Structural evaluation of phospholipid bicelles for solution-state studies of membrane-associated biomolecules.

doi:10.1016/S0006-3495(01)75864-X

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Structural evaluation of phospholipid bicelles for solution-state studies of membrane-associated biomolecules.

Journal Article•DOI•

Structural evaluation of phospholipid bicelles for solution-state studies of membrane-associated biomolecules.

Kerney Jebrell Glover¹, Jennifer A. Whiles¹, Guohua Wu², Nan Jun Yu³, Raymond A. Deems¹, Jochem Struppe¹, Ruth E. Stark², Elizabeth A. Komives¹, Regitze R. Vold¹ - Show less +5 more•Institutions (3)

University of California, San Diego¹, The Graduate Center, CUNY², University of California, Los Angeles³

01 Oct 2001-Biophysical Journal (The Biophysical Society)-Vol. 81, Iss: 4, pp 2163-2171

TL;DR: Results suggest that bicelles with low q retain the morphology and bilayer organization typical of their liquid-crystalline counterparts, making them useful membrane mimetics.

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About: This article is published in Biophysical Journal.The article was published on 2001-10-01 and is currently open access. It has received 270 citations till now. The article focuses on the topics: Model lipid bilayer.

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Journal Article•DOI•

Conformational Coupling across the Plasma Membrane in Activation of the EGF Receptor.

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Nicholas F. Endres¹, Rahul Das², Rahul Das¹, Adam W. Smith¹, Adam W. Smith³, Anton Arkhipov⁴, Erika Kovacs¹, Erika Kovacs², Yongjian Huang², Yongjian Huang¹, Jeffrey G. Pelton², Yibing Shan⁴, David E. Shaw⁵, David E. Shaw⁴, David E. Wemmer³, David E. Wemmer², David E. Wemmer¹, Jay T. Groves, John Kuriyan - Show less +15 more•Institutions (5)

University of California, Berkeley¹, California Institute for Quantitative Biosciences², Lawrence Berkeley National Laboratory³, D. E. Shaw Research⁴, Columbia University⁵

31 Jan 2013-Cell

TL;DR: It is concluded that EGF binding removes steric constraints in the extracellular module, promoting activation through N-terminal association of the transmembrane helices and promotes an antiparallel interaction between juxtamembrane segments and release of inhibition by the membrane.

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439 citations

Journal Article•DOI•

Regulation of T Cell Receptor Activation by Dynamic Membrane Binding of the CD3ɛ Cytoplasmic Tyrosine-Based Motif

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Chenqi Xu¹, Etienne Gagnon¹, Matthew E. Call¹, Jason R. Schnell¹, Charles D. Schwieters², Christopher V. Carman³, James J. Chou¹, Kai W. Wucherpfennig¹ - Show less +4 more•Institutions (3)

Harvard University¹, Center for Information Technology², Beth Israel Deaconess Medical Center³

14 Nov 2008-Cell

TL;DR: Receptor ligation needs to result in unbinding of the CD3epsilon ITAM from the membrane to render these tyrosines accessible to Src kinases and represents a previously unrecognized mechanism for control of receptor activation.

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395 citations

Cites methods from "Structural evaluation of phospholip..."

...8 bicelle is estimated to have a diameter of 72 Å according to the corrected Vold-Prosser model (Glover et al., 2001)....
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...A q = 0.8 bicelle is estimated to have a diameter of 72 Å according to the corrected Vold-Prosser model (Glover et al., 2001)....
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Journal Article•DOI•

Residual Dipolar Couplings in Structure Determination of Biomolecules

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James H. Prestegard¹, Catherine M. Bougault¹, Anita I. Kishore¹•Institutions (1)

University of Georgia¹

07 Jul 2004-Chemical Reviews

TL;DR: Since the recognition of the potential of RDCs in protein structure determination, applications have spread to nucleic acid structure, carbohydrate structure, protein-ligand interactions, protein domain relationships, high-throughput strategies for structural genomics, and studies of motional amplitudes in flexible assemblies.

