NMR paper Probing the Interaction between cHAVc3 Peptide and the EC1 Domain of E-cadherin using NMR and Molecular Dynamics Simulations.

		BioNMR > Educational resources > Journal club
[NMR paper] Probing the Interaction between cHAVc3 Peptide and the EC1 Domain of E-cadherin using NMR and Molecular Dynamics 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

01-07-2016, 08:36 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

Probing the Interaction between cHAVc3 Peptide and the EC1 Domain of E-cadherin using NMR and Molecular Dynamics Simulations.

Probing the Interaction between cHAVc3 Peptide and the EC1 Domain of E-cadherin using NMR and Molecular Dynamics Simulations.

Related Articles Probing the Interaction between cHAVc3 Peptide and the EC1 Domain of E-cadherin using NMR and Molecular Dynamics Simulations.

J Biomol Struct Dyn. 2016 Jan 5;:1-48

Authors: Alaofi A, Farokhi E, Prasasty VD, Anbanandam A, Kuczera K, Siahaan TJ

Abstract
The goal of this work is to probe the interaction between cyclic cHAVc3 peptide and the EC1 domain of human E-cadherin protein. Cyclic cHAVc3 peptide (cyclo(1,6)Ac-CSHAVC-NH2) binds to the EC1 domain as shown by chemical shift perturbations in the 2D (1)H,-(15)N-HSQC NMR spectrum. The molecular dynamics (MD) simulations of the EC1 domain showed folding of the C-terminal tail region into the main head region of the EC1 domain. For cHAVc3 peptide, replica exchange molecular dynamics (REMD) simulations generated five structural clusters of cHAVc3 peptide. Representative structures of cHAVc3 and the EC1 structure from MD simulations were used in molecular docking experiments with NMR-constraints to determine the binding site of the peptide on EC1. The results suggest that cHAVc3 binds to EC1 around residues Y36, S37, I38, I53, F77, S78, H79, and I94. The dissociation constants (Kd values) of cHAVc3 peptide to EC1 were estimated using the NMR chemical shifts data and the estimated Kds are in the range of 0.5 × 10(-5) to 7.0 × 10(-5) M.

PMID: 26728967 [PubMed - as supplied by publisher]

More...

