51
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Doktorova M, Heberle FA, Kingston RL, Khelashvili G, Cuendet MA, Wen Y, Katsaras J, Feigenson GW, Vogt VM, Dick RA. Cholesterol Promotes Protein Binding by Affecting Membrane Electrostatics and Solvation Properties. Biophys J 2017; 113:2004-2015. [PMID: 29117524 DOI: 10.1016/j.bpj.2017.08.055] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Revised: 08/07/2017] [Accepted: 08/09/2017] [Indexed: 01/28/2023] Open
Abstract
Binding of the retroviral structural protein Gag to the cellular plasma membrane is mediated by the protein's matrix (MA) domain. Prominent among MA-PM interactions is electrostatic attraction between the positively charged MA domain and the negatively charged plasma membrane inner leaflet. Previously, we reported that membrane association of HIV-1 Gag, as well as purified Rous sarcoma virus (RSV) MA and Gag, depends strongly on the presence of acidic lipids and is enhanced by cholesterol (Chol). The mechanism underlying this enhancement was unclear. Here, using a broad set of in vitro and in silico techniques we addressed molecular mechanisms of association between RSV MA and model membranes, and investigated how Chol enhances this association. In neutron scattering experiments with liposomes in the presence or absence of Chol, MA preferentially interacted with preexisting POPS-rich clusters formed by nonideal lipid mixing, binding peripherally to the lipid headgroups with minimal perturbation to the bilayer structure. Molecular dynamics simulations showed a stronger MA-bilayer interaction in the presence of Chol, and a large Chol-driven increase in lipid packing and membrane surface charge density. Although in vitro MA-liposome association is influenced by disparate variables, including ionic strength and concentrations of Chol and charged lipids, continuum electrostatic theory revealed an underlying dependence on membrane surface potential. Together, these results conclusively show that Chol affects RSV MA-membrane association by making the electrostatic potential at the membrane surface more negative, while decreasing the penalty for lipid headgroup desolvation. The presented approach can be applied to other viral and nonviral proteins.
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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
- The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, Tennessee; Joint Institute for Biological Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee; Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee.
| | - Richard L Kingston
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - George Khelashvili
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York
| | - Michel A Cuendet
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York
| | - Yi Wen
- Department of Biochemistry and Molecular Cell Biology, Cornell University, Ithaca, New York
| | - John Katsaras
- The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, Tennessee; Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee; Department of Physics and Astronomy, University of Tennessee, Knoxville, Tennessee; Shull Wollan Center, Oak Ridge National Laboratory, Oak Ridge, Tennessee
| | - Gerald W Feigenson
- Department of Biochemistry and Molecular Cell Biology, Cornell University, Ithaca, New York
| | - Volker M Vogt
- Department of Biochemistry and Molecular Cell Biology, Cornell University, Ithaca, New York
| | - Robert A Dick
- Department of Biochemistry and Molecular Cell Biology, Cornell University, Ithaca, New York.
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52
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Doktorova M, Heberle FA, Kingston RL, Khelashvili G, Cuendet MA, Wen Y, Katsaras J, Feigenson GW, Vogt VM, Dick RA. Cholesterol Promotes Protein Binding by Affecting Membrane Electrostatics and Solvation Properties. Biophys J 2017. [PMID: 29117524 DOI: 10.1016/j.bpj.2017.08.055.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Binding of the retroviral structural protein Gag to the cellular plasma membrane is mediated by the protein's matrix (MA) domain. Prominent among MA-PM interactions is electrostatic attraction between the positively charged MA domain and the negatively charged plasma membrane inner leaflet. Previously, we reported that membrane association of HIV-1 Gag, as well as purified Rous sarcoma virus (RSV) MA and Gag, depends strongly on the presence of acidic lipids and is enhanced by cholesterol (Chol). The mechanism underlying this enhancement was unclear. Here, using a broad set of in vitro and in silico techniques we addressed molecular mechanisms of association between RSV MA and model membranes, and investigated how Chol enhances this association. In neutron scattering experiments with liposomes in the presence or absence of Chol, MA preferentially interacted with preexisting POPS-rich clusters formed by nonideal lipid mixing, binding peripherally to the lipid headgroups with minimal perturbation to the bilayer structure. Molecular dynamics simulations showed a stronger MA-bilayer interaction in the presence of Chol, and a large Chol-driven increase in lipid packing and membrane surface charge density. Although in vitro MA-liposome association is influenced by disparate variables, including ionic strength and concentrations of Chol and charged lipids, continuum electrostatic theory revealed an underlying dependence on membrane surface potential. Together, these results conclusively show that Chol affects RSV MA-membrane association by making the electrostatic potential at the membrane surface more negative, while decreasing the penalty for lipid headgroup desolvation. The presented approach can be applied to other viral and nonviral proteins.
