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, 03:01 AM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 17,583
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 analysis of the residual structure in the denatured state of an unusual mutant of

NMR analysis of the residual structure in the denatured state of an unusual mutant of staphylococcal nuclease.

Related Articles NMR analysis of the residual structure in the denatured state of an unusual mutant of staphylococcal nuclease.

Structure. 1993 Oct 15;1(2):121-34

Authors: Shortle D, Abeygunawardana C

BACKGROUND: Staphylococcal nuclease is a well-developed model system for analyzing the effects of mutations on protein folding and stability. Substitution of glycine 88 with valine (Gly88Val) destabilizes staphylococcal nuclease by 1.0 kcal mole-1 and reduces its sensitivity to the denaturant guanidine hydrochloride, a phenomenon which may indicate an increase in residual structure in the denatured state. To assess its effects on denatured state structure, the Gly88Val mutation was incorporated into a 136 residue nonsense fragment which has been developed as a model of the wild type denatured state. RESULTS: Application of two- and three-dimensional NMR spectroscopy to the Gly88Val fragment uniformly labeled with 15N and 13C has led to the assignment of 93 of the 136 residues. Comparison of chemical shifts of backbone resonances to those of wild type native nuclease, analysis of the secondary shifts of the assigned resonances and nuclear Overhauser effects involving backbone protons indicate that, unlike the wild type fragment, most if not all of the five-stranded beta-barrel structure persists in this denatured state. CONCLUSION: One major effect of the Gly88Val mutation is to perturb the cooperative breakdown of the folded conformation, leading to a denatured state which is both more ordered and more stable than that formed by the wild type sequence. Since the equilibrium between the native and denatured states depends on the free energy difference between them, stabilization of the denatured state by the Gly88Val mutation indirectly destabilizes the native state.

