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 11-24-2010, 09:16 PM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 19,778
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 Rearrangement of charge-charge interactions in variant ubiquitins as detected by doub

Rearrangement of charge-charge interactions in variant ubiquitins as detected by double-mutant cycles and NMR.

Related Articles Rearrangement of charge-charge interactions in variant ubiquitins as detected by double-mutant cycles and NMR.

J Mol Biol. 2003 Sep 26;332(4):927-36

Authors: Sundd M, Robertson AD

Previous studies of ubiquitin disclosed numerous charge-charge interactions on the protein's surface. To investigate how neighboring residues influence the strength of these interactions, double-mutant cycles are combined with pK(a) determinations by 2D NMR. More specifically, the environment around the Asp21-Lys29 ion pair has been altered through mutations at position 25, which is an asparagine in mammalian ubiquitin and a positively-charged residue in many other ubiquitin-like proteins. The pK(a) value of Asp21 decreases by 0.4 to 0.7 pH unit when Asn25 is substituted with a positively charged residue, suggesting a new and favorable ion pair interaction between positions 21 and 25. However, analysis of double mutants reveals that the favorable interaction between Asp21 and Lys29 is weakened when position 25 is a positively charged residue. Interestingly, while the pK(a) value of His25 in the N25H variant agrees with model compound values, additional mutants reveal that this agreement is fortuitous, resulting from a balance of favorable and unfavorable interactions; similar results were observed previously for Glu34 in ubiquitin and His8 in staphylococcal nuclease. Ionizable groups may thus have pK(a) values similar to model compound values and yet still be involved in significant interactions with other protein groups. One surprising result of introducing positively charged residues at position 25 is a new interaction between Lys29 and Glu18, an interaction not present in wild-type ubiquitin. This unanticipated result illustrates a key advantage of using NMR to determine pK(a) values for many residues simultaneously in the variant proteins. Overall, the strength of an interaction between two residues at the surface of ubiquitin is sensitive to the identity of neighboring residues. The results also demonstrate that relatively conservative and common point mutations such as substitutions of polar with charged residues and vice versa can have effects on interactions beyond the site of mutation per se.

PMID: 12972262 [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 tweet] Q: Why is spin of the neutron included in NMR(nuclear magnetic resonance) ? It doesn't carry any charge? - A: http://tinyurl.com/3e3zjqj
Q: Why is spin of the neutron included in NMR(nuclear magnetic resonance) ? It doesn't carry any charge? - A: http://tinyurl.com/3e3zjqj Published by ikenedu (Iken.in) on 2011-05-19T09:13:48Z Source: Twitter
nmrlearner Twitter NMR 0 05-19-2011 09:40 AM
Solid-State NMR Study of the Charge-Transfer Complex between Ubiquinone-8 and Disulfide Bond Generating Membrane Protein DsbB.
Solid-State NMR Study of the Charge-Transfer Complex between Ubiquinone-8 and Disulfide Bond Generating Membrane Protein DsbB. Solid-State NMR Study of the Charge-Transfer Complex between Ubiquinone-8 and Disulfide Bond Generating Membrane Protein DsbB. J Am Chem Soc. 2011 Mar 4; Authors: Tang M, Sperling LJ, Berthold DA, Nesbitt AE, Gennis RB, Rienstra CM Ubiquinone (Coenzyme Q) plays an important role in the mitochondrial respiratory chain and also acts as an antioxidant in its reduced form, protecting cellular membranes from peroxidation....
nmrlearner Journal club 0 03-08-2011 01:40 PM
Solid-State NMR Study of the Charge-Transfer Complex between Ubiquinone-8 and Disulfide Bond Generating Membrane Protein DsbB
Solid-State NMR Study of the Charge-Transfer Complex between Ubiquinone-8 and Disulfide Bond Generating Membrane Protein DsbB Ming Tang, Lindsay J. Sperling, Deborah A. Berthold, Anna E. Nesbitt, Robert B. Gennis and Chad M. Rienstra http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jacsat/0/jacsat.ahead-of-print/ja107775w/aop/images/medium/ja-2010-07775w_0004.gif Journal of the American Chemical Society DOI: 10.1021/ja107775w http://feeds.feedburner.com/~ff/acs/jacsat?d=yIl2AUoC8zA http://feeds.feedburner.com/~r/acs/jacsat/~4/WdFsSgH1V7w
nmrlearner Journal club 0 03-05-2011 02:44 AM
[CNS Yahoo group] Double protonated His side chains have charge +1 independent of pH
Double protonated His side chains have charge +1 independent of pH Hi all, I am using ccpn/aria/cns combination for my structural work. I discovered a probably bad fact during the aria/cns structure calculation. In the ccpn More...
nmrlearner News from other NMR forums 0 01-20-2011 03:28 AM
[NMR paper] Large structure rearrangement of colicin ia channel domain after membrane binding fro
Large structure rearrangement of colicin ia channel domain after membrane binding from 2D 13C spin diffusion NMR. Related Articles Large structure rearrangement of colicin ia channel domain after membrane binding from 2D 13C spin diffusion NMR. J Am Chem Soc. 2005 May 4;127(17):6402-8 Authors: Luo W, Yao X, Hong M One of the main mechanisms of membrane protein folding is by spontaneous insertion into the lipid bilayer from the aqueous environment. The bacterial toxin, colicin Ia, is one such protein. To shed light on the conformational changes...
nmrlearner Journal club 0 11-25-2010 08:21 PM
[CSEARCH NMR-Database blog] CNMR-Predictions free of charge
CNMR-Predictions free of charge Chemspider has launched C13-NMR predictions using the NMRSHIFTDB-database system. An (again critical) evaluation can be found at http://nmrpredict.orc.univie.ac.at/chemspider_nmrshiftdb.html I strongly recommend to take a textbook on Carbon-NMR and to rerun the examples I have shown on my webpage - otherwise you won't believe ! Before somebody starts a 'blog-war', please convince me that 1000's of literature citations claiming that a terminal CH3 in an alkyl-chain resonates at 14ppm, are wrong - I will immediately publish here an "Erratum".
nmrlearner News from NMR blogs 0 08-22-2010 02:09 AM
[CSEARCH NMR-Database blog] CNMR-Predictions free of charge
CNMR-Predictions free of charge Chemspider has launched C13-NMR predictions using the NMRSHIFTDB-database system. An (again critical) evaluation can be found at http://nmrpredict.orc.univie.ac.at/chemspider_nmrshiftdb.html I strongly recommend to take a textbook on Carbon-NMR and to rerun the examples I have shown on my webpage - otherwise you won't believe ! Before somebody starts a 'blog-war', please convince me that 1000's of literature citations claiming that a terminal CH3 in an alkyl-chain resonates at 14ppm, are wrong - I will immediately publish here an "Erratum".
nmrlearner News from NMR blogs 0 08-22-2010 02:08 AM
[CSEARCH NMR-Database blog] CNMR-Predictions free of charge
CNMR-Predictions free of charge Chemspider has launched C13-NMR predictions using the NMRSHIFTDB-database system. An (again critical) evaluation can be found at http://nmrpredict.orc.univie.ac.at/chemspider_nmrshiftdb.html I strongly recommend to take a textbook on Carbon-NMR and to rerun the examples I have shown on my webpage - otherwise you won't believe ! Before somebody starts a 'blog-war', please convince me that 1000's of literature citations claiming that a terminal CH3 in an alkyl-chain resonates at 14ppm, are wrong - I will immediately publish here an "Erratum".
nmrlearner News from NMR blogs 0 08-22-2010 02:07 AM


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 - 2020, 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 08:33 PM.


Map