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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
- The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, Tennessee; Joint Institute for Biological Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee; Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee.
| | - Richard L Kingston
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - George Khelashvili
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York
| | - Michel A Cuendet
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York
| | - Yi Wen
- Department of Biochemistry and Molecular Cell Biology, Cornell University, Ithaca, New York
| | - John Katsaras
- The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, Tennessee; Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee; Department of Physics and Astronomy, University of Tennessee, Knoxville, Tennessee; Shull Wollan Center, Oak Ridge National Laboratory, Oak Ridge, Tennessee
| | - Gerald W Feigenson
- Department of Biochemistry and Molecular Cell Biology, Cornell University, Ithaca, New York
| | - Volker M Vogt
- Department of Biochemistry and Molecular Cell Biology, Cornell University, Ithaca, New York
| | - Robert A Dick
- Department of Biochemistry and Molecular Cell Biology, Cornell University, Ithaca, New York.
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53
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Prajapati JD, Fernández Solano CJ, Winterhalter M, Kleinekathöfer U. Characterization of Ciprofloxacin Permeation Pathways across the Porin OmpC Using Metadynamics and a String Method. J Chem Theory Comput 2017; 13:4553-4566. [PMID: 28816443 DOI: 10.1021/acs.jctc.7b00467] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The rapid spreading of antimicrobial resistance in Gram-negative bacteria has become a major threat for humans as well as animals. As one of the main factors involved, the permeability of the outer membrane has attracted a great deal of attention recently. However, the knowledge regarding the translocation mechanisms for most available antibiotics is so far rather limited. Here, a theoretical study concerning the diffusion route of ciprofloxacin across the outer membrane porin OmpC from E. coli is presented. To this end, we establish a protocol to characterize meaningful permeation pathways by combining metadynamics with the zero-temperature string method. It was found that the lowest-energy pathway requires a reorientation of ciprofloxacin in the extracellular side of the porin before reaching the constriction region with its carboxyl group ahead. Several affinity sites have been identified, and their metastability has been evaluated using unbiased simulations. Such a detailed understanding is potentially very helpful in guiding the development of next generation antibiotics.
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Affiliation(s)
- Jigneshkumar Dahyabhai Prajapati
- Department of Physics and Earth Sciences and ‡Department of Life Sciences and Chemistry, Jacobs University Bremen , 28759 Bremen, Germany
| | - Carlos José Fernández Solano
- Department of Physics and Earth Sciences and ‡Department of Life Sciences and Chemistry, Jacobs University Bremen , 28759 Bremen, Germany
| | - Mathias Winterhalter
- Department of Physics and Earth Sciences and ‡Department of Life Sciences and Chemistry, Jacobs University Bremen , 28759 Bremen, Germany
| | - Ulrich Kleinekathöfer
- Department of Physics and Earth Sciences and ‡Department of Life Sciences and Chemistry, Jacobs University Bremen , 28759 Bremen, Germany
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54
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Li H, Chowdhary J, Huang L, He X, MacKerell AD, Roux B. Drude Polarizable Force Field for Molecular Dynamics Simulations of Saturated and Unsaturated Zwitterionic Lipids. J Chem Theory Comput 2017; 13:4535-4552. [PMID: 28731702 DOI: 10.1021/acs.jctc.7b00262] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Additive force fields are designed to account for induced electronic polarization in a mean-field average way, using effective empirical fixed charges. The limitation of this approximation is cause for serious concerns, particularly in the case of lipid membranes, where the molecular environment undergoes dramatic variations over microscopic length scales. A polarizable force field based on the classical Drude oscillator offers a practical and computationally efficient framework for an improved representation of electrostatic interactions in molecular simulations. Building on the first-generation Drude polarizable force field for the dipalmitoylphosphatidylcholine 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) molecule, the present effort was undertaken to improve this initial model and expand the force field to a wider range of phospholipid molecules. New lipids parametrized include dimyristoylphosphatidylcholine (DMPC), dilauroylphosphatidylcholine (DLPC), 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC), 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC), dipalmitoylphosphatidylethanolamine (DPPE), 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine (POPE), and 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine (DOPE). The iterative optimization protocol employed in this effort led to lipid models that achieve a good balance between reproducing quantum mechanical data on model compound representative of phospholipids and reproducing a range of experimental condensed phase properties of bilayers. A parametrization strategy based on a restrained ensemble-maximum entropy methodology was used to help accurately match the experimental NMR order parameters in the polar headgroup region. All the parameters were developed to be compatible with the remainder of the Drude polarizable force field, which includes water, ions, proteins, DNA, and selected carbohydrates.
