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, 03:41 AM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 23,135
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 determinants of protein dynamics: analysis of 15N NMR relaxation measureme

Structural determinants of protein dynamics: analysis of 15N NMR relaxation measurements for main-chain and side-chain nuclei of hen egg white lysozyme.

Related Articles Structural determinants of protein dynamics: analysis of 15N NMR relaxation measurements for main-chain and side-chain nuclei of hen egg white lysozyme.

Biochemistry. 1995 Mar 28;34(12):4041-55

Authors: Buck M, Boyd J, Redfield C, MacKenzie DA, Jeenes DJ, Archer DB, Dobson CM

15N-labeled hen lysozyme has been studied by 2D and 3D NMR in order to characterize its dynamic behavior. The resonances of all main-chain amide nitrogen atoms were assigned, as were resonances of nitrogen atoms in 28 side chains. Relaxation measurements for the main-chain and arginine and tryptophan side-chain 15N nuclei used standard methods, and those for the 15N nuclei of asparagine and glutamine side chains used pulse sequences designed to remove unwanted relaxation pathways in the NH2 groups. The calculated order parameters (S2) show that the majority of main-chain amides undergo only small amplitude librational motions on a fast time scale (S2 > or = 0.8). Increased main-chain motion (0.5 < S2 < 0.8) is observed for a total of 19 residues located at the C-terminus, in loop and turn regions, and in the first strand of the main beta-sheet. Order parameters derived for the side chains range from 0.05 to 0.9; five of the six tryptophan residues have high order parameters (S2 > or = 0.8), consistent with their location in the closely packed core of the protein, whereas the order parameters between 0.05 and 0.3 for arginine residues confirm increased side-chain mobility at the protein surface. Order parameters for the side chains of asparagine and glutamine residues range from 0.2 to 0.8; high values are found for side chains that have low solvent accessible surfaces and well-defined chi 1 values, as measured by 3J alpha beta coupling constants. Many of the main-chain and side-chain groups with low order parameters have higher than average temperature factors in X-ray crystal structures and increased positional uncertainty in NMR solution structures. They also tend to lack persistent hydrogen bond interactions and protection against amide hydrogen exchange. The most significant correlations are found between residues with low order parameters and high surface accessibility in both crystal and solution structures. The results suggest that a lack of van der Waals contacts is a major determinant of side-chain and main-chain mobility in proteins.

