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  
Unread 07-13-2017, 12:02 PM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 23,174
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 Solvent-Driven Dynamical Cross-Over in the Phenylalanine Side-Chain from the Hydrophobic Core of Amyloid Fibrils Detected by (2)H NMR Relaxation.

Solvent-Driven Dynamical Cross-Over in the Phenylalanine Side-Chain from the Hydrophobic Core of Amyloid Fibrils Detected by (2)H NMR Relaxation.

Related Articles Solvent-Driven Dynamical Cross-Over in the Phenylalanine Side-Chain from the Hydrophobic Core of Amyloid Fibrils Detected by (2)H NMR Relaxation.

J Phys Chem B. 2017 Jul 12;:

Authors: Vugmeyster L, Ostrovsky D, Hoatson GL, Qiang W, Falconer IB

Abstract
Aromatic residues are important markers of dynamical changes in proteins' hydrophobic cores. In this work we investigated the dynamics of the F19 side-chain in the core of amyloid fibrils across a wide temperature range of 300 to 140 K. We utilized solid-state 2H NMR relaxation to demonstrate the presence of a solvent-driven dynamical cross-over between different motional regimes, often also referred to as the dynamical transition. In particular, the dynamics are dominated by small-angle fluctuations at low temperatures and by ?-flips of the aromatic ring at high temperatures. The cross-over temperature is more than 43 degrees lower for the hydrated state of the fibrils compared to the dry state, indicating that interactions with water facilitate ?-flips. Further, cross-over temperatures are shown to be very sensitive to polymorphic states of the fibrils, such as the 2-fold and 3-fold symmetric morphologies of the wild-type protein as well as D23N mutant protofibrils. We speculate that these differences can be attributed, at least partially, to enhanced interactions with water in the 3-fold polymorph, which has been shown to have a water-accessible cavity. Combined with previous studies of methyl group dynamics, the results highlight the presence of multiple dynamics modes in the core of the fibrils, which was originally believed to be quite rigid.


