scholarly journals Open-Bundle Structure as the Unfolding Intermediate of Cytochrome c′ Revealed by Small Angle Neutron Scattering

Biomolecules ◽  
2022 ◽  
Vol 12 (1) ◽  
pp. 95
Author(s):  
Takahide Yamaguchi ◽  
Kouhei Akao ◽  
Alexandros Koutsioubas ◽  
Henrich Frielinghaus ◽  
Takamitsu Kohzuma
Keyword(s):  
Neutron Scattering ◽  
Small Angle ◽  
Small Angle Neutron Scattering ◽  
Function Analysis ◽  
Dynamic Structure ◽  
Random Coil ◽  
Radius Of Gyration ◽  
Intermediate Structure ◽  
Cyt C ◽  
Bundle Structure

The dynamic structure changes, including the unfolding, dimerization, and transition from the compact to the open-bundle unfolding intermediate structure of Cyt c′, were detected by a small-angle neutron scattering experiment (SANS). The structure of Cyt c′ was changed into an unstructured random coil at pD = 1.7 (Rg = 25 Å for the Cyt c′ monomer). The four-α-helix bundle structure of Cyt c′ at neutral pH was transitioned to an open-bundle structure (at pD ~13), which is given by a numerical partial scattering function analysis as a joint-clubs model consisting of four clubs (α-helices) connected by short loops. The compactly folded structure of Cyt c′ (radius of gyration, Rg = 18 Å for the Cyt c′ dimer) at neutral or mildly alkaline pD transited to a remarkably larger open-bundle structure at pD ~13 (Rg = 25 Å for the Cyt c′ monomer). The open-bundle structure was also supported by ab initio modeling.

scholarly journals Open-Bundle Structure as the Unfolding Intermediate of Cytochrome c’ Revealed by Small Angle Neutron Scattering

2021 ◽  
Author(s):  
Takahide Yamaguchi ◽  
Kouhei Akao ◽  
Alexandros Koutsioubas ◽  
Henrich Frielinghaus ◽  
Takamitsu Kohzuma
Keyword(s):  
Cytochrome C ◽  
Neutron Scattering ◽  
Small Angle ◽  
Small Angle Neutron Scattering ◽  
Alpha Helix ◽  
Random Coil ◽  
Radius Of Gyration ◽  
Alpha Helices ◽  
Cyt C ◽  
Bundle Structure

The open-bundle structure of cytochrome c’ as an unfolding intermediate was determined by small-angle neutron scattering experiment (SANS). The four-α-helix bundle structure of Cyt c’ at neutral pH was transited to an open-bundle structure (at pD ~13), which is a joint-clubs consisting of four clubs (α-helices) connected by short loops. The compactly folded structure of Cyt c’ (radius of gyration, Rg = 18 Å for the Cyt c’ dimer) at neutral or mildly alkaline pD transitioned to a remarkably larger “open-bundle” structure at pD ~13 (Rg = 25 Å for the Cyt c’ monomer). Cyt c’ adopts an unstructured random coil structure at pD = 1.7 (Rg = 25 Å for the Cyt c’ monomer). Numerical partial scattering function analysis (joint-clubs) and ab initio modelling gave structures similar to the “open-bundle”, which retains the α-helices but loses the bundle structure.

scholarly journals Structural aspects of human lactoferrin in the iron-binding process studied by molecular dynamics and small-angle neutron scattering

2018 ◽  
Vol 41 (9) ◽  
Author(s):  
Lilia Anghel ◽  
Aurel Radulescu ◽  
Raul Victor Erhan
Keyword(s):  
Molecular Dynamics ◽  
Neutron Scattering ◽  
Small Angle ◽  
Small Angle Neutron Scattering ◽  
The Body ◽  
Human Lactoferrin ◽  
Radius Of Gyration ◽  
Scattering Method ◽  
Iron Binding ◽  
Binding Process

