1
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Scott HL, Burns-Casamayor V, Dixson AC, Standaert RF, Stanley CB, Stingaciu LR, Carrillo JMY, Sumpter BG, Katsaras J, Qiang W, Heberle FA, Mertz B, Ashkar R, Barrera FN. Neutron spin echo shows pHLIP is capable of retarding membrane thickness fluctuations. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2024; 1866:184349. [PMID: 38815687 PMCID: PMC11365786 DOI: 10.1016/j.bbamem.2024.184349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Revised: 04/03/2024] [Accepted: 05/21/2024] [Indexed: 06/01/2024]
Abstract
Cell membranes are responsible for a range of biological processes that require interactions between lipids and proteins. While the effects of lipids on proteins are becoming better understood, our knowledge of how protein conformational changes influence membrane dynamics remains rudimentary. Here, we performed experiments and computer simulations to study the dynamic response of a lipid membrane to changes in the conformational state of pH-low insertion peptide (pHLIP), which transitions from a surface-associated (SA) state at neutral or basic pH to a transmembrane (TM) α-helix under acidic conditions. Our results show that TM-pHLIP significantly slows down membrane thickness fluctuations due to an increase in effective membrane viscosity. Our findings suggest a possible membrane regulatory mechanism, where the TM helix affects lipid chain conformations, and subsequently alters membrane fluctuations and viscosity.
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Affiliation(s)
- Haden L Scott
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville 37996, United States of America
| | - Violeta Burns-Casamayor
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV 26506, United States of America
| | - Andrew C Dixson
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville 37996, United States of America
| | - Robert F Standaert
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville 37996, United States of America; C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV 26506, United States of America; Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, United States of America
| | - Christopher B Stanley
- Shull Wollan Center - a Joint Institute for Neutron Sciences, Oak Ridge, TN 37831, United States of America; Computational Sciences and Engineering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, United States of America
| | - Laura-Roxana Stingaciu
- Labs and Soft Matter Group, Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, United States of America; JCNS1, FZJ outstation at SNS, Oak Ridge National Laboratory, Oak Ridge, TN 37831, United States of America
| | - Jan-Michael Y Carrillo
- Computational Sciences and Engineering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, United States of America; Center for Nanophase Materials Sciences, Oak Ridge, TN 37831, United States of America
| | - Bobby G Sumpter
- Computational Sciences and Engineering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, United States of America; Center for Nanophase Materials Sciences, Oak Ridge, TN 37831, United States of America
| | - John Katsaras
- Shull Wollan Center - a Joint Institute for Neutron Sciences, Oak Ridge, TN 37831, United States of America; Labs and Soft Matter Group, Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, United States of America; Department of Physics and Astronomy, University of Tennessee, Knoxville, TN 37996, United States of America
| | - Wei Qiang
- Department of Chemistry, the State University of New York, Binghamton, NY 13902, United States of America
| | - Frederick A Heberle
- Department of Chemistry, University of Tennessee, Knoxville, TN 37920, United States of America
| | - Blake Mertz
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV 26506, United States of America; West Virginia University Cancer Institute, Morgantown, WV 26506, United States of America
| | - Rana Ashkar
- Department of Physics, Virginia Tech, Blacksburg, VA 24061, United States of America; Center for Soft Matter and Biological Physics, Virginia Tech, Blacksburg, VA 24061, United States of America.
| | - Francisco N Barrera
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville 37996, United States of America.
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2
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Sharma KD, Doktorova M, Waxham MN, Heberle FA. Cryo-EM images of phase-separated lipid bilayer vesicles analyzed with a machine-learning approach. Biophys J 2024; 123:2877-2891. [PMID: 38689500 DOI: 10.1016/j.bpj.2024.04.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 03/08/2024] [Accepted: 04/26/2024] [Indexed: 05/02/2024] Open
Abstract
Lateral lipid heterogeneity (i.e., raft formation) in biomembranes plays a functional role in living cells. Three-component mixtures of low- and high-melting lipids plus cholesterol offer a simplified experimental model for raft domains in which a liquid-disordered (Ld) phase coexists with a liquid-ordered (Lo) phase. Using such models, we recently showed that cryogenic electron microscopy (cryo-EM) can detect phase separation in lipid vesicles based on differences in bilayer thickness. However, the considerable noise within cryo-EM data poses a significant challenge for accurately determining the membrane phase state at high spatial resolution. To this end, we have developed an image-processing pipeline that utilizes machine learning (ML) to predict the bilayer phase in projection images of lipid vesicles. Importantly, the ML method exploits differences in both the thickness and molecular density of Lo compared to Ld, which leads to improved phase identification. To assess accuracy, we used artificial images of phase-separated lipid vesicles generated from all-atom molecular dynamics simulations of Lo and Ld phases. Synthetic ground-truth data sets mimicking a series of compositions along a tieline of Ld + Lo coexistence were created and then analyzed with various ML models. For all tieline compositions, we find that the ML approach can correctly identify the bilayer phase with >90% accuracy, thus providing a means to isolate the intensity profiles of coexisting Ld and Lo phases, as well as accurately determine domain-size distributions, number of domains, and phase-area fractions. The method described here provides a framework for characterizing nanoscopic lateral heterogeneities in membranes and paves the way for a more detailed understanding of raft properties in biological contexts.
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Affiliation(s)
- Karan D Sharma
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee
| | - Milka Doktorova
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia
| | - M Neal Waxham
- Department of Neurobiology and Anatomy, University of Texas Health Science Center, Houston, Texas
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3
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Park S, Kim J, Oh SS, Choi SQ. Arginine-Rich Cell-Penetrating Peptides Induce Lipid Rearrangements for Their Active Translocation across Laterally Heterogeneous Membranes. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2404563. [PMID: 38932459 PMCID: PMC11348069 DOI: 10.1002/advs.202404563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2024] [Revised: 06/01/2024] [Indexed: 06/28/2024]
Abstract
Arginine-rich cell-penetrating peptides (CPPs) have emerged as valuable tools for the intracellular delivery of bioactive molecules, but their membrane perturbation during cell penetration is not fully understood. Here, nona-arginine (R9)-mediated membrane reorganization that facilitates the translocation of peptides across laterally heterogeneous membranes is directly visualized. The electrostatic binding of cationic R9 to anionic phosphatidylserine (PS)-enriched domains on a freestanding lipid bilayer induces lateral lipid rearrangements; in particular, in real-time it is observed that R9 fluidizes PS-rich liquid-ordered (Lo) domains into liquid-disordered (Ld) domains, resulting in the membrane permeabilization. The experiments with giant unilamellar vesicles (GUVs) confirm the preferential translocation of R9 through Ld domains without pore formation, even when Lo domains are more negatively charged. Indeed, whenever R9 comes into contact with negatively charged Lo domains, it dissolves the Lo domains first, promoting translocation across phase-separated membranes. Collectively, the findings imply that arginine-rich CPPs modulate lateral membrane heterogeneity, including membrane fluidization, as one of the fundamental processes for their effective cell penetration across densely packed lipid bilayers.
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Affiliation(s)
- Sujin Park
- Department of Chemical and Biomolecular EngineeringKorea Advanced Institute of Science and Technology (KAIST)Daejeon34141Republic of Korea
| | - Jinmin Kim
- Department of Materials Science and EngineeringPohang University of Science and Technology (POSTECH)Pohang37673Republic of Korea
| | - Seung Soo Oh
- Department of Materials Science and EngineeringPohang University of Science and Technology (POSTECH)Pohang37673Republic of Korea
- Institute for Convergence Research and Education in Advanced Technology (I‐CREATE)Yonsei UniversityIncheon21983Republic of Korea
| | - Siyoung Q. Choi
- Department of Chemical and Biomolecular EngineeringKorea Advanced Institute of Science and Technology (KAIST)Daejeon34141Republic of Korea
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4
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Caselli L, Conti L, De Santis I, Berti D. Small-angle X-ray and neutron scattering applied to lipid-based nanoparticles: Recent advancements across different length scales. Adv Colloid Interface Sci 2024; 327:103156. [PMID: 38643519 DOI: 10.1016/j.cis.2024.103156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 02/28/2024] [Accepted: 04/08/2024] [Indexed: 04/23/2024]
Abstract
Lipid-based nanoparticles (LNPs), ranging from nanovesicles to non-lamellar assemblies, have gained significant attention in recent years, as versatile carriers for delivering drugs, vaccines, and nutrients. Small-angle scattering methods, employing X-rays (SAXS) or neutrons (SANS), represent unique tools to unveil structure, dynamics, and interactions of such particles on different length scales, spanning from the nano to the molecular scale. This review explores the state-of-the-art on scattering methods applied to unveil the structure of lipid-based nanoparticles and their interactions with drugs and bioactive molecules, to inform their rational design and formulation for medical applications. We will focus on complementary information accessible with X-rays or neutrons, ranging from insights on the structure and colloidal processes at a nanoscale level (SAXS) to details on the lipid organization and molecular interactions of LNPs (SANS). In addition, we will review new opportunities offered by Time-resolved (TR)-SAXS and -SANS for the investigation of dynamic processes involving LNPs. These span from real-time monitoring of LNPs structural evolution in response to endogenous or external stimuli (TR-SANS), to the investigation of the kinetics of lipid diffusion and exchange upon interaction with biomolecules (TR-SANS). Finally, we will spotlight novel combinations of SAXS and SANS with complementary on-line techniques, recently enabled at Large Scale Facilities for X-rays and neutrons. This emerging technology enables synchronized multi-method investigation, offering exciting opportunities for the simultaneous characterization of the structure and chemical or mechanical properties of LNPs.
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Affiliation(s)
- Lucrezia Caselli
- Physical Chemistry 1, University of Lund, S-221 00 Lund, Sweden.
| | - Laura Conti
- Consorzio Sistemi a Grande Interfase, Department of Chemistry, University of Florence, Sesto Fiorentino, Italy
| | - Ilaria De Santis
- Department of Chemistry, University of Florence, Via della Lastruccia 3, Sesto Fiorentino, Florence 50019, Italy
| | - Debora Berti
- Department of Chemistry, University of Florence, Via della Lastruccia 3, Sesto Fiorentino, Florence 50019, Italy; Consorzio Sistemi a Grande Interfase, Department of Chemistry, University of Florence, Sesto Fiorentino, Italy.
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5
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Doktorova M, Khelashvili G, Brown MF. Efficient calculation of orientation-dependent lipid dynamics from membrane simulations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.05.23.542012. [PMID: 37292992 PMCID: PMC10245828 DOI: 10.1101/2023.05.23.542012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Molecular dynamics simulations of lipid membranes have become increasingly impactful in biophysics because they offer atomistic resolution of structural fluctuations in relation to their functional outputs. Yet quantitative characterization of multiscale processes is a formidable challenge due to the distribution of motions that evade analysis of discrete simulation data. Here we investigate the efficient calculation of CH bond relaxation rates from membrane simulations. Widely used computational approaches offer numerical simplicity but fall short of capturing crucial aspects of the orientation dependence of the dynamics. To circumvent this problem, we introduced a robust framework based on liquid crystal theory which considers explicitly the CH bond motions with respect to the director axis (bilayer normal). Analysis of the orientation dependence of the dynamics shows excellent agreement with experiment, illustrating how the ordering potential affects the calculated relaxation rates. Furthermore, a fit-based resampling of the autocorrelation function of the bond fluctuations validates the new approach for low-temporal resolution data. The recovered relaxation rates indicate that at short timescales, both with and without cholesterol, the local motions of CH bonds describe the bilayer microviscosity and resemble liquid hydrocarbons. Our results establish the critical role of the orientational anisotropy in analysis of membrane simulations, explain fundamental aspects of lipid dynamics, and provide guidelines for extracting information that can be compared to experimental data.
