scholarly journals Visualization of lipid bilayer in the crystals by solvent contrast modulation

2014 ◽  
Vol 70 (a1) ◽  
pp. C1498-C1498
Author(s):  
Yoshiyuki Norimatsu ◽  
Junko Tsueda ◽  
Ayami Hirata ◽  
Shiho Iwasawa ◽  
Chikashi Toyoshima
Keyword(s):  
Lipid Bilayer ◽  
Electron Density ◽  
Lipid Bilayers ◽  
Transmembrane Helix ◽  
Real Space ◽  
New Method ◽  
Imaging Plate ◽  
Salt Bridges ◽  
Transmembrane Helices ◽  
X Ray

A new method of X-ray solvent contrast modulation was developed to visualize lipid bilayers in crystals of membrane proteins at a high enough resolution to resolve individual phospholipids molecules (~3.5 Å ). Visualization of lipid bilayer has been escaping from conventional crystallographic methods due to its extreme flexibility, and our knowledge on the behavior of lipid bilayer is still very much limited. Here we applied the new method of X-ray solvent contrast modulation to crystals of Ca2+-ATPase in 4 different physiological states. As phospholipids have to be added to make crystals of Ca2+-ATPase, it is expected that lipid bilayers are present in the crystals. Moreover, transmembrane helices of Ca2+-ATPase rearrange drastically during the reaction cycle and some of them show substantial movements perpendicular to the bilayer plane. Thus these crystals provide a rare opportunity to directly visualize phospholipids interacting with a membrane protein in different conformations. Complete diffraction data covering from 200 to 3.2 Å resolution were collected at BL41XU, Spring-8, using an R-Axis V imaging plate detector for crystals soaked in solvent of different electron density. A new concept "solvent exchange probability", which should be 1 in the bulk solvent, 0 inside the protein and an intermediate at interface, was introduced and used as a restraint for real space phase improvement. The electron density maps thus obtained clearly show that: (i) Phospholipid molecules surrounding the protein are fixed apparently by Arg/Lys-phosphate salt bridges or Trp-carbonyl hydrogen bonds and follow the movements of transmembrane helices. Movements of as large as 12 Å are allowed. (ii) If the movement of a transmembrane helix exceeds this limit, associated phospholipids change the partners for fixation or change the orientation of the entire protein molecule.

BILMIX: a new approach to restore the size polydispersity and electron density profiles of lipid bilayers from liposomes using small-angle X-ray scattering data

2020 ◽  
Vol 53 (1) ◽  
pp. 236-243
Author(s):  
Petr V. Konarev ◽  
Maxim V. Petoukhov ◽  
Liubov A. Dadinova ◽  
Natalia V. Fedorova ◽  
Pavel E. Volynsky ◽  
...  
Keyword(s):  
Lipid Bilayer ◽  
Electron Density ◽  
Lipid Bilayers ◽  
Density Profile ◽  
Small Angle ◽  
Electron Density Profile ◽  
Scattering Data ◽  
X Ray ◽  
X Ray Scattering ◽  
Ray Scattering

Small-angle X-ray scattering (SAXS) is one of the major tools for the study of model membranes, but interpretation of the scattering data remains non-trivial. Current approaches allow the extraction of some structural parameters and the electron density profile of lipid bilayers. Here it is demonstrated that parametric modelling can be employed to determine the polydispersity of spherical or ellipsoidal vesicles and describe the electron density profile across the lipid bilayer. This approach is implemented in the computer program BILMIX. BILMIX delivers a description of the electron density of a lipid bilayer from SAXS data and simultaneously generates the corresponding size distribution of the unilamellar lipid vesicles.

scholarly journals Structure of the DMPC lipid bilayer ripple phase

Soft Matter ◽  
2015 ◽  
Vol 11 (5) ◽  
pp. 918-926 ◽  
Author(s):  
Kiyotaka Akabori ◽  
John F. Nagle
Keyword(s):  
High Resolution ◽  
Lipid Bilayer ◽  
Lipid Bilayers ◽  
X Ray ◽  
Ripple Phase

High resolution X-ray study provides new insight for the enigmatic ripple phase in lipid bilayers.

