6CK2

Insulin analog containing a YB26W mutation

  • Classification: HORMONE
  • Organism(s): Homo sapiens
  • Mutation(s): 2 

  • Deposited: 2018-02-27 Released: 2018-06-13 
  • Deposition Author(s): Rege, N.K., Yee, V.C., Weiss, M.A.
  • Funding Organization(s): National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK) 

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.207 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history. 

Literature

Structure-based stabilization of insulin as a therapeutic protein assembly via enhanced aromatic-aromatic interactions.

Rege, N.K., Wickramasinghe, N.P., Tustan, A.N., Phillips, N.F.B., Yee, V.C., Ismail-Beigi, F., Weiss, M.A.

(2018) J. Biol. Chem. 293: 10895-10910

  • DOI: 10.1074/jbc.RA118.003650

  • PubMed Abstract: 

    • Key contributions to protein structure and stability are provided by weakly polar interactions, which arise from asymmetric electronic distributions within amino acids and peptide bonds. Of particular interest are aromatic side chains whose direction ...

    Key contributions to protein structure and stability are provided by weakly polar interactions, which arise from asymmetric electronic distributions within amino acids and peptide bonds. Of particular interest are aromatic side chains whose directional π-systems commonly stabilize protein interiors and interfaces. Here, we consider aromatic-aromatic interactions within a model protein assembly: the dimer interface of insulin. Semi-classical simulations of aromatic-aromatic interactions at this interface suggested that substitution of residue Tyr B26 by Trp would preserve native structure while enhancing dimerization (and hence hexamer stability). The crystal structure of a [Trp B26 ]insulin analog (determined as a T 3 R f 3 zinc hexamer at a resolution of 2.25 Å) was observed to be essentially identical to that of WT insulin. Remarkably and yet in general accordance with theoretical expectations, spectroscopic studies demonstrated a 150-fold increase in the in vitro lifetime of the variant hexamer, a critical pharmacokinetic parameter influencing design of long-acting formulations. Functional studies in diabetic rats indeed revealed prolonged action following subcutaneous injection. The potency of the Trp B26 -modified analog was equal to or greater than an unmodified control. Thus, exploiting a general quantum-chemical feature of protein structure and stability, our results exemplify a mechanism-based approach to the optimization of a therapeutic protein assembly.

    Organizational Affiliation: 

    From the Departments of Biochemistry and.,From the Departments of Biochemistry and weissma@iu.edu.,Medicine, Case Western Reserve University, Cleveland, Ohio 44106 and.,the Department of Biochemistry, Indiana University School of Medicine, Indianapolis, Indiana 46202.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Insulin A chain
A, C
21Homo sapiensMutation(s): 0 
Gene Names: INS
Find proteins for P01308 (Homo sapiens)
Go to Gene View: INS
Go to UniProtKB:  P01308
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Insulin B chain
B, D
30Homo sapiensMutation(s): 2 
Gene Names: INS
Find proteins for P01308 (Homo sapiens)
Go to Gene View: INS
Go to UniProtKB:  P01308
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN
Download SDF File 
Download CCD File 
B, D
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL
Download SDF File 
Download CCD File 
D
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
IPH
Query on IPH
Download SDF File 
Download CCD File 
C
PHENOL
C6 H6 O
ISWSIDIOOBJBQZ-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
ORN
Query on ORN
B, D
L-PEPTIDE LINKINGC5 H12 N2 O2ALA
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.207 
  • Space Group: H 3
Unit Cell:
Length (Å)Angle (°)
a = 79.755α = 90.00
b = 79.755β = 90.00
c = 37.610γ = 120.00
Software Package:
Software NamePurpose
REFMACphasing
PHENIXrefinement
Aimlessdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)United StatesR01 DK0409849
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)United States1F30DK112644

Revision History 

  • Version 1.0: 2018-06-13
    Type: Initial release
  • Version 1.1: 2018-06-27
    Type: Data collection, Database references
  • Version 1.2: 2018-07-25
    Type: Data collection, Database references
  • Version 1.3: 2019-12-25
    Type: Author supporting evidence