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Affiliation(s)
- Hui Li
- Department of Biochemistry and Molecular Biology, Gordon Center for Integrative Science, University of Chicago , Chicago, Illinois 60637, United States
| | - Janamejaya Chowdhary
- Department of Biochemistry and Molecular Biology, Gordon Center for Integrative Science, University of Chicago , Chicago, Illinois 60637, United States
| | - Lei Huang
- Department of Biochemistry and Molecular Biology, Gordon Center for Integrative Science, University of Chicago , Chicago, Illinois 60637, United States
| | - Xibing He
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore , Baltimore, Maryland 21201, United States
| | - Alexander D MacKerell
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore , Baltimore, Maryland 21201, United States
| | - Benoît Roux
- Department of Biochemistry and Molecular Biology, Gordon Center for Integrative Science, University of Chicago , Chicago, Illinois 60637, United States
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55
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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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56
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Uhríková D, Teixeira J, Hubčík L, Búcsi A, Kondela T, Murugova T, Ivankov OI. Lipid based drug delivery systems: Kinetics by SANS. ACTA ACUST UNITED AC 2017. [DOI: 10.1088/1742-6596/848/1/012007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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57
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Pan J, Sahoo PK, Dalzini A, Hayati Z, Aryal CM, Teng P, Cai J, Gutierrez HR, Song L. Membrane Disruption Mechanism of a Prion Peptide (106-126) Investigated by Atomic Force Microscopy, Raman and Electron Paramagnetic Resonance Spectroscopy. J Phys Chem B 2017; 121:5058-5071. [PMID: 28459565 PMCID: PMC5770145 DOI: 10.1021/acs.jpcb.7b02772] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
A fragment of the human prion protein spanning residues 106-126 (PrP106-126) recapitulates many essential properties of the disease-causing protein such as amyloidogenicity and cytotoxicity. PrP106-126 has an amphipathic characteristic that resembles many antimicrobial peptides (AMPs). Therefore, the toxic effect of PrP106-126 could arise from a direct association of monomeric peptides with the membrane matrix. Several experimental approaches are employed to scrutinize the impacts of monomeric PrP106-126 on model lipid membranes. Porous defects in planar bilayers are observed by using solution atomic force microscopy. Adding cholesterol does not impede defect formation. A force spectroscopy experiment shows that PrP106-126 reduces Young's modulus of planar lipid bilayers. We use Raman microspectroscopy to study the effect of PrP106-126 on lipid atomic vibrational dynamics. For phosphatidylcholine lipids, PrP106-126 disorders the intrachain conformation, while the interchain interaction is not altered; for phosphatidylethanolamine lipids, PrP106-126 increases the interchain interaction, while the intrachain conformational order remains similar. We explain the observed differences by considering different modes of peptide insertion. Finally, electron paramagnetic resonance spectroscopy shows that PrP106-126 progressively decreases the orientational order of lipid acyl chains in magnetically aligned bicelles. Together, our experimental data support the proposition that monomeric PrP106-126 can disrupt lipid membranes by using similar mechanisms found in AMPs.
