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 11-24-2010, 08:58 PM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 23,777
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 Residue-specific millisecond to microsecond fluctuations in bacteriorhodopsin induced

Residue-specific millisecond to microsecond fluctuations in bacteriorhodopsin induced by disrupted or disorganized two-dimensional crystalline lattice, through modified lipid-helix and helix-helix interactions, as revealed by 13C NMR.

Related Articles Residue-specific millisecond to microsecond fluctuations in bacteriorhodopsin induced by disrupted or disorganized two-dimensional crystalline lattice, through modified lipid-helix and helix-helix interactions, as revealed by 13C NMR.

Biochim Biophys Acta. 2002 Sep 20;1565(1):97-106

Authors: Saitô H, Tsuchida T, Ogawa K, Arakawa T, Yamaguchi S, Tuzi S

We have recorded 13C NMR spectra of [3-13C]-, [1-13C]Ala-, and [1-13C]Val-labeled bacteriorhodopsin (bR), W80L and W12L mutants and bacterio-opsin (bO) from retinal-deficient E1001 strain, in order to examine the possibility of their millisecond to microsecond local fluctuations with correlation time in the order of 10(-4) to 10(-5) s, induced or prevented by disruption or assembly of two-dimensional (2D) crystalline lattice, respectively, at ambient temperature. The presence of disrupted or disorganized 2D lattice for W12L, W80L and bO from E1001 strain was readily visualized by increased relative proportions of surrounding lipids per protein, together with their broadened 13C NMR signals of transmembrane alpha-helices and loops in [3-13C]Ala-labeled proteins, with reference to those of wild-type. In contrast, 13C CP-MAS NMR spectra of [1-13C]Ala- and Val-labeled these mutants were almost completely suppressed, owing to the presence of fluctuations with time scale of 10(-4) s interfered with magic angle spinning. In particular, 13C NMR signals of [1-13C]Ala-labeled transmembrane alpha-helices of wild-type were almost completely suppressed at the interface between the surface and inner part (up to 8.7 A deep from the surface) with reference to those of the similarly suppressed peaks by Mn(2+)-induced accelerated spin-spin relaxation rate. Such fluctuation-induced suppression of 13C NMR peaks from the interfacial regions, however, was less significant for [1-13C]Val-labeled proteins, because fluctuation motions in Val residues with bulky side-chains at the C(alpha) moiety were modified to those of longer correlation time (>10(-4) s), if any, by residue-specific manner. To support this view, we found that such suppressed 13C NMR signals of [1-13C]Ala-labeled peaks in the wild-type were recovered for D85N and bO in which correlation times of fluctuations were shifted to the order of 10(-5) s due to modified helix-helix interactions as previously pointed out [Biochemistry, 39 (2000) 14472; J. Biochem. (Tokyo) 127 (2000) 861].

PMID: 12225857 [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
Mapping residue-specific contacts of polymyxin B with lipopolysaccharide by saturation transfer difference NMR: insights into outer-membrane disruption and endotoxin neutralization.
Mapping residue-specific contacts of polymyxin B with lipopolysaccharide by saturation transfer difference NMR: insights into outer-membrane disruption and endotoxin neutralization. Mapping residue-specific contacts of polymyxin B with lipopolysaccharide by saturation transfer difference NMR: insights into outer-membrane disruption and endotoxin neutralization. Biopolymers. 2011;96(3):273-87 Authors: Bhunia A, Bhattacharjya S Abstract High-resolution interactions studies of molecules with lipopolysaccharide (LPS) or endotoxin are...
nmrlearner Journal club 0 09-21-2011 03:31 PM
[NMR paper] Millisecond protein folding studied by NMR spectroscopy.
Millisecond protein folding studied by NMR spectroscopy. Related Articles Millisecond protein folding studied by NMR spectroscopy. Protein Pept Lett. 2005 Feb;12(2):139-46 Authors: Zeeb M, Balbach J Proteins are involved in virtually every biological process and in order to function, it is necessary for these polypeptide chains to fold into the unique, native conformation. This folding process can take place rapidly. NMR line shape analyses and transverse relaxation measurements allow protein folding studies on a microsecond-to-millisecond...
nmrlearner Journal club 0 11-24-2010 11:14 PM
[NMR paper] Microsecond timescale backbone conformational dynamics in ubiquitin studied with NMR
Microsecond timescale backbone conformational dynamics in ubiquitin studied with NMR R1rho relaxation experiments. Related Articles Microsecond timescale backbone conformational dynamics in ubiquitin studied with NMR R1rho relaxation experiments. Protein Sci. 2005 Mar;14(3):735-42 Authors: Massi F, Grey MJ, Palmer AG NMR spin relaxation experiments are used to characterize the dynamics of the backbone of ubiquitin. Chemical exchange processes affecting residues Ile 23, Asn 25, Thr 55, and Val 70 are characterized using on- and off-resonance...
nmrlearner Journal club 0 11-24-2010 11:14 PM
[NMR paper] Real-time NMR kinetic studies provide global and residue-specific information on the
Real-time NMR kinetic studies provide global and residue-specific information on the non-cooperative unfolding of the beta-trefoil protein, interleukin-1beta. Related Articles Real-time NMR kinetic studies provide global and residue-specific information on the non-cooperative unfolding of the beta-trefoil protein, interleukin-1beta. J Mol Biol. 2003 May 2;328(3):693-703 Authors: Roy M, Jennings PA The interleukin-1beta (IL-1beta) structural motif is a beta-trefoil super fold created by six two-stranded beta-hairpins. Turns are thus...
nmrlearner Journal club 0 11-24-2010 09:01 PM
[NMR paper] Residue-specific real-time NMR diffusion experiments define the association states of
Residue-specific real-time NMR diffusion experiments define the association states of proteins during folding. Related Articles Residue-specific real-time NMR diffusion experiments define the association states of proteins during folding. J Am Chem Soc. 2002 Jun 19;124(24):7156-62 Authors: Buevich AV, Baum J Characterizing the association states of proteins during folding is critical for understanding the nature of protein-folding intermediates and protein-folding pathways, protein aggregation, and disease-related aggregation. To study the...
nmrlearner Journal club 0 11-24-2010 08:49 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] A residue-specific NMR view of the non-cooperative unfolding of a molten globule.
A residue-specific NMR view of the non-cooperative unfolding of a molten globule. Related Articles A residue-specific NMR view of the non-cooperative unfolding of a molten globule. Nat Struct Biol. 1997 Aug;4(8):630-4 Authors: Schulman BA, Kim PS, Dobson CM, Redfield C Molten globules are partially folded forms of proteins that are thought to be general intermediates in protein folding. Nonetheless, there is limited structural information about such species because they possess conformational heterogeneity and complex dynamical properties that...
nmrlearner Journal club 0 08-22-2010 05:08 PM
[NMR paper] High resolution 13C-solid state NMR of bacteriorhodopsin: assignment of specific aspa
High resolution 13C-solid state NMR of bacteriorhodopsin: assignment of specific aspartic acids and structural implications of single site mutations. Related Articles High resolution 13C-solid state NMR of bacteriorhodopsin: assignment of specific aspartic acids and structural implications of single site mutations. Eur Biophys J. 1990;18(1):17-24 Authors: Engelhard M, Hess B, Metz G, Kreutz W, Siebert F, Soppa J, Oesterhelt D Three mutant strains of Halobacterium sp. GRB with the site of mutation in the bacterioopsin gene (PM 326:...
nmrlearner Journal club 0 08-21-2010 10:48 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 03:08 PM.


Map