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

Go Back   BioNMR > NMR community > News from NMR blogs
Advanced Search



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  
Unread 05-10-2017, 09:55 PM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 23,134
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 Peptide and Protein Dynamics and Low-Temperature/DNP Magic Angle Spinning NMR #DNPNMR

From The DNP-NMR Blog:

Peptide and Protein Dynamics and Low-Temperature/DNP Magic Angle Spinning NMR #DNPNMR

p.p1 {margin: 0.0px 0.0px 0.0px 36.0px; text-indent: -36.0px; font: 12.0px Helvetica}
Ni, Q.Z., et al., Peptide and Protein Dynamics and Low-Temperature/DNP Magic Angle Spinning NMR. J Phys Chem B, 2017.


https://www.ncbi.nlm.nih.gov/pubmed/28437077


In DNP MAS NMR experiments at ~80-110 K, the structurally important -13CH3 and -15NH3+ signals in MAS spectra of biological samples disappear due to the interference of the molecular motions with the 1H decoupling. Here we investigate the effect of these dynamic processes on the NMR lineshapes and signal intensities in several typical systems: (1) microcrystalline APG, (2) membrane protein bR, (3) amyloid fibrils PI3-SH3, (4) monomeric alanine-CD3 and (5) the pro-tonated and deuterated dipeptide N-Ac-VL over 78-300 K. In APG, the 3-site hopping of the Ala-Cbeta peak disappears com-pletely at 112 K, concomitant with the attenuation of CP signals from other 13C's and 15N's. Similarly, the 15N signal from Ala-NH3+ disappears ~173 K, concurrent with the attenuation in CP experiments of other 15N's as well as 13C's. In bR and PI3-SH3, the methyl groups are attenuated at ~95 K while all other 13C's remain unaffected. However, both systems exhibit substantial losses of intensity at ~243 K. Finally, with spectra of Ala and N-Ac-VL we show that it is possible to extract site specific dynamic data from the temperature dependence of the intensity losses. Furthermore, 2H labeling can assist with re-covering the spectral intensity. Thus, our study provides insight into the dynamic behavior of biological systems over a wide range of temperatures, and serves as a guide to optimizing the sensitivity and resolution of structural data in low temperature DNP MAS NMR spectra.
p.p1 {margin: 0.0px 0.0px 0.0px 0.0px; font: 12.0px Helvetica} p.p1 {margin: 0.0px 0.0px 0.0px 0.0px; font: 12.0px Helvetica}

