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
Home Forums Wiki NMR feeds Downloads Register Today's Posts



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  
Old 11-17-2010, 11:15 PM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 23,697
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 Pressure-denatured state of Escherichia coli ribonuclease HI as monitored by Fourier

Pressure-denatured state of Escherichia coli ribonuclease HI as monitored by Fourier transform infrared and NMR spectroscopy.

Related Articles Pressure-denatured state of Escherichia coli ribonuclease HI as monitored by Fourier transform infrared and NMR spectroscopy.

Biochemistry. 1998 Dec 22;37(51):18001-9

Authors: Yamasaki K, Taniguchi Y, Takeda N, Nakano K, Yamasaki T, Kanaya S, Oobatake M

Pressure denaturation of Escherichia coli ribonuclease HI (RNase HI) was studied by Fourier transform infrared (FTIR) and two-dimensional NMR spectroscopy at pD* 3.0 and 25 degrees C. A reversible transition in the pressure range of 0.1-1090 MPa was observed with second-derivative FTIR experiments. A cooperative and gradual denaturation, involving both the secondary and tertiary structures, was observed between 240 and 450 MPa. The two peaks at 1629 and 1652 cm(-1), due to beta-strands and alpha-helices, respectively, did not fully disappear after the denaturation, and are different from the spectra of the random coil peptides. The hydrogen-deuterium exchange rates of the individual backbone amide protons were determined by heteronuclear NMR combined with the pressure-jump technique at 500, 650, and 850 MPa. Although most of the amides protected in the native structure are also highly protected in the pressure-denatured state, the rate constants (0.048 +/- 0.007 min(-1)) for the amide protons at 500 MPa are similar regardless of their locations, which is an indication of the EX1 mechanism of hydrogen-deuterium exchange. The pressure-denatured state of RNase HI at 500 MPa represents a novel denatured state, which is different from a typical molten globule state at atmospheric pressure (0.1 MPa), from the viewpoint of the homogeneous rate constants. The observations at 650 MPa are essentially the same as those at 500 MPa. However, at 850 MPa, the amide exchange rates for the highly hydrophobic C-terminal half of alpha-helix I are significantly slower than those for the other part of the protein, which can be interpreted as a hydrophobic collapse centered at the C-terminal half of alpha-helix I.

