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 11-18-2010, 09:15 PM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 23,137
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 NMR evidence for progressive stabilization of native-like structure upon aggregation

NMR evidence for progressive stabilization of native-like structure upon aggregation of acid-denatured LysN.

Related Articles NMR evidence for progressive stabilization of native-like structure upon aggregation of acid-denatured LysN.

J Mol Biol. 2000 Jan 14;295(2):239-55

Authors: Alexandrescu AT, Lamour FP, Jaravine VA

The acid-denatured form of the protein LysN aggregates reversibly at pH 2.0. The strength of self-association increases with increasing Cl(-) anion concentration. At low concentrations of protein or Cl(-) anion, resonances of denatured LysN are in slow exchange with a minor form of the protein, which shows native-like NMR chemical shifts. The minor native-like resonances increase in intensity with increasing protein concentration, demonstrating that a native-like monomer fold is stabilized on aggregation of the acid-denatured protein. At high concentrations of protein or Cl(-) anion, interconversion between the major and minor resonances appears to shift from slow to intermediate exchange on the NMR timescale. NMR line-broadening is more pronounced for the major resonances of the denatured protein, which show sigmoidal decay curves with increasing Cl(-) concentration. The mid-points of the decay curves for residues in different parts of the molecule are non-coincident. We propose that differences in the NMR line-broadening transitions of individual residues reflect a stepwise stabilization of native-like structure on aggregation, starting with the segments of the protein that form the initial association interface. The resonances of the denatured protein with the greatest sensitivity to self-association correspond roughly to those that are most perturbed in the native protein on binding of the natural substrate tRNA(Lys). This suggests that the hydrophobic surfaces that promote intermolecular misfolding of acid-denatured LysN, may resemble those used for substrate binding by the native protein.

PMID: 10623523 [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
[Question from NMRWiki Q&A forum] Can correct TAUc be a sufficient evidence of the absence of aggregation?
Can correct TAUc be a sufficient evidence of the absence of aggregation? Hello! I am studying the protein backbone dynamics using the standard set of NMR relaxation parameters (R1, R2, NOE). I would like to be sure that there is no aggregation in the sample, and I have doubts about it so far. The best evidence I have is that overall rotational correlation time TAUc, predicted by HYDRONMR, matches exactly the one calculated from averaged R2/R1 values. Can anyone tell me for sure it is enough and I can be sure that protein doesn't form dimers/oligomers? Thanks!
nmrlearner News from other NMR forums 0 06-10-2011 01:50 PM
[NMR paper] Prevention of aggregation after refolding by balanced stabilization-destabilization:
Prevention of aggregation after refolding by balanced stabilization-destabilization: production of the Arabidopsis thaliana protein APG8a (At4g21980) for NMR structure determination. Related Articles Prevention of aggregation after refolding by balanced stabilization-destabilization: production of the Arabidopsis thaliana protein APG8a (At4g21980) for NMR structure determination. Protein Expr Purif. 2004 Apr;34(2):280-3 Authors: Chae YK, Im H, Zhao Q, Doelling JH, Vierstra RD, Markley JL The gene coding for APG8a (At4g21980), a protein from...
nmrlearner Journal club 0 11-24-2010 09:51 PM
[NMR paper] Protein stabilization by compatible solutes. Effect of diglycerol phosphate on the dy
Protein stabilization by compatible solutes. Effect of diglycerol phosphate on the dynamics of Desulfovibrio gigas rubredoxin studied by NMR. Related Articles Protein stabilization by compatible solutes. Effect of diglycerol phosphate on the dynamics of Desulfovibrio gigas rubredoxin studied by NMR. Eur J Biochem. 2003 Dec;270(23):4606-14 Authors: Lamosa P, Turner DL, Ventura R, Maycock C, Santos H Heteronuclear NMR relaxation measurements and hydrogen exchange data have been used to characterize protein dynamics in the presence or absence of...
nmrlearner Journal club 0 11-24-2010 09:16 PM
[NMR paper] Native-like beta-hairpin structure in an isolated fragment from ferredoxin: NMR and C
Native-like beta-hairpin structure in an isolated fragment from ferredoxin: NMR and CD studies of solvent effects on the N-terminal 20 residues. Related Articles Native-like beta-hairpin structure in an isolated fragment from ferredoxin: NMR and CD studies of solvent effects on the N-terminal 20 residues. Protein Eng. 1996 Jul;9(7):559-65 Authors: Searle MS, Zerella R, Williams DH, Packman LC The conformational properties of protein fragments have been widely studied as models of the earliest initiation events in protein folding. While...
nmrlearner Journal club 0 08-22-2010 02:27 PM
[NMR paper] Native like structure and stability of apo AI in a n-propanol/water solution as deter
Native like structure and stability of apo AI in a n-propanol/water solution as determined by 13C NMR. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles Native like structure and stability of apo AI in a n-propanol/water solution as determined by 13C NMR. FEBS Lett. 1995 Mar 13;361(1):29-34 Authors: Leroy A, Lippens G, Wieruszeski JM, Parra HJ, Fruchart JC To elucidate the molecular details of the conformation of apolipoprotein AI (apo AI), we have developed an approach...
nmrlearner Journal club 0 08-22-2010 03:41 AM
[MWClarkson blog] How native-like is a cold-denatured structure?
How native-like is a cold-denatured structure? http://www.researchblogging.org/public/citation_icons/rb2_large_gray.pngA protein has several different levels of structure. The primary structure is the arrangements of atoms and bonds, and it is formed in the ribosome by the assembly of amino acids as directed by an RNA template. The secondary structure is the local topology, the helices and strands, and this forms mostly because of the release of energy through the formation of hydrogen bonds. The tertiary structure is the actual fold of the protein, the way helices, strands, and loops are...
nmrlearner News from NMR blogs 0 08-22-2010 01:58 AM
[NMR paper] Comparison of the X-ray structure of native rubredoxin from Pyrococcus furiosus with
Comparison of the X-ray structure of native rubredoxin from Pyrococcus furiosus with the NMR structure of the zinc-substituted protein. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www3.interscience.wiley.com-aboutus-images-wiley_interscience_pubmed_logo_FREE_120x27.gif http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www.pubmedcentral.nih.gov-corehtml-pmc-pmcgifs-pubmed-pmc.gif Related Articles Comparison of the X-ray structure of native rubredoxin from Pyrococcus furiosus with the NMR structure of the zinc-substituted protein. Protein Sci. 1992...
nmrlearner Journal club 0 08-21-2010 11:45 PM
Structure-based protein NMR assignments using native structural ensembles
Structure-based protein NMR assignments using native structural ensembles Mehmet Serkan Apaydın, Vincent Conitzer and Bruce Randall Donald Journal of Biomolecular NMR; 2008; 40(4); pp 263-276 Abstract: An important step in NMR protein structure determination is the assignment of resonances and NOEs to corresponding nuclei. Structure-based assignment (SBA) uses a model structure (“template”) for the target protein to expedite this process. Nuclear vector replacement (NVR) is an SBA framework that combines multiple sources of NMR data (chemical shifts, RDCs, sparse NOEs, amide exchange...
matthias Journal club 0 08-14-2008 12:54 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 10:15 AM.


Map