5BK1

Crystal structure of maltose binding protein in complex with an endosteric synthetic antibody


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.205 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Engineered synthetic antibodies as probes to quantify the energetic contributions of ligand binding to conformational changes in proteins.

Mukherjee, S.Griffin, D.H.Horn, J.R.Rizk, S.S.Nocula-Lugowska, M.Malmqvist, M.Kim, S.S.Kossiakoff, A.A.

(2018) J. Biol. Chem. --: --

  • DOI: 10.1074/jbc.RA117.000656
  • Primary Citation of Related Structures:  5BJZ, 5BK2

  • PubMed Abstract: 
  • Conformational changes in proteins due to ligand binding are ubiquitous in biological systems and are integral to many biological systems. However, it is often challenging to link ligand-induced conformational changes to a resulting biological functi ...

    Conformational changes in proteins due to ligand binding are ubiquitous in biological systems and are integral to many biological systems. However, it is often challenging to link ligand-induced conformational changes to a resulting biological function because it is difficult to distinguish between the energetic components associated with ligand-binding and those due to structural rearrangements. Here, we used a  unique approach exploiting conformation-specific and regio-specific synthetic antibodies (sABs) to probe the energetic contributions of ligand-binding to conformation changes. Using maltose binding protein (MBP) as a model system, customized phage display selections were performed to generate sABs that stabilize MBP in different conformational states, modulating ligand binding affinity in competitive, allosteric or peristeric manners. We determined that the binding of a closed conformation-specific sAB (sAB-11M) to MBP in the absence of maltose is entropically driven, providing new insight into designing antibody stabilized protein interactions. Crystal structures of sABs bound to MBP, together with biophysical data delineate the basis of free energy differences between different conformational states and confirm the use of the sABs as energy probes for dissecting enthalpic and entropic contributions to conformational transitions. Our work provides a foundation for investigating the energetic contributions of distinct conformational dynamics to specific biological outputs. We anticipate that our approach also may be valuable for analyzing the energy landscapes of regulatory proteins controlling biological responses to environmental changes.


    Organizational Affiliation

    University of Chicago.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Synthetic antibody, Fab fragment, Heavy Chain
H, C
236N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Synthetic antibody, Fab fragment, Light Chain
L, D
216N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Maltose binding protein
A, B
398N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
C
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
B, C
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.205 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 76.830α = 90.00
b = 120.810β = 90.00
c = 193.600γ = 90.00
Software Package:
Software NamePurpose
MD2data collection
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationCountryGrant Number
Chicago Biomedical ConsortiumUnited States--

Revision History 

  • Version 1.0: 2018-01-17
    Type: Initial release
  • Version 1.1: 2018-01-24
    Type: Database references