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 09-14-2017, 11:59 AM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 23,137
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 side chain 13 C chemical shifts in model peptides Ac-Gly-Gly-Xxx-Ala-NH 2

Pressure dependence of side chain 13 C chemical shifts in model peptides Ac-Gly-Gly-Xxx-Ala-NH 2

Abstract

For evaluating the pressure responses of folded as well as intrinsically unfolded proteins detectable by NMR spectroscopy the availability of data from well-defined model systems is indispensable. In this work we report the pressure dependence of 13C chemical shifts of the side chain atoms 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 a number of nuclei have a nonlinear dependence on pressure in the range from 0.1 to 200Â*MPa. The size of the polynomial pressure coefficients B 1 and B 2 is dependent on the type of atom and amino acid studied. For HN, N and Cα the first order pressure coefficient B 1 is also correlated to the chemical shift at atmospheric pressure. The first and second order pressure coefficients of a given type of carbon atom 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 also are weakly correlated. The downfield shifts of the methyl resonances suggest that gauche conformers of the side chains are not preferred with pressure. The valine and leucine methyl groups in the model peptides were assigned using stereospecifically 13C enriched amino acids with the pro-R carbons downfield shifted relative to the pro-S carbons.



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
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 13C� in the protected tetrapeptides Ac-Gly-Gly-Xxx-Ala-NH2 (Xxx one of the 20 canonical amino acids). Contrary to...
nmrlearner Journal club 0 06-22-2016 09:14 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] 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
A Simple Method to Measure Protein Side-Chain MobilityUsing NMR Chemical Shifts
A Simple Method to Measure Protein Side-Chain MobilityUsing NMR Chemical Shifts Mark V. Berjanskii and David S. Wishart http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jacsat/0/jacsat.ahead-of-print/ja407509z/aop/images/medium/ja-2013-07509z_0003.gif Journal of the American Chemical Society DOI: 10.1021/ja407509z http://feeds.feedburner.com/~ff/acs/jacsat?d=yIl2AUoC8zA http://feeds.feedburner.com/~r/acs/jacsat/~4/qRQjRZhXxAM
nmrlearner Journal club 0 09-23-2013 09:41 PM
[NMR paper] A simple method to measure protein side-chain mobility using NMR chemical shifts.
A simple method to measure protein side-chain mobility using NMR chemical shifts. http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--pubs.acs.org-images-pubmed-acspubs.jpg Related Articles A simple method to measure protein side-chain mobility using NMR chemical shifts. J Am Chem Soc. 2013 Sep 13; Authors: Berjanskii MV, Wishart DS Abstract Protein side-chain motions are involved in many important biological processes including enzymatic catalysis, allosteric regulation, and the mediation of protein-protein,...
nmrlearner Journal club 0 09-17-2013 11:36 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
[NMR paper] Backbone and side-chain heteronuclear resonance assignments and hyperfine NMR shifts
Backbone and side-chain heteronuclear resonance assignments and hyperfine NMR shifts in horse cytochrome c. Related Articles Backbone and side-chain heteronuclear resonance assignments and hyperfine NMR shifts in horse cytochrome c. Protein Sci. 2003 Sep;12(9):2104-8 Authors: Liu W, Rumbley J, Englander SW, Wand AJ The mutant of horse heart cytochrome c was expressed in E. coli during growth on isotopically enriched minimal media. Complete resonance assignments of both the diamagnetic reduced (spin zero) and paramagnetic oxidized (spin (1/2))...
nmrlearner Journal club 0 11-24-2010 09:16 PM
[NMR paper] Investigation of a side-chain-side-chain hydrogen bond by mutagenesis, thermodynamics
Investigation of a side-chain-side-chain hydrogen bond by mutagenesis, thermodynamics, and NMR spectroscopy. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www3.interscience.wiley.com-aboutus-images-wiley_interscience_pubmed_logo_FREE_120x27.gif http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www.pubmedcentral.nih.gov-corehtml-pmc-pmcgifs-pubmed-pmc.gif Related Articles Investigation of a side-chain-side-chain hydrogen bond by mutagenesis, thermodynamics, and NMR spectroscopy. Protein Sci. 1995 May;4(5):936-44 Authors: Hammen PK, Scholtz...
nmrlearner Journal club 0 08-22-2010 03:41 AM


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 10:13 AM.


Map