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 09-04-2014, 02:31 PM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 19,990
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 Conformational effects due to stereochemistry and C3-substituents in xylopyranoside derivatives as studied by NMR spectroscopy.

Conformational effects due to stereochemistry and C3-substituents in xylopyranoside derivatives as studied by NMR spectroscopy.

Related Articles Conformational effects due to stereochemistry and C3-substituents in xylopyranoside derivatives as studied by NMR spectroscopy.

Org Biomol Chem. 2014 Sep 3;

Authors: Rönnols J, Manner S, Ellervik U, Widmalm G

Abstract
Glycosaminoglycans contain a ?-d-xylopyranose residue at its reducing end, which links the polysaccharide to the protein in proteoglycans. 2-Naphthyl ?-d-xylopyranosides have shown inhibition of tumor growth and we herein investigate conformation and dynamics of compounds structurally and stereochemically modified at the C3 position as well as the influence of solvent. The 3-deoxygenated compound, the 3-C-methyl-substituted ?-d-xylopyranoside, ?-d-ribopyranoside, the 3-C-methyl-substituted ?-d-ribopyranoside as well as 2-naphthyl ?-d-xylopyranoside were analyzed by NMR spectroscopy. Conformational equilibria were dependent on the solvent of choice, either methanol-d4 or chloroform-d, with mainly (4)C1 and (1)C4 conformations present but also skew conformations to some extent. Intramolecular hydrogen bonding was concluded to be important for the 3-C-methyl-substituted ?-d-xylopyranosides in the non-polar solvent. Dynamic NMR (DNMR) spectroscopy was carried out for the 3-deoxygenated compound, which at 25 °C in methanol-d4 exists with equally populated states of the (4)C1 and the (1)C4 conformations, but at -100 °C only a few percent is present of the latter. Using (13)C NMR detection for DNMR, resonance lines were shown to broaden at -40 °C and to sharpen again below -90 °C, without the emergence of a second set of NMR resonances, a typical behavior for an unequally populated equilibrium. The enthalpy and entropy activation barriers were calculated and resulted in ?H(‡) = 47.3 kJ mol(-1) and ?S(‡) = 54 J mol(-1) K(-1).


