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 05-04-2013, 09:18 PM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 23,732
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 Relaxation in Proteins with Fast Internal Motions and Slow Conformational Exchange: Model Free Framework and Markov State Simulations.

NMR Relaxation in Proteins with Fast Internal Motions and Slow Conformational Exchange: Model Free Framework and Markov State Simulations.

NMR Relaxation in Proteins with Fast Internal Motions and Slow Conformational Exchange: Model Free Framework and Markov State Simulations.

J Phys Chem B. 2013 May 2;

Authors: Xia J, Deng NJ, Levy RM

Abstract
Calculating NMR relaxation effects for proteins with dynamics on multiple timescales generally requires very long trajectories based on conventional molecular dynamics simulations. In this report, we have built Markov state models from multiple MD trajectories and used the resulting MSM to capture the very fast internal motions of the protein within a free energy basin on a time scale up to hundreds of picoseconds and the more than three orders of magnitude slower conformational exchange between macrostates. To interpret the relaxation data, we derive new equations using the model free framework which includes two slowly exchanging macrostates, each of which also exhibits fast local motions.. Using simulations of HIV-1 Protease as an example, we show how the populations of slowly exchanging conformational states as well as order parameters for the different states can be determined from the NMR relaxation data.


PMID: 23638941 [PubMed - as supplied by publisher]



More...
Reply With Quote


Did you find this post helpful? Yes | No

Reply
Similar Threads
Thread Thread Starter Forum Replies Last Post
[NMR paper] Fast hydrogen exchange affects (15)N relaxation measurements in intrinsically disordered proteins.
Fast hydrogen exchange affects (15)N relaxation measurements in intrinsically disordered proteins. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--production.springer.de-OnlineResources-Logos-springerlink.gif Related Articles Fast hydrogen exchange affects (15)N relaxation measurements in intrinsically disordered proteins. J Biomol NMR. 2013 Jan 12; Authors: Kim S, Wu KP, Baum J Abstract Unprotected amide protons can undergo fast hydrogen exchange (HX) with protons from the solvent. Generally, NMR experiments using the out-and-back...
nmrlearner Journal club 0 02-03-2013 10:22 AM
Mathematical treatment of adiabatic fast passage pulses for the computation of nuclear spin relaxation rates in proteins with conformational exchange
Mathematical treatment of adiabatic fast passage pulses for the computation of nuclear spin relaxation rates in proteins with conformational exchange Abstract Although originally designed for broadband inversion and decoupling in NMR spectroscopy, recent methodological developments have introduced adiabatic fast passage (AFP) pulses into the field of protein dynamics. AFP pulses employ a frequency sweep, and have not only superior inversion properties with respect to offset effects, but they are also easily implemented into a pulse sequence. As magnetization is dragged from the +z to...
nmrlearner Journal club 0 09-30-2011 08:01 PM
Measuring Screw-Sense Preference in a Helical Oligomer by Comparison of 13C NMR Signal Separation at Slow and Fast Exchange
Measuring Screw-Sense Preference in a Helical Oligomer by Comparison of 13C NMR Signal Separation at Slow and Fast Exchange Jordi Sola?, Gareth A. Morris and Jonathan Clayden http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jacsat/0/jacsat.ahead-of-print/ja1097034/aop/images/medium/ja-2010-097034_0001.gif Journal of the American Chemical Society DOI: 10.1021/ja1097034 http://feeds.feedburner.com/~ff/acs/jacsat?d=yIl2AUoC8zA http://feeds.feedburner.com/~r/acs/jacsat/~4/NJjFWlcOo9Q
nmrlearner Journal club 0 02-26-2011 01:07 PM
TROSY-selected ZZ-exchange experiment for characterizing slow chemical exchange in large proteins
TROSY-selected ZZ-exchange experiment for characterizing slow chemical exchange in large proteins Abstract A TROSY-selected ZZ-exchange experiment is described for measuring slow chemical exchange rates by monitoring the TROSY component of 15N longitudinal magnetization. Application of the proposed pulse sequence to the cadherin 8 N-terminal extracelluar domain demonstrates that enhanced sensitivity is obtained, compared to a previously described TROSY-detected ZZ-exchange sequence (Sahu et al. J Am Chem Soc 129: 13232â??13237, 2007), by preserving the TROSY effect during the mixing...
nmrlearner Journal club 0 01-09-2011 12:46 PM
[NMR paper] Slow internal dynamics in proteins: application of NMR relaxation dispersion spectros
Slow internal dynamics in proteins: application of NMR relaxation dispersion spectroscopy to methyl groups in a cavity mutant of T4 lysozyme. Related Articles Slow internal dynamics in proteins: application of NMR relaxation dispersion spectroscopy to methyl groups in a cavity mutant of T4 lysozyme. J Am Chem Soc. 2002 Feb 20;124(7):1443-51 Authors: Mulder FA, Hon B, Mittermaier A, Dahlquist FW, Kay LE Recently developed carbon transverse relaxation dispersion experiments (Skrynnikov, N. R.; et al. J. Am. Chem. Soc. 2001, 123, 4556-4566) were...
nmrlearner Journal club 0 11-24-2010 08:49 PM
[NMR paper] NMR 15N relaxation and structural studies reveal slow conformational exchange in bars
NMR 15N relaxation and structural studies reveal slow conformational exchange in barstar C40/82A. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles NMR 15N relaxation and structural studies reveal slow conformational exchange in barstar C40/82A. J Mol Biol. 1997 May 2;268(2):494-511 Authors: Wong KB, Fersht AR, Freund SM Barstar an 89-residue protein consisting of four helices and a three-stranded parallel beta-sheet, is the intracellular inhibitor of the...
nmrlearner Journal club 0 08-22-2010 03:31 PM
[NMR paper] NMR 15N relaxation and structural studies reveal slow conformational exchange in bars
NMR 15N relaxation and structural studies reveal slow conformational exchange in barstar C40/82A. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles NMR 15N relaxation and structural studies reveal slow conformational exchange in barstar C40/82A. J Mol Biol. 1997 May 2;268(2):494-511 Authors: Wong KB, Fersht AR, Freund SM Barstar an 89-residue protein consisting of four helices and a three-stranded parallel beta-sheet, is the intracellular inhibitor of the...
nmrlearner Journal club 0 08-22-2010 03:03 PM
[NMR paper] Internal motions of apo-neocarzinostatin as studied by 13C NMR methine relaxation at
Internal motions of apo-neocarzinostatin as studied by 13C NMR methine relaxation at natural abundance. Related Articles Internal motions of apo-neocarzinostatin as studied by 13C NMR methine relaxation at natural abundance. J Biomol NMR. 1995 Apr;5(3):233-44 Authors: Mispelter J, Lefèvre C, Adjadj E, Quiniou E, Favaudon V Dynamics of the backbone and some side chains of apo-neocarzinostatin, a 10.7 kDa carrier protein, have been studied from 13C relaxation rates R1, R2 and steady-state 13C-(1H) NOEs, measured at natural abundance. Relaxation...
nmrlearner Journal club 0 08-22-2010 03:41 AM



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 02:22 AM.


Map