PMID: 7696270 [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
Conformational dynamics of recoverin's Ca(2+) -myristoyl switch probed by (15) N NMR relaxation dispersion and chemical shift analysis.
Conformational dynamics of recoverin's Ca(2+) -myristoyl switch probed by (15) N NMR relaxation dispersion and chemical shift analysis. Conformational dynamics of recoverin's Ca(2+) -myristoyl switch probed by (15) N NMR relaxation dispersion and chemical shift analysis. Proteins. 2011 Feb 16; Authors: Xu X, Ishima R, Ames JB Recoverin, a member of the neuronal calcium sensor (NCS) branch of the calmodulin superfamily, serves as a calcium sensor in retinal rod cells. Ca(2+) -induced conformational changes in recoverin promote extrusion of its...
nmrlearner Journal club 0 04-06-2011 10:54 AM
Structure, Dynamics, and Kinetics of Weak Protein-Protein Complexes from NMR Spin Relaxation Measurements of Titrated Solutions.
Structure, Dynamics, and Kinetics of Weak Protein-Protein Complexes from NMR Spin Relaxation Measurements of Titrated Solutions. Structure, Dynamics, and Kinetics of Weak Protein-Protein Complexes from NMR Spin Relaxation Measurements of Titrated Solutions. Angew Chem Int Ed Engl. 2011 Mar 18; Authors: Salmon L, Ortega Roldan JL, Lescop E, Licinio A, van Nuland N, Jensen MR, Blackledge M
nmrlearner Journal club 0 03-23-2011 05:41 PM
Integrated Computational Approach to the Analysis of NMR Relaxation in Proteins: Application to ps-ns Main Chain (15)N-(1)H and Global Dynamics of the Rho GTPase Binding Domain of Plexin-B1.
Integrated Computational Approach to the Analysis of NMR Relaxation in Proteins: Application to ps-ns Main Chain (15)N-(1)H and Global Dynamics of the Rho GTPase Binding Domain of Plexin-B1. Integrated Computational Approach to the Analysis of NMR Relaxation in Proteins: Application to ps-ns Main Chain (15)N-(1)H and Global Dynamics of the Rho GTPase Binding Domain of Plexin-B1. J Phys Chem B. 2010 Dec 10; Authors: Zerbetto M, Buck M, Meirovitch E, Polimeno A
nmrlearner Journal club 0 12-15-2010 12:03 PM
[NMR paper] QSAR-by-NMR: quantitative insights into structural determinants for binding affinity
QSAR-by-NMR: quantitative insights into structural determinants for binding affinity by analysis of 1H/15N chemical shift differences in MMP-3 ligands. Related Articles QSAR-by-NMR: quantitative insights into structural determinants for binding affinity by analysis of 1H/15N chemical shift differences in MMP-3 ligands. Bioorg Med Chem Lett. 2005 Apr 1;15(7):1779-83 Authors: Matter H, Schudok M, Elshorst B, Jacobs DM, Saxena K, Kogler H A novel strategy is applied to obtain quantitative insights on factors influencing biological affinity in...
nmrlearner Journal club 0 11-25-2010 08:21 PM
[NMR paper] Reorientational eigenmode dynamics: a combined MD/NMR relaxation analysis method for
Reorientational eigenmode dynamics: a combined MD/NMR relaxation analysis method for flexible parts in globular proteins. Related Articles Reorientational eigenmode dynamics: a combined MD/NMR relaxation analysis method for flexible parts in globular proteins. J Am Chem Soc. 2001 Aug 1;123(30):7305-13 Authors: Prompers JJ, Brüschweiler R An approach is presented for the interpretation of heteronuclear NMR spin relaxation data in mobile protein parts in terms of reorientational eigenmode dynamics. The method is based on the covariance matrix of...
nmrlearner Journal club 0 11-19-2010 08:44 PM
[NMR paper] Local structural plasticity of the prion protein. Analysis of NMR relaxation dynamics
Local structural plasticity of the prion protein. Analysis of NMR relaxation dynamics. Related Articles Local structural plasticity of the prion protein. Analysis of NMR relaxation dynamics. Biochemistry. 2001 Mar 6;40(9):2743-53 Authors: Viles JH, Donne D, Kroon G, Prusiner SB, Cohen FE, Dyson HJ, Wright PE A template-assisted conformational change of the cellular prion protein (PrP(C)) from a predominantly helical structure to an amyloid-type structure with a higher proportion of beta-sheet is thought to be the causative factor in prion...
nmrlearner Journal club 0 11-19-2010 08:32 PM
[NMR paper] Determinants of protein hyperthermostability: purification and amino acid sequence of
Determinants of protein hyperthermostability: purification and amino acid sequence of rubredoxin from the hyperthermophilic archaebacterium Pyrococcus furiosus and secondary structure of the zinc adduct by NMR. Related Articles Determinants of protein hyperthermostability: purification and amino acid sequence of rubredoxin from the hyperthermophilic archaebacterium Pyrococcus furiosus and secondary structure of the zinc adduct by NMR. Biochemistry. 1991 Nov 12;30(45):10885-95 Authors: Blake PR, Park JB, Bryant FO, Aono S, Magnuson JK, Eccleston E, Howard...
nmrlearner Journal club 0 08-21-2010 11:12 PM
[NMR paper] Determinants of protein hyperthermostability: purification and amino acid sequence of
Determinants of protein hyperthermostability: purification and amino acid sequence of rubredoxin from the hyperthermophilic archaebacterium Pyrococcus furiosus and secondary structure of the zinc adduct by NMR. Related Articles Determinants of protein hyperthermostability: purification and amino acid sequence of rubredoxin from the hyperthermophilic archaebacterium Pyrococcus furiosus and secondary structure of the zinc adduct by NMR. Biochemistry. 1991 Nov 12;30(45):10885-95 Authors: Blake PR, Park JB, Bryant FO, Aono S, Magnuson JK, Eccleston E, Howard...
nmrlearner Journal club 0 08-21-2010 11:12 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 - 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 01:50 AM.


Map