3BVG

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.216 

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
  • Primary Citation of Related Structures:  
    3BVG

  • 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 contributions to binding are unknown ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Enterotoxin type C-3A237Staphylococcus aureusMutation(s): 5 
Gene Names: entC3
Find proteins for P0A0L5 (Staphylococcus aureus)
Explore P0A0L5 
Go to UniProtKB:  P0A0L5
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.216 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.7α = 90
b = 42.7β = 90
c = 287.142γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
CrystalCleardata collection
CrystalCleardata reduction
CrystalCleardata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

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

Revision History  (Full details and data files)

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