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: 17,578
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 Demonstration of positionally disordered water within a protein hydrophobic cavity by

Demonstration of positionally disordered water within a protein hydrophobic cavity by NMR.

Related Articles Demonstration of positionally disordered water within a protein hydrophobic cavity by NMR.

Science. 1995 Mar 24;267(5205):1813-7

Authors: Ernst JA, Clubb RT, Zhou HX, Gronenborn AM, Clore GM

The presence and location of water of hydration (that is, bound water) in the solution structure of human interleukin-1 beta (hIL-1 beta) was investigated with water-selective two-dimensional heteronuclear magnetic resonance spectroscopy. It is shown here that in addition to water at the surface of the protein and ordered internal water molecules involved in bridging hydrogen bonds, positionally disordered water is present within a large, naturally occurring hydrophobic cavity located at the center of the molecule. These water molecules of hydration have residency times in the range of 1 to 2 nanoseconds to 100 to 200 microseconds and can be readily detected by nuclear magnetic resonance (NMR). Thus, large hydrophobic cavities in proteins may not be truly empty, as analysis of crystal structures appears to show, but may contain mobile water molecules that are crystallographically invisible but detectable by NMR.

PMID: 7892604 [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] Dynamics of xenon binding inside the hydrophobic cavity of pseudo-wild-type bacteriophage T4 lysozyme explored through xenon-based NMR spectroscopy.
Dynamics of xenon binding inside the hydrophobic cavity of pseudo-wild-type bacteriophage T4 lysozyme explored through xenon-based NMR spectroscopy. Related Articles Dynamics of xenon binding inside the hydrophobic cavity of pseudo-wild-type bacteriophage T4 lysozyme explored through xenon-based NMR spectroscopy. J Am Chem Soc. 2005 Aug 24;127(33):11676-83 Authors: Desvaux H, Dubois L, Huber G, Quillin ML, Berthault P, Matthews BW Wild-type bacteriophage T4 lysozyme contains a hydrophobic cavity with binding properties that have been...
nmrlearner Journal club 0 12-01-2010 06:56 PM
[NMR paper] Probing the hydrophobic cavity of lipid transfer protein from Nicotiana tabacum throu
Probing the hydrophobic cavity of lipid transfer protein from Nicotiana tabacum through xenon-based NMR spectroscopy. Related Articles Probing the hydrophobic cavity of lipid transfer protein from Nicotiana tabacum through xenon-based NMR spectroscopy. J Am Chem Soc. 2004 Dec 8;126(48):15738-46 Authors: Dubois L, Da Silva P, Landon C, Huber JG, Ponchet M, Vovelle F, Berthault P, Desvaux H The hydrophobic cavity of Lipid Transfer Protein 1 from Nicotiana tabacum is investigated in detail by NMR using xenon as a spy. The analysis of the (129)Xe...
nmrlearner Journal club 0 11-24-2010 10:03 PM
[NMR paper] Remodeling of HDL by phospholipid transfer protein: demonstration of particle fusion
Remodeling of HDL by phospholipid transfer protein: demonstration of particle fusion by 1H NMR spectroscopy. Related Articles Remodeling of HDL by phospholipid transfer protein: demonstration of particle fusion by 1H NMR spectroscopy. Biochem Biophys Res Commun. 1998 Aug 28;249(3):910-6 Authors: Korhonen A, Jauhiainen M, Ehnholm C, Kovanen PT, Ala-Korpela M There is evidence that phospholipid transfer protein (PLTP) can increase reverse cholesterol transport by inducing favorable subclass distribution in the high density lipoprotein (HDL)...
nmrlearner Journal club 0 11-17-2010 11:15 PM
[NMR paper] Demonstration of protein-protein interaction specificity by NMR chemical shift mappin
Demonstration of protein-protein interaction specificity by NMR chemical shift mapping. 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 Demonstration of protein-protein interaction specificity by NMR chemical shift mapping. Protein Sci. 1997 Dec;6(12):2624-7 Authors: Rajagopal P, Waygood EB, Reizer J, Saier MH, Klevit RE ...
nmrlearner Journal club 0 08-22-2010 05:08 PM
[NMR paper] NMR identification of hydrophobic cavities with low water occupancies in protein stru
NMR identification of hydrophobic cavities with low water occupancies in protein structures using small gas molecules. Related Articles NMR identification of hydrophobic cavities with low water occupancies in protein structures using small gas molecules. Nat Struct Biol. 1997 May;4(5):396-404 Authors: Otting G, Liepinsh E, Halle B, Frey U Magnetization transfer through dipole-dipole interactions (nuclear Overhauser effects, NOEs) between water protons and the protons lining two small hydrophobic cavities in hen egg-white lysozyme demonstrates...
nmrlearner Journal club 0 08-22-2010 03:31 PM
[NMR paper] NMR identification of hydrophobic cavities with low water occupancies in protein stru
NMR identification of hydrophobic cavities with low water occupancies in protein structures using small gas molecules. Related Articles NMR identification of hydrophobic cavities with low water occupancies in protein structures using small gas molecules. Nat Struct Biol. 1997 May;4(5):396-404 Authors: Otting G, Liepinsh E, Halle B, Frey U Magnetization transfer through dipole-dipole interactions (nuclear Overhauser effects, NOEs) between water protons and the protons lining two small hydrophobic cavities in hen egg-white lysozyme demonstrates...
nmrlearner Journal club 0 08-22-2010 03:03 PM
[NMR paper] Secondary structure in solution of the hydrophobic protein of soybean (HPS) as reveal
Secondary structure in solution of the hydrophobic protein of soybean (HPS) as revealed by 1H NMR. Related Articles Secondary structure in solution of the hydrophobic protein of soybean (HPS) as revealed by 1H NMR. J Biomol Struct Dyn. 1995 Apr;12(5):1009-22 Authors: Sodano P, Ptak M COSY, TOCSY and NOESY experiments have been used to assign sequentially the 1H 500 MHz NMR spectra of the Hydrophobic Protein of Soybean (HPS). Spin systems identification combined with sequential assignment allowed to identify the proton resonances of this 80...
nmrlearner Journal club 0 08-22-2010 03:41 AM
[NMR paper] 1H NMR study of the influence of hydrophobic contacts on protein-prosthetic group rec
1H NMR study of the influence of hydrophobic contacts on protein-prosthetic group recognition in bovine and rat ferricytochrome b5. Related Articles 1H NMR study of the influence of hydrophobic contacts on protein-prosthetic group recognition in bovine and rat ferricytochrome b5. Biochemistry. 1990 Oct 16;29(41):9623-31 Authors: Lee KB, La Mar GN, Kehres LA, Fujinari EM, Smith KM, Pochapsky TC, Sligar SG The proton nuclear magnetic resonance spectra of the soluble fragment of native bovine and genetically engineered wild-type rat...
nmrlearner Journal club 0 08-21-2010 11:04 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 04:23 PM.


Map