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



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 08-14-2010, 04:19 AM
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 Comparison of fast backbone dynamics at amide nitrogen and carbonyl sites in dematin

Abstract We perform a detailed comparison of fast backbone dynamics probed at amide nitrogen versus carbonyl carbon sites for dematin headpiece C-terminal domain (DHP) and its S74E mutant (DHPS74E). Carbonyl dynamics is probed via auto-correlated longitudinal rates and transverse Câ?²/Câ?²-Cα CSA/dipolar and Câ?²/Câ?²â??N CSA/dipolar cross-correlated rates, while 15N data are taken from a previous study. Resulting values of effective order parameters and internal correlation times support the conclusion that Câ?² relaxation reports on a different subset of fast motions compared to those probed at Nâ??H bond vectors in the same peptide planes. 13Câ?² order parameters are on the average 0.08 lower than 15N order parameters with the exception of the flexible loop region in DHP. The reduction of mobility in the loop region upon the S74E mutation can be seen from the 15N order parameters but not from the 13C order parameters. Internal correlation times at 13Câ?² sites are on the average an order of magnitude longer than those at 15N sites for the well-structured C-terminal subdomains, while the more flexible N-terminal subdomains have more comparable average internal correlation times.
  • Content Type Journal Article
  • DOI 10.1007/s10858-010-9417-9
  • Authors
    • Liliya Vugmeyster, University of Alaska at Anchorage Department of Chemistry and Environment and Natural Resources Institute 3211 Providence Drive Anchorage AK 99508 USA
    • Dmitry Ostrovsky, University of Alaska at Anchorage Department of Mathematical Sciences 3211 Providence Drive Anchorage AK 99508 USA
    • Ying Li, Columbia University Department of Biochemistry & Molecular Biophysics 630 West 168th Street New York NY 10032 USA

