Literature DB >> 22207767

Continuous distribution model for the investigation of complex molecular architectures near interfaces with scattering techniques.

Prabhanshu Shekhar, Hirsh Nanda, Mathias Lösche, Frank Heinrich.   

Abstract

Biological membranes are composed of a thermally disordered lipid matrix and therefore require non-crystallographic scattering approaches for structural characterization with x-rays or neutrons. Here we develop a continuous distribution (CD) model to refine neutron or x-ray reflectivity data from complex architectures of organic molecules. The new model is a flexible implementation of the composition-space refinement of interfacial structures to constrain the resulting scattering length density profiles. We show this model increases the precision with which molecular components may be localized within a sample, with a minimal use of free model parameters. We validate the new model by parameterizing all-atom molecular dynamics (MD) simulations of bilayers and by evaluating the neutron reflectivity of a phospholipid bilayer physisorbed to a solid support. The determination of the structural arrangement of a sparsely-tethered bilayer lipid membrane (stBLM) comprised of a multi-component phospholipid bilayer anchored to a gold substrate by a thiolated oligo(ethylene oxide) linker is also demonstrated. From the model we extract the bilayer composition and density of tether points, information which was previously inaccessible for stBLM systems. The new modeling strategy has been implemented into the ga_refl reflectivity data evaluation suite, available through the National Institute of Standards and Technology (NIST) Center for Neutron Research (NCNR).

Entities:  

Year:  2011        PMID: 22207767      PMCID: PMC3246012          DOI: 10.1063/1.3661986

Source DB:  PubMed          Journal:  J Appl Phys        ISSN: 0021-8979            Impact factor:   2.546


  36 in total

1.  Electrostatic interactions and binding orientation of HIV-1 matrix studied by neutron reflectivity.

Authors:  Hirsh Nanda; Siddhartha A K Datta; Frank Heinrich; Mathias Lösche; Alan Rein; Susan Krueger; Joseph E Curtis
Journal:  Biophys J       Date:  2010-10-20       Impact factor: 4.033

2.  Spontaneous formation of asymmetric lipid bilayers by adsorption of vesicles.

Authors:  Hanna P Wacklin; Robert K Thomas
Journal:  Langmuir       Date:  2007-06-01       Impact factor: 3.882

3.  Structure of functional Staphylococcus aureus alpha-hemolysin channels in tethered bilayer lipid membranes.

Authors:  Duncan J McGillivray; Gintaras Valincius; Frank Heinrich; Joseph W F Robertson; David J Vanderah; Wilma Febo-Ayala; Ilja Ignatjev; Mathias Lösche; John J Kasianowicz
Journal:  Biophys J       Date:  2009-02-18       Impact factor: 4.033

4.  Structure of myelin lipid bilayers. Changes during maturation.

Authors:  N P Franks; V Melchior; D A Kirshner; D L Caspar
Journal:  J Mol Biol       Date:  1982-02-25       Impact factor: 5.469

5.  Structure, composition, and peptide binding properties of detergent soluble bilayers and detergent resistant rafts.

Authors:  M Gandhavadi; D Allende; A Vidal; S A Simon; T J McIntosh
Journal:  Biophys J       Date:  2002-03       Impact factor: 4.033

6.  Comparing membrane simulations to scattering experiments: introducing the SIMtoEXP software.

Authors:  Norbert Kucerka; John Katsaras; John F Nagle
Journal:  J Membr Biol       Date:  2010-04-21       Impact factor: 1.843

7.  Structure of gel phase DMPC determined by X-ray diffraction.

Authors:  Stephanie Tristram-Nagle; Yufeng Liu; Justin Legleiter; John F Nagle
Journal:  Biophys J       Date:  2002-12       Impact factor: 4.033

8.  Structure and fluctuations of charged phosphatidylserine bilayers in the absence of salt.

Authors:  Horia I Petrache; Stephanie Tristram-Nagle; Klaus Gawrisch; Daniel Harries; V Adrian Parsegian; John F Nagle
Journal:  Biophys J       Date:  2004-03       Impact factor: 4.033

9.  Determining bilayer hydrocarbon thickness from neutron diffraction measurements using strip-function models.

Authors:  G I King; S H White
Journal:  Biophys J       Date:  1986-05       Impact factor: 4.033

10.  Structure and hydration of membranes embedded with voltage-sensing domains.

Authors:  Dmitriy Krepkiy; Mihaela Mihailescu; J Alfredo Freites; Eric V Schow; David L Worcester; Klaus Gawrisch; Douglas J Tobias; Stephen H White; Kenton J Swartz
Journal:  Nature       Date:  2009-11-26       Impact factor: 49.962

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  25 in total

1.  Membrane Anchoring of Hck Kinase via the Intrinsically Disordered SH4-U and Length Scale Associated with Subcellular Localization.