PMID: 25183410 [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] Effects of cholesterol on membrane molecular dynamics studied by fast field cycling NMR relaxometry.
Effects of cholesterol on membrane molecular dynamics studied by fast field cycling NMR relaxometry. Related Articles Effects of cholesterol on membrane molecular dynamics studied by fast field cycling NMR relaxometry. Phys Chem Chem Phys. 2013 Aug 22; Authors: Hsieh CJ, Chen YW, Hwang DW Abstract Biological membranes are complex structures composed of various lipids and proteins. Different membrane compositions affect viscoelastic and hydrodynamic properties of membranes, which are critical to their functions. Lipid bilayer vesicles...
nmrlearner Journal club 0 08-24-2013 04:53 PM
[NMR paper] Effects of a type I antifreeze protein (AFP) on the melting of frozen AFP and AFP+solute aqueous solutions studied by NMR microimaging experiment.
Effects of a type I antifreeze protein (AFP) on the melting of frozen AFP and AFP+solute aqueous solutions studied by NMR microimaging experiment. Related Articles Effects of a type I antifreeze protein (AFP) on the melting of frozen AFP and AFP+solute aqueous solutions studied by NMR microimaging experiment. J Biol Phys. 2013 Jan;39(1):131-44 Authors: Ba Y, Mao Y, Galdino L, Günsen Z Abstract The effects of a type I AFP on the bulk melting of frozen AFP solutions and frozen AFP+solute solutions were studied through an NMR...
nmrlearner Journal club 0 07-19-2013 09:20 PM
Conformational States of ADP Ribosylation Factor 1 Complexed with Different Guanosine Triphosphates As Studied by 31P NMR Spectroscopy
Conformational States of ADP Ribosylation Factor 1 Complexed with Different Guanosine Triphosphates As Studied by 31P NMR Spectroscopy http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/bichaw/0/bichaw.ahead-of-print/bi101573j/aop/images/medium/bi-2010-01573j_0005.gif Biochemistry DOI: 10.1021/bi101573j http://feeds.feedburner.com/~ff/acs/bichaw?d=yIl2AUoC8zA http://feeds.feedburner.com/~r/acs/bichaw/~4/C6EyTlTrUig More...
nmrlearner Journal club 0 07-06-2011 06:14 AM
Effects of substituents on the NMR features of basic bicyclic ring systems of fluoroquinolone antibiotics and the relationships between NMR chemical shifts, molecular descriptors and drug-likeness parameters.
Effects of substituents on the NMR features of basic bicyclic ring systems of fluoroquinolone antibiotics and the relationships between NMR chemical shifts, molecular descriptors and drug-likeness parameters. Related Articles Effects of substituents on the NMR features of basic bicyclic ring systems of fluoroquinolone antibiotics and the relationships between NMR chemical shifts, molecular descriptors and drug-likeness parameters. Acta Pharm. 2010 Sep 1;60(3):237-254 Authors: Taka? MJ In the present study, the NMR spectroscopic features of...
nmrlearner Journal club 0 12-08-2010 06:21 PM
[NMR paper] The effects of mutations on motions of side-chains in protein L studied by 2H NMR dyn
The effects of mutations on motions of side-chains in protein L studied by 2H NMR dynamics and scalar couplings. Related Articles The effects of mutations on motions of side-chains in protein L studied by 2H NMR dynamics and scalar couplings. J Mol Biol. 2003 Jun 6;329(3):551-63 Authors: Millet O, Mittermaier A, Baker D, Kay LE Recently developed 2H spin relaxation experiments are applied to study the dynamics of methyl-containing side-chains in the B1 domain of protein L and in a pair of point mutants of the domain, F22L and A20V. X-ray and...
nmrlearner Journal club 0 11-24-2010 09:01 PM
[NMR paper] Paramagnetic NMR Spectroscopy of Cobalt(II) and Copper(II) Derivatives of Pseudomonas
Paramagnetic NMR Spectroscopy of Cobalt(II) and Copper(II) Derivatives of Pseudomonas aeruginosa His46Asp Azurin. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--pubs.acs.org-images-acspubs.jpg Related Articles Paramagnetic NMR Spectroscopy of Cobalt(II) and Copper(II) Derivatives of Pseudomonas aeruginosa His46Asp Azurin. Inorg Chem. 1997 Sep 24;36(20):4567-4570 Authors: Vila AJ, Ramirez BE, Di Bilio AJ, Mizoguchi TJ, Richards JH, Gray HB NMR spectra of paramagnetic Co(II) and Cu(II) derivatives of Pseudomonas aeruginosa His46Asp...
nmrlearner Journal club 0 08-22-2010 05:08 PM
[NMR paper] Conformational differences between complexes of elongation factor Tu studied 19F-NMR
Conformational differences between complexes of elongation factor Tu studied 19F-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 Related Articles Conformational differences between complexes of elongation factor Tu studied 19F-NMR spectroscopy. Eur J Biochem. 1993 Dec 15;218(3):1041-7 Authors: Eccleston JF, Molloy DP, Hinds MG, King RW, Feeney J An analogue of elongation factor Tu (EF-Tu) from Escherichia coli was prepared by...
nmrlearner Journal club 0 08-22-2010 03:01 AM
NMR resonance assignments of thrombin reveal the conformational and dynamic effects o
NMR resonance assignments of thrombin reveal the conformational and dynamic effects of ligation Lechtenberg, B. C., Johnson, D. J. D., Freund, S. M. V., Huntington, J. A.... The serine protease thrombin is generated from its zymogen prothrombin at the end of the coagulation cascade. Thrombin functions as... Date: 2010-08-10 Source: PNAS Number: 32
nmrlearner Journal club 0 08-15-2010 10:45 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 - 2020, 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 10:23 AM.


Map