NMR paper Direct Evidence for Hydrogen Bonding Between Hydroxyl Groups in Glycans: A Combined NMR and Molecular Dynamics Study.

		BioNMR > Educational resources > Journal club
[NMR paper] Direct Evidence for Hydrogen Bonding Between Hydroxyl Groups in Glycans: A Combined NMR and Molecular Dynamics Study.

Webservers

NMR processing:

MDD

NMR assignment:

Backbone:

Side-chains:

NOEs:

Structure from NMR restraints:

Ab initio:

Fragment-based:

Rosetta-NMR (Robetta)

Template-based:

GeNMR

I-TASSER

Refinement:

Amber

Structure from chemical shifts:

Fragment-based:

Homology-based:

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:

NMR model quality:

NOEs, other restraints:

Chemical shifts:

RDCs:

Pseudocontact shifts:

Protein geomtery:

SAVES2 or SAVES4

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:

Isotope labeling:

Solid-state NMR:

Thread Tools

Search this Thread

Rate Thread

Display Modes

03-28-2013, 04:03 PM

nmrlearner

Senior Member

Join Date: Jan 2005

Posts: 23,734

Points: 193,617, Level: 100

Level up: 0%, 0 Points needed

Activity: 50.7%

Last Achievements

Award-Showcase

NMR Credits: 0

NMR Points: 193,617

Downloads: 0

Uploads: 0

Direct Evidence for Hydrogen Bonding Between Hydroxyl Groups in Glycans: A Combined NMR and Molecular Dynamics Study.

Direct Evidence for Hydrogen Bonding Between Hydroxyl Groups in Glycans: A Combined NMR and Molecular Dynamics Study.

Related Articles Direct Evidence for Hydrogen Bonding Between Hydroxyl Groups in Glycans: A Combined NMR and Molecular Dynamics Study.

J Phys Chem B. 2013 Mar 26;

Authors: Battistel MD, Pendrill R, Widmalm G, Freedberg DI

Abstract
With this report we introduce the abundant hydroxyl groups of glycans as NMR handles and structural probes that expand the repertoire of tools for structure-function studies on glycans in solution. To this end we present the facile detection and assignment of hydroxyl groups in a wide range of sample concentrations (0.5 to 1700 mM) and temperatures, ranging from -5 to 25 °C. We then exploit this information to directly detect hydrogen bonds, well known for their importance for molecular structural determination through NMR. Via HSQC-TOCSY we were able to determine directionality of these hydrogen bonds. Furthermore, by means of Molecular Dynamics simulations in conjunction with NMR, we establish that one out of the three detected hydrogen bonds arises from inter-molecular interactions, which may shed light in glycan-glycan interaction and their recognition by proteins.

PMID: 23531151 [PubMed - as supplied by publisher]

More...

