions indicate that the gA channel's effective hydrophobic length is ∼26 Å. Using this effective hydrophobic length, ΔG(DLPC → DMPC) determined here is in excellent agreement with predictions based on continuum elastic models (-3.0 to -2.2 kcal/mol) where the bilayer deformation energy is approximated as a harmonic function of the mismatch between the channel's effective hydrophobic length and the hydrophobic thickness of the bilayer. The free energy profile for gA in the BBS includes a barrier at the interface between the two bilayers which can be attributed to the line tension at the interface between two bilayers with different hydrophobic thicknesses. This observation implies that translation of a peptide between two different regions of a cell membrane (such as between the liquid ordered and disordered phases) may include effects of a barrier at the interface in addition to the relative free energies of the species far from the interface. The BBS allows for direct transfer free energy calculations between bilayers without a need of a reference medium, such as bulk water, and thus provides an efficient simulation protocol for the quantitative characterization of protein-lipid interactions at all-atom resolution.
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Affiliation(s)
- Soohyung Park
- Departments of Biological Sciences and Bioengineering , Lehigh University , Bethlehem , Pennsylvania 18015 , United States
| | - Min Sun Yeom
- Korean Institute of Science and Technology Information , Daejeon , Korea
| | - Olaf S Andersen
- Department of Physiology and Biophysics , Weill Cornell Medicine , New York , New York 10065 , United States
| | - Richard W Pastor
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute , National Institutes of Health , Bethesda , Maryland 20892 , United States
| | - Wonpil Im
- Departments of Biological Sciences and Bioengineering , Lehigh University , Bethlehem , Pennsylvania 18015 , United States.,School of Computational Sciences , Korea Institute for Advanced Study , Seoul 02455 , Republic of Korea
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167
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Das M, Dahal U, Mesele O, Liang D, Cui Q. Molecular Dynamics Simulation of Interaction between Functionalized Nanoparticles with Lipid Membranes: Analysis of Coarse-Grained Models. J Phys Chem B 2019; 123:10547-10561. [DOI: 10.1021/acs.jpcb.9b08259] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Mitradip Das
- School of Chemical Sciences, National Institute of Science Education and Research, Khordha, Odisha, India, 752050
- Homi Bhabha National Institute, Training School
Complex, Anushaktinagar, Mumbai, Maharashtra, India, 400094
| | - Udaya Dahal
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Oluwaseun Mesele
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Dongyue Liang
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin−Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Qiang Cui
- Departments of Chemistry, Physics and Biomedical Engineering, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
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168
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Yue Z, Li C, Voth GA, Swanson JMJ. Dynamic Protonation Dramatically Affects the Membrane Permeability of Drug-like Molecules. J Am Chem Soc 2019; 141:13421-13433. [PMID: 31382734 DOI: 10.1021/jacs.9b04387] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Permeability (Pm) across biological membranes is of fundamental importance and a key factor in drug absorption, distribution, and development. Although the majority of drugs will be charged at some point during oral delivery, our understanding of membrane permeation by charged species is limited. The canonical model assumes that only neutral molecules partition into and passively permeate across membranes, but there is mounting evidence that these processes are also facile for certain charged species. However, it is unknown whether such ionizable permeants dynamically neutralize at the membrane surface or permeate in their charged form. To probe protonation-coupled permeation in atomic detail, we herein apply continuous constant-pH molecular dynamics along with free energy sampling to study the permeation of a weak base propranolol (PPL), and evaluate the impact of including dynamic protonation on Pm. The simulations reveal that PPL dynamically neutralizes at the lipid-tail interface, which dramatically influences the permeation free energy landscape and explains why the conventional model overestimates the assigned intrinsic permeability. We demonstrate how fixed-charge-state simulations can account for this effect, and propose a revised model that better describes pH-coupled partitioning and permeation. Our results demonstrate how dynamic changes in protonation state may play a critical role in the permeation of ionizable molecules, including pharmaceuticals and drug-like molecules, thus requiring a revision of the standard picture.