Go to The DNP-NMR Blog for more info.
Reply With Quote


Did you find this post helpful? Yes | No

Reply
Similar Threads
Thread Thread Starter Forum Replies Last Post
[NMR paper] Peptide and Protein Dynamics and Low-Temperature/DNP Magic Angle Spinning NMR.
Peptide and Protein Dynamics and Low-Temperature/DNP Magic Angle Spinning NMR. Related Articles Peptide and Protein Dynamics and Low-Temperature/DNP Magic Angle Spinning NMR. J Phys Chem B. 2017 Apr 24;: Authors: Ni QZ, Markhasin E, Can TV, Corzilius B, Tan KO, Barnes AB, Daviso E, Su Y, Herzfeld J, Griffin RG Abstract In DNP MAS NMR experiments at ~80-110 K, the structurally important -13CH3 and -15NH3+ signals in MAS spectra of biological samples disappear due to the interference of the molecular motions with the 1H...
nmrlearner Journal club 0 04-25-2017 11:48 AM
Dynamic nuclear polarization at 40 kHz magic angle spinning #DNPNMR
From The DNP-NMR Blog: Dynamic nuclear polarization at 40 kHz magic angle spinning #DNPNMR Chaudhari, S.R., et al., Dynamic nuclear polarization at 40 kHz magic angle spinning. Phys Chem Chem Phys, 2016. 18(15): p. 10616-22. http://www.ncbi.nlm.nih.gov/pubmed/27035630
nmrlearner News from NMR blogs 0 08-23-2016 01:02 AM
Low-temperature dynamic nuclear polarization with helium-cooled samples and nitrogen-driven magic-angle spinning
From The DNP-NMR Blog: Low-temperature dynamic nuclear polarization with helium-cooled samples and nitrogen-driven magic-angle spinning Thurber, K. and R. Tycko, Low-temperature dynamic nuclear polarization with helium-cooled samples and nitrogen-driven magic-angle spinning. J Magn Reson, 2016. 264: p. 99-106. http://www.ncbi.nlm.nih.gov/pubmed/26920835
nmrlearner News from NMR blogs 0 04-11-2016 07:16 PM
Low-temperature dynamic nuclear polarization with helium-cooled samples and nitrogen-driven magic-angle spinning
Low-temperature dynamic nuclear polarization with helium-cooled samples and nitrogen-driven magic-angle spinning Publication date: March 2016 Source:Journal of Magnetic Resonance, Volume 264</br> Author(s): Kent Thurber, Robert Tycko</br> We describe novel instrumentation for low-temperature solid state nuclear magnetic resonance (NMR) with dynamic nuclear polarization (DNP) and magic-angle spinning (MAS), focusing on aspects of this instrumentation that have not been described in detail in previous publications. We characterize the performance of an extended...
nmrlearner Journal club 0 02-24-2016 01:30 AM
[NMR paper] Magic Angle Spinning NMR Reveals Sequence-Dependent Structural Plasticity, Dynamics, and the Spacer Peptide 1 Conformation in HIV-1 Capsid Protein Assemblies.
Magic Angle Spinning NMR Reveals Sequence-Dependent Structural Plasticity, Dynamics, and the Spacer Peptide 1 Conformation in HIV-1 Capsid Protein Assemblies. Magic Angle Spinning NMR Reveals Sequence-Dependent Structural Plasticity, Dynamics, and the Spacer Peptide 1 Conformation in HIV-1 Capsid Protein Assemblies. J Am Chem Soc. 2013 Oct 28; Authors: Han Y, Hou G, Suiter CL, Ahn J, Byeon IJ, Lipton AS, Burton SD, Hung I, Gor'kov PL, Gan Z, Brey WW, Rice D, Gronenborn AM, Polenova TE Abstract A key stage in HIV-1 maturation towards...
nmrlearner Journal club 0 10-30-2013 10:44 AM
[NMR paper] Probing Structure and Dynamics of Protein Assemblies by Magic Angle Spinning NMR Spectroscopy.
Probing Structure and Dynamics of Protein Assemblies by Magic Angle Spinning NMR Spectroscopy. Probing Structure and Dynamics of Protein Assemblies by Magic Angle Spinning NMR Spectroscopy. Acc Chem Res. 2013 Feb 13; Authors: Yan S, Suiter CL, Hou G, Zhang H, Polenova T Abstract In living organisms, biological molecules often organize into multicomponent complexes. Such assemblies consist of various proteins and carry out essential functions, ranging from cell division, transport, and energy transduction to catalysis, signaling, and viral...
nmrlearner Journal club 0 02-14-2013 02:37 PM
Combined Use of Replica-Exchange Molecular Dynamics and Magic-Angle-Spinning Solid-State NMR Spectral Simulations for Determining the Structure and Orientation of Membrane-Bound Peptide.
Combined Use of Replica-Exchange Molecular Dynamics and Magic-Angle-Spinning Solid-State NMR Spectral Simulations for Determining the Structure and Orientation of Membrane-Bound Peptide. Combined Use of Replica-Exchange Molecular Dynamics and Magic-Angle-Spinning Solid-State NMR Spectral Simulations for Determining the Structure and Orientation of Membrane-Bound Peptide. J Phys Chem B. 2011 Jun 13; Authors: Ikeda K, Kameda T, Harada E, Akutsu H, Fujiwara T We report an approach to determining membrane-peptides and -protein complex structures by...
nmrlearner Journal club 0 06-15-2011 01:15 PM
[NMR paper] 13C magic angle spinning NMR study of the light-induced and temperature-dependent cha
13C magic angle spinning NMR study of the light-induced and temperature-dependent changes in Rhodobacter sphaeroides R26 reaction centers enriched in tyrosine. Related Articles 13C magic angle spinning NMR study of the light-induced and temperature-dependent changes in Rhodobacter sphaeroides R26 reaction centers enriched in tyrosine. Biochemistry. 1992 Nov 17;31(45):11038-49 Authors: Fischer MR, de Groot HJ, Raap J, Winkel C, Hoff AJ, Lugtenburg J Solid-state 13C magic angle spinning (MAS) NMR has been used to investigate...
nmrlearner Journal club 0 08-21-2010 11:45 PM


Thread Tools Search this Thread
Search this Thread:

Advanced Search
Display Modes Rate This Thread
Rate This Thread:

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 Off
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 12:39 PM.


Map