5W88

NMR structure of the N-domain of troponin C bound to switch region of troponin I and 3-methyldiphenylamine (peptide mode)


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 80 
  • Conformers Submitted: 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation 3D Report Full Report



Literature

Structures reveal details of small molecule binding to cardiac troponin.

Cai, F.Li, M.X.Pineda-Sanabria, S.E.Gelozia, S.Lindert, S.West, F.Sykes, B.D.Hwang, P.M.

(2016) J Mol Cell Cardiol 101: 134-144

  • DOI: 10.1016/j.yjmcc.2016.10.016
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • In cardiac and skeletal muscle, the troponin complex turns muscle contraction on and off in a calcium-dependent manner. Many small molecules are known to bind to the troponin complex to modulate its calcium binding affinity, and this may be useful in ...

    In cardiac and skeletal muscle, the troponin complex turns muscle contraction on and off in a calcium-dependent manner. Many small molecules are known to bind to the troponin complex to modulate its calcium binding affinity, and this may be useful in a broad range of conditions in which striated muscle function is compromised, such as congestive heart failure. As a tool for developing drugs specific for the cardiac isoform of troponin, we have designed a chimeric construct (cChimera) consisting of the regulatory N-terminal domain of cardiac troponin C (cNTnC) fused to the switch region of cardiac troponin I (cTnI), mimicking the key binding event that turns on muscle contraction. We demonstrate by solution NMR spectroscopy that cChimera faithfully reproduces the native interface between cTnI and cNTnC. We determined that small molecules based on diphenylamine can bind to cChimera with a K D as low as 10μM. Solution NMR structures show that minimal structural perturbations in cChimera are needed to accommodate 3-methyldiphenylamine (3-mDPA), which is probably why it binds with higher affinity than previously studied compounds like bepridil, despite its significantly smaller size. The unsubstituted aromatic ring of 3-mDPA binds to an inner hydrophobic pocket adjacent to the central beta sheet of cNTnC. However, the methyl-substituted ring is able to bind in two different orientations, either inserting into the cNTnC-cTnI interface or "flipping out" to form contacts primarily with helix C of cNTnC. Our work suggests that preservation of the native interaction between cNTnC and cTnI is key to the development of a high affinity cardiac troponin-specific drug.


    Organizational Affiliation

    Department of Biochemistry, University of Alberta, Edmonton, AB, Canada; Department of Medicine, University of Alberta, Edmonton, AB, Canada. Electronic address: phwang1@ualberta.ca.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Troponin C, Troponin I
A
120Homo sapiensMutation(s): 2 
Gene Names: TNNC1TNNC
Find proteins for P19429 (Homo sapiens)
Go to UniProtKB:  P19429
NIH Common Fund Data Resources
PHAROS  P19429
Find proteins for P63316 (Homo sapiens)
Go to UniProtKB:  P63316
NIH Common Fund Data Resources
PHAROS  P63316
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
9XG
Query on 9XG

Download CCD File 
A
3-methyl-N-phenylaniline
C13 H13 N
TWPMMLHBHPYSMT-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 80 
  • Conformers Submitted: 
  • Selection Criteria: structures with the lowest energy 
  • OLDERADO: 5W88 Olderado

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Heart and Stroke Foundation of CanadaCanadaB.D.S., G-14-0005884

Revision History 

  • Version 1.0: 2017-07-12
    Type: Initial release