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Affiliation(s)
- Milka Doktorova
- Department of Molecular Physiology & Biological Physics, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - George Khelashvili
- Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University, New York, NY, USA
- Institute of Computational Biomedicine, Weill Cornell Medical College of Cornell University, New York, NY, USA
| | - Michael F. Brown
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, USA
- Department of Physics, University of Arizona, Tucson, AZ, USA
- Program in Applied Mathematics, University of Arizona, Tucson, AZ, USA
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6
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Javanainen M, Heftberger P, Madsen JJ, Miettinen MS, Pabst G, Ollila OHS. Quantitative Comparison against Experiments Reveals Imperfections in Force Fields' Descriptions of POPC-Cholesterol Interactions. J Chem Theory Comput 2023; 19:6342-6352. [PMID: 37616238 PMCID: PMC10536986 DOI: 10.1021/acs.jctc.3c00648] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Indexed: 08/26/2023]
Abstract
Cholesterol is a central building block in biomembranes, where it induces orientational order, slows diffusion, renders the membrane stiffer, and drives domain formation. Molecular dynamics (MD) simulations have played a crucial role in resolving these effects at the molecular level; yet, it has recently become evident that different MD force fields predict quantitatively different behavior. Although easily neglected, identifying such limitations is increasingly important as the field rapidly progresses toward simulations of complex membranes mimicking the in vivo conditions: pertinent multicomponent simulations must capture accurately the interactions between their fundamental building blocks, such as phospholipids and cholesterol. Here, we define quantitative quality measures for simulations of binary lipid mixtures in membranes against the C-H bond order parameters and lateral diffusion coefficients from NMR spectroscopy as well as the form factors from X-ray scattering. Based on these measures, we perform a systematic evaluation of the ability of commonly used force fields to describe the structure and dynamics of binary mixtures of palmitoyloleoylphosphatidylcholine (POPC) and cholesterol. None of the tested force fields clearly outperforms the others across the tested properties and conditions. Still, the Slipids parameters provide the best overall performance in our tests, especially when dynamic properties are included in the evaluation. The quality evaluation metrics introduced in this work will, particularly, foster future force field development and refinement for multicomponent membranes using automated approaches.
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Affiliation(s)
- Matti Javanainen
- Institute
of Organic Chemistry and Biochemistry, Academy
of Sciences of the Czech Republic, 16000 Prague 6, Czech Republic
- Institute
of Biotechnology, University of Helsinki, 00790 Helsinki, Finland
| | - Peter Heftberger
- Biophysics,
Institute of Molecular Biosciences, NAWI Graz, University of Graz, 8010 Graz, Austria
| | - Jesper J. Madsen
- Global
and Planetary Health, College of Public Health, University of South Florida, Tampa, Florida 33612, United States
- Center
for Global Health and Infectious Diseases Research, College of Public
Health, University of South Florida, Tampa, Florida 33612, United States
- Department
of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida 33612, United States
| | - Markus S. Miettinen
- Fachbereich
Physik, Freie Universität Berlin, 14195 Berlin, Germany
- Department
of Chemistry, University of Bergen, 5007 Bergen, Norway
- Computational
Biology Unit, Department of Informatics, University of Bergen, 5008 Bergen, Norway
| | - Georg Pabst
- Biophysics,
Institute of Molecular Biosciences, NAWI Graz, University of Graz, 8010 Graz, Austria
- BioTechMed-Graz, 8010 Graz, Austria
- Field of Excellence
BioHealth—University of Graz, 8010 Graz, Austria
| | - O. H. Samuli Ollila
- Institute
of Biotechnology, University of Helsinki, 00790 Helsinki, Finland
- VTT Technical Research Centre of Finland, 02150 Espoo, Finland
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7
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Sharma KD, Heberle FA, Waxham MN. Visualizing lipid membrane structure with cryo-EM: past, present, and future. Emerg Top Life Sci 2023; 7:55-65. [PMID: 36606590 PMCID: PMC10355340 DOI: 10.1042/etls20220090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/14/2022] [Accepted: 12/20/2022] [Indexed: 01/07/2023]
Abstract
The development of electron cryomicroscopy (cryo-EM) has evolved immensely in the last several decades and is now well-established in the analysis of protein structure both in isolation and in their cellular context. This review focuses on the history and application of cryo-EM to the analysis of membrane architecture. Parallels between the levels of organization of protein structure are useful in organizing the discussion of the unique parameters that influence membrane structure and function. Importantly, the timescales of lipid motion in bilayers with respect to the timescales of sample vitrification is discussed and reveals what types of membrane structure can be reliably extracted in cryo-EM images of vitrified samples. Appreciating these limitations, a review of the application of cryo-EM to examine the lateral organization of ordered and disordered domains in reconstituted and biologically derived membranes is provided. Finally, a brief outlook for further development and application of cryo-EM to the analysis of membrane architecture is provided.
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Affiliation(s)
- Karan D. Sharma
- Department of Chemistry, University of Tennessee, Knoxville, TN
| | | | - M. Neal Waxham
- Department of Neurobiology and Anatomy, University of Texas Health Science Center, Houston, TX
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8
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Bjørnestad V, Lund R. Pathways of Membrane Solubilization: A Structural Study of Model Lipid Vesicles Exposed to Classical Detergents. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:3914-3933. [PMID: 36893452 PMCID: PMC10035035 DOI: 10.1021/acs.langmuir.2c03207] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 02/17/2023] [Indexed: 06/18/2023]
Abstract
Understanding the pathways of solubilization of lipid membranes is of high importance for their use in biotechnology and industrial applications. Although lipid vesicle solubilization by classical detergents has been widely investigated, there are few systematic structural and kinetic studies where different detergents are compared under varying conditions. This study used small-angle X-ray scattering to determine the structures of lipid/detergent aggregates at different ratios and temperatures and studied the solubilization in time using the stopped-flow technique. Membranes composed of either of two zwitterionic lipids, DMPC or DPPC, and their interactions with three different detergents, sodium dodecyl sulfate (SDS), n-dodecyl-beta-maltoside (DDM), and Triton X-100 (TX-100), were tested. The detergent TX-100 can cause the formation of collapsed vesicles with a rippled bilayer structure that is highly resistant to TX-100 insertion at low temperatures, while at higher temperatures, it partitions and leads to the restructuring of vesicles. DDM also causes this restructuring into multilamellar structures at subsolubilizing concentrations. In contrast, partitioning of SDS does not alter the vesicle structure below the saturation limit. Solubilization is more efficient in the gel phase for TX-100 but only if the cohesive energy of the bilayer does not prevent sufficient partitioning of the detergent. DDM and SDS show less temperature dependence compared to TX-100. Kinetic measurements reveal that solubilization of DPPC largely occurs through a slow extraction of lipids, whereas DMPC solubilization is dominated by fast and burst-like solubilization of the vesicles. The final structures obtained seem to preferentially be discoidal micelles where the detergent can distribute in excess along the rim of the disc, although we do observe the formation of worm- and rodlike micelles in the case of solubilization of DDM. Our results are in line with the suggested theory that bilayer rigidity is the main factor influencing which aggregate is formed.
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9
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Castillo SR, Rickeard BW, DiPasquale M, Nguyen MHL, Lewis-Laurent A, Doktorova M, Kav B, Miettinen MS, Nagao M, Kelley EG, Marquardt D. Probing the Link between Pancratistatin and Mitochondrial Apoptosis through Changes in the Membrane Dynamics on the Nanoscale. Mol Pharm 2022; 19:1839-1852. [PMID: 35559658 DOI: 10.1021/acs.molpharmaceut.1c00926] [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: 11/28/2022]
Abstract
Pancratistatin (PST) is a natural antiviral alkaloid that has demonstrated specificity toward cancerous cells and explicitly targets the mitochondria. PST initiates apoptosis while leaving healthy, noncancerous cells unscathed. However, the manner by which PST induces apoptosis remains elusive and impedes the advancement of PST as a natural anticancer therapeutic agent. Herein, we use neutron spin-echo (NSE) spectroscopy, molecular dynamics (MD) simulations, and supporting small angle scattering techniques to study PST's effect on membrane dynamics using biologically representative model membranes. Our data suggests that PST stiffens the inner mitochondrial membrane (IMM) by being preferentially associated with cardiolipin, which would lead to the relocation and release of cytochrome c. Second, PST has an ordering effect on the lipids and disrupts their distribution within the IMM, which would interfere with the maintenance and functionality of the active forms of proteins in the electron transport chain. These previously unreported findings implicate PST's effect on mitochondrial apoptosis.
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Affiliation(s)
- Stuart R Castillo
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario N9B 3P4, Canada
| | - Brett W Rickeard
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario N9B 3P4, Canada
| | - Mitchell DiPasquale
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario N9B 3P4, Canada
| | - Michael H L Nguyen
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario N9B 3P4, Canada
| | - Aislyn Lewis-Laurent
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario N9B 3P4, Canada
| | - Milka Doktorova
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, Virginia 22903, United States
| | - Batuhan Kav
- Max-Planck Institute of Colloids and Interfaces, Potsdam 14476, Germany.,Institute of Biological Information Processing: Structural Biochemistry (IBI-7), Forschungszentrum Julich, Julich 52428, Germany
| | | | - Michihiro Nagao
- National Institute of Standards and Technology, Center for Neutron Research, Gaithersburg, Maryland 20899, United States.,Department of Materials Science and Engineering, University of Maryland, College Park, Maryland 20742, United States.,Department of Physics and Astronomy, University of Delaware, Newark, Delaware 19716, United States
| | - Elizabeth G Kelley
- National Institute of Standards and Technology, Center for Neutron Research, Gaithersburg, Maryland 20899, United States
| | - Drew Marquardt
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario N9B 3P4, Canada.,Department of Physics, University of Windsor, Windsor, Ontario N9B 3P4, Canada
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10
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Benedetto A, Kelley EG. Absorption of the [bmim][Cl] Ionic Liquid in DMPC Lipid Bilayers across Their Gel, Ripple, and Fluid Phases. J Phys Chem B 2022; 126:3309-3318. [PMID: 35472281 PMCID: PMC9082605 DOI: 10.1021/acs.jpcb.2c00710] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 04/11/2022] [Indexed: 12/19/2022]
Abstract
Lipid bilayers are a key component of cell membranes and play a crucial role in life and in bio-nanotechnology. As a result, controlling their physicochemical properties holds the promise of effective therapeutic strategies. Ionic liquids (ILs)─a vast class of complex organic electrolytes─have shown a high degree of affinity with lipid bilayers and can be exploited in this context. However, the chemical physics of IL absorption and partitioning into lipid bilayers is yet to be fully understood. This work focuses on the absorption of the model IL [bmim][Cl] into 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) lipid bilayers across their gel, ripple, and fluid phases. Here, by small-angle neutron scattering, we show that (i) the IL cations are absorbed in the lipid bilayer in all its thermodynamic phases and (ii) the amount of IL inserted into the lipid phase increased with increasing temperature, changing from three to four IL cations per 10 lipids with increasing temperature from 10 °C in the gel phase to 40 °C in the liquid phase, respectively. An explicative hypothesis, based on the entropy gain coming from the IL hydration water, is presented to explain the observed temperature trend. The ability to control IL absorption with temperature can be used as a handle to tune the effect of ILs on biomembranes and can be exploited in bio-nanotechnological applications.
