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

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

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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

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NMR sample preparation:

Protein disorder:

DisMeta

Protein solubility:

Isotope labeling:

Solid-state NMR:

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01-07-2016, 08:36 AM

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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]

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