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Abstract: The use of residual dipolar couplings (RDCs) in the analysis of biomolecular structure and dynamics has expanded rapidly since its potential as a source of structural information on proteins was demonstrated in the mid 1990s.1,2 Of course, this work on proteins rested on applications to smaller biomolecular systems that occurred much earlier,3 and even these early applications benefited from prior research on organic molecules in partially ordered liquid crystals.4 However, in the 1990s, the existence of efficient means of introducing magnetically active isotopic labels (13C and 15N) and the availability of triple resonance strategies for selective manipulation and assignment of NMR resonances made widespread application to large biomolecules possible. It was fortuitous that the 13C and 15N labels introduced had small magnetogyric ratios, allowing simple dipolar interactions with directly bonded protons to dominate RDC observations. Prior work had focused on systems with couplings coming from the much larger 1H-1H dipolar and 2H quadrupolar interactions. While large interactions and the resultant increased size of observable couplings may have seemed an advantage, these large interactions also lead to complex spectra and broader lines. In the case of 1H1H interactions, additional splittings of resonances from protons at long distances arose, and in both cases broader lines resulted from enhanced spin relaxation processes. Since the recognition of the potential of RDCs in protein structure determination, applications have spread to nucleic acid structure, carbohydrate structure, protein-ligand interactions, protein domain relationships, high-throughput strategies for structural genomics, and studies of motional amplitudes in flexible assemblies. Related pieces of data coming from interactions with paramagnetic sites and chemical shift anisotropy (CSA) offsets have also come onto the scene. Each new application demands parallel improvements in sample preparation, data acquisition, and data analysis methods. The development of RDC applications has been reviewed periodically since their introduction to the structural biology field,5-13 and the reader is referred to these reviews for a more complete description of the history and the underlying theory. Here, we will provide a brief introduction to RDCs and related data as they are used today. Advances that have been made in alignment techniques, data acquisition techniques, and analysis methods will be reviewed. In the course of this review, we will provide examples of applications that use these methods. Applications, per se, have become too numerous to attempt a comprehensive review. * To whom correspondence should be addressed. James H. Prestegard, Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA, 30602. Phone: (706) 542-6281. Fax: (706) 542-4412. E-mail: jpresteg@ccrc.uga.edu. † University of Georgia. ‡ Institut de Biologie Structurale. 3519 Chem. Rev. 2004, 104, 3519−3540

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359 citations

Journal Article•DOI•

Acoustically active liposomes for drug encapsulation and ultrasound-triggered release.

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Shaoling Huang¹, Robert C. MacDonald¹•Institutions (1)

Northwestern University¹

11 Oct 2004-Biochimica et Biophysica Acta

TL;DR: This research investigated the capacity of acoustically active liposomes for hydrophilic molecule encapsulation and to determine their sensitivity to ultrasound-triggered release, finding that release of contents was highly correlated with the loss of air induced either by ultrasound or rapid pressure reduction.

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278 citations

Journal Article•DOI•

Interactions of surfactants with lipid membranes.

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Heiko Heerklotz¹•Institutions (1)

University of Toronto¹

01 Nov 2008-Quarterly Reviews of Biophysics

TL;DR: The biophysics of the interactions of surfactants with membranes of insoluble, naturally occurring lipids is reviewed, including structural, thermodynamic and kinetic aspects of membrane–water partitioning, changes in membrane properties induced by surfactant properties, and other phases formed by lipid–surfactant systems are discussed.

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Abstract: Surfactants are surface-active, amphiphilic compounds that are water-soluble in the micro- to millimolar range, and self-assemble to form micelles or other aggregates above a critical concentration. This definition comprises synthetic detergents as well as amphiphilic peptides and lipopeptides, bile salts and many other compounds. This paper reviews the biophysics of the interactions of surfactants with membranes of insoluble, naturally occurring lipids. It discusses structural, thermodynamic and kinetic aspects of membrane-water partitioning, changes in membrane properties induced by surfactants, membrane solubilisation to micelles and other phases formed by lipid-surfactant systems. Each section defines and derives key parameters, mentions experimental methods for their measurement and compiles and discusses published data. Additionally, a brief overview is given of surfactant-like effects in biological systems, technical applications of surfactants that involve membrane interactions, and surfactant-based protocols to study biological membranes.

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270 citations

Cites methods from "Structural evaluation of phospholip..."

...Comprehensive studies using a large variety of methods have supported and refined this picture (Glover et al. 2001 ; Luchette et al. 2001)....
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References

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Journal Article•DOI•

Analysis of Macromolecular Polydispersity in Intensity Correlation Spectroscopy: The Method of Cumulants

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Dennis E. Koppel

01 Dec 1972-Journal of Chemical Physics

TL;DR: The first order electric field correlation function of laser light scattered by polydisperse solutions of macromolecules can be written as a sum or distribution of exponentials, with decay rates proportional to the diffusion coefficients of the solute molecules as discussed by the authors.

