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 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 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 Small-Angle Neutron Scattering Study of Bicelles and Proteobicelles with Incorporated Mitochondrial Cytochrome c Oxidase

2020 ◽  
Vol 65 (8) ◽  
pp. 662
Author(s):  
K. Siposova ◽  
V. I. Petrenko ◽  
O. I. Ivankov ◽  
L. A. Bulavin ◽  
A. Musatov
Keyword(s):  
Cytochrome C ◽  
Neutron Scattering ◽  
Cytochrome C Oxidase ◽  
Small Angle ◽  
Small Angle Neutron Scattering ◽  
Membrane System ◽  
Aggregation State ◽  
Structural Investigations ◽  
Neutron Scattering Study ◽  
Average Size

The structural investigations of a model membrane system, bicelles, and the aggregation state of isolated and purified bovine heart cytochrome c oxidase (CcO) in bicelles have been performed using small-angle neutron scattering (SANS), SANS contrast variation, and complemented by various biophysical and biochemical techniques. The average size of bicelles prepared from long-chain 1,2-dimyristoyl-sn-glycero-3-phosphocholine and short-chain 1,2-dihexanoyl-sn-glycero-3-phosphocholine was found to be about 22 nm with a thickness of about 4 nm. Enzyme in bicelles was remained active and structurally unaltered. The estimated volume of protein in bicelles of 240 nm3 corresponded well to the monomeric form of CcO. The ab initio modeling supports the experimental data and suggests that CcO in bicelles is a homogeneous monomeric complex incorporated into bicelles.

scholarly journals pH-Induced reorientation of cytochrome c on silica nanoparticles

Soft Matter ◽  
2019 ◽  
Vol 15 (3) ◽  
pp. 350-354 ◽  
Author(s):  
Jens Meissner ◽  
Yao Wu ◽  
Jacques Jestin ◽  
William A. Shelton ◽  
Gerhard H. Findenegg ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Cytochrome C ◽  
Neutron Scattering ◽  
Molecular Dynamics Simulations ◽  
Silica Nanoparticles ◽  
Small Angle ◽  
Small Angle Neutron Scattering ◽  
Wide Ph Range ◽  
Ph Range ◽  
Dynamics Simulations

The orientation of ellipsoidal cytochrome c molecules at the surface of silica nanoparticles was studied in a wide pH range by combining small-angle neutron scattering, adsorption measurements, and molecular dynamics simulations.

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