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 08-22-2010, 03:03 PM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 17,583
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 Solution NMR characterization of hydrogen bonds in a protein by indirect measurement

Solution NMR characterization of hydrogen bonds in a protein by indirect measurement of deuterium quadrupole couplings.

Related Articles Solution NMR characterization of hydrogen bonds in a protein by indirect measurement of deuterium quadrupole couplings.

J Magn Reson. 1997 Jul;127(1):54-64

Authors: Liwang AC, Bax A

Hydrogen bonds stabilize protein and nucleic acid structure, but little direct spectroscopic data have been available for characterizing these critical interactions in biological macromolecules. It is demonstrated that the electric field gradient at the nucleus of an amide hydrogen can be determined residue-specific by measurement of 15N NMR relaxation times in proteins dissolved in D2O, and uniformly enriched with 13C and 15N. In D2O, all backbone amide protons can be exchanged with solvent deuterons, and the T1 relaxation rate of a deuteron is dominated by its quadrupole coupling constant (QCC), which is directly proportional to the electric field gradient at the nucleus. 2HN T1 relaxation can be measured quantitatively through its effect on the T2 relaxation of its directly attached 15N. QCC values calculated from 2HN T1 and previously reported spectral densities correlate with the inverse cube of the X-ray crystal structure-derived hydrogen bond lengths: QCC = 228 + Sigmai 130 cos alphai/ri3 kHz, where alpha is the N-H...Oi angle and r is the backbone-backbone (N-)H...Oi(=C) hydrogen bond distance in ângstroms.

PMID: 9245630 [PubMed - indexed for MEDLINE]



Source: PubMed
Reply With Quote


Did you find this post helpful? Yes | No

Reply
Similar Threads
Thread Thread Starter Forum Replies Last Post
Measurement of protein unfolding/refolding kinetics and structural characterization of hidden intermediates by NMR relaxation dispersion.
Measurement of protein unfolding/refolding kinetics and structural characterization of hidden intermediates by NMR relaxation dispersion. Measurement of protein unfolding/refolding kinetics and structural characterization of hidden intermediates by NMR relaxation dispersion. Proc Natl Acad Sci U S A. 2011 May 11; Authors: Meinhold DW, Wright PE Detailed understanding of protein function and malfunction hinges on the ability to characterize transiently populated states and the transitions between them. Here, we use (15)N, , and (13)CO NMR R(2)...
nmrlearner Journal club 0 05-13-2011 02:40 PM
Methanol Strengthens Hydrogen Bonds and Weakens Hydrophobic Interactions in Proteins - A Combined Molecular Dynamics and NMR study.
Methanol Strengthens Hydrogen Bonds and Weakens Hydrophobic Interactions in Proteins - A Combined Molecular Dynamics and NMR study. Methanol Strengthens Hydrogen Bonds and Weakens Hydrophobic Interactions in Proteins - A Combined Molecular Dynamics and NMR study. J Phys Chem B. 2011 May 2; Authors: Hwang S, Shao Q, Williams H, Hilty C, Gao YQ A combined simulation and experimental study was performed to investigate how methanol affects the structure of a model peptide BBA5. BBA5 forms a stable ?-hairpin-?-helix structure in aqueous solutions....
nmrlearner Journal club 0 05-04-2011 04:14 PM
[NMR paper] Ligand-induced strain in hydrogen bonds of the c-Src SH3 domain detected by NMR.
Ligand-induced strain in hydrogen bonds of the c-Src SH3 domain detected by NMR. Related Articles Ligand-induced strain in hydrogen bonds of the c-Src SH3 domain detected by NMR. J Mol Biol. 2000 Dec 8;304(4):497-505 Authors: Cordier F, Wang C, Grzesiek S, Nicholson LK Changes in the molecular conformation of proteins can result from a variety of perturbations, and can play crucial roles in the regulation of biological activity. A new solution NMR method has been applied to monitor ligand-induced changes in hydrogen bond geometry in the...
nmrlearner Journal club 0 11-19-2010 08:29 PM
[NMR paper] Direct identification of NH...N hydrogen bonds in non-canonical base pairs of RNA by
Direct identification of NH...N hydrogen bonds in non-canonical base pairs of RNA by NMR spectroscopy. Related Articles Direct identification of NH...N hydrogen bonds in non-canonical base pairs of RNA by NMR spectroscopy. Nucleic Acids Res. 1999 Aug 1;27(15):3104-10 Authors: Wöhnert J, Dingley AJ, Stoldt M, Görlach M, Grzesiek S, Brown LR It is shown that the recently developed quantitative J(NN)HNN-COSY experiment can be used for the direct identification of hydrogen bonds in non-canonical base pairs in RNA. Scalar(2h)J(NN)couplings across...
nmrlearner Journal club 0 11-18-2010 08:31 PM
[NMR paper] NMR scalar couplings across Watson-Crick base pair hydrogen bonds in DNA observed by
NMR scalar couplings across Watson-Crick base pair hydrogen bonds in DNA observed by transverse relaxation-optimized spectroscopy. Related Articles NMR scalar couplings across Watson-Crick base pair hydrogen bonds in DNA observed by transverse relaxation-optimized spectroscopy. Proc Natl Acad Sci U S A. 1998 Nov 24;95(24):14147-51 Authors: Pervushin K, Ono A, Fernández C, Szyperski T, Kainosho M, Wüthrich K This paper describes the NMR observation of 15N---15N and 1H---15N scalar couplings across the hydrogen bonds in Watson-Crick base pairs...
nmrlearner Journal club 0 11-17-2010 11:15 PM
[NMR paper] Solution NMR characterization of hydrogen bonds in a protein by indirect measurement
Solution NMR characterization of hydrogen bonds in a protein by indirect measurement of deuterium quadrupole couplings. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles Solution NMR characterization of hydrogen bonds in a protein by indirect measurement of deuterium quadrupole couplings. J Magn Reson. 1997 Jul;127(1):54-64 Authors: Liwang AC, Bax A Hydrogen bonds stabilize protein and nucleic acid structure, but little direct spectroscopic data have been available for...
nmrlearner Journal club 0 08-22-2010 03:31 PM
[NMR paper] H NMR probes for inter-segmental hydrogen bonds in myoglobins.
H NMR probes for inter-segmental hydrogen bonds in myoglobins. Related Articles H NMR probes for inter-segmental hydrogen bonds in myoglobins. J Biochem. 1996 Jul;120(1):126-32 Authors: Yamamoto Y NMR signals arising from the HisB5 N delta H and HisEF5 N epsilon H protons in sperm whale skeletal and horse heart myoglobins have been located for the first time in the downfield shifted portion of the spectra. The shifts and hydrogen exchange rates indicate that these His imidazole ring NH protons are involved in the inter-segmental hydrogen bonds...
nmrlearner Journal club 0 08-22-2010 02:27 PM
[NMR paper] Transient hydrogen bonds identified on the surface of the NMR solution structure of H
Transient hydrogen bonds identified on the surface of the NMR solution structure of Hirudin. Related Articles Transient hydrogen bonds identified on the surface of the NMR solution structure of Hirudin. Biochemistry. 1994 Aug 9;33(31):9303-10 Authors: Szyperski T, Antuch W, Schick M, Betz A, Stone SR, Wüthrich K Recombinant desulfatohirudin retains largely the thrombin-inhibitory activity of natural hirudin from Hirudo medicinalis and causes at most minimal immune response in humans. With regard to potential pharmaceutical applications it is...
nmrlearner Journal club 0 08-22-2010 03:29 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 - 2017, 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 03:38 PM.


Map