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Abstract: The first order electric field correlation function of laser light scattered by polydisperse solutions of macromolecules can be written as a sum or distribution of exponentials, with decay rates proportional to the diffusion coefficients of the solute molecules. It is shown that the logarithm of this correlation function is formally equivalent to a cumulant generating function. A method is described by which the distribution function of the decay rates (and thus the extent of polydispersity) can be characterized, in a light scattering experiment, by calculation of the moments or cumulants. The systematic and random statistical errors in the calculated cumulants are discussed.

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2,613 citations

"Structural evaluation of phospholip..." refers methods in this paper

...5% (w/w); in both cases the measured hydrodynamic radii were determined by the method of cumulants (Koppel, 1972)....
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...radius and size distribution were determined for each bicelle solution using Cumulants, CONTIN, and NNLS algorithms (Koppel, 1972; Provencher, 1982; Morrison et al., 1985)....
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...…checking the particle sizes in samples of polystyrene beads and sodium dodecylsulfate micelles (Mazer et al., 1976), the mean radius and size distribution were determined for each bicelle solution using Cumulants, CONTIN, and NNLS algorithms (Koppel, 1972; Provencher, 1982; Morrison et al., 1985)....
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Journal Article•DOI•

A constrained regularization method for inverting data represented by linear algebraic or integral equations

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Stephen W. Provencher¹•Institutions (1)

European Bioinformatics Institute¹

01 Sep 1982-Computer Physics Communications

TL;DR: CONTIN as discussed by the authors is a portable Fortran IV package for inverting noisy linear operator equations, which can be used for the analysis of data from a wide variety of experiments, including photon correlation spectroscopy, multicomponent spectra, and Fourier-Bessel, Fourier and Laplace transforms.

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2,446 citations

"Structural evaluation of phospholip..." refers methods in this paper

...radius and size distribution were determined for each bicelle solution using Cumulants, CONTIN, and NNLS algorithms (Koppel, 1972; Provencher, 1982; Morrison et al., 1985)....
[...]
...…checking the particle sizes in samples of polystyrene beads and sodium dodecylsulfate micelles (Mazer et al., 1976), the mean radius and size distribution were determined for each bicelle solution using Cumulants, CONTIN, and NNLS algorithms (Koppel, 1972; Provencher, 1982; Morrison et al., 1985)....
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Journal Article•DOI•

Direct Measurement of Distances and Angles in Biomolecules by NMR in a Dilute Liquid Crystalline Medium

[...]

Nico Tjandra¹, Ad Bax¹•Institutions (1)

National Institutes of Health¹

07 Nov 1997-Science

TL;DR: The approach promises to improve the accuracy of structures determined by NMR, and extend the size limit, and distances and angles derived from dipolar couplings in human ubiquitin are in excellent agreement with its crystal structure.

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Abstract: In isotropic solution, internuclear dipolar couplings average to zero as a result of rotational diffusion. By dissolving macromolecules in a dilute aqueous nematic discotic liquid-crystalline medium containing widely spaced magnetically oriented particles, a tunable degree of solute alignment with the magnetic field can be created while retaining the high resolution and sensitivity of the regular isotropic nuclear magnetic resonance (NMR) spectrum. Dipolar couplings between1H-1H, 1H-13C,1H-15N, and 13C-13C pairs in such an oriented macromolecule no longer average to zero, and are readily measured. Distances and angles derived from dipolar couplings in human ubiquitin are in excellent agreement with its crystal structure. The approach promises to improve the accuracy of structures determined by NMR, and extend the size limit.

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1,634 citations

"Structural evaluation of phospholip..." refers methods in this paper

...2 andcL ' 3–5% (w/w)) have been used to achieve a small degree of orientation of nonmembrane-associated biomolecules for the purpose of obtaining residual dipolar couplings used in the refinement of high-resolution NMR structures (Tjandra and Bax, 1997; Struppe and Vold, 1998)....
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Journal Article•DOI•

An investigation of the micellar phase of sodium dodecyl sulfate in aqueous sodium chloride solutions using quasielastic light scattering spectroscopy

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Norman A. Mazer, George B. Benedek, Martin C. Carey

01 May 1976-The Journal of Physical Chemistry

551 citations

"Structural evaluation of phospholip..." refers methods in this paper

...After checking the particle sizes in samples of polystyrene beads and sodium dodecylsulfate micelles (Mazer et al., 1976), the mean radius and size distribution were determined for each bicelle solution using Cumulants, CONTIN, and NNLS algorithms (Koppel, 1972; Provencher, 1982; Morrison et al.,…...
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Journal Article•DOI•

Quasielastic light-scattering studies of aqueous biliary lipid systems. Mixed micelle formation in bile salt-lecithin solutions.

