NMR paper A detailed picture of a protein-carbohydrate hydrogen-bonding network revealed by NMR and MD simulations.

		BioNMR > Educational resources > Journal club
[NMR paper] A detailed picture of a protein-carbohydrate hydrogen-bonding network revealed by NMR and MD simulations.

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

09-13-2020, 09:18 AM

nmrlearner

Senior Member

Join Date: Jan 2005

Posts: 23,732

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

A detailed picture of a protein-carbohydrate hydrogen-bonding network revealed by NMR and MD simulations.

Related Articles A detailed picture of a protein-carbohydrate hydrogen-bonding network revealed by NMR and MD simulations.

Glycobiology. 2020 Sep 08;:

Authors: Nestor G, Ruda A, Anderson T, Oscarson S, Widmalm G, Gronenborn AM

Abstract
Cyanovirin-N (CV-N) is a cyanobacterial lectin with antiviral activity towards HIV and several other viruses. Here, we identify mannoside hydroxyl protons that are hydrogen bonded to the protein backbone of the CV-N domain B binding site, using NMR spectroscopy. For the two carbohydrate ligands Man?(1->2)Man?OMe and Man?(1->2) Man?(1->6)Man?OMe five hydroxyl protons are involved in hydrogen-bonding networks. Comparison with previous crystallographic results revealed that four of these hydroxyl protons donate hydrogen bonds to protein backbone carbonyl oxygens in solution and in the crystal. Hydrogen bonds were not detected between the side chains of Glu41 and Arg76 with sugar hydroxyls, as previously proposed for CV-N binding of mannosides. Molecular dynamics simulations of the CV-N/Man?(1->2)Man?(1->6)Man?OMe complex confirmed the NMR-determined hydrogen-bonding network. Detailed characterization of CV-N/mannoside complexes provides a better understanding of lectin-carbohydrate interactions and opens up to the use of CV-N and similar lectins as antiviral agents.

PMID: 32902635 [PubMed - as supplied by publisher]

More...