Abstract. Lactoferrin is a non-heme protein known for its ability to bind tightly Fe(III) ions in various physiological environments. Due to this feature lactoferrin plays an important role in the processes of iron regulation at the cellular level preventing the body from damages produced by high levels of free iron ions. The X-ray crystal structure of human lactoferrin shows that the iron-binding process leads to conformational changes within the protein structure. The present study was addressed to conformation stability of human lactoferrin in solution. Using molecular dynamics simulations, it was shown that Arg121 is the key amino acid in the stabilization of the Fe(III) ion in the N-lobe of human lactoferrin. The small-angle neutron scattering method allowed us to detect the structural differences between the open and closed conformation of human lactoferrin in solution. Our results indicate that the radius of gyration of apolactoferrin appears to be smaller than that of the hololactoferrin, $R_{g}=24.16(\pm 0.707)$ R g = 24 . 16 ( ± 0 . 707 ) Å and $R_{g}= 26.20(\pm 1.191)$ R g = 26 . 20 ( ± 1 . 191 ) Å, respectively. The low-resolution three-dimensional models computed for both forms of human lactoferrin in solution also show visible differences, both having a more compact conformation compared to the high-resolution structure. Graphical abstract

Determination of Deuterium Incorporation into RNA and Protein Components of the Escherichia Coli Ribosome at Biosynthetic Deuteration by Small-Angle Neutron Scattering

1997 ◽  
Vol 30 (1) ◽  
pp. 59-64
Author(s):  
L. Fan ◽  
E. I. Zgurskaya ◽  
I. Shcherbakova ◽  
I. N. Serdyuk
Keyword(s):  
Escherichia Coli ◽  
Neutron Scattering ◽  
Small Angle ◽  
Small Angle Neutron Scattering ◽  
Standard Procedure ◽  
Radius Of Gyration ◽  
Deuterium Incorporation ◽  
Simple Method ◽  
Protein Components

A simple method for the determination of deuterium incorporation into nonexchangeable (C-bonded) positions of RNA and protein components of the Escherichia coli ribosome at biosynthetic deuteration has been proposed using small-angle neutron scattering. The theory of the method is based on the joint use of two measurements: one of them is the dependence of neutron scattering intensity at zero angle on the contrast; the second is the dependence of the radius of gyration on the contrast. The main advantage of the method over the standard procedure is that it requires neither separation of the ribosome into RNA and protein components nor a subsequent time-consuming analysis of the hydrolysis products by nuclear magnetic resonance or mass spectrometry.

scholarly journals Small-angle neutron scattering studies suggest the mechanism of BinAB protein internalization

IUCrJ ◽  
2020 ◽  
Vol 7 (2) ◽  
pp. 166-172
Author(s):  
Mahima Sharma ◽  
Vinod K. Aswal ◽  
Vinay Kumar ◽  
R. Chidambaram
Keyword(s):  
Neutron Scattering ◽  
Conformational Changes ◽  
Small Angle ◽  
Small Angle Neutron Scattering ◽  
Solution Structure ◽  
Expression System ◽  
Radius Of Gyration ◽  
Macromolecular Systems ◽  
Approaches To Study ◽  
Protein Components

Small-angle neutron scattering (SANS) is one of the most widely used neutron-based approaches to study the solution structure of biological macromolecular systems. The selective deuterium labelling of different protein components of a complex provides a means to probe conformational changes in multiprotein complexes. The Lysinibacillus sphaericus mosquito-larvicidal BinAB proteins exert toxicity through interaction with the receptor Cqm1 protein; however, the nature of the complex is not known. Rationally engineered deuterated BinB (dBinB) protein from the L. sphaericus ISPC-8 species was synthesized using an Escherichia coli-based protein-expression system in M9 medium in D2O for `contrast-matched' SANS experiments. SANS data were independently analysed by ab initio indirect Fourier transform-based modelling and using crystal structures. These studies confirm the dimeric status of Cqm1 in 100% D2O with a longest intramolecular vector (D max) of ∼94 Å and a radius of gyration (R g) of ∼31 Å. Notably, BinB binds to Cqm1, forming a heterodimeric complex (D max of ∼129 Å and R g of ∼40 Å) and alters its oligomeric status from a dimer to a monomer, as confirmed by matched-out Cqm1–dBinB (D max of ∼70 Å and R g of ∼22 Å). The present study thus provides the first insight into the events involved in the internalization of larvicidal proteins, likely by raft-dependent endocytosis.

