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 04-11-2015, 01:51 PM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 23,135
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 Aggregation of a Tetrasaccharide Acceptor Observed by NMR: Synthesis of Pentasaccharide Fragments of the LeaLex Tumor-Associated Hexasaccharide Antigen.

Aggregation of a Tetrasaccharide Acceptor Observed by NMR: Synthesis of Pentasaccharide Fragments of the LeaLex Tumor-Associated Hexasaccharide Antigen.

Aggregation of a Tetrasaccharide Acceptor Observed by NMR: Synthesis of Pentasaccharide Fragments of the LeaLex Tumor-Associated Hexasaccharide Antigen.

J Org Chem. 2015 Apr 10;

Authors: Kuir D, Guillemineau M, Auzanneau FI

Abstract
We report the synthesis of a tetrasaccharide and two pentasaccharide fragments of the LeaLex tumor associated carbohydrate antigen alpha-L-Fuc-(1->4)-[beta-D-Gal-(1->3)]-beta-D-GlcNAc-(1->3)-beta-D-Gal-(1->4)-[alpha-L-Fuc-(1->3)]-beta-D-GlcNAc-(1->OR). The choice of protecting groups permitted a one-step global deprotection (Na/NH3(l)). The protected chlorohexyl glycoside pentasaccharide was the precursor to the hexyl glycoside, to be used as a soluble inhibitor, and the aminohexyl glycoside analogue, to be conjugated to proteins for surface immobilization and immunization experiments. We observed that a linear tetrasaccharide that contained two N-acetylglucosamine residues and a free OH group gave two distinct sets of 1H NMR signals when the data was acquired in deuterated chloroform. Data acquisition at variable concentrations and variable temperatures suggest that the second set of NMR signals results from aggregation of the tetrasaccharide driven by the formation of intermolecular H-bonds involving the NHAc. While the formation of intra- and intermolecular H-bonds involving N-acetylgucosamine residues has been reported in non-H-bonding solvents, this is, to our knowledge, the first time that these lead to the appearance of two distinct sets of signals in the NMR spectra. This aggregation, may explain the lack of reactivity observed when attempting to glycosylate such acceptor using non H-bonding solvents such as dichloromethane.