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
[NMR paper] Interresidual hydrogen bonding in carbohydrates unraveled by NMR spectroscopy and molecular dynamics simulations. Interresidual hydrogen bonding in carbohydrates unraveled by NMR spectroscopy and molecular dynamics simulations. http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--media.wiley.com-assets-7315-19-Wiley_FullText_120x30_orange.png Related Articles Interresidual hydrogen bonding in carbohydrates unraveled by NMR spectroscopy and molecular dynamics simulations. Chembiochem. 2019 May 08;: Authors: Rönnols J, Engström O, Schnupf U, Säwén E, Brady JW, Widmalm G Abstract Carbohydrates, also known as glycans in...	nmrlearner	Journal club	0	05-09-2019 11:40 PM
[NMR paper] Indirect use of deuterium in solution NMR studies of protein structure and hydrogen bonding. Indirect use of deuterium in solution NMR studies of protein structure and hydrogen bonding. Related Articles Indirect use of deuterium in solution NMR studies of protein structure and hydrogen bonding. Prog Nucl Magn Reson Spectrosc. 2014 Feb;77:49-68 Authors: Tugarinov V Abstract A description of the utility of deuteration in protein NMR is provided with an emphasis on quantitative evaluation of the effects of deuteration on a number of NMR parameters of proteins: (1) chemical shifts, (2) scalar coupling constants, (3) relaxation...	nmrlearner	Journal club	0	01-15-2014 05:16 PM
[NMR paper] Use of H/D isotope effects to gather information about hydrogen bonding and hydrogen exchange rates Use of H/D isotope effects to gather information about hydrogen bonding and hydrogen exchange rates Publication date: Available online 11 October 2013 Source:Journal of Magnetic Resonance</br> Author(s): Mitsuhiro Takeda , Yohei Miyanoiri , Tsutomu Terauchi , Chin-Jiun Yang , Masatsune Kainosho</br> Polar side-chains in proteins play important roles in formingand maintaining three-dimensional structures, and thus participate invarious biological functions. Until recently, most protein NMR studieshave focused onthe non-exchangeable protons of amino acid...	nmrlearner	Journal club	0	10-11-2013 10:43 AM
Indirect Use of Deuterium in Solution NMR Studies of Protein Structure and Hydrogen Bonding Indirect Use of Deuterium in Solution NMR Studies of Protein Structure and Hydrogen Bonding Publication date: Available online 28 August 2013 Source:Progress in Nuclear Magnetic Resonance Spectroscopy</br> Author(s): Vitali Tugarinov</br> A description of the utility of deuteration in protein NMR is provided with an emphasis on quantitative evaluation of the effects of deuteration on a number of NMR parameters of proteins: (1) chemical shifts, (2) scalar coupling constants, (3) relaxation properties (R 1 and R 2 rates) of nuclei directly attached to one or more...	nmrlearner	Journal club	0	08-29-2013 01:27 AM
[NMR paper] Hydrogen bonding on the ice-binding face of a beta-helical antifreeze protein indicat Hydrogen bonding on the ice-binding face of a beta-helical antifreeze protein indicated by amide proton NMR chemical shifts. Related Articles Hydrogen bonding on the ice-binding face of a beta-helical antifreeze protein indicated by amide proton NMR chemical shifts. Biochemistry. 2004 Oct 19;43(41):13012-7 Authors: Daley ME, Graether SP, Sykes BD The dependence of amide proton chemical shifts on temperature is used as an indication of the hydrogen bonding properties in a protein. The amide proton temperature coefficients of the beta-helical...	nmrlearner	Journal club	0	11-24-2010 10:01 PM
[NMR paper] Hydrogen bonding in high-resolution protein structures: a new method to assess NMR pr Hydrogen bonding in high-resolution protein structures: a new method to assess NMR protein geometry. Related Articles Hydrogen bonding in high-resolution protein structures: a new method to assess NMR protein geometry. J Am Chem Soc. 2002 Sep 4;124(35):10621-6 Authors: Lipsitz RS, Sharma Y, Brooks BR, Tjandra N An analysis of backbone hydrogen bonds has been performed on nine high-resolution protein X-ray crystal structures. Backbone hydrogen-bond geometry is compared in the context of X-ray crystal structure resolution. A strong correlation...	nmrlearner	Journal club	0	11-24-2010 08:58 PM
[NMR paper] NMR of hydrogen bonding in cold-shock protein A and an analysis of the influence of c NMR of hydrogen bonding in cold-shock protein A and an analysis of the influence of crystallographic resolution on comparisons of hydrogen bond lengths. Related Articles NMR of hydrogen bonding in cold-shock protein A and an analysis of the influence of crystallographic resolution on comparisons of hydrogen bond lengths. Protein Sci. 2001 Sep;10(9):1856-68 Authors: Alexandrescu AT, Snyder DR, Abildgaard F Hydrogen bonding in cold-shock protein A of Escherichia coli has been investigated using long-range HNCO spectroscopy. Nearly half of the...	nmrlearner	Journal club	0	11-19-2010 08:44 PM
[NMR paper] 1H NMR investigation of the distal hydrogen bonding network and ligand tilt in the cy 1H NMR investigation of the distal hydrogen bonding network and ligand tilt in the cyanomet complex of oxygen-avid Ascaris suum hemoglobin. Related Articles 1H NMR investigation of the distal hydrogen bonding network and ligand tilt in the cyanomet complex of oxygen-avid Ascaris suum hemoglobin. J Biol Chem. 1999 Nov 5;274(45):31819-26 Authors: Xia Z, Zhang W, Nguyen BD, Mar GN, Kloek AP, Goldberg DE The O(2)-avid hemoglobin from the parasitic nematode Ascaris suum exhibits one of the slowest known O(2) off rates. Solution (1)H NMR has been...	nmrlearner	Journal club	0	11-18-2010 08:31 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