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
[NMR paper] Summation solute hydrogen bonding acidity values for hydroxyl substituted flavones determined by NMR spectroscopy. Summation solute hydrogen bonding acidity values for hydroxyl substituted flavones determined by NMR spectroscopy. Related Articles Summation solute hydrogen bonding acidity values for hydroxyl substituted flavones determined by NMR spectroscopy. Nat Prod Commun. 2013 Jan;8(1):85-98 Authors: Whaley WL, Okoso-amaa EM, Womack CL, Vladimirova A, Rogers LB, Risher MJ, Abraham MH Abstract The flavonoids are a structurally diverse class of natural products that exhibit a broad spectrum of biochemical activities. The flavones are one of the most...	nmrlearner	Journal club	0	03-12-2013 07:09 PM
Rotational velocity rescaling of molecular dynamics trajectories for direct prediction of protein NMR relaxation Rotational velocity rescaling of molecular dynamics trajectories for direct prediction of protein NMR relaxation July 2012 Publication year: 2012 Source:Biophysical Chemistry, Volumes 168–169</br> </br> Rotational velocity rescaling (RVR) enables 15N relaxation data for the anisotropically tumbling B3 domain of Protein G (GB3) to be accurately predicted from 1?s of constant energy molecular dynamics simulation without recourse to any system-specific adjustable parameters. Superposition of adjacent trajectory frames yields the unique rotation axis and angle of rotation...	nmrlearner	Journal club	0	02-03-2013 10:13 AM
Methanol Strengthens Hydrogen Bonds and Weakens Hydrophobic Interactions in Proteins - A Combined Molecular Dynamics and NMR study. Methanol Strengthens Hydrogen Bonds and Weakens Hydrophobic Interactions in Proteins - A Combined Molecular Dynamics and NMR study. Methanol Strengthens Hydrogen Bonds and Weakens Hydrophobic Interactions in Proteins - A Combined Molecular Dynamics and NMR study. J Phys Chem B. 2011 May 2; Authors: Hwang S, Shao Q, Williams H, Hilty C, Gao YQ A combined simulation and experimental study was performed to investigate how methanol affects the structure of a model peptide BBA5. BBA5 forms a stable ?-hairpin-?-helix structure in aqueous solutions....	nmrlearner	Journal club	0	05-04-2011 04:14 PM
Methyl groups as probes of supra-molecular structure, dynamics and function Methyl groups as probes of supra-molecular structure, dynamics and function Abstract The development of new protein labeling strategies, along with optimized experiments that exploit the label, have significantly impacted on the types of biochemical problems that can now be addressed by solution NMR spectroscopy. Here we describe how methyl labeling of key residues in a highly deuterated protein background has facilitated studies of the structure, dynamics and interactions of supra-molecular particles. The methyl-labeling approach is briefly reviewed, followed by a summary of...	nmrlearner	Journal club	0	01-09-2011 12:46 PM
Alanine Methyl Groups as NMR Probes of Molecular Structure and Dynamics in High-Molecular-Weight Proteins Alanine Methyl Groups as NMR Probes of Molecular Structure and Dynamics in High-Molecular-Weight Proteins Raquel Godoy-Ruiz, Chenyun Guo and Vitali Tugarinov http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jacsat/0/jacsat.ahead-of-print/ja1083656/aop/images/medium/ja-2010-083656_0009.gif Journal of the American Chemical Society DOI: 10.1021/ja1083656 http://feeds.feedburner.com/~ff/acs/jacsat?d=yIl2AUoC8zA http://feeds.feedburner.com/~r/acs/jacsat/~4/hxZ4cabF688	nmrlearner	Journal club	0	12-08-2010 10:04 AM
[NMR paper] NMR-detected hydrogen exchange and molecular dynamics simulations provide structural NMR-detected hydrogen exchange and molecular dynamics simulations provide structural insight into fibril formation of prion protein fragment 106-126. Related Articles NMR-detected hydrogen exchange and molecular dynamics simulations provide structural insight into fibril formation of prion protein fragment 106-126. Proc Natl Acad Sci U S A. 2003 Dec 9;100(25):14790-5 Authors: Kuwata K, Matumoto T, Cheng H, Nagayama K, James TL, Roder H PrP106-126, a peptide corresponding to residues 107-127 of the human prion protein, induces neuronal cell...	nmrlearner	Journal club	0	11-24-2010 09:16 PM
[NMR paper] Solution (1)H NMR study of the influence of distal hydrogen bonding and N terminus ac Solution (1)H NMR study of the influence of distal hydrogen bonding and N terminus acetylation on the active site electronic and molecular structure of Aplysia limacina cyanomet myoglobin. Related Articles Solution (1)H NMR study of the influence of distal hydrogen bonding and N terminus acetylation on the active site electronic and molecular structure of Aplysia limacina cyanomet myoglobin. J Biol Chem. 2000 Jan 14;275(2):742-51 Authors: Nguyen BD, Xia Z, Cutruzzolá F, Allocatelli CT, Brunori M, La Mar GN The sea hare Aplysia limacina...	nmrlearner	Journal club	0	11-18-2010 09:15 PM
[NMR paper] Direct evidence for a two-state protein unfolding transition from hydrogen-deuterium Direct evidence for a two-state protein unfolding transition from hydrogen-deuterium exchange, mass spectrometry, and NMR. 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 Direct evidence for a two-state protein unfolding transition from hydrogen-deuterium exchange, mass spectrometry, and NMR. Protein Sci. 1996 Jun;5(6):1060-6 ...	nmrlearner	Journal club	0	08-22-2010 02:27 PM

« Previous Thread | Next 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