Accurate charge densities from powder X-ray diffraction – a new version of the Aarhus vacuum imaging-plate diffractometer

2017 ◽  
Vol 73 (4) ◽  
pp. 521-530 ◽  
Author(s):  
Kasper Tolborg ◽  
Mads R. V. Jørgensen ◽  
Sebastian Christensen ◽  
Hidetaka Kasai ◽  
Jacob Becker ◽  
...  
Keyword(s):  
Electron Density ◽  
High Energy ◽  
Imaging Plate ◽  
High Symmetry ◽  
X Rays ◽  
X Ray Diffraction ◽  
Core Electron ◽  
X Ray ◽  
Peak Broadening ◽  
Structure Factors

In recent years powder X-ray diffraction has proven to be a valuable alternative to single-crystal X-ray diffraction for determining electron-density distributions in high-symmetry inorganic materials, including subtle deformation in the core electron density. This was made possible by performing diffraction measurements in vacuum using high-energy X-rays at a synchrotron-radiation facility. Here we present a new version of our custom-built in-vacuum powder diffractometer with the sample-to-detector distance increased by a factor of four. In practice this is found to give a reduction in instrumental peak broadening by approximately a factor of three and a large improvement in signal-to-background ratio compared to the previous instrument. Structure factors of silicon at room temperature are extracted using a combined multipole–Rietveld procedure and compared withab initiocalculations and the results from the previous diffractometer. Despite some remaining issues regarding peak asymmetry, the new diffractometer yields structure factors of comparable accuracy to the previous diffractometer at low angles and improved accuracy at high angles. The high quality of the structure factors is further assessed by modelling of core electron deformation with results in good agreement with previous investigations.

scholarly journals Direct Observation of Molecular Orbitals Using Synchrotron X-ray Diffraction

Crystals ◽  
2020 ◽  
Vol 10 (11) ◽  
pp. 998
Author(s):  
Shunsuke Kitou ◽  
Yuto Hosogi ◽  
Ryo Kitaura ◽  
Toshio Naito ◽  
Toshikazu Nakamura ◽  
...  
Keyword(s):  
Degrees Of Freedom ◽  
Real Space ◽  
Molecular Orbitals ◽  
New Method ◽  
C60 Fullerene ◽  
X Ray Diffraction ◽  
Fourier Synthesis ◽  
Orbital State ◽  
X Ray ◽  
Valence Electron Density

The physical properties of molecular crystals are governed by the frontier orbitals of molecules. A molecular orbital, which is formed by superposing the atomic orbitals of constituent elements, has complicated degrees of freedom in the crystal because of the influence of electron correlation and crystal field. Therefore, in general, it is difficult to experimentally observe the whole picture of a frontier orbital. Here, we introduce a new method called “core differential Fourier synthesis” (CDFS) using synchrotron X-ray diffraction to observe the valence electron density in materials. By observing the valence electrons occupied in molecular orbitals, the orbital state can be directly determined in a real space. In this study, we applied the CDFS method to molecular materials such as diamond, C60 fullerene, (MV)I2, and (TMTTF)2X. Our results not only demonstrate the typical orbital states in some materials, but also provide a new method for studying intramolecular degrees of freedom.

scholarly journals CryoEM structures of membrane pore and prepore complex reveal cytolytic mechanism of Pneumolysin

eLife ◽  
2017 ◽  
Vol 6 ◽  
Author(s):  
Katharina van Pee ◽  
Alexander Neuhaus ◽  
Edoardo D'Imprima ◽  
Deryck J Mills ◽  
Werner Kühlbrandt ◽  
...  
Keyword(s):  
Streptococcus Pneumoniae ◽  
Lipid Bilayer ◽  
Virulence Factor ◽  
Pathogenic Bacteria ◽  
Soluble Form ◽  
Salt Bridges ◽  
Membrane Pore ◽  
X Ray ◽  
Target Membrane ◽  
Domain 3