[...]

Norman A. Mazer, George B. Benedek, Martin C. Carey

19 Feb 1980-Biochemistry

TL;DR: The inclusion of bile salts in a fixed stoichiometry within the interior of the bilayers is shown to provide a quantitative explanation for the divergence of the mixed micellar sizes, their temperature dependence, and the origin of the lecithin-bile salt phase limit.

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Abstract: From measurements of the autocorrelation function and time-averaged intensity of light scattered from aqueous bile salt-lecithin solutions, we deduced the mean hydrodynamic radius (Rh), shape, and polydispersity of bile salt-lecithin mixed micelles as functions of bile salt species, lecithin to bile salt (L/BS) molar ratio, total lipid concentration (0.625-10 g/dL), temperature (20-60 degrees C), and NaCl concentration (0.15-0.6 M). Our data suggest that at low L/BS ratios (0 to approximately 0.6) simple bile salt micelles coexist in varying proportions with minimum-sized mixed micelles (Rh, 18-35 A). These solutions are highly polydisperse and display features dependent upon the particular bile salt species. At high L/BS ratios (greater than 0.6), only mixed micelles are present, and their sizes increase markedly (Rh, 20 leads to 300 A) with increases in L/BS ratio and appear to diverge as the lecithin-bile salt phase limit is approached. The shape of the mixed micelles as deduced from light-scattering measurements and confirmed by transmission electron microscopy is disklike. The radii of the disks, however, are not compatible with Small's model of mixed micellar structure [Small, D.M. (1967a) Gastroenterology 52, 607-a1 but are consistent with a new model proposed here in which bile salts and lecithin interact to form a mixed bilayer disk which is surrounded on its perimeter by bile salts. The inclusion of bile salts in a fixed stoichiometry within the interior of the bilayers is shown to provide a quantitative explanation for the divergence of the mixed micellar sizes, their temperature dependence, and the origin of the lecithin-bile salt phase limit. The influence of total lipid concentration on both mixed micellar size and the lecithin-bile salt phase limit is explained by the "mixed disk" model by taking account of the equilibrium between mixed micelles and bile salt monomers in the intermicellar solution. By use of this concept, deductions of the intermicellar bile salt concentration in taurocholate-lecithin solutions are made and are shown to vary as a function of mixed micellar size and temperature. The range of values obtained, 3-6 mM, is comparable in magnitude to the critical micellar concentration of the pure bile salt.

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489 citations

"Structural evaluation of phospholip..." refers background or methods in this paper

...…salt-lecithin mixed micelles and noted earlier, the aggregates are expected to grow in more dilute solutions, presumably because a greater proportion of the available DHPC is drawn out of the bicellar particles to maintain the interaggregate concentration (Mazer et al., 1980; Cohen et al., 1998)....
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...Qualitatively similar variations in size have also been observed for phospholipidbile salt mixtures ( Mazer et al., 1980; Stark and Roberts, 1984); overall dilution enhances the proportion of the bilesalt detergent that exists in free form to maintain the intermicellar concentration, and results in the formation of a larger detergent-poor mixed-lipid aggregate....
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...Shape information was deduced from semilog plots of normalized scattered light intensity/cL versus hydrodynamic radius using analyses devised to distinguish spheres, disks, and rods in bile-saltphospholipid mixtures (Mazer et al., 1980; Cohen et al., 1998)....
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...Qualitatively similar variations in size have also been observed for phospholipidbile salt mixtures (Mazer et al., 1980; Stark and Roberts, 1984); overall dilution enhances the proportion of the bilesalt detergent that exists in free form to maintain the intermicellar concentration, and results in…...
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...As reported previously in bile salt-lecithin mixed micelles and noted earlier, the aggregates are expected to grow in more dilute solutions, presumably because a greater proportion of the available DHPC is drawn out of the bicellar particles to maintain the interaggregate concentration ( Mazer et al., 1980; Cohen et al., 1998)....
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