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, 08:32 PM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 23,700
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 What is the average conformation of bacteriophage T4 lysozyme in solution? A domain o

What is the average conformation of bacteriophage T4 lysozyme in solution? A domain orientation study using dipolar couplings measured by solution NMR.

Related Articles What is the average conformation of bacteriophage T4 lysozyme in solution? A domain orientation study using dipolar couplings measured by solution NMR.

J Mol Biol. 2001 May 11;308(4):745-64

Authors: Goto NK, Skrynnikov NR, Dahlquist FW, Kay LE

Lysozyme from T4 bacteriophage is comprised of two domains that are both involved in binding substrate. Although wild-type lysozyme has been exclusively crystallized in a closed form that is similar to the peptidoglycan-bound conformation, a more open structure is thought to be required for ligand binding. To determine the relative arrangement of domains within T4 lysozyme in the solution state, dipolar couplings were measured in several different dilute liquid crystalline media by solution NMR methods. The dipolar coupling data were analyzed with a domain orientation procedure described previously that utilizes high- resolution X-ray structures. The cleft between the domains is significantly larger in the average solution structure than what is observed in the X-ray structure of the ligand-free form of the protein (approximately 17 degrees closure from solution to X-ray structures). A comparison of the solution domain orientation with X-ray-derived structures in the protein data base shows that the solution structure resembles a crystal structure obtained for the M6I mutant. Dipolar couplings were also measured on the lysozyme mutant T21C/T142C, which was oxidized to form an inter-domain disulfide bond (T4SS). In this case, the inter-domain solution structure was found to be more closed than was observed in the crystal (approximately 11 degrees). Direct refinement of lysozyme crystal structures with the measured dipolar couplings using the program CNS, establishes that this degree of closure can be accommodated whilst maintaining the inter-domain cystine bond. The differences between the average solution conformations obtained using dipolar couplings and the crystal conformations for both forms of lysozyme investigated in this study illustrate the impact that crystal packing interactions can have on the arrangement of domains within proteins and the importance of alternative methods to X-ray crystallography for evaluating inter-domain structure.

