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, 03:03 PM
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 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 the presence of water molecules with occupancies of approximately 10-50%. Similarly, NOEs were observed between the cavity protons and the protons of hydrogen, methane, ethylene or cyclopropane applied at 1-200 bar pressure. These gases can thus be used as general NMR indicators of empty or partially hydrated hydrophobic cavities in proteins. All gases reside in the cavities for longer than 1 ns in marked contrast to common belief that gas diffusion in proteins is not much slower than in water. Binding to otherwise empty cavities may be a major aspect of the anesthetic effect of small organic gas molecules.

PMID: 9145111 [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] Water-protein hydrogen exchange in the micro-crystalline protein crh as observed by solid state NMR spectroscopy.
Water-protein hydrogen exchange in the micro-crystalline protein crh as observed by solid state NMR spectroscopy. Related Articles Water-protein hydrogen exchange in the micro-crystalline protein crh as observed by solid state NMR spectroscopy. J Biomol NMR. 2005 Jul;32(3):195-207 Authors: Böckmann A, Juy M, Bettler E, Emsley L, Galinier A, Penin F, Lesage A We report site-resolved observation of hydrogen exchange in the micro-crystalline protein Crh. Our approach is based on the use of proton T2' -selective 1H-13C-13C correlation spectra for...
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] Exploring surfaces and cavities in lipoxygenase and other proteins by hyperpolarized
Exploring surfaces and cavities in lipoxygenase and other proteins by hyperpolarized xenon-129 NMR. Related Articles Exploring surfaces and cavities in lipoxygenase and other proteins by hyperpolarized xenon-129 NMR. J Am Chem Soc. 1999 Oct 13;121(40):9370-7 Authors: Bowers CR, Storhaug V, Webster CE, Bharatam J, Cottone A, Gianna R, Betsey K, Gaffney BJ This paper presents an exploratory study of the binding interactions of xenon with the surface of several different proteins in the solution and solid states using both conventional and...
nmrlearner Journal club 0 11-18-2010 08:31 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 03:31 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] 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...
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
[NMR paper] Identification and localization of bound internal water in the solution structure of
Identification and localization of bound internal water in the solution structure of interleukin 1 beta by heteronuclear three-dimensional 1H rotating-frame Overhauser 15N-1H multiple quantum coherence NMR spectroscopy. Related Articles Identification and localization of bound internal water in the solution structure of interleukin 1 beta by heteronuclear three-dimensional 1H rotating-frame Overhauser 15N-1H multiple quantum coherence NMR spectroscopy. Biochemistry. 1990 Jun 19;29(24):5671-6 Authors: Clore GM, Bax A, Wingfield PT, Gronenborn AM ...
nmrlearner Journal club 0 08-21-2010 10:48 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 07:04 AM.


Map