PMID: 8069625 [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
Chemical Shifts for the Unusual DNA Structure in Pf1 Bacteriophage from Dynamic-Nuclear-Polarization-Enhanced Solid-State NMR Spectroscopy
Chemical Shifts for the Unusual DNA Structure in Pf1 Bacteriophage from Dynamic-Nuclear-Polarization-Enhanced Solid-State NMR Spectroscopy Ivan V. Sergeyev, Loren A. Day, Amir Goldbourt and Ann E. McDermott http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jacsat/0/jacsat.ahead-of-print/ja2043062/aop/images/medium/ja-2011-043062_0007.gif Journal of the American Chemical Society DOI: 10.1021/ja2043062 http://feeds.feedburner.com/~ff/acs/jacsat?d=yIl2AUoC8zA http://feeds.feedburner.com/~r/acs/jacsat/~4/EeKgo5vg1K0
nmrlearner Journal club 0 11-30-2011 10:45 PM
Chemical Shifts for the Unusual DNA Structure in Pf1 Bacteriophage from Dynamic-Nuclear-Polarization-Enhanced Solid-State NMR Spectroscopy.
Chemical Shifts for the Unusual DNA Structure in Pf1 Bacteriophage from Dynamic-Nuclear-Polarization-Enhanced Solid-State NMR Spectroscopy. Chemical Shifts for the Unusual DNA Structure in Pf1 Bacteriophage from Dynamic-Nuclear-Polarization-Enhanced Solid-State NMR Spectroscopy. J Am Chem Soc. 2011 Aug 22; Authors: Sergeyev IV, Day LA, Goldbourt A, McDermott AE Abstract Solid state NMR spectra, including dynamic nuclear polarization enhanced 400 MHz spectra acquired at 100K, as well as non-DNP spectra at a variety of field strengths and...
nmrlearner Journal club 0 08-23-2011 04:03 PM
NMR insights into the core of GED assembly by H/D exchange coupled with DMSO dissociation and analysis of the denatured state.
NMR insights into the core of GED assembly by H/D exchange coupled with DMSO dissociation and analysis of the denatured state. NMR insights into the core of GED assembly by H/D exchange coupled with DMSO dissociation and analysis of the denatured state. J Mol Biol. 2011 Feb 4;405(5):1202-14 Authors: Chakraborty S, Hosur RV GTPase effector domain (GED) of dynamin forms megadalton-sized assembly in vitro, rendering its structural characterization highly challenging. To probe the core of the GED assembly, we performed H/D exchange in native...
nmrlearner Journal club 0 02-25-2011 08:54 PM
[NMR paper] Residual dipolar couplings in NMR structure analysis.
Residual dipolar couplings in NMR structure analysis. Related Articles Residual dipolar couplings in NMR structure analysis. Annu Rev Biophys Biomol Struct. 2004;33:387-413 Authors: Lipsitz RS, Tjandra N Residual dipolar couplings (RDCs) have recently emerged as a new tool in nuclear magnetic resonance (NMR) with which to study macromolecular structure and function in a solution environment. RDCs are complementary to the more conventional use of NOEs to provide structural information. While NOEs are local-distance restraints, RDCs provide...
nmrlearner Journal club 0 11-24-2010 09:25 PM
[NMR paper] Solid-state NMR studies of the secondary structure of a mutant prion protein fragment
Solid-state NMR studies of the secondary structure of a mutant prion protein fragment of 55 residues that induces neurodegeneration. Related Articles Solid-state NMR studies of the secondary structure of a mutant prion protein fragment of 55 residues that induces neurodegeneration. Proc Natl Acad Sci U S A. 2001 Sep 25;98(20):11686-90 Authors: Laws DD, Bitter HM, Liu K, Ball HL, Kaneko K, Wille H, Cohen FE, Prusiner SB, Pines A, Wemmer DE The secondary structure of a 55-residue fragment of the mouse prion protein, MoPrP(89-143), was studied in...
nmrlearner Journal club 0 11-19-2010 08:44 PM
[NMR paper] NMR characterization of residual structure in the denatured state of protein L.
NMR characterization of residual structure in the denatured state of protein L. Related Articles NMR characterization of residual structure in the denatured state of protein L. J Mol Biol. 2000 Jun 23;299(5):1341-51 Authors: Yi Q, Scalley-Kim ML, Alm EJ, Baker D Triple-resonance NMR experiments were used to assign the (13)C(alpha), (13)C(beta), (15)N and NH resonances for all the residues in the denatured state of a destabilized protein L variant in 2 M guanidine. The chemical shifts of most resonances were very close to their random coil...
nmrlearner Journal club 0 11-18-2010 09:15 PM
[NMR paper] Structure and dynamics of the acid-denatured molten globule state of alpha-lactalbumi
Structure and dynamics of the acid-denatured molten globule state of alpha-lactalbumin: a two-dimensional NMR study. Related Articles Structure and dynamics of the acid-denatured molten globule state of alpha-lactalbumin: a two-dimensional NMR study. Biochemistry. 1993 Feb 23;32(7):1707-18 Authors: Alexandrescu AT, Evans PA, Pitkeathly M, Baum J, Dobson CM Two-dimensional 1H-NMR spectroscopy has been used to study the acid-denatured molten globule (A-state) of alpha-lactalbumin. The NMR spectra show that chemical shift dispersion is limited...
nmrlearner Journal club 0 08-21-2010 11:53 PM
[NMR paper] NMR determination of residual structure in a urea-denatured protein, the 434-represso
NMR determination of residual structure in a urea-denatured protein, the 434-repressor. Related Articles NMR determination of residual structure in a urea-denatured protein, the 434-repressor. Science. 1992 Sep 11;257(5076):1559-63 Authors: Neri D, Billeter M, Wider G, Wüthrich K A nuclear magnetic resonance (NMR) structure determination is reported for the polypeptide chain of a globular protein in strongly denaturing solution. Nuclear Overhauser effect (NOE) measurements with a 7 molar urea solution of the amino-terminal 63-residue domain...
nmrlearner Journal club 0 08-21-2010 11:45 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 03:46 PM.


Map