NMR paper Capturing the dynamic association between a tris-dipicolinate lanthanide complex and a decapeptide: a combined paramagnetic NMR and molecular dynamics exploration

		BioNMR > Educational resources > Journal club
[NMR paper] Capturing the dynamic association between a tris-dipicolinate lanthanide complex and a decapeptide: a combined paramagnetic NMR and molecular dynamics exploration

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

05-20-2021, 12:45 PM

nmrlearner

Senior Member

Join Date: Jan 2005

Posts: 23,777

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

Capturing the dynamic association between a tris-dipicolinate lanthanide complex and a decapeptide: a combined paramagnetic NMR and molecular dynamics exploration

Capturing the dynamic association between a tris-dipicolinate lanthanide complex and a decapeptide: a combined paramagnetic NMR and molecular dynamics exploration

In the realm of biomolecules, peptides can present a large diversity of structures. Our study sheds new light on the structural interplay between a tris-dipicolinate lanthanide probe and a decapeptide SASYKTLPRG. Although a rather trivial, electrostatically driven interaction was expected, the combination of paramagnetic NMR and molecular dynamics simulations reveals a highly dynamic association process and allows for providing extensive insights into the interaction sites and their occupancy....

More...

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
[NMR paper] Unravelling the Fast Alkali-Ion Dynamics in Paramagnetic Battery Materials Combined with NMR and Deep-Potential Molecular Dynamics Simulation Unravelling the Fast Alkali-Ion Dynamics in Paramagnetic Battery Materials Combined with NMR and Deep-Potential Molecular Dynamics Simulation Angewandte Chemie International Edition, Volume 60, Issue 22, Page 12547-12553, May 25, 2021. More...	nmrlearner	Journal club	0	05-17-2021 02:04 PM
Capturing a Dynamic Chaperone–Substrate Interaction Using NMR-Informed Molecular Modeling Capturing a Dynamic Chaperone–Substrate Interaction Using NMR-Informed Molecular Modeling Loi?c Salmon, Logan S. Ahlstrom, Scott Horowitz, Alex Dickson, Charles L. Brooks and James C. A. Bardwell http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jacsat/0/jacsat.ahead-of-print/jacs.6b02382/20160802/images/medium/ja-2016-02382u_0007.gif Journal of the American Chemical Society DOI: 10.1021/jacs.6b02382 http://feeds.feedburner.com/~ff/acs/jacsat?d=yIl2AUoC8zA http://feeds.feedburner.com/~r/acs/jacsat/~4/ihnI-EXnn5s	nmrlearner	Journal club	0	08-03-2016 04:58 AM
[NMR paper] Capturing a dynamic chaperone-substrate interaction using NMR-informed molecular modeling. Capturing a dynamic chaperone-substrate interaction using NMR-informed molecular modeling. Capturing a dynamic chaperone-substrate interaction using NMR-informed molecular modeling. J Am Chem Soc. 2016 Jul 14; Authors: Salmon L, Ahlstrom LS, Horowitz S, Dickson A, Brooks CL, Bardwell JC Abstract Chaperones maintain a healthy proteome by preventing aggregation and by aiding in protein folding. Precisely how chaperones influence the conformational properties of their substrates, however, remains unclear. To achieve a detailed...	nmrlearner	Journal club	0	07-16-2016 04:54 AM
[NMR paper] Combined molecular dynamics, STD-NMR, and CORCEMA protocol yields structural model for a UDP-galactopyranose mutase-inhibitor complex. Combined molecular dynamics, STD-NMR, and CORCEMA protocol yields structural model for a UDP-galactopyranose mutase-inhibitor complex. http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles Combined molecular dynamics, STD-NMR, and CORCEMA protocol yields structural model for a UDP-galactopyranose mutase-inhibitor complex. Bioorg Med Chem Lett. 2015 Mar 15;25(6):1284-7 Authors: Shi Y, Ardá A, Pinto BM Abstract UDP-galactopyranose mutase (UGM) is...	nmrlearner	Journal club	0	12-29-2015 08:05 PM
[NMR paper] Capturing Conformational States in Proteins Using Sparse Paramagnetic NMR Data. Capturing Conformational States in Proteins Using Sparse Paramagnetic NMR Data. Related Articles Capturing Conformational States in Proteins Using Sparse Paramagnetic NMR Data. PLoS One. 2015;10(5):e0127053 Authors: Pilla KB, Leman JK, Otting G, Huber T Abstract Capturing conformational changes in proteins or protein-protein complexes is a challenge for both experimentalists and computational biologists. Solution nuclear magnetic resonance (NMR) is unique in that it permits structural studies of proteins under greatly varying...	nmrlearner	Journal club	0	05-21-2015 04:28 PM
Dynamic Nuclear Polarization of 1H, 13C, and 59Co in a Tris(ethylenediamine)cobalt(III) Crystalline Lattice Doped with Cr(III) From The DNP-NMR Blog: Dynamic Nuclear Polarization of 1H, 13C, and 59Co in a Tris(ethylenediamine)cobalt(III) Crystalline Lattice Doped with Cr(III) Corzilius, B., et al., Dynamic Nuclear Polarization of H, C, and Co in a Tris(ethylenediamine)cobalt(III) Crystalline Lattice Doped with Cr(III). J Am Chem Soc, 2014. http://www.ncbi.nlm.nih.gov/pubmed/25069794	nmrlearner	News from NMR blogs	0	08-11-2014 02:21 PM
[NMR paper] Exploration of the supramolecular interactions involving tris-dipicolinate lanthanide complexes in protein crystals by a combined biostructural, computational and NMR study. Exploration of the supramolecular interactions involving tris-dipicolinate lanthanide complexes in protein crystals by a combined biostructural, computational and NMR study. Related Articles Exploration of the supramolecular interactions involving tris-dipicolinate lanthanide complexes in protein crystals by a combined biostructural, computational and NMR study. Phys Chem Chem Phys. 2013 Sep 24; Authors: Dumont E, Pompidor G, D'Aléo A, Vicat J, Toupet L, Kahn R, Girard E, Maury O, Giraud N Abstract Incorporating in a non-covalent...	nmrlearner	Journal club	0	09-27-2013 03:28 AM
[NMR paper] A caged lanthanide complex as a paramagnetic shift agent for protein NMR. A caged lanthanide complex as a paramagnetic shift agent for protein NMR. Related Articles A caged lanthanide complex as a paramagnetic shift agent for protein NMR. Chemistry. 2004 Jul 5;10(13):3252-60 Authors: Prudêncio M, Rohovec J, Peters JA, Tocheva E, Boulanger MJ, Murphy ME, Hupkes HJ, Kosters W, Impagliazzo A, Ubbink M A lanthanide complex, named CLaNP (caged lanthanide NMR probe) has been developed for the characterisation of proteins by paramagnetic NMR spectroscopy. The probe consists of a lanthanide chelated by a derivative of DTPA...	nmrlearner	Journal club	0	11-24-2010 09:51 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