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, 03:41 AM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 17,587
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 Internal motions of apo-neocarzinostatin as studied by 13C NMR methine relaxation at

Internal motions of apo-neocarzinostatin as studied by 13C NMR methine relaxation at natural abundance.

Related Articles Internal motions of apo-neocarzinostatin as studied by 13C NMR methine relaxation at natural abundance.

J Biomol NMR. 1995 Apr;5(3):233-44

Authors: Mispelter J, Lefèvre C, Adjadj E, Quiniou E, Favaudon V

Dynamics of the backbone and some side chains of apo-neocarzinostatin, a 10.7 kDa carrier protein, have been studied from 13C relaxation rates R1, R2 and steady-state 13C-(1H) NOEs, measured at natural abundance. Relaxation data were obtained for 79 nonoverlapping C alpha resonances and for 11 threonine C beta single resonances. Except for three C alpha relaxation rates, all data were analysed from a simple two-parameter spectral density function using the model-free approach of Lipari and Szabo. The corresponding C-H fragments exhibit fast (tau e < 40 ps) restricted libration motions (S2 = 0.73 to 0.95). Global examination of the microdynamical parameters S2 and tau e along the amino acid sequence gives no immediate correlation with structural elements. However, different trends for the three loops involved in the binding site are revealed. The beta-ribbon comprising residues 37 to 47 is spatially restricted, with relatively large tau e values in its hairpin region. The other beta-ribbon (residues 72 to 87) and the large disordered loop ranging between residues 97-107 experience small-amplitude motions on a much faster (picosecond) time scale. The two N-terminal residues, Ala1 and Ala2, and the C-terminal residue Asn113, exhibit an additional slow motion on a subnanosecond time scale (400-500 ps). Similarly, the relaxation data for eight threonine side-chain C beta must be interpreted in terms of a three-parameter spectral density function. They exhibit slower motions, on the nanosecond time scale (500-3000 ps). Three threonine (Thr65, Thr68, Thr81) side chains do not display a slow component, but an exchange contribution to the observed transverse relaxation rate R2 could no be excluded at these sites. The microdynamical parameter (S2, tau e and R2ex) or (S(slow)2, S(fast)2 and tauslow) were obtained from a straightforward solution of the equations describing the relaxation data. They were calculated assuming an overall isotropic rotational correlation time tau c for the protein of 5.7 ns, determined using standard procedures from R2/R1 ratios. However, it is shown that the product (1-S2) x tau e is nearly independent of tau c for residues not exhibiting slow motions on the nanosecond time scale. In addition, this parameter very closely follows the heteronuclear NOEs, which therefore could be good indices for local fast motions on the picosecond time scale.