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Affiliation(s)
- Antonio Benedetto
- Department
of Science, University of Roma Tre, 00146 Rome, Italy
- School
of Physics, and Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin 4, Ireland
- Laboratory
for Neutron Scattering, Paul Scherrer Institute, 5232 Villigen, Switzerland
| | - Elizabeth G. Kelley
- NIST
Center for Neutron Research, National Institute
of Standards and Technology, Gaithersburg, Maryland 20899, United States
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11
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Lewis-Laurent A, Doktorova M, Heberle FA, Marquardt D. Vesicle Viewer: Online visualization and analysis of small-angle scattering from lipid vesicles. Biophys J 2021; 120:4639-4648. [PMID: 34571013 DOI: 10.1016/j.bpj.2021.09.018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 07/26/2021] [Accepted: 09/09/2021] [Indexed: 10/20/2022] Open
Abstract
Small-angle X-ray and neutron scattering are among the most powerful experimental techniques for investigating the structure of biological membranes. Much of the critical information contained in small-angle scattering (SAS) data is not easily accessible to researchers who have limited time to analyze results by hand or to nonexperts who may lack the necessary scientific background to process such data. Easy-to-use data visualization software can allow them to take full advantage of their SAS data and maximize the use of limited resources. To this end, we developed an internet-based application called Vesicle Viewer to visualize and analyze SAS data from unilamellar lipid bilayer vesicles. Vesicle Viewer utilizes a modified scattering density profile (SDP) analysis called EZ-SDP in which key bilayer structural parameters, such as area per lipid and bilayer thickness, are easily and robustly determined. Notably, we introduce a bilayer model that is able to describe an asymmetric bilayer, whether it be chemically or isotopically asymmetric. The application primarily uses Django, a Python package specialized for the development of robust web applications. In addition, several other libraries are used to support the more technical aspects of the project; notable examples are Matplotlib (for graphs) and NumPy (for calculations). By eliminating the barrier of downloading and installing software, this web-based application will allow scientists to analyze their own vesicle scattering data using their preferred operating system. The web-based application can be found at https://vesicleviewer.dmarquardt.ca/.
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Affiliation(s)
- Aislyn Lewis-Laurent
- Department of Chemistry & Biochemistry, University of Windsor, Windsor, Ontario, Canada
| | - Milka Doktorova
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, Virginia
| | | | - Drew Marquardt
- Department of Chemistry & Biochemistry, University of Windsor, Windsor, Ontario, Canada; Department of Physics, University of Windsor, Windsor, Ontario, Canada.
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12
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Abstract
Cell membranes - primarily composed of lipids, sterols, and proteins - form a dynamic interface between living cells and their environment. They act as a mechanical barrier around the cell while selectively facilitating material transport, signal transduction, and various other functions necessary for the cell viability. The complex functionality of cell membranes and the hierarchical motions and responses they exhibit demand a thorough understanding of the origin of different membrane dynamics and how they are influenced by molecular additives and environmental cues. These dynamic modes include single-molecule diffusion, thermal fluctuations, and large-scale membrane deformations, to name a few. This review highlights advances in investigating structure-driven dynamics associated with model cell membranes, with a particular focus on insights gained from neutron scattering and spectroscopy experiments. We discuss the uniqueness of neutron contrast variation and its remarkable potential in probing selective membrane structure and dynamics on spatial and temporal scales over which key biological functions occur. We also present a summary of current and future opportunities in synergistic combinations of neutron scattering with molecular dynamics (MD) simulations to gain further understanding of the molecular mechanisms underlying complex membrane functions.
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Affiliation(s)
- Sudipta Gupta
- Department of Physics, Virginia Tech, Blacksburg, VA 24061, USA. and Center for Soft Matter and Biological Physics, Virginia Tech, Blacksburg, VA 24061, USA
| | - Rana Ashkar
- Department of Physics, Virginia Tech, Blacksburg, VA 24061, USA. and Center for Soft Matter and Biological Physics, Virginia Tech, Blacksburg, VA 24061, USA
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Kinnun JJ, Scott HL, Ashkar R, Katsaras J. Biomembrane Structure and Material Properties Studied With Neutron Scattering. Front Chem 2021; 9:642851. [PMID: 33987167 PMCID: PMC8110834 DOI: 10.3389/fchem.2021.642851] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 03/16/2021] [Indexed: 12/12/2022] Open
Abstract
Cell membranes and their associated structures are dynamical supramolecular structures where different physiological processes take place. Detailed knowledge of their static and dynamic structures is therefore needed, to better understand membrane biology. The structure–function relationship is a basic tenet in biology and has been pursued using a range of different experimental approaches. In this review, we will discuss one approach, namely the use of neutron scattering techniques as applied, primarily, to model membrane systems composed of lipid bilayers. An advantage of neutron scattering, compared to other scattering techniques, is the differential sensitivity of neutrons to isotopes of hydrogen and, as a result, the relative ease of altering sample contrast by substituting protium for deuterium. This property makes neutrons an ideal probe for the study of hydrogen-rich materials, such as biomembranes. In this review article, we describe isotopic labeling studies of model and viable membranes, and discuss novel applications of neutron contrast variation in order to gain unique insights into the structure, dynamics, and molecular interactions of biological membranes. We specifically focus on how small-angle neutron scattering data is modeled using different contrast data and molecular dynamics simulations. We also briefly discuss neutron reflectometry and present a few recent advances that have taken place in neutron spin echo spectroscopy studies and the unique membrane mechanical data that can be derived from them, primarily due to new models used to fit the data.
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Affiliation(s)
- Jacob J Kinnun
- Large Scale Structures Group, Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States.,Oak Ridge National Laboratory, Shull-Wollan Center, Oak Ridge, TN, United States
| | - Haden L Scott
- Large Scale Structures Group, Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States.,Oak Ridge National Laboratory, Shull-Wollan Center, Oak Ridge, TN, United States
| | - Rana Ashkar
- Department of Physics, Virginia Tech, Blacksburg, VA, United States.,Center for Soft Matter and Biological Physics, Virginia Tech, Blacksburg, VA, United States
| | - John Katsaras
- Oak Ridge National Laboratory, Shull-Wollan Center, Oak Ridge, TN, United States.,Sample Environment Group, Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States.,Department of Physics and Astronomy, University of Tennessee, Knoxville, TN, United States
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14
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Chappa V, Smirnova Y, Komorowski K, Müller M, Salditt T. The effect of polydispersity, shape fluctuations and curvature on small unilamellar vesicle small-angle X-ray scattering curves. J Appl Crystallogr 2021; 54:557-568. [PMID: 33953656 PMCID: PMC8056763 DOI: 10.1107/s1600576721001461] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 02/08/2021] [Indexed: 11/27/2022] Open
Abstract
It is a challenge to distinguish the effect of shape fluctuations and size polydispersity on experimental small-angle X-ray scattering curves of small unilamellar vesicles. Here it is shown that both effects have distinguishable spectral patterns, and an efficient simulation tool is presented for simulating and analysing experimental data. The importance of curvature-induced electron-density profile asymmetry for estimating the vesicle size from SAXS scattering curves is also demonstrated. Small unilamellar vesicles (20–100 nm diameter) are model systems for strongly curved lipid membranes, in particular for cell organelles. Routinely, small-angle X-ray scattering (SAXS) is employed to study their size and electron-density profile (EDP). Current SAXS analysis of small unilamellar vesicles (SUVs) often employs a factorization into the structure factor (vesicle shape) and the form factor (lipid bilayer electron-density profile) and invokes additional idealizations: (i) an effective polydispersity distribution of vesicle radii, (ii) a spherical vesicle shape and (iii) an approximate account of membrane asymmetry, a feature particularly relevant for strongly curved membranes. These idealizations do not account for thermal shape fluctuations and also break down for strong salt- or protein-induced deformations, as well as vesicle adhesion and fusion, which complicate the analysis of the lipid bilayer structure. Presented here are simulations of SAXS curves of SUVs with experimentally relevant size, shape and EDPs of the curved bilayer, inferred from coarse-grained simulations and elasticity considerations, to quantify the effects of size polydispersity, thermal fluctuations of the SUV shape and membrane asymmetry. It is observed that the factorization approximation of the scattering intensity holds even for small vesicle radii (∼30 nm). However, the simulations show that, for very small vesicles, a curvature-induced asymmetry arises in the EDP, with sizeable effects on the SAXS curve. It is also demonstrated that thermal fluctuations in shape and the size polydispersity have distinguishable signatures in the SAXS intensity. Polydispersity gives rise to low-q features, whereas thermal fluctuations predominantly affect the scattering at larger q, related to membrane bending rigidity. Finally, it is shown that simulation of fluctuating vesicle ensembles can be used for analysis of experimental SAXS curves.
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Affiliation(s)
- Veronica Chappa
- Faculty of Physics, University of Göttingen, Friedrich-Hund-Platz 1, Göttingen 37077, Germany
| | - Yuliya Smirnova
- Faculty of Physics, University of Göttingen, Friedrich-Hund-Platz 1, Göttingen 37077, Germany
| | - Karlo Komorowski
- Faculty of Physics, University of Göttingen, Friedrich-Hund-Platz 1, Göttingen 37077, Germany
| | - Marcus Müller
- Faculty of Physics, University of Göttingen, Friedrich-Hund-Platz 1, Göttingen 37077, Germany
| | - Tim Salditt
- Faculty of Physics, University of Göttingen, Friedrich-Hund-Platz 1, Göttingen 37077, Germany
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15
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Semeraro EF, Marx L, Frewein MPK, Pabst G. Increasing complexity in small-angle X-ray and neutron scattering experiments: from biological membrane mimics to live cells. SOFT MATTER 2021; 17:222-232. [PMID: 32104874 DOI: 10.1039/c9sm02352f] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Small-angle X-ray and neutron scattering are well-established, non-invasive experimental techniques to interrogate global structural properties of biological membrane mimicking systems under physiologically relevant conditions. Recent developments, both in bottom-up sample preparation techniques for increasingly complex model systems, and in data analysis techniques have opened the path toward addressing long standing issues of biological membrane remodelling processes. These efforts also include emerging quantitative scattering studies on live cells, thus enabling a bridging of molecular to cellular length scales. Here, we review recent progress in devising compositional models for joint small-angle X-ray and neutron scattering studies on diverse membrane mimics - with a specific focus on membrane structural coupling to amphiphatic peptides and integral proteins - and live Escherichia coli. In particular, we outline the present state-of-the-art in small-angle scattering methods applied to complex membrane systems, highlighting how increasing system complexity must be followed by an advance in compositional modelling and data-analysis tools.
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Affiliation(s)
- Enrico F Semeraro
- University of Graz, Institute of Molecular Biosciences, Biophysics Division, NAWI Graz, 8010 Graz, Austria. and BioTechMed Graz, 8010 Graz, Austria
| | - Lisa Marx
- University of Graz, Institute of Molecular Biosciences, Biophysics Division, NAWI Graz, 8010 Graz, Austria. and BioTechMed Graz, 8010 Graz, Austria
| | - Moritz P K Frewein
- University of Graz, Institute of Molecular Biosciences, Biophysics Division, NAWI Graz, 8010 Graz, Austria. and BioTechMed Graz, 8010 Graz, Austria and Institut Laue-Langevin, 38000 Grenoble, France
| | - Georg Pabst
- University of Graz, Institute of Molecular Biosciences, Biophysics Division, NAWI Graz, 8010 Graz, Austria. and BioTechMed Graz, 8010 Graz, Austria
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16
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Tan L, Elkins JG, Davison BH, Kelley EG, Nickels J. Implementation of a self-consistent slab model of bilayer structure in the SasView suite. J Appl Crystallogr 2021; 54:10.1107/s1600576720015526. [PMID: 37965294 PMCID: PMC10644672 DOI: 10.1107/s1600576720015526] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 11/23/2020] [Indexed: 11/10/2022] Open
Abstract
Slab models are simple and useful structural descriptions which have long been used to describe lyotropic lamellar phases, such as lipid bilayers. Typically, slab models assume a midline symmetry and break a bilayer structure into three pieces, a central solvent-free core and two symmetric outer layers composed of the soluble portion of the amphiphile and associated solvent. This breakdown matches reasonably well to the distribution of neutron scattering length density and therefore is a convenient and common approach for the treatment of small-angle scattering data. Here, an implementation of this model within the SasView software suite is reported. The implementation is intended to provide physical consistency through the area per amphiphile molecule and number of solvent molecules included within the solvent-exposed outer layer. The proper use of this model requires knowledge of (or good estimates for) the amphiphile and solvent molecule volume and atomic composition, ultimately providing a self-consistent data treatment with only two free parameters: the lateral area per amphiphile molecule and the number of solvent molecules included in the outer region per amphiphile molecule. The use of this code is demonstrated in the fitting of standard lipid bilayer data sets, obtaining structural parameters consistent with prior literature and illustrating the typical and ideal cases of fitting for neutron scattering data obtained using single or multiple contrast conditions. While demonstrated here for lipid bilayers, this model is intended for general application to block copolymers, surfactants, and other lyotropic lamellar phase structures for which a slab model is able to reasonably estimate the neutron scattering length density/electron-density profile of inner and outer layers of the lamellae.
