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 11-24-2010, 09:25 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 Insights into conformation and dynamics of protein GB1 during folding and unfolding b

Insights into conformation and dynamics of protein GB1 during folding and unfolding by NMR.

Related Articles Insights into conformation and dynamics of protein GB1 during folding and unfolding by NMR.

J Mol Biol. 2004 Jan 30;335(5):1299-307

Authors: Ding K, Louis JM, Gronenborn AM

Understanding protein stability requires characterization of structural determinants of the folded and unfolded states. Many proteins are capable of populating partially folded states under specific solution conditions. Occasionally, coexistence of the folded and an unfolded state under non- or mildly denaturing conditions can be observed by NMR, allowing us to structurally probe these states under identical conditions. Here we report on a destabilized mutant of the B1 domain of protein G (GB1) whose equilibrium unfolding was systematically investigated. Backbone amide residual dipolar couplings (RDCs), the tryptophan Nepsilon-H resonance and the amide nitrogen transverse relaxation rates (R2s) for varying pH values and different temperatures were measured. The backbone amide RDCs indicate that prior to complete unfolding, two melting hot spots are formed at the turn around T11, L12 and K13 and the N terminus of the helix at A24 and T25. The RDCs for the low pH, thermally unfolded state of GB1 are very small and do not indicate the presence of any native-like structure. Amide nitrogen transverse relaxation rates for GB1 in the folded state at different temperatures exhibit large contributions from exchange processes and the associated dynamics display considerable heterogeneity. Our data provide clear evidence for intermediate conformations and multi-state equilibrium un/folding for this GB1 variant.

PMID: 14729345 [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
Structure and dynamics of cationic membrane peptides and proteins: Insights from solid-state NMR.
Structure and dynamics of cationic membrane peptides and proteins: Insights from solid-state NMR. Structure and dynamics of cationic membrane peptides and proteins: Insights from solid-state NMR. Protein Sci. 2011 Feb 22; Authors: Hong M, Su Y Many membrane peptides and protein domains contain functionally important cationic Arg and Lys residues, whose insertion into the hydrophobic interior of the lipid bilayer encounters significant energy barriers. To understand how these cationic molecules overcome the free energy barrier to insert into the...
nmrlearner Journal club 0 02-24-2011 11:04 AM
[NMR paper] NMR dynamics-derived insights into the binding properties of a peptide interacting wi
NMR dynamics-derived insights into the binding properties of a peptide interacting with an SH2 domain. Related Articles NMR dynamics-derived insights into the binding properties of a peptide interacting with an SH2 domain. Biochemistry. 2005 Jan 18;44(2):694-703 Authors: Finerty PJ, Mittermaier AK, Muhandiram R, Kay LE, Forman-Kay JD The signal transduction protein phospholipase C-gamma1 (PLC-gamma1) is activated when its C-terminal SH2 domain (PLCC) binds the phosphorylated Tyr-1021 site (pTyr-1021) in the beta-platelet-derived growth factor...
nmrlearner Journal club 0 11-24-2010 11:14 PM
[NMR paper] NMR structure of the alpha-hemoglobin stabilizing protein: insights into conformation
NMR structure of the alpha-hemoglobin stabilizing protein: insights into conformational heterogeneity and binding. Related Articles NMR structure of the alpha-hemoglobin stabilizing protein: insights into conformational heterogeneity and binding. J Biol Chem. 2004 Aug 13;279(33):34963-70 Authors: Santiveri CM, Pérez-Cañadillas JM, Vadivelu MK, Allen MD, Rutherford TJ, Watkins NA, Bycroft M The structure of alpha-hemoglobin stabilizing protein (AHSP), a molecular chaperone for free alpha-hemoglobin, has been determined using NMR spectroscopy....
nmrlearner Journal club 0 11-24-2010 09:51 PM
[NMR paper] Mechanical unfolding of a titin Ig domain: structure of unfolding intermediate reveal
Mechanical unfolding of a titin Ig domain: structure of unfolding intermediate revealed by combining AFM, molecular dynamics simulations, NMR and protein engineering. Related Articles Mechanical unfolding of a titin Ig domain: structure of unfolding intermediate revealed by combining AFM, molecular dynamics simulations, NMR and protein engineering. J Mol Biol. 2002 Sep 27;322(4):841-9 Authors: Fowler SB, Best RB, Toca Herrera JL, Rutherford TJ, Steward A, Paci E, Karplus M, Clarke J The mechanical unfolding of an immunoglobulin domain from the...
nmrlearner Journal club 0 11-24-2010 08:58 PM
[NMR paper] Alteration of conformation and dynamics of bacteriorhodopsin induced by protonation o
Alteration of conformation and dynamics of bacteriorhodopsin induced by protonation of Asp 85 and deprotonation of Schiff base as studied by 13C NMR. Related Articles Alteration of conformation and dynamics of bacteriorhodopsin induced by protonation of Asp 85 and deprotonation of Schiff base as studied by 13C NMR. Biochemistry. 2000 Nov 28;39(47):14472-80 Authors: Kawase Y, Tanio M, Kira A, Yamaguchi S, Tuzi S, Naito A, Kataoka M, Lanyi JK, Needleman R, Saitô H According to previous X-ray diffraction studies, the D85N mutant of...
nmrlearner Journal club 0 11-19-2010 08:29 PM
[NMR paper] Conformation and backbone dynamics of bacteriorhodopsin revealed by (13)C-NMR.
Conformation and backbone dynamics of bacteriorhodopsin revealed by (13)C-NMR. Related Articles Conformation and backbone dynamics of bacteriorhodopsin revealed by (13)C-NMR. Biochim Biophys Acta. 2000 Aug 30;1460(1):39-48 Authors: Saitô H, Tuzi S, Yamaguchi S, Tanio M, Naito A It is demonstrated here how the secondary structure and dynamics of transmembrane helices, as well as surface residues, such as interhelical loops and N- or C-terminus of bacteriorhodopsin (bR) in purple membrane, can be determined at ambient temperature based on very...
nmrlearner Journal club 0 11-19-2010 08:29 PM
[NMR paper] Insights into protein folding from NMR.
Insights into protein folding from NMR. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--arjournals.annualreviews.org-images-AnnualReviews100x25.gif Related Articles Insights into protein folding from NMR. Annu Rev Phys Chem. 1996;47:369-95 Authors: Dyson HJ, Wright PE NMR has emerged as an important tool for studies of protein folding because of the unique structural insights it can provide into many aspects of the folding process. Applications include measurements of kinetic folding events and structural characterization of folding...
nmrlearner Journal club 0 08-22-2010 02:27 PM
[NMR paper] Conformation of parathyroid hormone antagonists by CD, NMR, and molecular dynamics si
Conformation of parathyroid hormone antagonists by CD, NMR, and molecular dynamics simulations. Related Articles Conformation of parathyroid hormone antagonists by CD, NMR, and molecular dynamics simulations. Biopolymers. 1995 Oct;36(4):485-95 Authors: Chorev M, Behar V, Yang Q, Rosenblatt M, Mammi S, Maretto S, Pellegrini M, Peggion E The conformation of two highly potent parathyroid hormone (PTH) antagonists was investigated in water/2,2,2-trifluoroethanol mixtures. The two peptides are derived from the sequence (7-34) of PTH and of...
nmrlearner Journal club 0 08-22-2010 03:50 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 08:11 AM.


Map