PMID: 9922168 [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
[NMR paper] Ribonuclease Sa conformational stability studied by NMR-monitored hydrogen exchange.
Ribonuclease Sa conformational stability studied by NMR-monitored hydrogen exchange. Related Articles Ribonuclease Sa conformational stability studied by NMR-monitored hydrogen exchange. Biochemistry. 2005 May 31;44(21):7644-55 Authors: Laurents DV, Scholtz JM, Rico M, Pace CN, Bruix M The conformational stability of ribonuclease Sa (RNase Sa) has been measured at the per-residue level by NMR-monitored hydrogen exchange at pH* 5.5 and 30 degrees C. In these conditions, the exchange mechanism was found to be EXII. The conformational stability...
nmrlearner Journal club 0 11-25-2010 08:21 PM
[NMR paper] Acid-induced denaturation of Escherichia coli ribonuclease HI analyzed by CD and NMR
Acid-induced denaturation of Escherichia coli ribonuclease HI analyzed by CD and NMR spectroscopies. Related Articles Acid-induced denaturation of Escherichia coli ribonuclease HI analyzed by CD and NMR spectroscopies. Biopolymers. 2003 Jun;69(2):176-88 Authors: Yamasaki K, Yamasaki T, Kanaya S, Oobatake M Acid-induced denaturation of the ribonuclease HI protein from Escherichia coli was analyzed by CD and NMR spectroscopies. The CD measurement revealed that the acid denaturation at 10 degrees C proceeds from the native state (N-state) to a...
nmrlearner Journal club 0 11-24-2010 09:01 PM
[NMR paper] High pressure NMR reveals active-site hinge motion of folate-bound Escherichia coli d
High pressure NMR reveals active-site hinge motion of folate-bound Escherichia coli dihydrofolate reductase. Related Articles High pressure NMR reveals active-site hinge motion of folate-bound Escherichia coli dihydrofolate reductase. Biochemistry. 2000 Oct 24;39(42):12789-95 Authors: Kitahara R, Sareth S, Yamada H, Ohmae E, Gekko K, Akasaka K A high-pressure (15)N/(1)H two-dimensional NMR study has been carried out on folate-bound dihydrofolate reductase (DHFR) from Escherichia coli in the pressure range between 30 and 2000 bar. Several...
nmrlearner Journal club 0 11-19-2010 08:29 PM
[NMR paper] NMR structure of ribonuclease HI from Escherichia coli.
NMR structure of ribonuclease HI from Escherichia coli. Related Articles NMR structure of ribonuclease HI from Escherichia coli. Biol Pharm Bull. 2000 Oct;23(10):1147-52 Authors: Fujiwara M, Kato T, Yamazaki T, Yamasaki K, Nagayam K The solution structure of ribonuclease HI (RNase HI) from Escherichia coli (E. coli), a protein of 155 residues, was determined. Three-dimensional nuclear Overhauser enhancement spectroscopy (NOESY) was used to obtain 1,424 distance constraints between individually assigned polypeptide chain hydrogen atoms....
nmrlearner Journal club 0 11-19-2010 08:29 PM
[NMR paper] The pressure-temperature free energy-landscape of staphylococcal nuclease monitored b
The pressure-temperature free energy-landscape of staphylococcal nuclease monitored by (1)H NMR. Related Articles The pressure-temperature free energy-landscape of staphylococcal nuclease monitored by (1)H NMR. J Mol Biol. 2000 Apr 28;298(2):293-302 Authors: Lassalle MW, Yamada H, Akasaka K The thermodynamic stability of staphylococcal nuclease was studied against the variation of both temperature and pressure by utilizing (1)H NMR spectroscopy at 750 MHz in 20 mM Mes buffer containing 99.9 % (2)H(2)O, pH 5.3. Equilibrium fractions of folded...
nmrlearner Journal club 0 11-18-2010 09:15 PM
[NMR paper] Folding pathway of Escherichia coli ribonuclease HI: a circular dichroism, fluorescen
Folding pathway of Escherichia coli ribonuclease HI: a circular dichroism, fluorescence, and NMR study. Related Articles Folding pathway of Escherichia coli ribonuclease HI: a circular dichroism, fluorescence, and NMR study. Biochemistry. 1995 Dec 26;34(51):16552-62 Authors: Yamasaki K, Ogasahara K, Yutani K, Oobatake M, Kanaya S The unfolding and refolding processes of Escherichia coli ribonuclease HI at 25 degrees C, induced by concentration jumps of either guanidine hydrochloride (GuHCl) or urea, were investigated using stopped-flow...
nmrlearner Journal club 0 08-22-2010 03:50 AM
[NMR paper] NMR study of the cold, heat, and pressure unfolding of ribonuclease A.
NMR study of the cold, heat, and pressure unfolding of ribonuclease A. Related Articles NMR study of the cold, heat, and pressure unfolding of ribonuclease A. Biochemistry. 1995 Jul 11;34(27):8631-41 Authors: Zhang J, Peng X, Jonas A, Jonas J The reversible cold, heat, and pressure unfolding of RNase A and RNase A--inhibitor complex were studied by 1D and 2D 1H NMR spectroscopy. The reversible pressure denaturation experiments in the pressure range from 1 bar to 5 kbar were carried out at pH 2.0 and 10 degrees C. The cold denaturation was...
nmrlearner Journal club 0 08-22-2010 03:50 AM
[NMR paper] Complete assignments of magnetic resonances of ribonuclease H from Escherichia coli b
Complete assignments of magnetic resonances of ribonuclease H from Escherichia coli by double- and triple-resonance 2D and 3D NMR spectroscopies. Related Articles Complete assignments of magnetic resonances of ribonuclease H from Escherichia coli by double- and triple-resonance 2D and 3D NMR spectroscopies. Biochemistry. 1993 Jun 1;32(21):5656-69 Authors: Yamazaki T, Yoshida M, Nagayama K Assignments of 1H, 15N, and 13C magnetic resonances for ribonuclease H from Escherichia coli have been completed using double- and triple-resonance 2D and 3D...
nmrlearner Journal club 0 08-21-2010 11:53 PM



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 02:32 PM.


Map