Radius of Gyration Scaling in the Semidilute Regime

1994 ◽  
Vol 376 ◽  
Author(s):  
J.G. Barker ◽  
A.M. Mayes ◽  
R.M. Briber ◽  
W.J. Orts
Keyword(s):  
Carbon Tetrachloride ◽  
Theoretical Prediction ◽  
Neutron Scattering ◽  
Small Angle ◽  
Small Angle Neutron Scattering ◽  
Radius Of Gyration ◽  
Scaling Exponent ◽  
Review Of The Literature ◽  
In Cis

ABSTRACTSmall-angle neutron scattering is used to investigate swelling effects of polystyrene in carbon tetrachloride and cis-decalin in the semidilute regime. The observed scaling exponent m where Rg2 ~ ф-m was m=0.15±0.01 both in carbon tetrachloride and in cis-decalin at T=180 C, which is much weaker than the theoretical prediction m=0.25. A review of the literature has found the scaling exponent to vary from 0.1 to 0.25. Possible causes for this variation in the observed scaling exponent are discussed.

scholarly journals Kinetics of the urea-induced dissociation of human plasma α2-macroglobulin as measured by small-angle neutron scattering

1991 ◽  
Vol 278 (2) ◽  
pp. 325-328 ◽  
Author(s):  
B Sjöberg ◽  
S Pap ◽  
S E Järnberg ◽  
K Mortensen
Keyword(s):  
Neutron Scattering ◽  
Human Plasma ◽  
Small Angle ◽  
Small Angle Neutron Scattering ◽  
Binding Activity ◽  
Radius Of Gyration ◽  
Covalent Interaction ◽  
Α2 Macroglobulin ◽  
Relative Change ◽  
Kinetics Of

The kinetics of the urea-induced dissociation of human plasma alpha 2-macroglobulin into two half-molecular fragments was investigated at 21.0 degrees C by using small-angle neutron scattering. The relative change in molecular mass that occurs upon dissociation was monitored by recording the forward scattering of neutrons as a function of time. All these kinetic data can be explained by a reaction that is first-order with respect to the concentration of undissociated alpha 2-macroglobulin. The velocity constant is a function of urea concentration and it varies within wide limits. For instance, the half-life of the reaction at the lowest concentration of [2H]urea studied (2.70 M) is 328 h, whereas the same value at the highest concentration of [2H]urea (6.24 M) is only 8 min. Measurements were made both with [1H]urea in 1H2O and with [2H]urea in 99% 2H2O, and it was found that there is a pronounced kinetic isotope effect, i.e. the dissociation is 4 times faster in the 1H-containing medium as compared with the 2H-containing medium at the same molar concentration of urea. From the angular dependence of the neutron scattering it can be concluded that the dissociation is associated with a drastic change in structure. This is directly shown by the radius of gyration, which increases from about 7.4 nm immediately after the addition of urea up to about 9.4 nm when the protein is fully dissociated. A structural analysis shows that the scattering curve of urea-dissociated alpha 2-macroglobulin can best be explained by that of a Gaussian coil with a radius of gyration equal to 9.44 nm. These data indicate that the so-called non-covalent interaction of alpha 2-macroglobulin probably is more complicated than just a pure hydrophobic interaction. Finally, it is also shown that the dissociation is accompanied by a loss in trypsin-binding activity, which is directly related to the fraction of dissociated protein.