Source: Journal of Biomolecular NMR
Reply With Quote


Did you find this post helpful? Yes | No

Reply
Similar Threads
Thread Thread Starter Forum Replies Last Post
Temperature dependence of fast carbonyl backbone dynamics in chicken villin headpiece subdomain
Temperature dependence of fast carbonyl backbone dynamics in chicken villin headpiece subdomain Abstract Temperature-dependence of protein dynamics can provide information on details of the free energy landscape by probing the characteristics of the potential responsible for the fluctuations. We have investigated the temperature-dependence of picosecond to nanosecond backbone dynamics at carbonyl carbon sites in chicken villin headpiece subdomain protein using a combination of three NMR relaxation rates: 13Câ?² longitudinal rate, and two cross-correlated rates involving dipolar and...
nmrlearner Journal club 0 03-20-2011 07:14 PM
[NMR paper] Temperature dependence of protein backbone motion from carbonyl 13C and amide 15N NMR
Temperature dependence of protein backbone motion from carbonyl 13C and amide 15N NMR relaxation. Related Articles Temperature dependence of protein backbone motion from carbonyl 13C and amide 15N NMR relaxation. J Magn Reson. 2005 May;174(1):43-53 Authors: Chang SL, Tjandra N The NMR spin-lattice relaxation rate (R1) and the rotating-frame spin-lattice relaxation rate (R1rho) of amide 15N and carbonyl 13C (13C') of the uniformly 13C- and 15N-labeled ubiquitin were measured at different temperatures and field strengths to investigate the...
nmrlearner Journal club 0 11-25-2010 08:21 PM
[NMR paper] Comparison of backbone dynamics of oxidized and reduced putidaredoxin by 15N NMR rela
Comparison of backbone dynamics of oxidized and reduced putidaredoxin by 15N NMR relaxation measurements. Related Articles Comparison of backbone dynamics of oxidized and reduced putidaredoxin by 15N NMR relaxation measurements. Biochemistry. 1999 Aug 3;38(31):9862-71 Authors: Sari N, Holden MJ, Mayhew MP, Vilker VL, Coxon B The backbone dynamics of uniformly 15N-labeled reduced and oxidized putidaredoxin (Pdx) have been studied by 2D 15N NMR relaxation measurements. 15N T1 and T2 values and 1H-15N NOEs have been measured for the diamagnetic...
nmrlearner Journal club 0 11-18-2010 08:31 PM
NMR backbone dynamics studies of human PED/PEA-15 outline protein functional sites.
NMR backbone dynamics studies of human PED/PEA-15 outline protein functional sites. NMR backbone dynamics studies of human PED/PEA-15 outline protein functional sites. FEBS J. 2010 Sep 3; Authors: Farina B, Pirone L, Russo L, Viparelli F, Doti N, Pedone C, Pedone EM, Fattorusso R PED/PEA-15 (phosphoprotein enriched in diabetes/phosphoprotein enriched in astrocytes) is a ubiquitously expressed protein and a key regulator of cell growth and glucose metabolism. PED/PEA-15 mediates both homotypic and heterotypic interactions and is constituted by...
nmrlearner Journal club 0 09-10-2010 11:53 PM
Backbone Amide Dynamics Studies of Apo-L75F-TrpR, a Temperature-Sensitive Mutant of t
Backbone Amide Dynamics Studies of Apo-L75F-TrpR, a Temperature-Sensitive Mutant of the Tryptophan Repressor Protein (TrpR): Comparison with the 15N NMR Relaxation Profiles of Wild-Type and A77V Mutant Apo-TrpR Repressors http://pubs.acs.org//appl/literatum/publisher/achs/journals/content/bichaw/0/bichaw.ahead-of-print/bi100508u/aop/images/medium/bi-2010-00508u_0005.gifBiochemistry, Volume 0, Issue 0, Articles ASAP (As Soon As Publishable). More...
nmrlearner Journal club 0 08-31-2010 10:50 PM
[NMR paper] Comparison of backbone dynamics of reduced and oxidized Escherichia coli glutaredoxin
Comparison of backbone dynamics of reduced and oxidized Escherichia coli glutaredoxin-1 using 15N NMR relaxation measurements. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--pubs.acs.org-images-acspubs.jpg Related Articles Comparison of backbone dynamics of reduced and oxidized Escherichia coli glutaredoxin-1 using 15N NMR relaxation measurements. Biochemistry. 1997 Apr 22;36(16):5029-44 Authors: Kelley JJ, Caputo TM, Eaton SF, Laue TM, Bushweller JH NMR-based structure determination of Escherichia coli glutaredoxin-1 in its reduced...
nmrlearner Journal club 0 08-22-2010 03:31 PM
[NMR paper] Backbone dynamics, amide hydrogen exchange, and resonance assignments of the DNA meth
Backbone dynamics, amide hydrogen exchange, and resonance assignments of the DNA methylphosphotriester repair domain of Escherichia coli Ada using NMR. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--pubs.acs.org-images-acspubs.jpg Related Articles Backbone dynamics, amide hydrogen exchange, and resonance assignments of the DNA methylphosphotriester repair domain of Escherichia coli Ada using NMR. Biochemistry. 1996 Jul 23;35(29):9335-48 Authors: Habazettl J, Myers LC, Yuan F, Verdine GL, Wagner G The 10kDa amino-terminal fragment of...
nmrlearner Journal club 0 08-22-2010 02:20 PM
Backbone amide dynamics studies of apo-L75F-TrpR, a temperature sensitive mutant of t
Backbone amide dynamics studies of apo-L75F-TrpR, a temperature sensitive mutant of the tryptophan repressor protein (TrpR): comparison with the 15N NMR relaxation profiles of wild type and A77V mutant apo-TrpR repressors. Related Articles Backbone amide dynamics studies of apo-L75F-TrpR, a temperature sensitive mutant of the tryptophan repressor protein (TrpR): comparison with the 15N NMR relaxation profiles of wild type and A77V mutant apo-TrpR repressors. Biochemistry. 2010 Aug 18; Authors: Goel A, Tripet BP, Tyler RC, Nebert LD, Copie V ...
nmrlearner Journal club 0 08-21-2010 01:02 AM


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 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 09:53 AM.


Map