PMID: 7787421 [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
Can Enzyme Engineering Benefit from the Modulation of Protein Motions? Lessons Learned from NMR Relaxation Dispersion Experiments.
Can Enzyme Engineering Benefit from the Modulation of Protein Motions? Lessons Learned from NMR Relaxation Dispersion Experiments. Can Enzyme Engineering Benefit from the Modulation of Protein Motions? Lessons Learned from NMR Relaxation Dispersion Experiments. Protein Pept Lett. 2011 Jan 11; Authors: Despite impressive progress in protein engineering and design, our ability to create new and efficient enzyme activities remains a laborious and time-consuming endeavor. In the past few years, intricate combinations of rational mutagenesis, directed...
nmrlearner Journal club 0 01-13-2011 12:00 PM
[NMR paper] The effects of mutations on motions of side-chains in protein L studied by 2H NMR dyn
The effects of mutations on motions of side-chains in protein L studied by 2H NMR dynamics and scalar couplings. Related Articles The effects of mutations on motions of side-chains in protein L studied by 2H NMR dynamics and scalar couplings. J Mol Biol. 2003 Jun 6;329(3):551-63 Authors: Millet O, Mittermaier A, Baker D, Kay LE Recently developed 2H spin relaxation experiments are applied to study the dynamics of methyl-containing side-chains in the B1 domain of protein L and in a pair of point mutants of the domain, F22L and A20V. X-ray and...
nmrlearner Journal club 0 11-24-2010 09:01 PM
[NMR paper] Slow internal dynamics in proteins: application of NMR relaxation dispersion spectros
Slow internal dynamics in proteins: application of NMR relaxation dispersion spectroscopy to methyl groups in a cavity mutant of T4 lysozyme. Related Articles Slow internal dynamics in proteins: application of NMR relaxation dispersion spectroscopy to methyl groups in a cavity mutant of T4 lysozyme. J Am Chem Soc. 2002 Feb 20;124(7):1443-51 Authors: Mulder FA, Hon B, Mittermaier A, Dahlquist FW, Kay LE Recently developed carbon transverse relaxation dispersion experiments (Skrynnikov, N. R.; et al. J. Am. Chem. Soc. 2001, 123, 4556-4566) were...
nmrlearner Journal club 0 11-24-2010 08:49 PM
[NMR paper] Characterization of the internal motions of a chimeric protein by 13C NMR highlights
Characterization of the internal motions of a chimeric protein by 13C NMR highlights the important dynamic consequences of the engineering on a millisecond time scale. Related Articles Characterization of the internal motions of a chimeric protein by 13C NMR highlights the important dynamic consequences of the engineering on a millisecond time scale. Eur J Biochem. 2000 Nov;267(22):6519-33 Authors: Wolff N, Guenneugues M, Gilquin B, Drakopoulou E, Vita C, Ménez A, Zinn-Justin S By transferring the central curaremimetic beta hairpin of the...
nmrlearner Journal club 0 11-19-2010 08:29 PM
[NMR paper] Backbone motions in a crystalline protein from field-dependent 2H-NMR relaxation and
Backbone motions in a crystalline protein from field-dependent 2H-NMR relaxation and line-shape analysis. Related Articles Backbone motions in a crystalline protein from field-dependent 2H-NMR relaxation and line-shape analysis. Biopolymers. 2000 Jan;53(1):9-18 Authors: Mack JW, Usha MG, Long J, Griffin RG, Wittebort RJ We have used 2H-nmr to study backbone dynamics of the 2H-labeled, slowly exchanging amide sites of fully hydrated, crystalline hen egg white lysozyme. Order parameters are determined from the residual quadrupole coupling and...
nmrlearner Journal club 0 11-18-2010 09:15 PM
[NMR paper] Assignment of 13C resonances and analysis of relaxation properties and internal dynam
Assignment of 13C resonances and analysis of relaxation properties and internal dynamics of pike parvalbumin by 13C-NMR at natural abundance. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www3.interscience.wiley.com-aboutus-images-wiley_interscience_pubmed_logo_FREE_120x27.gif Related Articles Assignment of 13C resonances and analysis of relaxation properties and internal dynamics of pike parvalbumin by 13C-NMR at natural abundance. Eur J Biochem. 1996 May 1;237(3):561-74 Authors: Alattia T, Padilla A, Cavé A Pike parvalbumin is an...
nmrlearner Journal club 0 08-22-2010 02:27 PM
[NMR paper] Backbone dynamics of trp repressor studied by 15N NMR relaxation.
Backbone dynamics of trp repressor studied by 15N NMR relaxation. Related Articles Backbone dynamics of trp repressor studied by 15N NMR relaxation. Biochemistry. 1995 Apr 18;34(15):5212-23 Authors: Zheng Z, Czaplicki J, Jardetzky O Backbone dynamics of trp repressor, a 25 kDa DNA binding protein, have been studied using 15N relaxation data measured by proton-detected two-dimensional 1H-15N NMR spectroscopy. 15N spin-lattice relaxation time (T1), spin-spin relaxation time (T2), and heteronuclear NOEs were determined for all visible backbone...
nmrlearner Journal club 0 08-22-2010 03:41 AM
[NMR paper] Effect of antibody binding on protein motions studied by hydrogen-exchange labeling a
Effect of antibody binding on protein motions studied by hydrogen-exchange labeling and two-dimensional NMR. Related Articles Effect of antibody binding on protein motions studied by hydrogen-exchange labeling and two-dimensional NMR. Biochemistry. 1992 Nov 10;31(44):10678-85 Authors: Mayne L, Paterson Y, Cerasoli D, Englander SW We have used hydrogen-exchange labeling detected by 2D NMR to study antibody-protein interactions for two monoclonal antibodies raised against horse cytochrome c. The data show that these antibodies bind mainly to the...
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 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 12:43 AM.


Map