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Affiliation(s)
- Luoxi Tan
- Department of Chemical and Environmental Engineering, University of Cincinnati, 2901 Woodside Drive, Cincinnati, OH 45221, USA
| | - James G. Elkins
- Biosciences Division, Oak Ridge National Laboratory, PO Box 2008, Oak Ridge, TN 37831, USA
| | - Brian H. Davison
- Biosciences Division, Oak Ridge National Laboratory, PO Box 2008, Oak Ridge, TN 37831, USA
| | - Elizabeth G. Kelley
- Center for Neutron Research, National Institute of Standards and Technology, Gaithersberg, MD 20899, USA
| | - Jonathan Nickels
- Department of Chemical and Environmental Engineering, University of Cincinnati, 2901 Woodside Drive, Cincinnati, OH 45221, USA
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17
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Zienkiewicz-Strzałka M, Deryło-Marczewska A. Small AgNP in the Biopolymer Nanocomposite System. Int J Mol Sci 2020; 21:ijms21249388. [PMID: 33317218 PMCID: PMC7763337 DOI: 10.3390/ijms21249388] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 12/06/2020] [Accepted: 12/07/2020] [Indexed: 12/25/2022] Open
Abstract
In this work, ultra-small and stable silver nanoparticles (AgNP) on chitosan biopolymer (BP/AgP) were prepared by in situ reduction of the diamminesilver(I) complex ([Ag(NH3)2]+) to create a biostatic membrane system. The small AgNP (3 nm) as a stable source of silver ions, their crystal form, and homogeneous distribution in the whole solid membrane were confirmed by transmission electron microscopy (TEM), scanning electron microscopy (SEM), and atomic force microscopy (AFM). The X-ray photoelectron spectroscopy (XPS) and Auger analysis were applied to investigate the elemental composition, concentration, and chemical state of surface atoms. It was found that ultra-small metallic nanoparticles might form a steady source of silver ions and enhance the biostatic properties of solid membranes. Ultra-small AgNP with disturbed electronic structure and plasmonic properties may generate interaction between amine groups of the biopolymer for improving the homogeneity of the nanometallic layer. In this work, the significant differences between the typical way (deposition of ex-situ-prepared AgNP) and the proposed in-situ synthesis approach were determined. The improved thermal stability (by thermogravimetry and differential scanning calorimetry (TG/DSC) analysis) for BP/AgP was observed and explained by the presence of the protective layer of a low-molecular silver phase. Finally, the antibacterial activity of the BP/AgP nanocomposite was tested using selected bacteria biofilms. The grafted membrane showed clear inhibition properties by destruction and multiple damages of bacteria cells. The possible mechanisms of biocidal activity were discussed, and the investigation of the AgNP influence on the bacteria body was illustrated by AFM measurements. The results obtained concluded that the biopolymer membrane properties were significantly improved by the integration with ultra-small Ag nanoparticles, which added value to its applications as a biostatic membrane system for filtration and separation issues.
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18
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Andersson J, Bilotto P, Mears LLE, Fossati S, Ramach U, Köper I, Valtiner M, Knoll W. Solid-supported lipid bilayers - A versatile tool for the structural and functional characterization of membrane proteins. Methods 2020; 180:56-68. [PMID: 32920130 DOI: 10.1016/j.ymeth.2020.09.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 09/07/2020] [Accepted: 09/08/2020] [Indexed: 02/07/2023] Open
Abstract
The cellular membrane is central to the development of single-and multicellular life, as it separates the delicate cellular interior from the hostile environment. It exerts tight control over entry and exit of substances, is responsible for signaling with other cells in multicellular organisms and prevents pathogens from entering the cell. In the case of bacteria and viruses, the cellular membrane also hosts the proteins enabling invasion of the host organism. In a very real sense therefore, the cellular membrane is central to all life. The study of the cell membrane and membrane proteins in particular has therefore attracted significant attention. Due to the enormous variety of tasks performed by the membrane, it is a highly complex and challenging structure to study. Ideally, membrane components would be studied in isolation from this environment, but unlike water soluble proteins, the amphiphilic environment provided by the cellular membrane is key to the structure and function of the cell membrane. Therefore, model membranes have been developed to provide an environment in which a membrane protein can be studied. This review presents a set of tools that enable the comprehensive characterization of membrane proteins: electrochemical tools, surface plasmon resonance, neutron scattering, the surface forces apparatus and atomic force microscopy are discussed, with a particular focus on experimental technique and data evaluation.
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Affiliation(s)
| | - Pierluigi Bilotto
- Institute of Applied Physics, Vienna University of Technology, Vienna 1040, Austria
| | - Laura L E Mears
- Institute of Applied Physics, Vienna University of Technology, Vienna 1040, Austria
| | - Stefan Fossati
- AIT Austrian Institute of Technology, 1210 Vienna, Austria; Institute of Applied Physics, Vienna University of Technology, Vienna 1040, Austria
| | - Ulrich Ramach
- Institute of Applied Physics, Vienna University of Technology, Vienna 1040, Austria; CEST Kompetenzzentrum für elektrochemische Oberflächentechnologie, Wiener Neustadt 2700, Austria
| | - Ingo Köper
- Flinders Institute for Nanoscale Science and Technology, College of Science and Engineering, Flinders University, Adelaide, SA, Australia
| | - Markus Valtiner
- Institute of Applied Physics, Vienna University of Technology, Vienna 1040, Austria; CEST Kompetenzzentrum für elektrochemische Oberflächentechnologie, Wiener Neustadt 2700, Austria
| | - Wolfgang Knoll
- AIT Austrian Institute of Technology, 1210 Vienna, Austria; CEST Kompetenzzentrum für elektrochemische Oberflächentechnologie, Wiener Neustadt 2700, Austria
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19
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Direct label-free imaging of nanodomains in biomimetic and biological membranes by cryogenic electron microscopy. Proc Natl Acad Sci U S A 2020; 117:19943-19952. [PMID: 32759206 DOI: 10.1073/pnas.2002200117] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The nanoscale organization of biological membranes into structurally and compositionally distinct lateral domains is believed to be central to membrane function. The nature of this organization has remained elusive due to a lack of methods to directly probe nanoscopic membrane features. We show here that cryogenic electron microscopy (cryo-EM) can be used to directly image coexisting nanoscopic domains in synthetic and bioderived membranes without extrinsic probes. Analyzing a series of single-component liposomes composed of synthetic lipids of varying chain lengths, we demonstrate that cryo-EM can distinguish bilayer thickness differences as small as 0.5 Å, comparable to the resolution of small-angle scattering methods. Simulated images from computational models reveal that features in cryo-EM images result from a complex interplay between the atomic distribution normal to the plane of the bilayer and imaging parameters. Simulations of phase-separated bilayers were used to predict two sources of contrast between coexisting ordered and disordered phases within a single liposome, namely differences in membrane thickness and molecular density. We observe both sources of contrast in biomimetic membranes composed of saturated lipids, unsaturated lipids, and cholesterol. When extended to isolated mammalian plasma membranes, cryo-EM reveals similar nanoscale lateral heterogeneities. The methods reported here for direct, probe-free imaging of nanodomains in unperturbed membranes open new avenues for investigation of nanoscopic membrane organization.
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20
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Cheu C, Yang L, Nieh MP. Refining internal bilayer structure of bicelles resolved by extended-q small angle X-ray scattering. Chem Phys Lipids 2020; 231:104945. [PMID: 32621811 DOI: 10.1016/j.chemphyslip.2020.104945] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Revised: 06/18/2020] [Accepted: 06/26/2020] [Indexed: 11/15/2022]
Abstract
The internal profile across the bilayer reveals important structural information regarding the crystallinity of acyl chains or the positions of encapsulated species. Here, we demonstrate that a simple five-layer-core-shell discoidal model can be employed to best fit the extended-q small angle X-ray scattering (SAXS) data and resolve the bilayer internal structure (with sub-nanometer resolution) of a nanoscale discoidal system comprised of a mixture of long- and short- chain lipids (known as "bicelles"). In contrast to the traditional core-shell discoidal model, the detailed structure in the hydrophobic core such as the methylene and methyl groups can be distinguished via this model. The refined model is validated by the SAXS data of bicelles whose electron scattering length density of the hydrophobic core is adjusted by the addition of a long-chain lipid with a fluorine-end group. The higher resolution of the bilayer internal structure can be employed to advance our understanding of the interaction and conformation of the membrane and associated molecules, such as membrane-associated proteins and locations of entrapped species in the lipid nanoparticles.
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Affiliation(s)
- Catherine Cheu
- Polymer Program, Institute of Materials Science, University of Connecticut, Storrs, CT 06269, USA
| | - Lin Yang
- Brookhaven National Laboratory, PO Box 5000, Upton, NY 11973-5000, USA
| | - Mu-Ping Nieh
- Polymer Program, Institute of Materials Science, University of Connecticut, Storrs, CT 06269, USA; Department of Chemical and Biomolecular Engineering, University of Connecticut, Storrs, CT 06269, USA; Department of Biomedical Engineering, University of Connecticut, Storrs, CT 06269, USA.
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21
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Doktorova M, Kučerka N, Kinnun JJ, Pan J, Marquardt D, Scott HL, Venable RM, Pastor RW, Wassall SR, Katsaras J, Heberle FA. Molecular Structure of Sphingomyelin in Fluid Phase Bilayers Determined by the Joint Analysis of Small-Angle Neutron and X-ray Scattering Data. J Phys Chem B 2020; 124:5186-5200. [PMID: 32468822 DOI: 10.1021/acs.jpcb.0c03389] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
We have determined the fluid bilayer structure of palmitoyl sphingomyelin (PSM) and stearoyl sphingomyelin (SSM) by simultaneously analyzing small-angle neutron and X-ray scattering data. Using a newly developed scattering density profile (SDP) model for sphingomyelin lipids, we report structural parameters including the area per lipid, total bilayer thickness, and hydrocarbon thickness, in addition to lipid volumes determined by densitometry. Unconstrained all-atom simulations of PSM bilayers at 55 °C using the C36 CHARMM force field produced a lipid area of 56 Å2, a value that is 10% lower than the one determined experimentally by SDP analysis (61.9 Å2). Furthermore, scattering form factors calculated from the unconstrained simulations were in poor agreement with experimental form factors, even though segmental order parameter (SCD) profiles calculated from the simulations were in relatively good agreement with SCD profiles obtained from NMR experiments. Conversely, constrained area simulations at 61.9 Å2 resulted in good agreement between the simulation and experimental scattering form factors, but not with SCD profiles from NMR. We discuss possible reasons for the discrepancies between these two types of data that are frequently used as validation metrics for molecular dynamics force fields.