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Affiliation(s)
- Jianjun Pan
- Department of Physics, University of South Florida, Tampa, Florida 33620, United States
| | - Prasana K. Sahoo
- Department of Physics, University of South Florida, Tampa, Florida 33620, United States
| | - Annalisa Dalzini
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida 32310, United States
| | - Zahra Hayati
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida 32310, United States
| | - Chinta M. Aryal
- Department of Physics, University of South Florida, Tampa, Florida 33620, United States
| | - Peng Teng
- Department of Chemistry, University of South Florida, Tampa, Florida 33620, United States
| | - Jianfeng Cai
- Department of Chemistry, University of South Florida, Tampa, Florida 33620, United States
| | | | - Likai Song
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida 32310, United States
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58
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Bera I, Klauda JB. Molecular Simulations of Mixed Lipid Bilayers with Sphingomyelin, Glycerophospholipids, and Cholesterol. J Phys Chem B 2017; 121:5197-5208. [DOI: 10.1021/acs.jpcb.7b00359] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Indrani Bera
- Department
of Chemical and Biomolecular Engineering and ‡Biophysics Program, University of Maryland, College Park, Maryland 20742, United States
| | - Jeffery B. Klauda
- Department
of Chemical and Biomolecular Engineering and ‡Biophysics Program, University of Maryland, College Park, Maryland 20742, United States
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59
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Van Oosten B, Marquardt D, Harroun TA. Testing High Concentrations of Membrane Active Antibiotic Chlorhexidine Via Computational Titration and Calorimetry. J Phys Chem B 2017; 121:4657-4668. [DOI: 10.1021/acs.jpcb.6b12510] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Brad Van Oosten
- Department
of Physics, Brock University, St. Catharines, Ontario L2S 3A1, Canada
| | - Drew Marquardt
- Institute
of Molecular Biosciences, University of Graz, 8010 Graz, Austria
| | - Thad A. Harroun
- Department
of Physics, Brock University, St. Catharines, Ontario L2S 3A1, Canada
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60
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A novel pathway for amyloids self-assembly in aggregates at nanomolar concentration mediated by the interaction with surfaces. Sci Rep 2017; 7:45592. [PMID: 28358113 PMCID: PMC5372363 DOI: 10.1038/srep45592] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 02/27/2017] [Indexed: 11/09/2022] Open
Abstract
A limitation of the amyloid hypothesis in explaining the development of neurodegenerative diseases is that the level of amyloidogenic polypeptide in vivo is below the critical concentration required to form the aggregates observed in post-mortem brains. We discovered a novel, on-surface aggregation pathway of amyloidogenic polypeptide that eliminates this long-standing controversy. We applied atomic force microscope (AFM) to demonstrate directly that on-surface aggregation takes place at a concentration at which no aggregation in solution is observed. The experiments were performed with the full-size Aβ protein (Aβ42), a decapeptide Aβ(14-23) and α-synuclein; all three systems demonstrate a dramatic preference of the on-surface aggregation pathway compared to the aggregation in the bulk solution. Time-lapse AFM imaging, in solution, show that over time, oligomers increase in size and number and release in solution, suggesting that assembled aggregates can serve as nuclei for aggregation in bulk solution. Computational modeling performed with the all-atom MD simulations for Aβ(14-23) peptide shows that surface interactions induce conformational transitions of the monomer, which facilitate interactions with another monomer that undergoes conformational changes stabilizing the dimer assembly. Our findings suggest that interactions of amyloidogenic polypeptides with cellular surfaces play a major role in determining disease onset.
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61
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Fosso-Tande J, Black C, G. Aller S, Lu L, D. Hills Jr R. Simulation of lipid-protein interactions with the CgProt force field. AIMS MOLECULAR SCIENCE 2017. [DOI: 10.3934/molsci.2017.3.352] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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62
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Marquardt D, Heberle FA, Greathouse DV, Koeppe RE, Standaert RF, Van Oosten BJ, Harroun TA, Kinnun JJ, Williams JA, Wassall SR, Katsaras J. Lipid bilayer thickness determines cholesterol's location in model membranes. SOFT MATTER 2016; 12:9417-9428. [PMID: 27801465 DOI: 10.1039/c6sm01777k] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Cholesterol is an essential biomolecule of animal cell membranes, and an important precursor for the biosynthesis of certain hormones and vitamins. It is also thought to play a key role in cell signaling processes associated with functional plasma membrane microdomains (domains enriched in cholesterol), commonly referred to as rafts. In all of these diverse biological phenomena, the transverse location of cholesterol in the membrane is almost certainly an important structural feature. Using a combination of neutron scattering and solid-state 2H NMR, we have determined the location and orientation of cholesterol in phosphatidylcholine (PC) model membranes having fatty acids of different lengths and degrees of unsaturation. The data establish that cholesterol reorients rapidly about the bilayer normal in all the membranes studied, but is tilted and forced to span the bilayer midplane in the very thin bilayers. The possibility that cholesterol lies flat in the middle of bilayers, including those made from PC lipids containing polyunsaturated fatty acids (PUFAs), is ruled out. These results support the notion that hydrophobic thickness is the primary determinant of cholesterol's location in membranes.