PMID: 11350172 [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] Dynamics of xenon binding inside the hydrophobic cavity of pseudo-wild-type bacteriophage T4 lysozyme explored through xenon-based NMR spectroscopy.
Dynamics of xenon binding inside the hydrophobic cavity of pseudo-wild-type bacteriophage T4 lysozyme explored through xenon-based NMR spectroscopy. Related Articles Dynamics of xenon binding inside the hydrophobic cavity of pseudo-wild-type bacteriophage T4 lysozyme explored through xenon-based NMR spectroscopy. J Am Chem Soc. 2005 Aug 24;127(33):11676-83 Authors: Desvaux H, Dubois L, Huber G, Quillin ML, Berthault P, Matthews BW Wild-type bacteriophage T4 lysozyme contains a hydrophobic cavity with binding properties that have been...
nmrlearner Journal club 0 12-01-2010 06:56 PM
[NMR paper] NMR solution structure of the monomeric form of the bacteriophage lambda capsid stabi
NMR solution structure of the monomeric form of the bacteriophage lambda capsid stabilizing protein gpD. Related Articles NMR solution structure of the monomeric form of the bacteriophage lambda capsid stabilizing protein gpD. J Biomol NMR. 2005 Apr;31(4):351-6 Authors: Iwai H, Forrer P, Plückthun A, Güntert P
nmrlearner Journal club 0 11-25-2010 08:21 PM
[NMR paper] NMR structure of Citrobacter freundii AmpD, comparison with bacteriophage T7 lysozyme
NMR structure of Citrobacter freundii AmpD, comparison with bacteriophage T7 lysozyme and homology with PGRP domains. Related Articles NMR structure of Citrobacter freundii AmpD, comparison with bacteriophage T7 lysozyme and homology with PGRP domains. J Mol Biol. 2003 Apr 4;327(4):833-42 Authors: Liepinsh E, Généreux C, Dehareng D, Joris B, Otting G AmpD is a bacterial amidase involved in the recycling of cell-wall fragments in Gram-negative bacteria. Inactivation of AmpD leads to derepression of beta-lactamase expression, presenting a major...
nmrlearner Journal club 0 11-24-2010 09:01 PM
[NMR paper] Conformation of the cytoplasmic domain of phospholamban by NMR and CD.
Conformation of the cytoplasmic domain of phospholamban by NMR and CD. Related Articles Conformation of the cytoplasmic domain of phospholamban by NMR and CD. Mol Membr Biol. 1994 Oct-Dec;11(4):263-9 Authors: Hubbard JA, MacLachlan LK, Meenan E, Salter CJ, Reid DG, Lahouratate P, Humphries J, Stevens N, Bell D, Neville WA Nuclear magnetic resonance (NMR) and circular dichroism (CD) spectroscopy have been used to characterize the conformation of the putative cytoplasmic domain of phospholamban (PLB), an oligomeric membrane-bound protein which...
nmrlearner Journal club 0 08-22-2010 03:29 AM
[NMR paper] Exploring the DNA binding domain of gene V protein encoded by bacteriophage M13 with
Exploring the DNA binding domain of gene V protein encoded by bacteriophage M13 with the aid of spin-labeled oligonucleotides in combination with 1H-NMR. Related Articles Exploring the DNA binding domain of gene V protein encoded by bacteriophage M13 with the aid of spin-labeled oligonucleotides in combination with 1H-NMR. Biochemistry. 1993 Sep 14;32(36):9407-16 Authors: Folkers PJ, van Duynhoven JP, van Lieshout HT, Harmsen BJ, van Boom JH, Tesser GI, Konings RN, Hilbers CW The DNA binding domain of the single-stranded DNA binding protein...
nmrlearner Journal club 0 08-22-2010 03:01 AM
[NMR paper] The influence of hydration on the conformation of lysozyme studied by solid-state 13C
The influence of hydration on the conformation of lysozyme studied by solid-state 13C-NMR spectroscopy. Related Articles The influence of hydration on the conformation of lysozyme studied by solid-state 13C-NMR spectroscopy. Biopolymers. 1993 Apr;33(4):513-9 Authors: Gregory RB, Gangoda M, Gilpin RK, Su W 13C proton decoupled cross-polarization magic-angle spinning nmr spectra of lysozyme are reported as a function of hydration. Increases in hydration level enhance the resolution of the spectra, particularly in the aliphatic region, but has no...
nmrlearner Journal club 0 08-21-2010 11:53 PM
[NMR paper] Analysis of phi and chi 1 torsion angles for hen lysozyme in solution from 1H NMR spi
Analysis of phi and chi 1 torsion angles for hen lysozyme in solution from 1H NMR spin-spin coupling constants. Related Articles Analysis of phi and chi 1 torsion angles for hen lysozyme in solution from 1H NMR spin-spin coupling constants. Biochemistry. 1991 Jan 29;30(4):986-96 Authors: Smith LJ, Sutcliffe MJ, Redfield C, Dobson CM Three-bond 3JHN alpha coupling constants have been determined for 106 residues and 3J alpha beta coupling constants have been measured for 57 residues of the 129-residue protein hen egg white lysozyme. These NMR...
nmrlearner Journal club 0 08-21-2010 11:16 PM
[NMR paper] Assignment of the backbone 1H and 15N NMR resonances of bacteriophage T4 lysozyme.
Assignment of the backbone 1H and 15N NMR resonances of bacteriophage T4 lysozyme. Related Articles Assignment of the backbone 1H and 15N NMR resonances of bacteriophage T4 lysozyme. Biochemistry. 1990 Jul 10;29(27):6341-62 Authors: McIntosh LP, Wand AJ, Lowry DF, Redfield AG, Dahlquist FW The proton and nitrogen (15NH-H alpha-H beta) resonances of bacteriophage T4 lysozyme were assigned by 15N-aided 1H NMR. The assignments were directed from the backbone amide 1H-15N nuclei, with the heteronuclear single-multiple-quantum coherence (HSMQC)...
nmrlearner Journal club 0 08-21-2010 11:04 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 09:17 AM.


Map