Concentration Dependence of Radius of Gyration of Sodium Poly(styrenesulfonate) over a Wide Range of Concentration Studied by Small-Angle Neutron Scattering†

Langmuir ◽  
1999 ◽  
Vol 15 (12) ◽  
pp. 4120-4122 ◽  
Author(s):  
Yoshiaki Takahashi ◽  
Naoki Matsumoto ◽  
Shinji Iio ◽  
Hidemi Kondo ◽  
Ichiro Noda ◽  
...  
Keyword(s):  
Neutron Scattering ◽  
Concentration Dependence ◽  
Small Angle ◽  
Small Angle Neutron Scattering ◽  
Radius Of Gyration ◽  
Wide Range

scholarly journals Structural Characterization of a Polymer Substituted Fullerene (Flagellene) by Small Angle Neutron Scattering

1994 ◽  
Vol 359 ◽  
Author(s):  
K.A. Affholter ◽  
G.J. Bunick ◽  
J.M. Desimone ◽  
M.O. Hunt ◽  
Y.Z. Menceloglu ◽  
...  
Keyword(s):  
Neutron Scattering ◽  
Small Angle ◽  
Small Angle Neutron Scattering ◽  
Virial Coefficient ◽  
Scattering Length ◽  
Second Virial Coefficient ◽  
Radius Of Gyration ◽  
Polystyrene Sample ◽  
Negative Scattering Length

ABSTRACTSmall-angle neutron scattering (SANS) can structurally characterize fullerenes1in solvents with strong SANS contrast (e.g. CS2). Deuterated solvents (e.g. toluene-d8) have a high scattering length density (SLD), which is close to that of C60and C70moieties. Hence, there is virtually no SANS contrast with the solvent and these particles are practically “invisible” in such media. On the other hand, the negative scattering length of hydrogen means that the SLD of H1-containing materials is much lower, so they have strong contrast with toluene-d8. Thus, SANS makes it possible to study the size and shapes of modified buckyballs such as the polymer-substituted fullerenes, or flagellenes2. These consist of C60cores to which 1-4 polystyrene chains (with a molecular weight, MW ≃ 2000) are attached. The extrapolated cross section at zero angle of scatter [dΣ/dΩ(0)]s is a function of the number of pendant chains, so SANS can be used to assess the number of “arms” which are covalently attached to the fullerene “sphere”. Close agreement (± 4%) between the measured and calculated values of dΣ/dΩ(0) along with independent estimates of the radius of gyration (Rg) and second virial coefficient (A2) for a calibration linear polystyrene sample serves as a cross check on the validity of this methodology.

Real-space interpretation of spin-echo small-angle neutron scattering

2003 ◽  
Vol 36 (1) ◽  
pp. 117-124 ◽  
Author(s):  
Timofei Krouglov ◽  
Ignatz M. de Schepper ◽  
Wim G. Bouwman ◽  
M. Theo Rekveldt
Keyword(s):  
Neutron Scattering ◽  
Small Angle ◽  
Small Angle Neutron Scattering ◽  
Spin Echo ◽  
Scattering Length ◽  
Structural Parameters ◽  
Pair Correlation ◽  
Real Space ◽  
Radius Of Gyration ◽  
Solid Spheres

Spin-echo small-angle neutron scattering (SESANS) is a novel real-space scattering technique. SESANS measures a correlation-like functionG(Z), the meaning of which was unknown until now. Here a direct real-space interpretation ofG(Z) through the particle scattering density and pair correlation function is given. One-dimensional and two-dimensional SESANS are compared. The case of non-interacting particles is considered in detail with an explicit geometrical interpretation. General methods for the calculation of structural parameters, such as the total scattering length and the radius of gyration, are developed. Analytical expressions ofG(Z) for non-interacting solid spheres, hollow spheres and Gaussian coils are derived. The case of solid spheres is compared with experimental data.

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