Many pathogenic bacteria produce pore-forming toxins to attack and kill human cells. We have determined the 4.5 Å structure of the ~2.2 MDa pore complex of pneumolysin, the main virulence factor of Streptococcus pneumoniae, by cryoEM. The pneumolysin pore is a 400 Å ring of 42 membrane-inserted monomers. Domain 3 of the soluble toxin refolds into two ~85 Å β-hairpins that traverse the lipid bilayer and assemble into a 168-strand β-barrel. The pore complex is stabilized by salt bridges between β-hairpins of adjacent subunits and an internal α-barrel. The apolar outer barrel surface with large sidechains is immersed in the lipid bilayer, while the inner barrel surface is highly charged. Comparison of the cryoEM pore complex to the prepore structure obtained by electron cryo-tomography and the x-ray structure of the soluble form reveals the detailed mechanisms by which the toxin monomers insert into the lipid bilayer to perforate the target membrane.

scholarly journals XGen: Real-Space Fitting of Complex Ligand Conformational Ensembles to X-ray Electron Density Maps

2020 ◽  
Vol 63 (18) ◽  
pp. 10509-10528
Author(s):  
Ajay N. Jain ◽  
Ann E. Cleves ◽  
Alexander C. Brueckner ◽  
Charles A. Lesburg ◽  
Qiaolin Deng ◽  
...  
Keyword(s):  
Electron Density ◽  
Real Space ◽  
X Ray ◽  
Conformational Ensembles ◽  
Density Maps ◽  
Complex Ligand

scholarly journals X-ray scattering from unilamellar lipid vesicles

2005 ◽  
Vol 38 (1) ◽  
pp. 126-131 ◽  
Author(s):  
Michael R. Brzustowicz ◽  
Axel T. Brunger
Keyword(s):  
Form Factor ◽  
Lipid Bilayer ◽  
Electron Density ◽  
Lipid Vesicles ◽  
Lipid Vesicle ◽  
Asymmetric Structure ◽  
Bilayer Structure ◽  
X Ray ◽  
X Ray Scattering ◽  
Ray Scattering

An improved small-angle X-ray scattering (SAXS) method for determining asymmetric lipid bilayer structure in unilamellar vesicles is presented. From scattering theory, analytic expressions are derived for the bilayer form factor over flat and spherical geometries, assuming the lipid bilayer electron density to be composed of a series of Gaussian shells. This is in contrast to both classic diffraction and Guinier hard-shell SAXS methods which, respectively, are capable only of ascertaining symmetric bilayer structure and limited-resolution asymmetric structure. Using model fitting and direct calculation of the form factor, using only one equation, an asymmetric electron density profile of the lipid vesicle is obtained with high accuracy, as well as the average radius. The analysis suggests that the inner leaflet of a unilamellar lipid vesicle is `rougher' than the outer one.

Electron density and electrostatic potential of KNiF3: multipole, orbital and topological analyses of vacuum-camera-imaging plate and four-circle diffractometer data

1999 ◽  
Vol 55 (6) ◽  
pp. 923-930 ◽  
Author(s):  
Yury Ivanov ◽  
Elizabeth A. Zhurova ◽  
Vladimir V. Zhurov ◽  
Kiyoaki Tanaka ◽  
Vladimir Tsirelson
Keyword(s):  
Electron Density ◽  
Electrostatic Potential ◽  
Atomic Displacement ◽  
Imaging Plate ◽  
X Ray Diffraction ◽  
X Ray ◽  
Camera Imaging ◽  
Model Treatment ◽  
Atomic Displacement Parameters ◽  
Good Agreement

The electron density and electrostatic potential of KNiF3, nickel potassium trifluoride, were studied using multipole and orbital model treatment of the precision X-ray diffraction data measured by vacuum-camera-imaging plate and four-circle diffractometer methods. Different experimental methods lead to similar multipole and atomic displacement parameters and to qualitatively the same electron densities. Good agreement was also achieved for the Laplacians of the electron density and the electrostatic potentials. Some pitfalls of the vacuum-camera-imaging plate method that could be improved are discussed.

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