Structure Analysis by Small-Angle X-Ray and Neutron Scattering

Svergun, Dmitri I.; Feĭgin, L. A.; Taylor, George William

doi:10.1007/978-1-4757-6624-0

Cited by 1,890 publications

(2,135 citation statements)

References 0 publications

Supporting

Mentioning

2,056

Contrasting

Unclassified

Order By: Relevance

“…SAXS is a label-free technique that provides information about the average composition, size, and shape of macromolecules. Interpretation of SAXS experimental results in biology is most reliable for monodisperse systems (84); given the diversity and flexibility of PANS, the corresponding SAXS experimental data may be challenging to interpret. A detailed comparison between experimental and theoretical curves based on atomistic models of PANS can both validate the all-atom models and provide a more detailed interpretation to SAXS measurements.…”

Section: Interpretation Of Saxs Spectra Of Subnucleosomal Particlesmentioning

confidence: 99%

Partially Assembled Nucleosome Structures at Atomic Detail

Rychkov

Ilatovskiy

Nazarov

et al. 2017

Biophysical Journal

View full text Add to dashboard Cite

The evidence is now overwhelming that partially assembled nucleosome states (PANS) are as important as the canonical nucleosome structure for the understanding of how accessibility to genomic DNA is regulated in cells. We use a combination of molecular dynamics simulation and atomic force microscopy to deliver, in atomic detail, structural models of three key PANS: the hexasome (H2A$H2B)$(H3$H4) 2 , the tetrasome (H3$H4) 2 , and the disome (H3$H4). Despite fluctuations of the conformation of the free DNA in these structures, regions of protected DNA in close contact with the histone core remain stable, thus establishing the basis for the understanding of the role of PANS in DNA accessibility regulation. On average, the length of protected DNA in each structure is roughly 18 basepairs per histone protein. Atomistically detailed PANS are used to explain experimental observations; specifically, we discuss interpretation of atomic force microscopy, Fö rster resonance energy transfer, and small-angle x-ray scattering data obtained under conditions when PANS are expected to exist. Further, we suggest an alternative interpretation of a recent genome-wide study of DNA protection in active chromatin of fruit fly, leading to a conclusion that the three PANS are present in actively transcribing regions in a substantial amount. The presence of PANS may not only be a consequence, but also a prerequisite for fast transcription in vivo.

show abstract

Section: Interpretation Of Saxs Spectra Of Subnucleosomal Particlesmentioning

confidence: 99%

Partially Assembled Nucleosome Structures at Atomic Detail

Rychkov

Ilatovskiy

Nazarov

et al. 2017

Biophysical Journal

View full text Add to dashboard Cite

show abstract

“…In this study, we consider form factor models for three different micellar shapes: ellipsoids, rigid cylinders, and flexible cylinders. 1,2 In the expressions below, (∆ρ) is the difference in scattering length density between the micelle and the solvent, so that (∆ρ) 2 is the scattering contrast. The models were implemented using software modules supplied by NIST.…”

Section: Sans Modelingmentioning

confidence: 99%

“…[1][2][3][4][5][6] These micelles are inverted cylindrical chains that grow to lengths of several microns while also maintaining a local flexibility. Because of their flexibility, the micelles have been referred to as wormlike, threadlike, or polymer-like structures.…”

Section: Introductionmentioning

confidence: 99%

“…The first examples of such micellar systems were ternary mixtures of the type lecithin/ water/oil. 1 Lecithin is a zwitterionic phospholipid with two alkyl tails (Figure 1a), which when added alone to oil gives rise to reverse spherical or ellipsoidal micelles. When a small quantity of water is added to these fluids, the micelles grow axially into flexible cylinders.…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

A New Reverse Wormlike Micellar System: Mixtures of Bile Salt and Lecithin in Organic Liquids

2006

View full text Add to dashboard Cite

Abstract:We report a new route for forming reverse wormlike micelles (i.e., long, flexible micellar chains) in nonpolar organic liquids such as cyclohexane and n-decane. This route involves the addition of a bile salt (e.g., sodium deoxycholate) in trace amounts to solutions of the phospholipid lecithin. Previous recipes for reverse wormlike micelles have usually required the addition of water to induce reverse micellar growth; here, we show that bile salts, due to their unique "facially amphiphilic" structure, can play a role analogous to that of water and promote the longitudinal aggregation of lecithin molecules into reverse micellar chains. The formation of transient entangled networks of these reverse micelles transforms low-viscosity lecithin organosols into strongly viscoelastic fluids. The zero-shear viscosity increases by more than 5 orders of magnitude, and it is the molar ratio of bile salt to lecithin that controls the viscosity enhancement. The growth of reverse wormlike micelles is also confirmed by small-angle neutron scattering (SANS) experiments on these fluids.

show abstract

“…In case of monodispersed population of ULVs with radius R and the bilayer thickness d, the SANS intensity is determined as follows [22]:…”

Section: The Separated Form Factors Methodsmentioning

confidence: 99%

The Small-Angle Neutron Scattering Data Analysis of the Phospholipid Transport Nanosystem Structure

Zemlyanaya

Киселев

Zhabitskaya

et al. 2018

J. Phys.: Conf. Ser.

View full text Add to dashboard Cite

Abstract. The small-angle neutron scattering technique (SANS) is employed for investigation of structure of the phospholipid transport nanosystem (PTNS) elaborated in the V.N.Orekhovich Institute of Biomedical Chemistry (Moscow, Russia). The SANS spectra have been measured at the YuMO small-angle spectrometer of IBR-2 reactor (Joint Institute of Nuclear Research, Dubna, Russia). Basic characteristics of polydispersed population of PTNS unilamellar vesicles (average radius of vesicles, polydispersity, thickness of membrane, etc.) have been determined in three cases of the PTNS concentrations in D2O: 5%, 10%, and 25%. Numerical analysis is based on the separated form factors method (SFF). The results are discussed in comparison with the results of analysis of the small-angle X-ray scattering spectra collected at the Kurchatov Synchrotron Radiation

show abstract

Structure Analysis by Small-Angle X-Ray and Neutron Scattering

Cited by 1,890 publications

References 0 publications

Partially Assembled Nucleosome Structures at Atomic Detail

Partially Assembled Nucleosome Structures at Atomic Detail

A New Reverse Wormlike Micellar System: Mixtures of Bile Salt and Lecithin in Organic Liquids

The Small-Angle Neutron Scattering Data Analysis of the Phospholipid Transport Nanosystem Structure

Contact Info

Product

Resources

About