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Affiliation(s)
- Milka Doktorova
- Department of Integrative Biology and Pharmacology, University of Texas Health Science Center, Houston, Texas 77030, United States
| | - Norbert Kučerka
- Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, 141980 Dubna, Russia.,Department of Physical Chemistry of Drugs, Faculty of Pharmacy, Comenius University, 814 99 Bratislava, Slovakia
| | - Jacob J Kinnun
- Department of Physics, Indiana University-Purdue University Indianapolis, Indianapolis, Indiana 46202, United States
| | - Jianjun Pan
- Department of Physics, University of South Florida, Tampa, Florida 33620, United States
| | - Drew Marquardt
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, ON N9B 3P4, Canada
| | - Haden L Scott
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Richard M Venable
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Richard W Pastor
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Stephen R Wassall
- Department of Physics, Indiana University-Purdue University Indianapolis, Indianapolis, Indiana 46202, United States
| | - John Katsaras
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, United States
| | - Frederick A Heberle
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee 37996, United States
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22
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Komorowski K, Schaeper J, Sztucki M, Sharpnack L, Brehm G, Köster S, Salditt T. Vesicle adhesion in the electrostatic strong-coupling regime studied by time-resolved small-angle X-ray scattering. SOFT MATTER 2020; 16:4142-4154. [PMID: 32319505 DOI: 10.1039/d0sm00259c] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
We have used time-resolved small-angle X-ray scattering (SAXS) to study the adhesion of lipid vesicles in the electrostatic strong-coupling regime induced by divalent ions. The bilayer structure and the interbilayer distance dw between adhered vesicles was studied for different DOPC:DOPS mixtures varying the surface charge density of the membrane, as well as for different divalent ions, such as Ca2+, Sr2+, and Zn2+. The results are in good agreement with the strong coupling theory predicting the adhesion state and the corresponding like-charge attraction based on ion-correlations. Using SAXS combined with the stopped-flow rapid mixing technique, we find that in highly charged bilayers the adhesion state is only of transient nature, and that the adhering vesicles subsequently transform to a phase of multilamellar vesicles, again with an inter-bilayer distance according to the theory of strong binding. Aside from the stopped-flow SAXS instrumentations used primarily for these results, we also evaluate microfluidic sample environments for vesicle SAXS in view of future extension of this work.
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Affiliation(s)
- Karlo Komorowski
- Institute for X-Ray Physics, University of Göttingen, Friedrich-Hund-Platz 1, 37077 Göttingen, Germany.
| | - Jannis Schaeper
- Institute for X-Ray Physics, University of Göttingen, Friedrich-Hund-Platz 1, 37077 Göttingen, Germany.
| | - Michael Sztucki
- European Synchrotron Radiation Facility, CS 40220, 38043 Grenoble Cedex 9, France
| | - Lewis Sharpnack
- European Synchrotron Radiation Facility, CS 40220, 38043 Grenoble Cedex 9, France
| | - Gerrit Brehm
- Institute for X-Ray Physics, University of Göttingen, Friedrich-Hund-Platz 1, 37077 Göttingen, Germany.
| | - Sarah Köster
- Institute for X-Ray Physics, University of Göttingen, Friedrich-Hund-Platz 1, 37077 Göttingen, Germany.
| | - Tim Salditt
- Institute for X-Ray Physics, University of Göttingen, Friedrich-Hund-Platz 1, 37077 Göttingen, Germany.
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23
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Petukhov MV, Konarev PV, Dadinova LA, Fedorova NV, Volynsky PE, Svergun DI, Batishchev OV, Shtykova EV. Quasi-Atomistic Approach to Modeling of Liposomes. CRYSTALLOGR REP+ 2020. [DOI: 10.1134/s1063774520020182] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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24
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Scott HL, Skinkle A, Kelley EG, Waxham MN, Levental I, Heberle FA. On the Mechanism of Bilayer Separation by Extrusion, or Why Your LUVs Are Not Really Unilamellar. Biophys J 2019; 117:1381-1386. [PMID: 31586522 DOI: 10.1016/j.bpj.2019.09.006] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 08/18/2019] [Accepted: 09/10/2019] [Indexed: 11/18/2022] Open
Abstract
Extrusion through porous filters is a widely used method for preparing biomimetic model membranes. Of primary importance in this approach is the efficient production of single bilayer (unilamellar) vesicles that eliminate the influence of interlamellar interactions and strictly define the bilayer surface area available to external reagents such as proteins. Submicroscopic vesicles produced using extrusion are widely assumed to be unilamellar, and large deviations from this assumption would impact interpretations from many model membrane experiments. Using three probe-free methods-small angle X-ray and neutron scattering and cryogenic electron microscopy-we report unambiguous evidence of extensive multilamellarity in extruded vesicles composed of neutral phosphatidylcholine lipids, including for the common case of neutral lipids dispersed in physiological buffer and extruded through 100-nm diameter pores. In such preparations, only ∼35% of lipids are externally accessible and this fraction is highly dependent on preparation conditions. Charged lipids promote unilamellarity as does decreasing solvent ionic strength, indicating the importance of electrostatic interactions in determining the lamellarity of extruded vesicles. Smaller extrusion pore sizes also robustly increase the fraction of unilamellar vesicles, suggesting a role for membrane bending. Taken together, these observations suggest a mechanistic model for extrusion, wherein the formation of unilamellar vesicles involves competition between bilayer bending and adhesion energies. The findings presented here have wide-ranging implications for the design and interpretation of model membrane studies, especially ensemble-averaged observations relying on the assumption of unilamellarity.
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Affiliation(s)
- Haden L Scott
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee; Shull Wollan Center, Oak Ridge National Laboratory, Oak Ridge, Tennessee
| | - Allison Skinkle
- Department of Biosciences, Rice University, Houston, Texas; Department of Integrative Biology and Pharmacology, University of Texas Health Science Center, Houston, Texas
| | - Elizabeth G Kelley
- NIST Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland
| | - M Neal Waxham
- Department of Neurobiology and Anatomy, University of Texas Health Science Center, Houston, Texas
| | - Ilya Levental
- Department of Integrative Biology and Pharmacology, University of Texas Health Science Center, Houston, Texas.
| | - Frederick A Heberle
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee; Department of Integrative Biology and Pharmacology, University of Texas Health Science Center, Houston, Texas.
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25
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A biophysical study of the interactions between the antimicrobial peptide indolicidin and lipid model systems. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2019; 1861:1355-1364. [DOI: 10.1016/j.bbamem.2019.04.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 03/22/2019] [Accepted: 04/07/2019] [Indexed: 12/19/2022]
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26
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Komorowski K, Salditt A, Xu Y, Yavuz H, Brennich M, Jahn R, Salditt T. Vesicle Adhesion and Fusion Studied by Small-Angle X-Ray Scattering. Biophys J 2019; 114:1908-1920. [PMID: 29694868 PMCID: PMC5936998 DOI: 10.1016/j.bpj.2018.02.040] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 02/19/2018] [Accepted: 02/28/2018] [Indexed: 12/02/2022] Open
Abstract
We have studied the adhesion state (also denoted by docking state) of lipid vesicles as induced by the divalent ions Ca2+ or Mg2+ at well-controlled ion concentration, lipid composition, and charge density. The bilayer structure and the interbilayer distance in the docking state were analyzed by small-angle x-ray scattering. A strong adhesion state was observed for DOPC:DOPS vesicles, indicating like-charge attraction resulting from ion correlations. The observed interbilayer separations of ∼1.6 nm agree quantitatively with the predictions of electrostatics in the strong coupling regime. Although this phenomenon was observed when mixing anionic and zwitterionic (or neutral) lipids, pure anionic membranes (DOPS) with highest charge density σ resulted in a direct phase transition to a multilamellar state, which must be accompanied by rupture and fusion of vesicles. To extend the structural assay toward protein-controlled docking and fusion, we have characterized reconstituted N-ethylmaleimide-sensitive factor attachment protein receptors in controlled proteoliposome suspensions by small-angle x-ray scattering.
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Affiliation(s)
- Karlo Komorowski
- Institut für Röntgenphysik, Georg-August-Universität Göttingen, Göttingen, Germany; Department of Neurobiology, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany
| | - Annalena Salditt
- Institut für Röntgenphysik, Georg-August-Universität Göttingen, Göttingen, Germany
| | - Yihui Xu
- Institut für Röntgenphysik, Georg-August-Universität Göttingen, Göttingen, Germany
| | - Halenur Yavuz
- Department of Neurobiology, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany
| | - Martha Brennich
- European Molecular Biology Laboratory, Grenoble Outstation, Grenoble, France
| | - Reinhard Jahn
- Department of Neurobiology, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany
| | - Tim Salditt
- Institut für Röntgenphysik, Georg-August-Universität Göttingen, Göttingen, Germany.
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27
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Marrink SJ, Corradi V, Souza PC, Ingólfsson HI, Tieleman DP, Sansom MS. Computational Modeling of Realistic Cell Membranes. Chem Rev 2019; 119:6184-6226. [PMID: 30623647 PMCID: PMC6509646 DOI: 10.1021/acs.chemrev.8b00460] [Citation(s) in RCA: 422] [Impact Index Per Article: 84.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Indexed: 12/15/2022]
Abstract
Cell membranes contain a large variety of lipid types and are crowded with proteins, endowing them with the plasticity needed to fulfill their key roles in cell functioning. The compositional complexity of cellular membranes gives rise to a heterogeneous lateral organization, which is still poorly understood. Computational models, in particular molecular dynamics simulations and related techniques, have provided important insight into the organizational principles of cell membranes over the past decades. Now, we are witnessing a transition from simulations of simpler membrane models to multicomponent systems, culminating in realistic models of an increasing variety of cell types and organelles. Here, we review the state of the art in the field of realistic membrane simulations and discuss the current limitations and challenges ahead.
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Affiliation(s)
- Siewert J. Marrink
- Groningen
Biomolecular Sciences and Biotechnology Institute & Zernike Institute
for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Valentina Corradi
- Centre
for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Paulo C.T. Souza
- Groningen
Biomolecular Sciences and Biotechnology Institute & Zernike Institute
for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Helgi I. Ingólfsson
- Biosciences
and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94550, United States
| | - D. Peter Tieleman
- Centre
for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Mark S.P. Sansom
- Department
of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, U.K.
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28
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Doktorova M, Heberle FA, Marquardt D, Rusinova R, Sanford RL, Peyear TA, Katsaras J, Feigenson GW, Weinstein H, Andersen OS. Gramicidin Increases Lipid Flip-Flop in Symmetric and Asymmetric Lipid Vesicles. Biophys J 2019; 116:860-873. [PMID: 30755300 PMCID: PMC6400823 DOI: 10.1016/j.bpj.2019.01.016] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 01/03/2019] [Accepted: 01/09/2019] [Indexed: 01/06/2023] Open
Abstract
Unlike most transmembrane proteins, phospholipids can migrate from one leaflet of the membrane to the other. Because this spontaneous lipid translocation (flip-flop) tends to be very slow, cells facilitate the process with enzymes that catalyze the transmembrane movement and thereby regulate the transbilayer lipid distribution. Nonenzymatic membrane-spanning proteins with unrelated primary functions have also been found to accelerate lipid flip-flop in a nonspecific manner and by various hypothesized mechanisms. Using deuterated phospholipids, we examined the acceleration of flip-flop by gramicidin channels, which have well-defined structures and known functions, features that make them ideal candidates for probing the protein-membrane interactions underlying lipid flip-flop. To study compositionally and isotopically asymmetric proteoliposomes containing gramicidin, we expanded a recently developed protocol for the preparation and characterization of lipid-only asymmetric vesicles. Channel incorporation, conformation, and function were examined with small angle x-ray scattering, circular dichroism, and a stopped-flow spectrofluorometric assay, respectively. As a measure of lipid scrambling, we used differential scanning calorimetry to monitor the effect of gramicidin on the melting transition temperatures of the two bilayer leaflets. The two calorimetric peaks of the individual leaflets merged into a single peak over time, suggestive of scrambling, and the effect of the channel on the transbilayer lipid distribution in both symmetric 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine and asymmetric 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine/1,2-dimyristoyl-sn-glycero-3-phosphocholine vesicles was quantified from proton NMR measurements. Our results show that gramicidin increases lipid flip-flop in a complex, concentration-dependent manner. To determine the molecular mechanism of the process, we used molecular dynamics simulations and further computational analysis of the trajectories to estimate the extent of membrane deformation. Together, the experimental and computational approaches were found to constitute an effective means for studying the effects of transmembrane proteins on lipid distribution in both symmetric and asymmetric model membranes.