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
Molecular dynamics simulations on PGLa using NMR orientational constraints Molecular dynamics simulations on PGLa using NMR orientational constraints Abstract NMR data obtained by solid state NMR from anisotropic samples are used as orientational constraints in molecular dynamics simulations for determining the structure and dynamics of the PGLa peptide within a membrane environment. For the simulation the recently developed molecular dynamics with orientational constraints technique (MDOC) is used. This method introduces orientation dependent pseudo-forces into the COSMOS-NMR force field. Acting during a molecular dynamics...	nmrlearner	Journal club	0	09-11-2015 06:48 AM
[NMR paper] Structure and dynamics of a fusion peptide helical hairpin on the membrane surface: comparison of molecular simulations and NMR. Structure and dynamics of a fusion peptide helical hairpin on the membrane surface: comparison of molecular simulations and NMR. http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--pubs.acs.org-images-pubmed-acspubs.jpg http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www.pubmedcentral.nih.gov-corehtml-pmc-pmcgifs-pubmed-pmc.gif Related Articles Structure and dynamics of a fusion peptide helical hairpin on the membrane surface: comparison of molecular simulations and NMR. J Phys Chem B. 2014 May 1;118(17):4461-70 ...	nmrlearner	Journal club	0	05-13-2015 12:28 AM
[NMR paper] Lipid dynamics studied by calculation of 31P solid-state NMR spectra using ensembles from molecular dynamics simulations. Lipid dynamics studied by calculation of 31P solid-state NMR spectra using ensembles from molecular dynamics simulations. http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--pubs.acs.org-images-pubmed-acspubs.jpg Related Articles Lipid dynamics studied by calculation of 31P solid-state NMR spectra using ensembles from molecular dynamics simulations. J Phys Chem B. 2014 May 15;118(19):5119-29 Authors: Hansen SK, Vestergaard M, Thøgersen L, Schiøtt B, Nielsen NC, Vosegaard T Abstract We present a method to...	nmrlearner	Journal club	0	04-22-2015 03:33 PM
[NMR paper] Assessment of the Use of NMR Chemical Shifts as Replica-Averaged Structural Restraints in Molecular Dynamics Simulations to Characterize the Dynamics of Proteins. Assessment of the Use of NMR Chemical Shifts as Replica-Averaged Structural Restraints in Molecular Dynamics Simulations to Characterize the Dynamics of Proteins. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--pubs.acs.org-images-pubmed-acspubs.jpg Related Articles Assessment of the Use of NMR Chemical Shifts as Replica-Averaged Structural Restraints in Molecular Dynamics Simulations to Characterize the Dynamics of Proteins. J Phys Chem B. 2013 Feb 1; Authors: Camilloni C, Cavalli A, Vendruscolo M Abstract It has been recently...	nmrlearner	Journal club	0	02-03-2013 10:19 AM
Membrane binding of an acyl-lactoferricin B antimicrobial peptide from solid-state NMR experiments and molecular dynamics simulations. Membrane binding of an acyl-lactoferricin B antimicrobial peptide from solid-state NMR experiments and molecular dynamics simulations. Membrane binding of an acyl-lactoferricin B antimicrobial peptide from solid-state NMR experiments and molecular dynamics simulations. Biochim Biophys Acta. 2011 Aug;1808(8):2019-30 Authors: Romo TD, Bradney LA, Greathouse DV, Grossfield A Abstract One approach to the growing health problem of antibiotic resistant bacteria is the development of antimicrobial peptides (AMPs) as alternative treatments. The...	nmrlearner	Journal club	0	08-19-2011 02:56 PM
Structure and Dynamics of the A?21–30 Peptide from the Interplay of NMR Experiments and Molecular Simulations Structure and Dynamics of the A?21–30 Peptide from the Interplay of NMR Experiments and Molecular Simulations Nicolas L. Fawzi, Aaron H. Phillips, Jory Z. Ruscio, Michaeleen Doucleff, David E. Wemmer and Teresa Head-Gordon Journal of the American Chemical Society DOI: 10.1021/ja204315n http://feeds.feedburner.com/~ff/acs/jacsat?d=yIl2AUoC8zA http://feeds.feedburner.com/~r/acs/jacsat/~4/bEQEah_ik60	nmrlearner	Journal club	0	07-09-2011 07:11 AM
Combined Use of Replica-Exchange Molecular Dynamics and Magic-Angle-Spinning Solid-State NMR Spectral Simulations for Determining the Structure and Orientation of Membrane-Bound Peptide. Combined Use of Replica-Exchange Molecular Dynamics and Magic-Angle-Spinning Solid-State NMR Spectral Simulations for Determining the Structure and Orientation of Membrane-Bound Peptide. Combined Use of Replica-Exchange Molecular Dynamics and Magic-Angle-Spinning Solid-State NMR Spectral Simulations for Determining the Structure and Orientation of Membrane-Bound Peptide. J Phys Chem B. 2011 Jun 13; Authors: Ikeda K, Kameda T, Harada E, Akutsu H, Fujiwara T We report an approach to determining membrane-peptides and -protein complex structures by...	nmrlearner	Journal club	0	06-15-2011 01:15 PM
[NMR paper] Probing conformational disorder in neurotensin by two-dimensional solid-state NMR and comparison to molecular dynamics simulations. Probing conformational disorder in neurotensin by two-dimensional solid-state NMR and comparison to molecular dynamics simulations. Related Articles Probing conformational disorder in neurotensin by two-dimensional solid-state NMR and comparison to molecular dynamics simulations. Biophys J. 2005 Sep;89(3):2113-20 Authors: Heise H, Luca S, de Groot BL, Grubmüller H, Baldus M An approach is introduced to characterize conformational ensembles of intrinsically unstructured peptides on the atomic level using two-dimensional solid-state NMR data and...	nmrlearner	Journal club	0	12-01-2010 06:56 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