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Affiliation(s)
- Drew Marquardt
- Department of Physics, Brock University, St. Catharines, Ontario L2S 3A1, Canada and Institute of Molecular Biosciences, University of Graz, Graz, Austria
| | - Frederick A Heberle
- The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, Tennessee 37996, USA and Joint Institute for Biological Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA and Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA.
| | - Denise V Greathouse
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701, USA
| | - Roger E Koeppe
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701, USA
| | - Robert F Standaert
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA and Department of Biochemistry and Cellular & Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Brad J Van Oosten
- Department of Physics, Brock University, St. Catharines, Ontario L2S 3A1, Canada
| | - Thad A Harroun
- Department of Physics, Brock University, St. Catharines, Ontario L2S 3A1, Canada
| | - Jacob J Kinnun
- Department of Physics, Indiana University - Purdue University Indianapolis, Indianapolis, Indiana 46202, USA.
| | - Justin A Williams
- Department of Physics, Indiana University - Purdue University Indianapolis, Indianapolis, Indiana 46202, USA.
| | - Stephen R Wassall
- Department of Physics, Indiana University - Purdue University Indianapolis, Indianapolis, Indiana 46202, USA.
| | - John Katsaras
- Department of Physics, Brock University, St. Catharines, Ontario L2S 3A1, Canada and The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, Tennessee 37996, USA and Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA. and Shull Wollan Center-a Joint Institute for Neutron Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA and Department of Physics and Astronomy, University of Tennessee, Knoxville, Tennessee 37996, USA
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63
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An extensive simulation study of lipid bilayer properties with different head groups, acyl chain lengths, and chain saturations. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:3093-3104. [PMID: 27664502 DOI: 10.1016/j.bbamem.2016.09.016] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Revised: 09/14/2016] [Accepted: 09/19/2016] [Indexed: 12/21/2022]
Abstract
Previous MD simulations of six phosphocholine (PC) lipid bilayers demonstrated the accuracy of the CHARMM36 force field (C36FF) for PC bilayer simulation at varied temperatures (BBA-Biomembranes, 1838 (2014): 2520-2529). In this work, we further examine the accuracy of C36FF over a wide temperature range for a broader range of lipid types such as various head groups (phosphatidic acid (PA), PC, phosphoethanolamine (PE), phosphoglycerol (PG), and phosphoserine (PS)), and tails (saturated, mono-, mixed- and poly-unsaturated acyl chains with varied chain lengths). The structural properties (surface area per lipid (SA/lip), overall bilayer thickness, hydrophobic thickness, headgroup-to-headgroup thickness, deuterium order parameter (SCD), and spin-lattice relaxation time (T1)) obtained from simulations agree well with nearly all available experimental data. Our analyses indicate that PS lipids have the most inter-lipid hydrogen bonds, while PG lipids have the most intra-lipid hydrogen bonds, which play the main role in their low SA/lip in PS lipids and low thicknesses in PG lipids, respectively. PS, PE, and PA lipids have the largest contact clusters with on average 5-8 lipids per cluster, while PC and PG have clusters of 4 lipids based on a cutoff distance of 6.5Å. PS lipids have much slower lipid wobble (i.e., higher correlation time) than other head groups at a given temperature as the hydrogen bonded network significantly reduces a lipid's mobility, and the rate of lipid wobble increases dramatically as temperature increases. These in-depth analyses facilitate further understanding of lipid bilayers at the atomic level.