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Affiliation(s)
- Milka Doktorova
- Tri-Institutional PhD Program in Computational Biology and Medicine, Weill Cornell Medical College, New York, New York.
| | - Frederick A Heberle
- Department of Integrative Biology and Pharmacology, University of Texas Health Science Center, Houston, Texas; The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, Tennessee
| | | | - Radda Rusinova
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York
| | - R Lea Sanford
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York
| | - Thasin A Peyear
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York
| | - John Katsaras
- Large Scale Structures Group, Oak Ridge National Laboratory, Oak Ridge, Tennessee, Oak Ridge National Laboratory, Oak Ridge, Tennessee; Shull Wollan Center, Oak Ridge National Laboratory, Oak Ridge, Tennessee
| | - Gerald W Feigenson
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York
| | - Harel Weinstein
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Greenberg Center, New York, New York
| | - Olaf S Andersen
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York
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29
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Nielsen JE, Bjørnestad VA, Lund R. Resolving the structural interactions between antimicrobial peptides and lipid membranes using small-angle scattering methods: the case of indolicidin. SOFT MATTER 2018; 14:8750-8763. [PMID: 30358793 DOI: 10.1039/c8sm01888j] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Using small angle X-ray and neutron scattering (SAXS/SANS) and detailed theoretical modelling we have elucidated the structure of the antimicrobial peptide, indolicidin, and the interaction with model lipid membranes of different anionic lipid compositions mimicking typical charge densities found in the cytoplasmic membrane of bacteria. First, we show that indolicidin displays a predominantly disordered, random chain conformation in solution with a small fraction (≈1%) of fiber-like nanostructures that are not dissolved at higher temperatures. The peptide is shown to strongly interact with the membranes at all charge densities without significantly perturbing the lipid bilayer structure. Instead, the results show that indolicidin inserts into the outer leaflet of the lipid vesicles causing a reduced local order of the lipid packing. This result is supported by an observed change in the melting point of the lipids upon addition of the peptide, as seen by differential scanning calorimetry experiments. The peptide does not to our observation affect the thickness of the membrane or form distinct structural pores in the membrane at physiologically relevant concentrations as has been previously suggested as an important mode of action. Finally, using sophisticated contrast variation SANS, we show that the peptide does not affect the random lateral distribution of anionic lipids in the membrane. Together, these results demonstrate that the structural aspects of the mode of action of antimicrobial peptides can be elucidated in detail using SAS techniques with liposomes as model systems.
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30
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Li J, Jiao A, Chen S, Wu Z, Xu E, Jin Z. RETRACTED: Application of the small-angle X-ray scattering technique for structural analysis studies: A review. J Mol Struct 2018. [DOI: 10.1016/j.molstruc.2017.12.031] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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31
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Tesei G, Hellstrand E, Sanagavarapu K, Linse S, Sparr E, Vácha R, Lund M. Aggregate Size Dependence of Amyloid Adsorption onto Charged Interfaces. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:1266-1273. [PMID: 29284092 PMCID: PMC5828364 DOI: 10.1021/acs.langmuir.7b03155] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Amyloid aggregates are associated with a range of human neurodegenerative disorders, and it has been shown that neurotoxicity is dependent on aggregate size. Combining molecular simulation with analytical theory, a predictive model is proposed for the adsorption of amyloid aggregates onto oppositely charged surfaces, where the interaction is governed by an interplay between electrostatic attraction and entropic repulsion. Predictions are experimentally validated against quartz crystal microbalance-dissipation experiments of amyloid beta peptides and fragmented fibrils in the presence of a supported lipid bilayer. Assuming amyloids as rigid, elongated particles, we observe nonmonotonic trends for the extent of adsorption with respect to aggregate size and preferential adsorption of smaller aggregates over larger ones. Our findings describe a general phenomenon with implications for stiff polyions and rodlike particles that are electrostatically attracted to a surface.
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Affiliation(s)
- Giulio Tesei
- Theoretical
Chemistry, Biophysical Chemistry, Biochemistry & Structural Biology,
and Physical Chemistry, Lund University, 221 00 Lund, Sweden
- E-mail: (G.T.)
| | - Erik Hellstrand
- Theoretical
Chemistry, Biophysical Chemistry, Biochemistry & Structural Biology,
and Physical Chemistry, Lund University, 221 00 Lund, Sweden
| | - Kalyani Sanagavarapu
- Theoretical
Chemistry, Biophysical Chemistry, Biochemistry & Structural Biology,
and Physical Chemistry, Lund University, 221 00 Lund, Sweden
| | - Sara Linse
- Theoretical
Chemistry, Biophysical Chemistry, Biochemistry & Structural Biology,
and Physical Chemistry, Lund University, 221 00 Lund, Sweden
| | - Emma Sparr
- Theoretical
Chemistry, Biophysical Chemistry, Biochemistry & Structural Biology,
and Physical Chemistry, Lund University, 221 00 Lund, Sweden
| | - Robert Vácha
- Central European Institute of Technology and Faculty of Science, Masaryk University, 625
00 Brno, Czech Republic
- E-mail: (R.V.)
| | - Mikael Lund
- Theoretical
Chemistry, Biophysical Chemistry, Biochemistry & Structural Biology,
and Physical Chemistry, Lund University, 221 00 Lund, Sweden
- E-mail: (M.L.)
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32
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Heberle FA, Pabst G. Complex biomembrane mimetics on the sub-nanometer scale. Biophys Rev 2017; 9:353-373. [PMID: 28717925 PMCID: PMC5578918 DOI: 10.1007/s12551-017-0275-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 06/26/2017] [Indexed: 12/12/2022] Open
Abstract
Biomimetic lipid vesicles are indispensable tools for gaining insight into the biophysics of cell physiology on the molecular level. The level of complexity of these model systems has steadily increased, and now spans from domain-forming lipid mixtures to asymmetric lipid bilayers. Here, we review recent progress in the development and application of elastic neutron and X-ray scattering techniques for studying these systems in situ and under physiologically relevant conditions on the nanometer to sub-nanometer length scales. In particular, we focus on: (1) structural details of coexisting liquid-ordered and liquid-disordered domains, including their thickness and lipid packing mismatch as a function of a size transition from nanoscopic to macroscopic domains; (2) membrane-mediated protein partitioning into lipid domains; (3) the role of the aqueous medium in tuning interactions between membranes and domains; and (4) leaflet-specific structure in asymmetric bilayers and passive lipid flip-flop.
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Affiliation(s)
- Frederick A Heberle
- The Bredesen Center, University of Tennessee, Knoxville, TN, 37996, USA.,Joint Institute for Biological Sciences and Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Georg Pabst
- Institute of Molecular Biosciences, Biophysics Division, NAWI Graz, University of Graz, 8010, Graz, Austria. .,BioTechMed-Graz, 8010, Graz, Austria.
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33
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Marquardt D, Van Oosten BJ, Ghelfi M, Atkinson J, Harroun TA. Vitamin E Circular Dichroism Studies: Insights into Conformational Changes Induced by the Solvent's Polarity. MEMBRANES 2016; 6:membranes6040056. [PMID: 27983631 PMCID: PMC5192412 DOI: 10.3390/membranes6040056] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Revised: 12/07/2016] [Accepted: 12/08/2016] [Indexed: 11/16/2022]
Abstract
We used circular dichroism (CD) to study differences in CD spectra between α-, δ-, and methylated-α-tocopherol in solvents with different polarities. CD spectra of the different tocopherol structures differ from each other in intensity and peak locations, which can be attributed to chromanol substitution and the ability to form hydrogen bonds. In addition, each structure was examined in different polarity solvents using the Reichardt index-a measure of the solvent's ionizing ability, and a direct measurement of solvent-solute interactions. Differences across solvents indicate that hydrogen bonding is a key contributor to CD spectra at 200 nm. These results are a first step in examining the hydrogen bonding abilities of vitamin E in a lipid bilayer.
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Affiliation(s)
- Drew Marquardt
- Department of Physics, Brock University, St. Catharines, ON L2S 3A1, Canada.
- Institute of Molecular Biosciences, Biophysics Division, NAWI Graz, University of Graz, Graz 8010, Austria.
- BioTechMed-Graz, Graz 8010, Austria.
| | - Brad J Van Oosten
- Department of Physics, Brock University, St. Catharines, ON L2S 3A1, Canada.
| | - Mikel Ghelfi
- Department of Chemistry, Brock University, St. Catharines, ON L2S 3A1, Canada.
| | - Jeffrey Atkinson
- Department of Chemistry, Brock University, St. Catharines, ON L2S 3A1, Canada.
| | - Thad A Harroun
- Department of Physics, Brock University, St. Catharines, ON L2S 3A1, Canada.
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34
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Martin-Bertelsen B, Yaghmur A, Franzyk H, Justesen S, Kirkensgaard JJK, Foged C. Conserved Molecular Superlattices in a Series of Homologous Synthetic Mycobacterial Cell-Wall Lipids Forming Interdigitated Bilayers. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:12693-12701. [PMID: 27934510 DOI: 10.1021/acs.langmuir.6b01720] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Synthetic analogues of the cell-wall lipid monomycoloyl glycerol (MMG) are promising as next-generation vaccine adjuvants. In the present study, the thermotropic phase behavior of an array of synthetic MMG analogues was examined by using simultaneous small- and wide-angle X-ray scattering under excess water conditions. The MMG analogues differed in the alkyl chain lengths and in the stereochemistry of the polar glycerol headgroup or of the lipid tails (native-like versus alternative compounds). All MMG analogues formed poorly hydrated lamellar phases at low temperatures and inverse hexagonal (H2) phases at higher temperatures prior to melting. MMG analogues with a native-like lipid acid configuration self-assembled into noninterdigitated bilayers whereas the analogues displaying an alternative lipid acid configuration formed interdigitated bilayers in a subgel (Lc') state. This is in contrast to previously described interdigitated phases for other lipids, which are usually in a gel (Lβ) state. All investigated MMG analogues displayed an abrupt direct temperature-induced phase transition from Lc' to H2. This transition is ultimately driven by the lipid chain melting and the accompanying change in molecular shape. No intermediate structures were found, but the entire array of MMG analogues displayed phase coexistence during the lamellar to H2 transition. The structural data also showed that the headgroups of the MMG analogues adopting the alternative lipid acid configuration were ordered and formed a two-dimensional molecular superlattice, which was conserved regardless of the lipid tail length. To our knowledge, the MMG analogues with an alternative lipid acid configuration represent the first example of a lipid system showing both interdigitation and superlattice formation, and as such could serve as an interesting model system for future studies. The MMG analogues are also relevant from a subunit vaccine perspective because they are well-tolerated and display promising immunopotentiating activity. The structural characterization described here will serve as a prerequisite for the rational design of nanoparticulate adjuvants with specific and tailored structural features.
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Affiliation(s)
| | | | | | | | - Jacob J K Kirkensgaard
- Niels Bohr Institute, Faculty of Science, University of Copenhagen , Universitetsparken 5, 2100 Copenhagen, Denmark
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35
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Rai DK, Sharma VK, Anunciado D, O'Neill H, Mamontov E, Urban V, Heller WT, Qian S. Neutron Scattering Studies of the Interplay of Amyloid β Peptide(1-40) and An Anionic Lipid 1,2-dimyristoyl-sn-glycero-3-phosphoglycerol. Sci Rep 2016; 6:30983. [PMID: 27503057 PMCID: PMC4995599 DOI: 10.1038/srep30983] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Accepted: 07/05/2016] [Indexed: 12/19/2022] Open
Abstract
The interaction between lipid bilayers and Amyloid β peptide (Aβ) plays a critical role in proliferation of Alzheimer’s disease (AD). AD is expected to affect one in every 85 humans by 2050, and therefore, deciphering the interplay of Aβ and lipid bilayers at the molecular level is of profound importance. In this work, we applied an array of neutron scattering methods to study the structure and dynamics of Aβ(1–40) interacting 1,2-dimyristoyl-sn-glycero-3-phosphoglycerol (DMPG) bilayers. In the structural investigations of lipid bilayer’s response to Aβ binding, Small Angle Neutron Scattering and Neutron Membrane Diffraction revealed that the Aβ anchors firmly to the highly charged DMPG bilayers in the interfacial region between water and hydrocarbon chain, and it doesn’t penetrate deeply into the bilayer. This association mode is substantiated by the dynamics studies with high resolution Quasi-Elastic Neutron Scattering experiments, showing that the addition of Aβ mainly affects the slower lateral motion of lipid molecules, especially in the fluid phase, but not the faster internal motion. The results revealed that Aβ associates with the highly charged membrane in surface with limited impact on the structure, but the altered membrane dynamics could have more influence on other membrane processes.