PMID: 28699757 [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] NMR Spectroscopic Assignment of Backbone and Side-Chain Protons in Fully Protonated Proteins: Microcrystals, Sedimented Assemblies, and Amyloid Fibrils.
NMR Spectroscopic Assignment of Backbone and Side-Chain Protons in Fully Protonated Proteins: Microcrystals, Sedimented Assemblies, and Amyloid Fibrils. NMR Spectroscopic Assignment of Backbone and Side-Chain Protons in Fully Protonated Proteins: Microcrystals, Sedimented Assemblies, and Amyloid Fibrils. Angew Chem Int Ed Engl. 2016 Nov 16;: Authors: Stanek J, Andreas LB, Jaudzems K, Cala D, Lalli D, Bertarello A, Schubeis T, Akopjana I, Kotelovica S, Tars K, Pica A, Leone S, Picone D, Xu ZQ, Dixon NE, Martinez D, Berbon M, El Mammeri N, Noubhani...
nmrlearner Journal club 0 11-20-2016 09:20 PM
[NMR paper] Dynamics of Hydrophobic Core Phenylalanine Residues Probed by Solid-State Deuteron NMR.
Dynamics of Hydrophobic Core Phenylalanine Residues Probed by Solid-State Deuteron NMR. http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--pubs.acs.org-images-pubmed-acspubs.jpg Related Articles Dynamics of Hydrophobic Core Phenylalanine Residues Probed by Solid-State Deuteron NMR. J Phys Chem B. 2015 Nov 3; Authors: Vugmeyster L, Ostrovsky D, Villafranca TR, Sharp J, Xu W, Lipton AS, Hoatson GL, Vold RL Abstract We conducted a detailed investigation of the dynamics of two phenylalanine side chains in the...
nmrlearner Journal club 0 11-09-2015 02:00 AM
[NMR paper] Polyglutamine amyloid core boundaries and flanking domain dynamics in huntingtin fragment fibrils determined by solid-state NMR.
Polyglutamine amyloid core boundaries and flanking domain dynamics in huntingtin fragment fibrils determined by solid-state NMR. Related Articles Polyglutamine amyloid core boundaries and flanking domain dynamics in huntingtin fragment fibrils determined by solid-state NMR. Biochemistry. 2014 Oct 3; Authors: Hoop CL, Lin HK, Kar K, Hou Z, Poirier MA, Wetzel R, van der Wel PC Abstract In Huntington's Disease (HD), expansion of a polyglutamine (polyQ) domain in the huntingtin (htt) protein leads to misfolding and aggregation....
nmrlearner Journal club 0 10-04-2014 05:16 PM
A Studyof Phenylalanine Side-Chain Dynamics in Surface-AdsorbedPeptides Using Solid-State Deuterium NMR and Rotamer Library Statistics
A Studyof Phenylalanine Side-Chain Dynamics in Surface-AdsorbedPeptides Using Solid-State Deuterium NMR and Rotamer Library Statistics Kun Li, Prashant S. Emani, Jason Ash, Michael Groves and Gary P. Drobny http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jacsat/0/jacsat.ahead-of-print/ja504677d/aop/images/medium/ja-2014-04677d_0008.gif Journal of the American Chemical Society DOI: 10.1021/ja504677d http://feeds.feedburner.com/~ff/acs/jacsat?d=yIl2AUoC8zA http://feeds.feedburner.com/~r/acs/jacsat/~4/d2WMAZNh-I4
nmrlearner Journal club 0 08-06-2014 07:59 AM
[NMR paper] A Study of Phenylalanine Side Chain Dynamics in Surface-Adsorbed Peptides Using Solid State Deuterium NMR and Rotamer Library Statistics.
A Study of Phenylalanine Side Chain Dynamics in Surface-Adsorbed Peptides Using Solid State Deuterium NMR and Rotamer Library Statistics. A Study of Phenylalanine Side Chain Dynamics in Surface-Adsorbed Peptides Using Solid State Deuterium NMR and Rotamer Library Statistics. J Am Chem Soc. 2014 Jul 23; Authors: Li K, Emani PS, Ash J, Groves M, Drobny GP Abstract Extracellular matrix proteins adsorbed onto mineral surfaces exist in a unique environment where the structure and dynamics of the protein can be altered...
nmrlearner Journal club 0 07-24-2014 11:56 AM
The Core of Ure2p Prion Fibrils Is Formed by the N-Terminal Segment in a Parallel Cross-? Structure: Evidence from Solid-State NMR.
The Core of Ure2p Prion Fibrils Is Formed by the N-Terminal Segment in a Parallel Cross-? Structure: Evidence from Solid-State NMR. The Core of Ure2p Prion Fibrils Is Formed by the N-Terminal Segment in a Parallel Cross-? Structure: Evidence from Solid-State NMR. J Mol Biol. 2011 Apr 8; Authors: Kryndushkin DS, Wickner RB, Tycko R Intracellular fibril formation by Ure2p produces the non-Mendelian genetic element in Saccharomyces cerevisiae, making Ure2p a prion protein. We show that solid-state NMR spectra of full-length Ure2p fibrils, seeded...
nmrlearner Journal club 0 04-19-2011 11:01 PM
Side chain: backbone projections in aromatic and ASX residues from NMR cross-correlated relaxation
Side chain: backbone projections in aromatic and ASX residues from NMR cross-correlated relaxation Abstract The measurements of cross-correlated relaxation rates between HNā??N and CĪ²ā??CĪ³ intraresidual and sequential dipolar interactions is demonstrated in ASN, ASP and aromatic residues. The experiment can be used for deuterated samples and no additional knowledge such as Karplus parametrizations is required for the analysis. The data constitutes a new type of information since no other method relates the CĪ²ā??CĪ³ bond to HNā??N. Using this method the dominant populations of rotamer...
nmrlearner Journal club 0 01-09-2011 12:46 PM
[NMR paper] Probing solvent accessibility of amyloid fibrils by solution NMR spectroscopy.
Probing solvent accessibility of amyloid fibrils by solution NMR spectroscopy. Related Articles Probing solvent accessibility of amyloid fibrils by solution NMR spectroscopy. Proc Natl Acad Sci U S A. 2002 Jun 25;99(13):8648-53 Authors: Ippel JH, Olofsson A, Schleucher J, Lundgren E, Wijmenga SS Amyloid is the result of an anomalous protein and peptide aggregation, leading to the formation of insoluble fibril deposits. At present, 18 human diseases have been associated with amyloid deposits-e.g., Alzheimer's disease and Prion-transmissible...
nmrlearner Journal club 0 11-24-2010 08:49 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 10:59 AM.


Map