scholarly journals Small-angle neutron scattering and molecular dynamics structural study of gelling DNA nanostars

2016 ◽  
Vol 145 (8) ◽  
pp. 084910 ◽  
Author(s):  
J. Fernandez-Castanon ◽  
F. Bomboi ◽  
L. Rovigatti ◽  
M. Zanatta ◽  
A. Paciaroni ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Neutron Scattering ◽  
Structural Study ◽  
Small Angle ◽  
Small Angle Neutron Scattering

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

scholarly journals Solution structure of macromolecules using small angle neutron scattering and molecular simulations

2020 ◽  
Vol 236 ◽  
pp. 03003
Author(s):  
Jayesh S. Bhatt
Keyword(s):  
Molecular Dynamics ◽  
Monte Carlo ◽  
Neutron Scattering ◽  
Small Angle ◽  
Small Angle Neutron Scattering ◽  
Solution Structure ◽  
Molecular Simulations ◽  
Liquid Solution ◽  
Scattering Data ◽  
Monte Carlo Techniques

An introductory account of using molecular simulations to deduce solution structure of macromolecules using small angle neutron scattering data is presented for biologists. The presence of a liquid solution provides mobility to the molecules, making it difficult to pin down their structure. Here a simple introduction to molecular dynamics and Monte Carlo techniques is followed by a recipe to use the output of the simulations along with the scattering data in order to infer the structure of macromolecules when they are placed in a liquid solution. Some practical issues to be watched for are also highlighted.

Conformations and Structures of Poly(oxyethylene) Melts from Molecular Dynamics Simulations and Small-Angle Neutron Scattering Experiments

1996 ◽  
Vol 29 (10) ◽  
pp. 3462-3469 ◽  
Author(s):  
Grant D. Smith ◽  
Do Y. Yoon ◽  
Richard L. Jaffe ◽  
Ralph H. Colby ◽  
Ramanan Krishnamoorti ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Neutron Scattering ◽  
Molecular Dynamics Simulations ◽  
Small Angle ◽  
Small Angle Neutron Scattering ◽  
Dynamics Simulations

Cholesterol solubility limit in lipid membranes probed by small angle neutron scattering and MD simulations

Soft Matter ◽  
2014 ◽  
Vol 10 (46) ◽  
pp. 9313-9317 ◽  
Author(s):  
Sumit Garg ◽  
Francisco Castro-Roman ◽  
Lionel Porcar ◽  
Paul Butler ◽  
Pedro Jesus Bautista ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Neutron Scattering ◽  
Small Angle ◽  
Lipid Membranes ◽  
Small Angle Neutron Scattering ◽  
Md Simulations ◽  
Solubility Limit ◽  
Coarse Grained ◽  
Small Unilamellar Vesicles ◽  
Cholesterol Solubility

The solubility limits of cholesterol in small unilamellar vesicles made of POPS and POPC were probed using Small Angle Neutron Scattering (SANS) and coarse grained (CG) molecular dynamics (MD) simulations.

scholarly journals Exploring the bulk-phase structure of ionic liquid mixtures using small-angle neutron scattering

2018 ◽  
Vol 206 ◽  
pp. 265-289 ◽  
Author(s):  
Christopher P. Cabry ◽  
Lucía D’Andrea ◽  
Karina Shimizu ◽  
Isabelle Grillo ◽  
Peixun Li ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Ionic Liquid ◽  
Neutron Scattering ◽  
Small Angle ◽  
Small Angle Neutron Scattering ◽  
Liquid Mixture ◽  
Liquid Mixtures ◽  
System P ◽  
Dynamics Simulations ◽  
Mixture System

Small-angle neutron scattering experiments, supported by molecular dynamics simulations, have been performed on a range of compositions of the [C2mim]1−x[C12mim]x[Tf2N] ionic liquid mixture system.

Effect of the solute–solvent interface on small-angle neutron scattering from organic solutions of short alkyl chain molecules as revealed by molecular dynamics simulation

2013 ◽  
Vol 46 (2) ◽  
pp. 372-378 ◽  
Author(s):  
Roman A. Eremin ◽  
Kholmirzo Kholmurodov ◽  
Viktor I. Petrenko ◽  
László Rosta ◽  
Mikhail V. Avdeev
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Neutron Scattering ◽  
Small Angle ◽  
Small Angle Neutron Scattering ◽  
Scattering Length ◽  
Solvent Molecule ◽  
Dynamics Simulation ◽  
Time Averaging ◽  
Acid Molecule

The problem of describing the experimental small-angle neutron scattering (SANS) from diluted solutions of saturated monocarboxylic acids with short chain lengths (myristic and stearic acids) in deuterated decalin is considered. The method of classical molecular dynamics simulation (MDS) is used to obtain the atomic number density distributions, and, as a consequence, the scattering length density (SLD) distribution in the solute–solvent interface area (about 1 nm around the acid molecules), assuming the acid molecules to be rigid and non-associated in the solutions. MDS is performed for solutions in a parallelepiped cell of 5.5 × 5.3 × 5.3 nm (one acid molecule per cell) under normal conditions. The time averaging of the obtained distributions is done over 2 ns (after the system thermalization). It is shown that a specific short-range ordering organization of the solvent molecules in the vicinity of the acid molecules has a significant effect on the scattering, which is mainly determined by a relatively large ratio between the effective size of the solvent molecule and the cross-section diameter of the acid molecule. Various approximations to the simulated SLD distributions, based on the cylinder-type symmetry of the acid molecules, are probed to achieve the best consistency with the experimental SANS curves by varying the residual incoherent background.

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