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Affiliation(s)
- Durgesh K Rai
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Veerendra K Sharma
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Divina Anunciado
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Hugh O'Neill
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Eugene Mamontov
- Chemical and Engineering Materials Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Volker Urban
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - William T Heller
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Shuo Qian
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
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36
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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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37
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Marquardt D, Heberle FA, Nickels JD, Pabst G, Katsaras J. On scattered waves and lipid domains: detecting membrane rafts with X-rays and neutrons. SOFT MATTER 2015; 11:9055-72. [PMID: 26428538 PMCID: PMC4719199 DOI: 10.1039/c5sm01807b] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 09/21/2015] [Indexed: 05/28/2023]
Abstract
In order to understand the biological role of lipids in cell membranes, it is necessary to determine the mesoscopic structure of well-defined model membrane systems. Neutron and X-ray scattering are non-invasive, probe-free techniques that have been used extensively in such systems to probe length scales ranging from angstroms to microns, and dynamics occurring over picosecond to millisecond time scales. Recent developments in the area of phase separated lipid systems mimicking membrane rafts will be presented, and the underlying concepts of the different scattering techniques used to study them will be discussed in detail.
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Affiliation(s)
- Drew Marquardt
- University of Graz, Institute of Molecular Biosciences, Biophysics Division, NAWI Graz, Humboldtstr. 50/III, Graz, Austria. and BioTechMed-Graz, Graz, Austria
| | - Frederick A Heberle
- Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA. and Joint Institute for Neutron Sciences, Oak Ridge, Tennessee 37831, USA
| | - Jonathan D Nickels
- Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA. and Joint Institute for Neutron Sciences, Oak Ridge, Tennessee 37831, USA
| | - Georg Pabst
- University of Graz, Institute of Molecular Biosciences, Biophysics Division, NAWI Graz, Humboldtstr. 50/III, Graz, Austria. and BioTechMed-Graz, Graz, Austria
| | - John Katsaras
- Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA. and Joint Institute for Neutron Sciences, Oak Ridge, Tennessee 37831, USA
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38
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The interactions of peripheral membrane proteins with biological membranes. Chem Phys Lipids 2015; 192:51-59. [DOI: 10.1016/j.chemphyslip.2015.07.015] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Revised: 07/14/2015] [Accepted: 07/25/2015] [Indexed: 11/22/2022]
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39
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Structural Significance of Lipid Diversity as Studied by Small Angle Neutron and X-ray Scattering. MEMBRANES 2015; 5:454-72. [PMID: 26402708 PMCID: PMC4584290 DOI: 10.3390/membranes5030454] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 09/15/2015] [Indexed: 11/17/2022]
Abstract
We review recent developments in the rapidly growing field of membrane biophysics, with a focus on the structural properties of single lipid bilayers determined by different scattering techniques, namely neutron and X-ray scattering. The need for accurate lipid structural properties is emphasized by the sometimes conflicting results found in the literature, even in the case of the most studied lipid bilayers. Increasingly, accurate and detailed structural models require more experimental data, such as those from contrast varied neutron scattering and X-ray scattering experiments that are jointly refined with molecular dynamics simulations. This experimental and computational approach produces robust bilayer structural parameters that enable insights, for example, into the interplay between collective membrane properties and its components (e.g., hydrocarbon chain length and unsaturation, and lipid headgroup composition). From model studies such as these, one is better able to appreciate how a real biological membrane can be tuned by balancing the contributions from the lipid's different moieties (e.g., acyl chains, headgroups, backbones, etc.).
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40
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Belička M, Gerelli Y, Kučerka N, Fragneto G. The component group structure of DPPC bilayers obtained by specular neutron reflectometry. SOFT MATTER 2015; 11:6275-6283. [PMID: 26160133 DOI: 10.1039/c5sm00274e] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Specular neutron reflectometry was measured on a floating bilayer system consisting of 1,2-dipalmitoyl-d62-sn-glycero-3-phosphocholine deposited over a 1,2-dibehenoyl-sn-glycero-3-phosphocholine bilayer at 25 and 55 °C. The internal structure of lipid bilayers was described by a one-dimensional neutron scattering length density profile model, originally developed for the evaluation of small-angle scattering data. The reflectivity data from the supported bilayer were evaluated separately and used further as constraints in modeling the floating bilayer reflectivity curves. The model reflectivity curves successfully describe the experimental reflectivities of the supported bilayer in the gel phase and the floating bilayer system in the liquid-crystalline phase. The results yield an internal structure of a deposited bilayer and a floating bilayer on the level of component groups of lipid molecules. The obtained structure of the floating d62-diC16:0PC bilayer displays high resemblance of the bilayer structure in the form of unilamellar vesicles. At the same time, however, the results show differences in comparison to unilamellar vesicle bilayers, most likely due to the undulations of supported bilayers.
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Affiliation(s)
- Michal Belička
- Department of Physical Chemistry of Drugs, Faculty of Pharmacy, Comenius University, Odbojárov 10, SK-832 32 Bratislava, Slovakia.
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Heberle FA, Anghel VN, Katsaras J. Scattering from phase-separated vesicles. I. An analytical form factor for multiple static domains. J Appl Crystallogr 2015. [DOI: 10.1107/s160057671501362x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023] Open
Abstract
This is the first in a series of papers considering elastic scattering from laterally heterogeneous lipid vesicles containing multiple domains. Unique among biophysical tools, small-angle neutron scattering can in principle give detailed information about the size, shape and spatial arrangement of domains. A general theory for scattering from laterally heterogeneous vesicles is presented, and the analytical form factor for static domains with arbitrary spatial configuration is derived, including a simplification for uniformly sized round domains. The validity of the model, including series truncation effects, is assessed by comparison with simulated data obtained from a Monte Carlo method. Several aspects of the analytical solution for scattering intensity are discussed in the context of small-angle neutron scattering data, including the effect of varying domain size and number, as well as solvent contrast. The analysis indicates that effects of domain formation are most pronounced when the vesicle's average scattering length density matches that of the surrounding solvent.
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Heberle FA, Myles DAA, Katsaras J. Biomembranes research using thermal and cold neutrons. Chem Phys Lipids 2015; 192:41-50. [PMID: 26241882 DOI: 10.1016/j.chemphyslip.2015.07.020] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2015] [Revised: 07/25/2015] [Accepted: 07/27/2015] [Indexed: 01/26/2023]
Abstract
In 1932 James Chadwick discovered the neutron using a polonium source and a beryllium target (Chadwick, 1932). In a letter to Niels Bohr dated February 24, 1932, Chadwick wrote: "whatever the radiation from Be may be, it has most remarkable properties." Where it concerns hydrogen-rich biological materials, the "most remarkable" property is the neutron's differential sensitivity for hydrogen and its isotope deuterium. Such differential sensitivity is unique to neutron scattering, which unlike X-ray scattering, arises from nuclear forces. Consequently, the coherent neutron scattering length can experience a dramatic change in magnitude and phase as a result of resonance scattering, imparting sensitivity to both light and heavy atoms, and in favorable cases to their isotopic variants. This article describes recent biomembranes research using a variety of neutron scattering techniques.
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Affiliation(s)
- F A Heberle
- Biology and Soft Matter Division, Neutron Sciences Directorate, Oak Ridge, TN, 37831, United States; Joint Institute for Neutron Sciences, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, United States
| | - D A A Myles
- Biology and Soft Matter Division, Neutron Sciences Directorate, Oak Ridge, TN, 37831, United States
| | - J Katsaras
- Biology and Soft Matter Division, Neutron Sciences Directorate, Oak Ridge, TN, 37831, United States; Joint Institute for Neutron Sciences, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, United States; Department of Physics and Astronomy, University of Tennessee, Knoxville, TN, 37996, United States.
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Mangiarotti A, Wilke N. Energetics of the Phase Transition in Free-Standing versus Supported Lipid Membranes. J Phys Chem B 2015; 119:8718-24. [DOI: 10.1021/acs.jpcb.5b04397] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Agustín Mangiarotti
- Centro
de Investigaciones
en Química Biológica de Córdoba (CIQUIBIC, UNC−CONICET),
Departamento de Química Biológica, Facultad de Ciencias
Químicas, Universidad Nacional de Córdoba, Haya de la Torre y Medina
Allende, Ciudad Universitaria, X5000HUA Córdoba, Argentina
| | - Natalia Wilke
- Centro
de Investigaciones
en Química Biológica de Córdoba (CIQUIBIC, UNC−CONICET),
Departamento de Química Biológica, Facultad de Ciencias
Químicas, Universidad Nacional de Córdoba, Haya de la Torre y Medina
Allende, Ciudad Universitaria, X5000HUA Córdoba, Argentina
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Pan J, Cheng X, Sharp M, Ho CS, Khadka N, Katsaras J. Structural and mechanical properties of cardiolipin lipid bilayers determined using neutron spin echo, small angle neutron and X-ray scattering, and molecular dynamics simulations. SOFT MATTER 2015; 11:130-138. [PMID: 25369786 DOI: 10.1039/c4sm02227k] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The detailed structural and mechanical properties of a tetraoleoyl cardiolipin (TOCL) bilayer were determined using neutron spin echo (NSE) spectroscopy, small angle neutron and X-ray scattering (SANS and SAXS, respectively), and molecular dynamics (MD) simulations. We used MD simulations to develop a scattering density profile (SDP) model, which was then utilized to jointly refine SANS and SAXS data. In addition to commonly reported lipid bilayer structural parameters, component distributions were obtained, including the volume probability, electron density and neutron scattering length density. Of note, the distance between electron density maxima DHH (39.4 Å) and the hydrocarbon chain thickness 2DC (29.1 Å) of TOCL bilayers were both found to be larger than the corresponding values for dioleoyl phosphatidylcholine (DOPC) bilayers. Conversely, TOCL bilayers have a smaller overall bilayer thickness DB (36.7 Å), primarily due to their smaller headgroup volume per phosphate. SDP analysis yielded a lipid area of 129.8 Å(2), indicating that the cross-sectional area per oleoyl chain in TOCL bilayers (i.e., 32.5 Å(2)) is smaller than that for DOPC bilayers. Multiple sets of MD simulations were performed with the lipid area constrained at different values. The calculated surface tension versus lipid area resulted in a lateral area compressibility modulus KA of 342 mN m(-1), which is slightly larger compared to DOPC bilayers. Model free comparison to experimental scattering data revealed the best simulated TOCL bilayer from which detailed molecular interactions were determined. Specifically, Na(+) cations were found to interact most strongly with the glycerol hydroxyl linkage, followed by the phosphate and backbone carbonyl oxygens. Inter- and intra-lipid interactions were facilitated by hydrogen bonding between the glycerol hydroxyl and phosphate oxygen, but not with the backbone carbonyl. Finally, analysis of the intermediate scattering functions from NSE spectroscopy measurements of TOCL bilayers yielded a bending modulus KC of 1.06 × 10(-19) J, which was larger than that observed in DOPC bilayers. Our results show the physicochemical properties of cardiolin bilayers that may be important in explaining their functionality in the inner mitochondrial membrane.
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Affiliation(s)
- Jianjun Pan
- Department of Physics, University of South Florida, Tampa, FL 33620, USA.