PMID: 25860389 [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] Evaluation of Michael-type Acceptor Reactivity of 5-Benzylidenebarbiturates, 5-benzylidenerhodanines, and Related Heterocycles Using NMR.
Evaluation of Michael-type Acceptor Reactivity of 5-Benzylidenebarbiturates, 5-benzylidenerhodanines, and Related Heterocycles Using NMR. Related Articles Evaluation of Michael-type Acceptor Reactivity of 5-Benzylidenebarbiturates, 5-benzylidenerhodanines, and Related Heterocycles Using NMR. Acta Chim Slov. 2014 Sep;61(3):637-644 Authors: Arsovska E, Trontelj J, Zidar N, Tomaši? T, Maši? LP, Kikelj D, Plavec J, Zega A Abstract Despite existing experimental and computational tools to assess the risk, the non-specific chemical...
nmrlearner Journal club 0 10-07-2014 02:31 PM
NMR characterization of the conformational fluctuations of the human lymphocyte function-associated antigen-1 I-domain
NMR characterization of the conformational fluctuations of the human lymphocyte function-associated antigen-1 I-domain Abstract Lymphocyte function-associated antigen-1 (LFA-1) is an integrin protein that transmits information across the plasma membrane through the so-called inside-out and outside-in signaling mechanisms. To investigate these mechanisms, we carried out an NMR analysis of the dynamics of the LFA-1 I-domain, which has enabled us to characterize the motions of this domain on a broad range of timescales. We studied first the internal motions on the nanosecond timescale by...
nmrlearner Journal club 0 09-05-2014 03:03 PM
[NMR paper] NMR characterisation of the conformational fluctuations of the human lymphocyte function associated antigen-1 i domain.
NMR characterisation of the conformational fluctuations of the human lymphocyte function associated antigen-1 i domain. Related Articles NMR characterisation of the conformational fluctuations of the human lymphocyte function associated antigen-1 i domain. Protein Sci. 2014 Aug 21; Authors: Leung HT, Kukic P, Camilloni C, Bemporad F, DeSimone A, Aprile FA, Kumita J, Vendruscolo M Abstract Lymphocyte function-associated antigen-1 (LFA-1) is an integrin protein that transmits information across the plasma membrane through the...
nmrlearner Journal club 0 08-26-2014 01:25 PM
[NMR paper] Unraveling the interaction between the LPS O-antigen of Burkholderia anthina and the 5D8 monoclonal antibody by using a multidisciplinary chemical approach, with synthesis, NMR, and molecular modeling methods.
Unraveling the interaction between the LPS O-antigen of Burkholderia anthina and the 5D8 monoclonal antibody by using a multidisciplinary chemical approach, with synthesis, NMR, and molecular modeling methods. http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--media.wiley.com-assets-2250-98-WileyOnlineLibrary-Button_120x27px_FullText.gif Related Articles Unraveling the interaction between the LPS O-antigen of Burkholderia anthina and the 5D8 monoclonal antibody by using a multidisciplinary chemical approach, with synthesis, NMR, and molecular modeling methods....
nmrlearner Journal club 0 03-04-2014 06:37 PM
[NMR paper] Expression and structural characterization of anti-T-antigen single chain antibodies (scFvs) and analysis of their binding to T-antigen by surface plasmon resonance and NMR spectroscopy.
Expression and structural characterization of anti-T-antigen single chain antibodies (scFvs) and analysis of their binding to T-antigen by surface plasmon resonance and NMR spectroscopy. Expression and structural characterization of anti-T-antigen single chain antibodies (scFvs) and analysis of their binding to T-antigen by surface plasmon resonance and NMR spectroscopy. J Biochem. 2013 Oct 4; Authors: Yuasa N, Koyama T, Subedi GP, Yamaguchi Y, Matsushita M, Fujita-Yamaguchi Y Abstract T-antigen (Gal?1-3GalNAc?-1-Ser/Thr), also known as...
nmrlearner Journal club 0 10-08-2013 02:04 PM
Light-Induced Spin Polarization in Porphyrin-Based Donor–Acceptor Dyads and Triads
From The DNP-NMR Blog: Light-Induced Spin Polarization in Porphyrin-Based Donor–Acceptor Dyads and Triads van der Est, A. and P. Poddutoori, Light-Induced Spin Polarization in Porphyrin-Based Donor–Acceptor Dyads and Triads. Appl. Magn. Reson., 2013. 44(1-2): p. 301-318. http://dx.doi.org/10.1007/s00723-012-0420-z
nmrlearner News from NMR blogs 0 08-01-2013 12:26 AM
[NMR paper] NMR study on the interaction between MHC class I protein and its antigen peptide.
NMR study on the interaction between MHC class I protein and its antigen peptide. Related Articles NMR study on the interaction between MHC class I protein and its antigen peptide. Biochem Biophys Res Commun. 2000 Nov 30;278(3):609-13 Authors: Nakagawa M, Chiba-Kamoshida K, Udaka K, Nakanishi H A major histcompatibility complex (MHC) class I protein H-2K(b) was expressed in a large scale as a fusion protein with thioredoxin and hexahistidine at the N-terminus to analyze the interaction with the antigen peptide SIYRYYGL. NMR spectra of the...
nmrlearner Journal club 0 11-19-2010 08:29 PM
[NMR paper] NMR analysis of tRNA acceptor stem microhelices: discriminator base change affects tR
NMR analysis of tRNA acceptor stem microhelices: discriminator base change affects tRNA conformation at the 3' end. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www.pubmedcentral.nih.gov-corehtml-pmc-pmcgifs-pubmed-pmc.gif Related Articles NMR analysis of tRNA acceptor stem microhelices: discriminator base change affects tRNA conformation at the 3' end. Proc Natl Acad Sci U S A. 1994 Nov 22;91(24):11467-71 Authors: Puglisi EV, Puglisi JD, Williamson JR, RajBhandary UL An important step in initiation of protein synthesis in...
nmrlearner Journal club 0 08-22-2010 03:29 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 06:49 AM.


Map