Authors:  Matthew P Pond; Rebecca Eells; Bradley W Treece; Frank Heinrich; Mathias Lösche; Benoît Roux
Journal:  J Mol Biol       Date:  2019-12-23       Impact factor: 5.469

2.  Structural features and lipid binding domain of tubulin on biomimetic mitochondrial membranes.

Authors:  David P Hoogerheide; Sergei Y Noskov; Daniel Jacobs; Lucie Bergdoll; Vitalii Silin; David L Worcester; Jeff Abramson; Hirsh Nanda; Tatiana K Rostovtseva; Sergey M Bezrukov
Journal:  Proc Natl Acad Sci U S A       Date:  2017-04-18       Impact factor: 11.205

3.  Myristoylation restricts orientation of the GRASP domain on membranes and promotes membrane tethering.

Authors:  Frank Heinrich; Hirsh Nanda; Haw Zan Goh; Collin Bachert; Mathias Lösche; Adam D Linstedt
Journal:  J Biol Chem       Date:  2014-02-06       Impact factor: 5.157

4.  Information gain from isotopic contrast variation in neutron reflectometry on protein-membrane complex structures.

Authors:  Frank Heinrich; Paul A Kienzle; David P Hoogerheide; Mathias Lösche
Journal:  J Appl Crystallogr       Date:  2020-05-29       Impact factor: 3.304

5.  Association of Model Neurotransmitters with Lipid Bilayer Membranes.

Authors:  Brian P Josey; Frank Heinrich; Vitalii Silin; Mathias Lösche
Journal:  Biophys J       Date:  2020-01-28       Impact factor: 4.033

Review 6.  Zooming in on disordered systems: neutron reflection studies of proteins associated with fluid membranes.

Authors:  Frank Heinrich; Mathias Lösche
Journal:  Biochim Biophys Acta       Date:  2014-03-25

7.  Structure and properties of tethered bilayer lipid membranes with unsaturated anchor molecules.

Authors:  Rima Budvytyte; Gintaras Valincius; Gediminas Niaura; Vladislava Voiciuk; Mindaugas Mickevicius; Hilary Chapman; Haw-Zan Goh; Prabhanshu Shekhar; Frank Heinrich; Siddharth Shenoy; Mathias Lösche; David J Vanderah
Journal:  Langmuir       Date:  2013-06-26       Impact factor: 3.882

8.  Molecular Structure of Sphingomyelin in Fluid Phase Bilayers Determined by the Joint Analysis of Small-Angle Neutron and X-ray Scattering Data.

Authors:  Milka Doktorova; Norbert Kučerka; Jacob J Kinnun; Jianjun Pan; Drew Marquardt; Haden L Scott; Richard M Venable; Richard W Pastor; Stephen R Wassall; John Katsaras; Frederick A Heberle
Journal:  J Phys Chem B       Date:  2020-06-16       Impact factor: 2.991

9.  Membrane association of the PTEN tumor suppressor: electrostatic interaction with phosphatidylserine-containing bilayers and regulatory role of the C-terminal tail.

Authors:  Siddharth S Shenoy; Hirsh Nanda; Mathias Lösche
Journal:  J Struct Biol       Date:  2012-10-13       Impact factor: 2.867

10.  Uncovering a membrane-distal conformation of KRAS available to recruit RAF to the plasma membrane.

Authors:  Que N Van; Cesar A López; Marco Tonelli; Troy Taylor; Ben Niu; Christopher B Stanley; Debsindhu Bhowmik; Timothy H Tran; Peter H Frank; Simon Messing; Patrick Alexander; Daniel Scott; Xiaoying Ye; Matt Drew; Oleg Chertov; Mathias Lösche; Arvind Ramanathan; Michael L Gross; Nicolas W Hengartner; William M Westler; John L Markley; Dhirendra K Simanshu; Dwight V Nissley; William K Gillette; Dominic Esposito; Frank McCormick; S Gnanakaran; Frank Heinrich; Andrew G Stephen
Journal:  Proc Natl Acad Sci U S A       Date:  2020-09-10       Impact factor: 11.205

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