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Kučerka N, van Oosten B, Pan J, Heberle FA, Harroun TA, Katsaras J. Molecular structures of fluid phosphatidylethanolamine bilayers obtained from simulation-to-experiment comparisons and experimental scattering density profiles. J Phys Chem B 2014; 119:1947-56. [PMID: 25436970 DOI: 10.1021/jp511159q] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Following our previous efforts in determining the structures of commonly used PC, PG, and PS bilayers, we continue our studies of fully hydrated, fluid phase PE bilayers. The newly designed parsing scheme for PE bilayers was based on extensive MD simulations, and is utilized in the SDP analysis of both X-ray and neutron (contrast varied) scattering measurements. Obtained experimental scattering form factors are directly compared to our simulation results, and can serve as a benchmark for future developed force fields. Among the evaluated structural parameters, namely, area per lipid A, overall bilayer thickness DB, and hydrocarbon region thickness 2DC, the PE bilayer response to changing temperature is similar to previously studied bilayers with different headgroups. On the other hand, the reduced hydration of PE headgroups, as well as the strong hydrogen bonding between PE headgroups, dramatically affects lateral packing within the bilayer. Despite sharing the same glycerol backbone, a markedly smaller area per lipid distinguishes PE from other bilayers (i.e., PC, PG, and PS) studied to date. Overall, our data are consistent with the notion that lipid headgroups govern bilayer packing, while hydrocarbon chains dominate the bilayer's response to temperature changes.
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Affiliation(s)
- Norbert Kučerka
- Canadian Neutron Beam Centre, National Research Council , Chalk River, Ontario K0J 1J0, Canada
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Pan J, Marquardt D, Heberle FA, Kučerka N, Katsaras J. Revisiting the bilayer structures of fluid phase phosphatidylglycerol lipids: Accounting for exchangeable hydrogens. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2014; 1838:2966-9. [PMID: 25135659 DOI: 10.1016/j.bbamem.2014.08.009] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Revised: 08/06/2014] [Accepted: 08/08/2014] [Indexed: 11/30/2022]
Abstract
We recently published two papers detailing the structures of fluid phase phosphatidylglycerol (PG) lipid bilayers (Kučerka et al., 2012 J. Phys. Chem. B 116: 232-239; Pan et al., 2012 Biochim. Biophys. Acta Biomembr. 1818: 2135-2148), which were determined using the scattering density profile model. This hybrid experimental/computational technique utilizes molecular dynamics simulations to parse a lipid bilayer into components whose volume probabilities follow simple analytical functional forms. Given the appropriate scattering densities, these volume probabilities are then translated into neutron scattering length density (NSLD) and electron density (ED) profiles, which are used to jointly refine experimentally obtained small angle neutron and X-ray scattering data. However, accurate NSLD and ED profiles can only be obtained if the bilayer's chemical composition is known. Specifically, in the case of neutron scattering, the lipid's exchangeable hydrogens with aqueous D2O must be accounted for, as they can have a measureable effect on the resultant lipid bilayer structures. This was not done in our above-mentioned papers. Here we report on the molecular structures of PG lipid bilayers by appropriately taking into account the exchangeable hydrogens. Analysis indicates that the temperature-averaged PG lipid areas decrease by 1.5 to 3.8Å(2), depending on the lipid's acyl chain length and unsaturation, compared to PG areas when hydrogen exchange was not taken into account.
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Affiliation(s)
- Jianjun Pan
- Department of Physics, University of South Florida, Tampa, FL 33620, USA.
| | - Drew Marquardt
- Department of Physics, Brock University, St. Catharines, ON L2S 3A1, Canada
| | - Frederick A Heberle
- Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Norbert Kučerka
- Department of Physical Chemistry of Drugs, Comenius University, 832 32 Bratislava, Slovakia; Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, 141980 Dubna, Russia
| | - John Katsaras
- Department of Physics, Brock University, St. Catharines, ON L2S 3A1, Canada; Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; Joint Institute for Neutron Scattering, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; Department of Physics and Astronomy, University of Tennessee, Knoxville, TN 37996, USA.
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Schmiele M, Schindler T, Westermann M, Steiniger F, Radulescu A, Kriele A, Gilles R, Unruh T. Mesoscopic Structures of Triglyceride Nanosuspensions Studied by Small-Angle X-ray and Neutron Scattering and Computer Simulations. J Phys Chem B 2014; 118:8808-18. [DOI: 10.1021/jp502580a] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Martin Schmiele
- Friedrich-Alexander-Universität Erlangen—Nürnberg, Physik
Department, Staudtstrasse
3, 91058 Erlangen, Germany
| | - Torben Schindler
- Friedrich-Alexander-Universität Erlangen—Nürnberg, Physik
Department, Staudtstrasse
3, 91058 Erlangen, Germany
| | - Martin Westermann
- Center for Electron Microscopy of the Jena University Hospital, Ziegelmühlenweg 1, 07743 Jena, Germany
| | - Frank Steiniger
- Center for Electron Microscopy of the Jena University Hospital, Ziegelmühlenweg 1, 07743 Jena, Germany
| | - Aurel Radulescu
- Jülich Centre for Neutron Science (JCNS), Lichtenbergstrasse 1, 85747 Garching, Germany
| | - Armin Kriele
- Outstation
at Heinz Maier-Leibnitz Zentrum (MLZ), Helmholtz-Zentrum Geesthacht (HZG), Lichtenbergstrasse
1, 85747 Garching, Germany
| | - Ralph Gilles
- Heinz
Maier-Leibnitz Zentrum (MLZ), Technische Universität München, Lichtenbergstrasse 1, 85747 Garching, Germany
| | - Tobias Unruh
- Friedrich-Alexander-Universität Erlangen—Nürnberg, Physik
Department, Staudtstrasse
3, 91058 Erlangen, Germany
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Pan J, Cheng X, Monticelli L, Heberle FA, Kučerka N, Tieleman DP, Katsaras J. The molecular structure of a phosphatidylserine bilayer determined by scattering and molecular dynamics simulations. SOFT MATTER 2014; 10:3716-3725. [PMID: 24807693 DOI: 10.1039/c4sm00066h] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Phosphatidylserine (PS) lipids play essential roles in biological processes, including enzyme activation and apoptosis. We report on the molecular structure and atomic scale interactions of a fluid bilayer composed of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylserine (POPS). A scattering density profile model, aided by molecular dynamics (MD) simulations, was developed to jointly refine different contrast small-angle neutron and X-ray scattering data, which yielded a lipid area of 62.7 Å(2) at 25 °C. MD simulations with POPS lipid area constrained at different values were also performed using all-atom and aliphatic united-atom models. The optimal simulated bilayer was obtained using a model-free comparison approach. Examination of the simulated bilayer, which agrees best with the experimental scattering data, reveals a preferential interaction between Na(+) ions and the terminal serine and phosphate moieties. Long-range inter-lipid interactions were identified, primarily between the positively charged ammonium, and the negatively charged carboxylic and phosphate oxygens. The area compressibility modulus KA of the POPS bilayer was derived by quantifying lipid area as a function of surface tension from area-constrained MD simulations. It was found that POPS bilayers possess a much larger KA than that of neutral phosphatidylcholine lipid bilayers. We propose that the unique molecular features of POPS bilayers may play an important role in certain physiological functions.
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Affiliation(s)
- Jianjun Pan
- Department of Physics, University of South Florida, Tampa, FL 33620, USA.
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Koshy C, Ziegler C. Structural insights into functional lipid-protein interactions in secondary transporters. Biochim Biophys Acta Gen Subj 2014; 1850:476-87. [PMID: 24859688 DOI: 10.1016/j.bbagen.2014.05.010] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Revised: 05/09/2014] [Accepted: 05/12/2014] [Indexed: 12/22/2022]
Abstract
BACKGROUND Structural evidences with functional corroborations have revealed distinct features of lipid-protein interactions especially in channels and receptors. Many membrane embedded transporters are also known to require specific lipids for their functions and for some of them cellular and biochemical data suggest tight regulation by the lipid bilayer. However, molecular details on lipid-protein interactions in transporters are sparse since lipids are either depleted from the detergent solubilized transporters in three-dimensional crystals or not readily resolved in crystal structures. Nevertheless the steady increase in the progress of transporter structure determination contributed more examples of structures with resolved lipids. SCOPE OF REVIEW This review gives an overview on transporter structures in complex with lipids reported to date and discusses commonly encountered difficulties in the identification of functionally significant lipid-protein interactions based on those structures and functional in vitro data. Recent structures provided molecular details into regulation mechanism of transporters by specific lipids. The review highlights common findings and conserved patterns for distantly related transporter families to draw a more general picture on the regulatory role of lipid-protein interactions. MAJOR CONCLUSIONS Several common themes of the manner in which lipids directly influence membrane-mediated folding, oligomerization and structure stability can be found. Especially for LeuT-like fold transporters similarities in structurally resolved lipid-protein interactions suggest a common way in which transporter conformations are affected by lipids even in evolutionarily distinct transporters. Lipids appear to play an additional role as joints mechanically reinforcing the inverted repeat topology, which is a major determinant in the alternating access mechanism of secondary transporters. GENERAL SIGNIFICANCE This review brings together and adds to the repertoire of knowledge on lipid-protein interactions of functional significance presented in structures of membrane transporters. Knowledge of specific lipid-binding sites and modes of lipid influence on these proteins not only accomplishes the molecular description of transport cycle further, but also sheds light into localization dependent differences of transporter function. This article is part of a Special Issue entitled Structural biochemistry and biophysics of membrane proteins.
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Affiliation(s)
- Caroline Koshy
- Max Planck Institute of Biophysics, Structural Biology Department, Frankfurt am Main, Germany; Max-Planck Institute of Biophysics, Computational Structural Biology Group, Frankfurt am Main, Germany
| | - Christine Ziegler
- Max Planck Institute of Biophysics, Structural Biology Department, Frankfurt am Main, Germany; Institute of Biophysics and Physical Biochemistry, University of Regensburg, Regensburg, Germany.
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Daily MD, Olsen BN, Schlesinger PH, Ory DS, Baker NA. Improved Coarse-Grained Modeling of Cholesterol-Containing Lipid Bilayers. J Chem Theory Comput 2014; 10:2137-2150. [PMID: 24910542 PMCID: PMC4044725 DOI: 10.1021/ct401028g] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Cholesterol trafficking, which is an essential function in mammalian cells, is intimately connected to molecular-scale interactions through cholesterol modulation of membrane structure and dynamics and interaction with membrane receptors. Since these effects of cholesterol occur on micro- to millisecond timescales, it is essential to develop accurate coarse-grained simulation models that can reach these timescales. Cholesterol has been shown experimentally to thicken the membrane and increase phospholipid tail order between 0-40% cholesterol, above which these effects plateau or slightly decrease. Here, we showed that the published MARTINI coarse-grained force-field for phospholipid (POPC) and cholesterol fails to capture these effects. Using reference atomistic simulations, we systematically modified POPC and cholesterol bonded parameters in MARTINI to improve its performance. We showed that the corrections to pseudo-bond angles between glycerol and the lipid tails and around the oleoyl double bond particle (the "angle-corrected model") slightly improves the agreement of MARTINI with experimentally measured thermal, elastic, and dynamic properties of POPC membranes. The angle-corrected model improves prediction of the thickening and ordering effects up to 40% cholesterol but overestimates these effects at higher cholesterol concentration. In accordance with prior work that showed the cholesterol rough face methyl groups are important for limiting cholesterol self-association, we revised the coarse-grained representation of these methyl groups to better match cholesterol-cholesterol radial distribution functions from atomistic simulations. In addition, by using a finer-grained representation of the branched cholesterol tail than MARTINI, we improved predictions of lipid tail order and bilayer thickness across a wide range of concentrations. Finally, transferability testing shows that a model incorporating our revised parameters into DOPC outperforms other CG models in a DOPC/cholesterol simulation series, which further argues for its efficacy and generalizability. These results argue for the importance of systematic optimization for coarse-graining biologically important molecules like cholesterol with complicated molecular structure.
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Affiliation(s)
- Michael D Daily
- Computational and Statistical Analytics Division, Pacific Northwest National Laboratory, Richland, Washington
| | - Brett N Olsen
- Department of Medicine, Diabetic Cardiovascular Disease Center, Washington University School of Medicine, St. Louis, Missouri
| | - Paul H Schlesinger
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, Missouri
| | - Daniel S Ory
- Department of Medicine, Diabetic Cardiovascular Disease Center, Washington University School of Medicine, St. Louis, Missouri
| | - Nathan A Baker
- Computational and Statistical Analytics Division, Pacific Northwest National Laboratory, Richland, Washington
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