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Affiliation(s)
- Zhi Yue
- Department of Chemistry, James Frank Institute, and Institute for Biophysical Dynamics , The University of Chicago , Chicago , Illinois 60637 , United States
| | - Chenghan Li
- Department of Chemistry, James Frank Institute, and Institute for Biophysical Dynamics , The University of Chicago , Chicago , Illinois 60637 , United States
| | - Gregory A Voth
- Department of Chemistry, James Frank Institute, and Institute for Biophysical Dynamics , The University of Chicago , Chicago , Illinois 60637 , United States
| | - Jessica M J Swanson
- Department of Chemistry, James Frank Institute, and Institute for Biophysical Dynamics , The University of Chicago , Chicago , Illinois 60637 , United States
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169
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Ramezanpour M, Schmidt ML, Bodnariuc I, Kulkarni JA, Leung SSW, Cullis PR, Thewalt JL, Tieleman DP. Ionizable amino lipid interactions with POPC: implications for lipid nanoparticle function. NANOSCALE 2019; 11:14141-14146. [PMID: 31334542 DOI: 10.1039/c9nr02297j] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Lipid nanoparticles (LNPs) composed of ionizable cationic lipids are currently the leading systems for siRNA delivery in liver disease, with the major limitation of low siRNA release efficacy into the cytoplasm. Ionizable cationic lipids are known to be of critical importance in LNP structure and stability, siRNA entrapment, and endosomal disruption. However, their distribution inside the LNPs and their exact role in cytoplasmic delivery remain unclear. A recent study [Kulkarni et al., On the formation and morphology of lipid nanoparticles containing ionizable cationic lipids and siRNA, ACS Nano, 2018, 12(5), 4787-4795] on LNP-siRNA systems containing the ionizable lipid DLin-KC2-DMA (also known as KC2 with an apparent pKa of ca. 6.7) suggested that neutral KC2 segregates from other components and forms an amorphous oil droplet in the core of LNPs. In this paper, we present evidence supporting the model proposed by Kulkarni et al. We studied KC2 segregation in the presence of POPC using molecular dynamics simulation, deuterium NMR, SAXS, and cryo-TEM experiments, and found that neutral KC2 has a high tendency to separate from POPC dispersions. KC2 confinement, upon raising the pH during the formulation process, could result in rearrangement of the internal structure of LNPs. As interactions between cationic KC2 and anionic endosomal lipids are thought to be a key factor in cargo release, KC2 confinement inside the LNP may be responsible for the observed low release efficacy.
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Affiliation(s)
- M Ramezanpour
- Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada.
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170
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Kim AV, Shelepova EA, Selyutina OY, Meteleva ES, Dushkin AV, Medvedev NN, Polyakov NE, Lyakhov NZ. Glycyrrhizin-Assisted Transport of Praziquantel Anthelmintic Drug through the Lipid Membrane: An Experiment and MD Simulation. Mol Pharm 2019; 16:3188-3198. [PMID: 31198045 DOI: 10.1021/acs.molpharmaceut.9b00390] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Praziquantel (PZQ) is one of the most widespread anthelmintic drugs. However, the frequent insufficient application of PZQ after oral administration is associated with its low solubility, penetration rate, and bioavailability. In the present study, the permeation of PZQ through a 1,2-dioleoyl- sn-glycero-3-phosphocholine (DOPC) membrane was investigated to probe glycyrrhizin-assisted transport. Glycyrrhizin (or glycyrrhizic acid, GA), a natural saponin, shows the ability to enhance the therapeutic activity of various drugs when it is used as a drug delivery system. However, the molecular mechanism of this effect is still under debate. In the present study, the transport rate was measured experimentally by a parallel artificial membrane permeation assay (PAMPA) and molecular dynamics (MD) simulation with DOPC lipid bilayers. The formation of the noncovalent supramolecular complex of PZQ with disodium salt of GA (Na2GA) in an aqueous solution was proved by the NMR relaxation technique. PAMPA experiments show a strong increase in the amount of the penetrating praziquantel molecules in comparison with a saturated aqueous solution of pure drug used as a control. MD simulation of PZQ penetration through the bilayer demonstrates an increase in permeability into the membrane in the presence of a glycyrrhizin molecule. A decrease in the free energy barrier in the middle of the lipid bilayer was obtained, associated with the hydrogen bond between PZQ and GA. Also, GA reduces the local bilayer surface resistance to penetration of PZQ by rearranging the surface lipid headgroups. This study clarifies the mechanism of increasing the drug's bioavailability in the presence of glycyrrhizin.