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64
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Pluhackova K, Kirsch SA, Han J, Sun L, Jiang Z, Unruh T, Böckmann RA. A Critical Comparison of Biomembrane Force Fields: Structure and Dynamics of Model DMPC, POPC, and POPE Bilayers. J Phys Chem B 2016; 120:3888-903. [DOI: 10.1021/acs.jpcb.6b01870] [Citation(s) in RCA: 107] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Kristyna Pluhackova
- Computational
Biology, Department of Biology, Friedrich-Alexander-University of Erlangen-Nürnberg, Staudtstr. 5, 91058 Erlangen, Germany
| | - Sonja A. Kirsch
- Computational
Biology, Department of Biology, Friedrich-Alexander-University of Erlangen-Nürnberg, Staudtstr. 5, 91058 Erlangen, Germany
| | - Jing Han
- Computational
Biology, Department of Biology, Friedrich-Alexander-University of Erlangen-Nürnberg, Staudtstr. 5, 91058 Erlangen, Germany
| | - Liping Sun
- Computational
Biology, Department of Biology, Friedrich-Alexander-University of Erlangen-Nürnberg, Staudtstr. 5, 91058 Erlangen, Germany
| | - Zhenyan Jiang
- Computational
Biology, Department of Biology, Friedrich-Alexander-University of Erlangen-Nürnberg, Staudtstr. 5, 91058 Erlangen, Germany
| | - Tobias Unruh
- Lehrstuhl
für Kristallografie und Strukturphysik, Department Physik, Friedrich-Alexander-University of Erlangen-Nürnberg, Staudtstr. 3, 91058 Erlangen, Germany
| | - Rainer A. Böckmann
- Computational
Biology, Department of Biology, Friedrich-Alexander-University of Erlangen-Nürnberg, Staudtstr. 5, 91058 Erlangen, Germany
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65
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Skjevik ÅA, Madej BD, Dickson CJ, Lin C, Teigen K, Walker RC, Gould IR. Simulation of lipid bilayer self-assembly using all-atom lipid force fields. Phys Chem Chem Phys 2016; 18:10573-84. [PMID: 27034995 DOI: 10.1039/c5cp07379k] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
In this manuscript we expand significantly on our earlier communication by investigating the bilayer self-assembly of eight different types of phospholipids in unbiased molecular dynamics (MD) simulations using three widely used all-atom lipid force fields. Irrespective of the underlying force field, the lipids are shown to spontaneously form stable lamellar bilayer structures within 1 microsecond, the majority of which display properties in satisfactory agreement with the experimental data. The lipids self-assemble via the same general mechanism, though at formation rates that differ both between lipid types, force fields and even repeats on the same lipid/force field combination. In addition to zwitterionic phosphatidylcholine (PC) and phosphatidylethanolamine (PE) lipids, anionic phosphatidylserine (PS) and phosphatidylglycerol (PG) lipids are represented. To our knowledge this is the first time bilayer self-assembly of phospholipids with negatively charged head groups is demonstrated in all-atom MD simulations.
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Affiliation(s)
- Åge A Skjevik
- San Diego Supercomputer Center, University of California San Diego, 9500 Gilman Drive MC0505, La Jolla, California 92093-0505, USA.
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66
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Poyton MF, Sendecki AM, Cong X, Cremer PS. Cu2+ Binds to Phosphatidylethanolamine and Increases Oxidation in Lipid Membranes. J Am Chem Soc 2016; 138:1584-90. [DOI: 10.1021/jacs.5b11561] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Matthew F. Poyton
- Department
of Chemistry, Penn State University, University Park, Pennsylvania 16801, United States
| | - Anne M. Sendecki
- Department
of Chemistry, Penn State University, University Park, Pennsylvania 16801, United States
| | - Xiao Cong
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Paul S. Cremer
- Department
of Chemistry, Penn State University, University Park, Pennsylvania 16801, United States
- Department
of Biochemistry and Molecular Biology, Penn State University, University Park, Pennsylvania 16801, United States
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67
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A MARTINI extension for Pseudomonas aeruginosa PAO1 lipopolysaccharide. J Mol Graph Model 2016; 63:125-33. [DOI: 10.1016/j.jmgm.2015.12.002] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Revised: 11/16/2015] [Accepted: 12/11/2015] [Indexed: 11/24/2022]
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68
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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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69
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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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70
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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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