BioNMR
NMR aggregator & online community since 2003
BioNMR    
Learn or help to learn NMR - get free NMR books!
 

Go Back   BioNMR > Educational resources > Journal club
Advanced Search
Home Forums Wiki NMR feeds Downloads Register Today's Posts



Jobs Groups Conferences Literature Pulse sequences Software forums Programs Sample preps Web resources BioNMR issues


Webservers
NMR processing:
MDD
NMR assignment:
Backbone:
Autoassign
MARS
UNIO Match
PINE
Side-chains:
UNIO ATNOS-Ascan
NOEs:
UNIO ATNOS-Candid
UNIO Candid
ASDP
Structure from NMR restraints:
Ab initio:
GeNMR
Cyana
XPLOR-NIH
ASDP
UNIO ATNOS-Candid
UNIO Candid
Fragment-based:
BMRB CS-Rosetta
Rosetta-NMR (Robetta)
Template-based:
GeNMR
I-TASSER
Refinement:
Amber
Structure from chemical shifts:
Fragment-based:
WeNMR CS-Rosetta
BMRB CS-Rosetta
Homology-based:
CS23D
Simshift
Torsion angles from chemical shifts:
Preditor
TALOS
Promega- Proline
Secondary structure from chemical shifts:
CSI (via RCI server)
TALOS
MICS caps, β-turns
d2D
PECAN
Flexibility from chemical shifts:
RCI
Interactions from chemical shifts:
HADDOCK
Chemical shifts re-referencing:
Shiftcor
UNIO Shiftinspector
LACS
CheckShift
RefDB
NMR model quality:
NOEs, other restraints:
PROSESS
PSVS
RPF scores
iCing
Chemical shifts:
PROSESS
CheShift2
Vasco
iCing
RDCs:
DC
Anisofit
Pseudocontact shifts:
Anisofit
Protein geomtery:
Resolution-by-Proxy
PROSESS
What-If
iCing
PSVS
MolProbity
SAVES2 or SAVES4
Vadar
Prosa
ProQ
MetaMQAPII
PSQS
Eval123D
STAN
Ramachandran Plot
Rampage
ERRAT
Verify_3D
Harmony
Quality Control Check
NMR spectrum prediction:
FANDAS
MestReS
V-NMR
Flexibility from structure:
Backbone S2
Methyl S2
B-factor
Molecular dynamics:
Gromacs
Amber
Antechamber
Chemical shifts prediction:
From structure:
Shiftx2
Sparta+
Camshift
CH3shift- Methyl
ArShift- Aromatic
ShiftS
Proshift
PPM
CheShift-2- Cα
From sequence:
Shifty
Camcoil
Poulsen_rc_CS
Disordered proteins:
MAXOCC
Format conversion & validation:
CCPN
From NMR-STAR 3.1
Validate NMR-STAR 3.1
NMR sample preparation:
Protein disorder:
DisMeta
Protein solubility:
camLILA
ccSOL
Camfold
camGroEL
Zyggregator
Isotope labeling:
UPLABEL
Solid-state NMR:
sedNMR


Reply
 
Thread Tools Search this Thread Rate Thread Display Modes
  #1  
Old 03-19-2017, 10:38 PM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 23,777
Points: 193,617, Level: 100
Points: 193,617, Level: 100 Points: 193,617, Level: 100 Points: 193,617, Level: 100
Level up: 0%, 0 Points needed
Level up: 0% Level up: 0% Level up: 0%
Activity: 50.7%
Activity: 50.7% Activity: 50.7% Activity: 50.7%
Last Achievements
Award-Showcase
NMR Credits: 0
NMR Points: 193,617
Downloads: 0
Uploads: 0
Default Combining Diffusion NMR and Small-Angle Neutron Scattering Enables Precise Measurements of Polymer Chain Compression in a Crowded Environment.

Combining Diffusion NMR and Small-Angle Neutron Scattering Enables Precise Measurements of Polymer Chain Compression in a Crowded Environment.

Related Articles Combining 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.


PMID: 28306301 [PubMed - in process]



More...
Reply With Quote


Did you find this post helpful? Yes | No

Reply
Similar Threads
Thread Thread Starter Forum Replies Last Post
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...
nmrlearner Journal club 0 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...
nmrlearner Journal club 0 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...
nmrlearner Journal club 0 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...
nmrlearner Journal club 0 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...
nmrlearner Journal club 0 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 http://www.bionmr.com//nt1.ggpht.com/news/tbn/iU2tlbV3PRWsOM/6.jpg Azom.com <img alt="" height="1" width="1" /> Small Angle X-Ray Scattering and the Determination of Protein Shape Azom.com 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 ... and more &raquo;
nmrlearner Online News 0 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)...
Abe Journal club 0 09-21-2008 11:30 PM
Multidomain Protein Structures from NMR & Solution Small-Angle X-ray Scattering
http://pubs.acs.org/isubscribe/journals/jacsat/127/i47/figures/ja054342mn00001.gif 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 -...
nmrlearner Journal club 0 01-12-2006 08:23 PM



Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is On
Trackbacks are Off
Pingbacks are Off
Refbacks are Off



BioNMR advertisements to pay for website hosting and domain registration. Nobody does it for us.



Powered by vBulletin® Version 3.7.3
Copyright ©2000 - 2024, Jelsoft Enterprises Ltd.
Copyright, BioNMR.com, 2003-2013
Search Engine Friendly URLs by vBSEO 3.6.0

All times are GMT. The time now is 02:59 PM.


Map