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Affiliation(s)
- Alexandra V Kim
- Institute of Chemical Kinetics and Combustion , Institutskaya Street, 3 , 630090 , Novosibirsk , Russia.,Novosibirsk State University , 630090 Novosibirsk , Russia
| | - Ekaterina A Shelepova
- Institute of Chemical Kinetics and Combustion , Institutskaya Street, 3 , 630090 , Novosibirsk , Russia.,Novosibirsk State University , 630090 Novosibirsk , Russia
| | - Olga Yu Selyutina
- Institute of Chemical Kinetics and Combustion , Institutskaya Street, 3 , 630090 , Novosibirsk , Russia
| | - Elizaveta S Meteleva
- Institute of Solid State Chemistry and Mechanochemistry , 630128 Novosibirsk , Russia
| | - Alexander V Dushkin
- Institute of Solid State Chemistry and Mechanochemistry , 630128 Novosibirsk , Russia
| | - Nikolai N Medvedev
- Institute of Chemical Kinetics and Combustion , Institutskaya Street, 3 , 630090 , Novosibirsk , Russia.,Novosibirsk State University , 630090 Novosibirsk , Russia
| | - Nikolay E Polyakov
- Institute of Chemical Kinetics and Combustion , Institutskaya Street, 3 , 630090 , Novosibirsk , Russia.,Institute of Solid State Chemistry and Mechanochemistry , 630128 Novosibirsk , Russia
| | - Nikolay Z Lyakhov
- Institute of Solid State Chemistry and Mechanochemistry , 630128 Novosibirsk , Russia
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171
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Krämer A, Pickard FC, Huang J, Venable RM, Simmonett AC, Reith D, Kirschner KN, Pastor RW, Brooks BR. Interactions of Water and Alkanes: Modifying Additive Force Fields to Account for Polarization Effects. J Chem Theory Comput 2019; 15:3854-3867. [PMID: 31002505 DOI: 10.1021/acs.jctc.9b00016] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Atomistic biomolecular simulations predominantly utilize additive force fields (FF), where the electrostatic potential is modeled by fixed point charges. Among other consequences, the lack of polarizability in these models undermines the balance of hydrophilic/hydrophobic nonbonded interactions. Simulations of water/alkane systems using the TIP3P water model and CHARMM36 parameters reveal a 1 kcal/mol overestimate of the experimental transfer free energy of water to hexadecane; more recent optimized water models (SPC/E, TIP4P/2005, TIP4P-Ew, TIP3P-FB, TIP4P-FB, OPC, TIP4P-D) overestimate this transfer free energy by approximately 2 kcal/mol. In contrast, the polarizable SWM4-NDP and SWM6 water models reproduce experimental values to within statistical error. As an alternative to explicitly modeling polarizability, this paper develops an efficient automated workflow to optimize pair-specific Lennard-Jones parameters within an additive FF. Water/hexadecane is used as a prototype and the free energy of water transfer to hexadecane as a target. The optimized model yields quantitative agreement with the experimental transfer free energy and improves the water/hexadecane interfacial tension by 6%. Simulations of five different lipid bilayers show a strong increase of water permeabilities compared to the unmodified CHARMM36 lipid FF which consistently improves match with experiment: the order-of-magnitude underestimate for monounsaturated bilayers is rectified and the factor of 2.8-4 underestimate for saturated bilayers is turned into a factor of 1.5-3 overestimate. While agreement with experiment is decreased for the diffusion constant of water in hexadecane, alkane transfer free energies, and the bilayers' area per lipid, the method provides a permeant-specific route to achieve a wide range of heterogeneous observables via rapidly optimized pairwise parameters.
