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 11-19-2010, 08:29 PM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 23,775
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 Structural preordering in the N-terminal region of ribosomal protein S4 revealed by h

Structural preordering in the N-terminal region of ribosomal protein S4 revealed by heteronuclear NMR spectroscopy.

Related Articles Structural preordering in the N-terminal region of ribosomal protein S4 revealed by heteronuclear NMR spectroscopy.

Biochemistry. 2000 Nov 7;39(44):13602-13

Authors: Sayers EW, Gerstner RB, Draper DE, Torchia DA

Protein S4, a component of the 30S subunit of the prokaryotic ribosome, is one of the first proteins to interact with rRNA in the process of ribosome assembly and is known to be involved in the regulation of this process. While the structure of the C-terminal 158 residues of Bacillus stearothermophilus S4 has been solved by both X-ray crystallography and NMR, that of the N-terminal 41 residues is unknown. Evidence suggests that the N-terminus is necessary both for the assembly of functional ribosomes and for full binding to 16S RNA, and so we present NMR data collected on the full-length protein (200 aa). Our data indicate that the addition of the N-terminal residues does not significantly change the structure of the C-terminal 158 residues. The data further indicate that the N-terminus is highly flexible in solution, without discernible secondary structure. Nevertheless, structure calculations based on nuclear Overhauser effect spectroscopic data combined with (15)N relaxation data revealed that two short segments in the N-terminus, S(12)RRL(15) and P(30)YPP(33), adopt transiently ordered states in solution. The major conformation of S(12)RRL(15) appears to orient the arginine side chains outward toward the solvent in a parallel fashion, while that of P(30)YPP(33) forms a nascent turn of a polyproline II helix. These segments contain residues that are highly conserved across many prokaryotic species, and thus they are reasonable candidates respectively for sites of interaction with RNA and other ribosomal proteins within the intact ribosome.

PMID: 11063598 [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
Insulin-like growth factor binding protein-2: NMR analysis and structural characterization of the N-terminal domain.
Insulin-like growth factor binding protein-2: NMR analysis and structural characterization of the N-terminal domain. Insulin-like growth factor binding protein-2: NMR analysis and structural characterization of the N-terminal domain. Biochimie. 2011 Sep 22; Authors: Galea CA, Mobli M, McNeil KA, Mulhern TD, Wallace JC, King GF, Forbes BE, Norton RS Abstract The insulin-like growth factor binding proteins are a family of six proteins (IGFBP-1 to 6) that bind insulin-like growth factors-I and -II (IGF-I/II) with high affinity. In addition...
nmrlearner Journal club 0 09-30-2011 06:00 AM
Insulin-like growth factor binding protein-2: NMR analysis and structural characterization of the N-terminal domain.
Insulin-like growth factor binding protein-2: NMR analysis and structural characterization of the N-terminal domain. Insulin-like growth factor binding protein-2: NMR analysis and structural characterization of the N-terminal domain. Biochimie. 2011 Sep 22; Authors: Galea CA, Mobli M, McNeil KA, Mulhern TD, Wallace JC, King GF, Forbes BE, Norton RS Abstract The insulin-like growth factor binding proteins are a family of six proteins (IGFBP-1 to 6) that bind insulin-like growth factors-I and -II (IGF-I/II) with high affinity. In...
nmrlearner Journal club 0 09-30-2011 05:59 AM
[NMR paper] Structural model of the UbcH5B/CNOT4 complex revealed by combining NMR, mutagenesis,
Structural model of the UbcH5B/CNOT4 complex revealed by combining NMR, mutagenesis, and docking approaches. Related Articles Structural model of the UbcH5B/CNOT4 complex revealed by combining NMR, mutagenesis, and docking approaches. Structure. 2004 Apr;12(4):633-44 Authors: Dominguez C, Bonvin AM, Winkler GS, van Schaik FM, Timmers HT, Boelens R The protein CNOT4 possesses an N-terminal RING finger domain that acts as an E3 ubiquitin ligase and specifically interacts with UbcH5B, a ubiquitin-conjugating enzyme. The structure of the CNOT4...
nmrlearner Journal club 0 11-24-2010 09:51 PM
[NMR paper] Structural features of the binding site for ribosomal protein S8 in Escherichia coli
Structural features of the binding site for ribosomal protein S8 in Escherichia coli 16S rRNA defined using NMR spectroscopy. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--highwire.stanford.edu-icons-externalservices-pubmed-custom-pnas_full_free.gif http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www.pubmedcentral.nih.gov-corehtml-pmc-pmcgifs-pubmed-pmc.gif Related Articles Structural features of the binding site for ribosomal protein S8 in Escherichia coli 16S rRNA defined using NMR spectroscopy. Proc Natl Acad Sci U S A. 1997 Mar 18;94(6):2139-44 ...
nmrlearner Journal club 0 08-22-2010 03:31 PM
[NMR paper] Structural features of the binding site for ribosomal protein S8 in Escherichia coli
Structural features of the binding site for ribosomal protein S8 in Escherichia coli 16S rRNA defined using NMR spectroscopy. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--highwire.stanford.edu-icons-externalservices-pubmed-custom-pnas_full_free.gif http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www.pubmedcentral.nih.gov-corehtml-pmc-pmcgifs-pubmed-pmc.gif Related Articles Structural features of the binding site for ribosomal protein S8 in Escherichia coli 16S rRNA defined using NMR spectroscopy. Proc Natl Acad Sci U S A. 1997 Mar 18;94(6):2139-44 ...
nmrlearner Journal club 0 08-22-2010 03:03 PM
[NMR paper] Determination of the structure of the N-terminal splice region of the cyclic AMP-spec
Determination of the structure of the N-terminal splice region of the cyclic AMP-specific phosphodiesterase RD1 (RNPDE4A1) by 1H NMR and identification of the membrane association domain using chimeric constructs. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--highwire.stanford.edu-icons-externalservices-pubmed-standard-jbc_full_free.gif Related Articles Determination of the structure of the N-terminal splice region of the cyclic AMP-specific phosphodiesterase RD1 (RNPDE4A1) by 1H NMR and identification of the membrane association domain using chimeric constructs. ...
nmrlearner Journal club 0 08-22-2010 02:20 PM
[NMR paper] Structural and dynamic characterization of the phosphotyrosine binding region of a Sr
Structural and dynamic characterization of the phosphotyrosine binding region of a Src homology 2 domain--phosphopeptide complex by NMR relaxation, proton exchange, and chemical shift approaches. Related Articles Structural and dynamic characterization of the phosphotyrosine binding region of a Src homology 2 domain--phosphopeptide complex by NMR relaxation, proton exchange, and chemical shift approaches. Biochemistry. 1995 Sep 12;34(36):11353-62 Authors: Pascal SM, Yamazaki T, Singer AU, Kay LE, Forman-Kay JD Arginine side chains are often...
nmrlearner Journal club 0 08-22-2010 03:50 AM
[NMR paper] The carboxyl-terminal region of human interferon gamma is important for biological ac
The carboxyl-terminal region of human interferon gamma is important for biological activity: mutagenic and NMR analysis. Related Articles The carboxyl-terminal region of human interferon gamma is important for biological activity: mutagenic and NMR analysis. Protein Eng. 1991 Feb;4(3):335-41 Authors: Lundell D, Lunn C, Dalgarno D, Fossetta J, Greenberg R, Reim R, Grace M, Narula S Deletion of nine amino acids from the carboxyl terminus of human IFN gamma (residues 138--146; LFRGRRASQ) resulted in a 7-fold increase in specific antiviral...
nmrlearner Journal club 0 08-21-2010 11:16 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 04:18 PM.


Map