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 06-22-2016, 09:14 PM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 23,134
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 Pressure dependence of backbone chemical shifts in the model peptides Ac-Gly-Gly-Xxx-Ala-NH 2

Pressure dependence of backbone chemical shifts in the model peptides Ac-Gly-Gly-Xxx-Ala-NH 2

Abstract

For a better understanding of nuclear magnetic resonance (NMR) detected pressure responses of folded as well as unstructured proteins the availability of data from well-defined model systems are indispensable. In this work we report the pressure dependence of chemical shifts of the backbone atoms 1Hα, 13Cα and 13Câ?² in the protected tetrapeptides Ac-Gly-Gly-Xxx-Ala-NH2 (Xxx one of the 20 canonical amino acids). Contrary to expectation the chemical shifts of these nuclei have a nonlinear dependence on pressure in the range from 0.1 to 200Â*MPa. The polynomial pressure coefficients B 1 and B 2 are dependent on the type of amino acid studied. The coefficients of a given nucleus show significant linear correlations suggesting that the NMR observable pressure effects in the different amino acids have at least partly the same physical cause. In line with this observation the magnitude of the second order coefficients of nuclei being direct neighbors in the chemical structure are also weakly correlated.

Graphical Abstract





Source: Journal of Biomolecular NMR
Reply With Quote


Did you find this post helpful? Yes | No

Reply
Similar Threads
Thread Thread Starter Forum Replies Last Post
[NMR paper] Sensitivity of ab Initio vs Empirical Methods in Computing Structural Effects on NMR Chemical Shifts for the Example of Peptides.
Sensitivity of ab Initio vs Empirical Methods in Computing Structural Effects on NMR Chemical Shifts for the Example of Peptides. Related Articles Sensitivity of ab Initio vs Empirical Methods in Computing Structural Effects on NMR Chemical Shifts for the Example of Peptides. J Chem Theory Comput. 2014 Jan 14;10(1):122-33 Authors: Sumowski CV, Hanni M, Schweizer S, Ochsenfeld C Abstract The structural sensitivity of NMR chemical shifts as computed by quantum chemical methods is compared to a variety of empirical approaches for...
nmrlearner Journal club 0 11-22-2015 01:36 AM
Easy and unambiguous sequential assignments of intrinsically disordered proteins by correlating the backbone 15 N or 13 Câ?² chemical shifts of multiple contiguous residues in highly resolved 3D spectra
Easy and unambiguous sequential assignments of intrinsically disordered proteins by correlating the backbone 15 N or 13 Câ?² chemical shifts of multiple contiguous residues in highly resolved 3D spectra Abstract Sequential resonance assignment strategies are typically based on matching one or two chemical shifts of adjacent residues. However, resonance overlap often leads to ambiguity in resonance assignments in particular for intrinsically disordered proteins. We investigated the potential of establishing connectivity through the three-bond couplings...
nmrlearner Journal club 0 01-12-2015 11:31 PM
Pressure response of amide one-bond J-couplings in model peptides and proteins
Pressure response of amide one-bond J-couplings in model peptides and proteins Abstract The pressure dependence of the one-bond indirect spinâ??spin coupling constants 1 J Nâ??H was studied in the protected tetrapeptides Ac-Gly-Gly-Xxx-Ala-NH2 (with Xxx being one of the 20 proteinogenic amino acids). The response of the 1 J Nâ??H coupling constants is amino acid type specific, with an average...
nmrlearner Journal club 0 08-13-2014 07:49 AM
[NMR paper] Protein backbone and sidechain torsion angles predicted from NMR chemical shifts using artificial neural networks.
Protein backbone and sidechain torsion angles predicted from NMR chemical shifts using artificial neural networks. Related Articles Protein backbone and sidechain torsion angles predicted from NMR chemical shifts using artificial neural networks. J Biomol NMR. 2013 Jun 2; Authors: Shen Y, Bax A Abstract A new program, TALOS-N, is introduced for predicting protein backbone torsion angles from NMR chemical shifts. The program relies far more extensively on the use of trained artificial neural networks than its predecessor, TALOS+....
nmrlearner Journal club 0 06-04-2013 06:31 PM
Pressure-induced chemical shifts as probes for conformational fluctuations in proteins
Pressure-induced chemical shifts as probes for conformational fluctuations in proteins Available online 19 January 2013 Publication year: 2013 Source:Progress in Nuclear Magnetic Resonance Spectroscopy</br> </br> </br> </br></br>
nmrlearner Journal club 0 01-20-2013 07:56 PM
Local protein backbone folds determined by calculated NMR chemical shifts.
Local protein backbone folds determined by calculated NMR chemical shifts. Local protein backbone folds determined by calculated NMR chemical shifts. J Comput Chem. 2011 Sep 9; Authors: Czajlik A, Hudáky I, Perczel A Abstract NMR chemical shifts (CSs: ?N(NH) , ?C(?) , ?C(?) , ?C', ?H(NH) , and ?H(?) ) were computed for the amino acid backbone conformers (?(L) , ?(L) , ?(L) , ?(L) , ?(L) , ?(D) , ?(D) , ?(D) , and ?(D) ) modeled by oligoalanine structures. Topological differences of the extended fold were investigated on single ?-strands,...
nmrlearner Journal club 0 09-10-2011 06:51 PM
[NMR paper] A protein backbone psi and phi angle dependence of 2J(N(i),C alpha(i-1)): the new NMR
A protein backbone psi and phi angle dependence of 2J(N(i),C alpha(i-1)): the new NMR experiment and quantum chemical calculations. Related Articles A protein backbone psi and phi angle dependence of 2J(N(i),C alpha(i-1)): the new NMR experiment and quantum chemical calculations. J Biomol NMR. 2005 Feb;31(2):87-95 Authors: Ko?mi?ski W, Zhukov I, Pecul M, Sadlej J A new pulse sequence exploiting double- and zero-quantum evolution of two-spin 15N-13C' coherence is proposed for the accurate measurements of 2J(N(i),C alpha(i-1)) coupling...
nmrlearner Journal club 0 11-24-2010 11:14 PM
Rapid, Accurate and Simple Model to Predict NMR Chemical Shifts for Biological Molecu
Rapid, Accurate and Simple Model to Predict NMR Chemical Shifts for Biological Molecules. Rapid, Accurate and Simple Model to Predict NMR Chemical Shifts for Biological Molecules. J Phys Chem B. 2010 Nov 18; Authors: Atieh Z, Aubert-Fre?con M, Allouche AR We present a new model to predict chemical shifts for biological molecules. It is simple, fast, and involves a limited number of parameters. It is particularly adapted to be used in molecular dynamics studies with a molecular mechanic potential. We test the model for polyamines, which are rather...
nmrlearner Journal club 0 11-20-2010 06:01 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 05:25 PM.


Map