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Affiliation(s)
- Andreas Krämer
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute , National Institutes of Health , Bethesda , Maryland 20892 , United States.,Institute of Technology, Resource and Energy-Efficient Engineering , Bonn-Rhein-Sieg University of Applied Sciences , Grantham-Allee 20 , 53757 Sankt Augustin , Germany
| | - Frank C Pickard
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute , National Institutes of Health , Bethesda , Maryland 20892 , United States
| | - Jing Huang
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute , National Institutes of Health , Bethesda , Maryland 20892 , United States.,School of Life Sciences , Westlake University , 18 Shilongshan Road , Hangzhou 310024 , Zhejiang China.,Department of Pharmaceutical Science, School of Pharmacy , University of Maryland , 20 Penn Street , Baltimore , Maryland 21201 , United States
| | - Richard M Venable
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute , National Institutes of Health , Bethesda , Maryland 20892 , United States
| | - Andrew C Simmonett
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute , National Institutes of Health , Bethesda , Maryland 20892 , United States
| | - Dirk Reith
- Institute of Technology, Resource and Energy-Efficient Engineering , Bonn-Rhein-Sieg University of Applied Sciences , Grantham-Allee 20 , 53757 Sankt Augustin , Germany
| | - Karl N Kirschner
- Institute of Technology, Resource and Energy-Efficient Engineering , Bonn-Rhein-Sieg University of Applied Sciences , Grantham-Allee 20 , 53757 Sankt Augustin , Germany
| | - Richard W Pastor
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute , National Institutes of Health , Bethesda , Maryland 20892 , United States
| | - Bernard R Brooks
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute , National Institutes of Health , Bethesda , Maryland 20892 , United States
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172
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Kumari P, Kashyap HK. Sensitivity and Resilience of Phosphatidylcholine and Phosphatidylethanolamine Lipid Membranes against Cholinium Glycinate Biocompatible Ionic Liquid. J Phys Chem B 2019; 123:4550-4561. [DOI: 10.1021/acs.jpcb.9b02800] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Pratibha Kumari
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Hemant K. Kashyap
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
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173
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Abstract
Membranes surrounding the biological cell and its internal compartments host proteins that catalyze chemical reactions essential for the functioning of the cell. Rather than being a passive structural matrix that holds membrane-embedded proteins in place, the membrane can largely shape the conformational energy landscape of membrane proteins and impact the energetics of their chemical reaction. Here, we highlight the challenges in understanding how lipids impact the conformational energy landscape of macromolecular membrane complexes whose functioning involves chemical reactions including proton transfer. We review here advances in our understanding of how chemical reactions occur at membrane interfaces gleaned with both theoretical and experimental advances using simple protein systems as guides. Our perspective is that of bridging experiments with theory to understand general physicochemical principles of membrane reactions, with a long term goal of furthering our understanding of the role of the lipids on the functioning of complex macromolecular assemblies at the membrane interface.
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Affiliation(s)
- Ana-Nicoleta Bondar
- Freie Universität Berlin , Department of Physics, Theoretical Molecular Biophysics Group , Arnimallee 14 , D-14195 Berlin , Germany
| | - M Joanne Lemieux
- University of Alberta , Department of Biochemistry, Membrane Protein Disease Research Group , Edmonton , Alberta T6G 2H7 , Canada
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