3BVG

Manipulating the coupled folding and binding process drives affinity maturation in a protein-protein complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.213 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Assessing energetic contributions to binding from a disordered region in a protein-protein interaction

Cho, S.Swaminathan, C.P.Bonsor, D.A.Kerzic, M.C.Guan, R.Yang, J.Kieke, M.C.Andersen, P.S.Kranz, D.M.Mariuzza, R.A.Sundberg, E.J.

(2010) Biochemistry 49: 9256-9268

  • DOI: 10.1021/bi1008968

  • PubMed Abstract: 
  • Many functional proteins are at least partially disordered prior to binding. Although the structural transitions upon binding of disordered protein regions can influence the affinity and specificity of protein complexes, their precise energetic contr ...

    Many functional proteins are at least partially disordered prior to binding. Although the structural transitions upon binding of disordered protein regions can influence the affinity and specificity of protein complexes, their precise energetic contributions to binding are unknown. Here, we use a model protein-protein interaction system in which a locally disordered region has been modified by directed evolution to quantitatively assess the thermodynamic and structural contributions to binding of disorder-to-order transitions. Through X-ray structure determination of the protein binding partners before and after complex formation and isothermal titration calorimetry of the interactions, we observe a correlation between protein ordering and binding affinity for complexes along this affinity maturation pathway. Additionally, we show that discrepancies between observed and calculated heat capacities based on buried surface area changes in the protein complexes can be explained largely by heat capacity changes that would result solely from folding the locally disordered region. Previously developed algorithms for predicting binding energies of protein-protein interactions, however, are unable to correctly model the energetic contributions of the structural transitions in our model system. While this highlights the shortcomings of current computational methods in modeling conformational flexibility, it suggests that the experimental methods used here could provide training sets of molecular interactions for improving these algorithms and further rationalizing molecular recognition in protein-protein interactions.


    Organizational Affiliation

    W. M. Keck Laboratory for Structural Biology, University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD 20850, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Enterotoxin type C-3
A
237Staphylococcus aureusMutation(s): 0 
Gene Names: entC3
Find proteins for P0A0L5 (Staphylococcus aureus)
Go to UniProtKB:  P0A0L5
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.213 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 42.700α = 90.00
b = 42.700β = 90.00
c = 287.142γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
PDB_EXTRACTdata extraction
CrystalCleardata collection
CrystalCleardata scaling
REFMACrefinement
CrystalCleardata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2008-01-07 
  • Released Date: 2009-01-27 
  • Deposition Author(s): Cho, S., Eric, J.S.

Revision History 

  • Version 1.0: 2009-01-27
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance