[NMR paper] Combining Diffusion NMR and Small-Angle Neutron Scattering Enables Precise Measurements of Polymer Chain Compression in a Crowded Environment.
Related ArticlesCombining Diffusion NMR and Small-Angle Neutron Scattering Enables Precise Measurements of Polymer Chain Compression in a Crowded Environment.
Phys Rev Lett. 2017 Mar 03;118(9):097801
Authors: Palit S, He L, Hamilton WA, Yethiraj A, Yethiraj A
Abstract
The effect of particles on the behavior of polymers in solution is important in a number of important phenomena such as the effect of "crowding" proteins in cells, colloid-polymer mixtures, and nanoparticle "fillers" in polymer solutions and melts. In this Letter, we study the effect of spherical inert nanoparticles (which we refer to as "crowders") on the diffusion coefficient and radius of gyration of polymers in solution using pulsed-field-gradient NMR and small-angle neutron scattering (SANS), respectively. The diffusion coefficients exhibit a plateau below a characteristic polymer concentration, which we identify as the overlap threshold concentration c^{?}. Above c^{?}, in a crossover region between the dilute and semidilute regimes, the (long-time) self-diffusion coefficients are found, universally, to decrease exponentially with polymer concentration at all crowder packing fractions, consistent with a structural basis for the long-time dynamics. The radius of gyration obtained from SANS in the crossover regime changes linearly with an increase in polymer concentration, and must be extrapolated to c^{?} in order to obtain the radius of gyration of an individual polymer chain. When the polymer radius of gyration and crowder size are comparable, the polymer size is very weakly affected by the presence of crowders, consistent with recent computer simulations. There is significant chain compression, however, when the crowder size is much smaller than the polymer radius gyration.
The dynamic duo: Combining NMR and small angle scattering in structural biology
The dynamic duo: Combining NMR and small angle scattering in structural biology
Abstract
Structural biology provides essential information for elucidating molecular mechanisms that underlie biological function. Advances in hardware, sample preparation, experimental methods, and computational approaches now enable structural analysis of protein complexes with increasing complexity that more closely represent biologically entities in the cellular environment. Integrated multidisciplinary approaches are required to overcome limitations of individual methods and take advantage of...
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04-17-2014 12:03 PM
Using Small Angle Solution Scattering Data in Xplor-NIH Structure Calculations
Using Small Angle Solution Scattering Data in Xplor-NIH Structure Calculations
Publication date: Available online 3 April 2014
Source:Progress in Nuclear Magnetic Resonance Spectroscopy</br>
Author(s): Charles D. Schwieters , G. Marius Clore</br>
This contribution describes the use of small and wide angle X-ray and small angle neutron scattering for biomolecular structure calculation using the program Xplor-NIH, both with and without NMR data. The current algorithms used for calculating scattering curves are described, and the use of scattering data as a...
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04-04-2014 01:19 PM
[NMR paper] The Dynamic Duo: Combining NMR and Small Angle Scattering in Structural Biology.
The Dynamic Duo: Combining NMR and Small Angle Scattering in Structural Biology.
The Dynamic Duo: Combining NMR and Small Angle Scattering in Structural Biology.
Protein Sci. 2014 Mar 29;
Authors: Hennig J, Sattler M
Abstract
Structural biology provides essential information for elucidating molecular mechanisms that underlie biological function. Advances in hardware, sample preparation, experimental methods and computational approaches now enable structural analysis of protein complexes with increasing complexity that more...
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04-02-2014 11:54 PM
The Dynamic Duo: Combining NMR and Small Angle Scattering in Structural Biology
The Dynamic Duo: Combining NMR and Small Angle Scattering in Structural Biology
Abstract
Structural biology provides essential information for elucidating molecular mechanisms that underlie biological function. Advances in hardware, sample preparation, experimental methods and computational approaches now enable structural analysis of protein complexes with increasing complexity that more closely represent biologically entities in the cellular environment. Integrated multi-disciplinary approaches are required to overcome limitations of individual methods and take advantage of...
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03-29-2014 01:00 PM
[NMR paper] Combining NMR and small angle X-ray and neutron scattering in the structural analysis of a ternary protein-RNA complex.
Combining NMR and small angle X-ray and neutron scattering in the structural analysis of a ternary protein-RNA complex.
Combining NMR and small angle X-ray and neutron scattering in the structural analysis of a ternary protein-RNA complex.
J Biomol NMR. 2013 Mar 3;
Authors: Hennig J, Wang I, Sonntag M, Gabel F, Sattler M
Abstract
Many processes in the regulation of gene expression and signaling involve the formation of protein complexes involving multi-domain proteins. Individual domains that mediate protein-protein and protein-nucleic...
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03-05-2013 03:25 PM
Small Angle X-Ray Scattering and the Determination of Protein Shape - Azom.com
Small Angle X-Ray Scattering and the Determination of Protein Shape - Azom.com
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Small Angle X-Ray Scattering and the Determination of Protein Shape
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The low resolution 3D structure obtained by ab-initio methods is an important additional data to the high resolution structures obtained by protein crystallography and NMR. This article discusses the application of SAXSess mc system from Anton Paar to ...
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02-20-2013 06:24 PM
A structure refinement protocol combining NMR residual dipolar couplings and small angle scattering restraints
A structure refinement protocol combining NMR residual dipolar couplings and small angle scattering restraints
F. Gabel, B. Simon, M. Nilges, M. Petoukhov, D. Svergun and M. Sattler
Journal of Biomolecular NMR; 2008; 41(4); pp 199-208
Abstract:
We present the implementation of a target function based on Small Angle Scattering data (Gabel et al. Eur Biophys J 35(4):313–327, 2006) into the Crystallography and NMR Systems (CNS) and demonstrate its utility in NMR structure calculations by simultaneous application of small angle scattering (SAS) and residual dipolar coupling (RDC)...
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09-21-2008 11:30 PM
Multidomain Protein Structures from NMR & Solution Small-Angle X-ray Scattering
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Refinement of Multidomain Protein Structures by Combination of Solution Small-Angle X-ray Scattering and NMR Data
Alexander Grishaev,* Justin Wu, Jill Trewhella, and Ad Bax*
Contribution from the Laboratory of Chemical Physics, NIDDK, National Institutes of Health, Bethesda, Maryland 20892-0520, Department of Biochemistry, The Ohio State University, Columbus, Ohio 43210, and Department of Chemistry, University of Utah, Salt Lake City, Utah 84112-0850
J. Am. Chem. Soc.; 2005; 127(47) pp 16621 -...