1JCA

Non-standard Design of Unstable Insulin Analogues with Enhanced Activity

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.204 

wwPDB Validation   3D Report Full Report


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


Literature

Non-standard insulin design: structure-activity relationships at the periphery of the insulin receptor.

Weiss, M.A., Wan, Z., Zhao, M., Chu, Y.C., Nakagawa, S.H., Burke, G.T., Jia, W., Hellmich, R., Katsoyannis, P.G.

(2002) J Mol Biol 315: 103-111

  • DOI: 10.1006/jmbi.2001.5224
  • Primary Citation of Related Structures:  
    1J73, 1JCA

  • PubMed Abstract: 

    • The design of insulin analogues has emphasized stabilization or destabilization of structural elements according to established principles of protein folding. To this end, solvent-exposed side-chains extrinsic to the receptor-binding surface provide convenient sites of modification ...

    The design of insulin analogues has emphasized stabilization or destabilization of structural elements according to established principles of protein folding. To this end, solvent-exposed side-chains extrinsic to the receptor-binding surface provide convenient sites of modification. An example is provided by an unfavorable helical C-cap (Thr(A8)) whose substitution by favorable amino acids (His(A8) or Arg(A8)) has yielded analogues of improved stability. Remarkably, these analogues also exhibit enhanced activity, suggesting that activity may correlate with stability. Here, we test this hypothesis by substitution of diaminobutyric acid (Dab(A8)), like threonine an amino acid of low helical propensity. The crystal structure of Dab(A8)-insulin is similar to those of native insulin and the related analogue Lys(A8)-insulin. Although no more stable than native insulin, the non-standard analogue is twice as active. Stability and affinity can therefore be uncoupled. To investigate alternative mechanisms by which A8 substitutions enhance activity, multiple substitutions were introduced. Surprisingly, diverse aliphatic, aromatic and polar side-chains enhance receptor binding and biological activity. Because no relationship is observed between activity and helical propensity, we propose that local interactions between the A8 side-chain and an edge of the hormone-receptor interface modulate affinity. Dab(A8)-insulin illustrates the utility of non-standard amino acids in hypothesis-driven protein design.

    Related Citations: 
    • A Proposed Interaction Model of Insulin Molecules with its Receptor
      Liang, D.C., Chang, W.R., Wan, Z.L., Vijayan, N.M.
      (1994) Biophys Chem 50: 63
    • Diabetes-associated Mutations in a beta-Cell Transcription Factor Destabilize an Antiparallel "mini-zipper" in a Dimerization Interface
      Hua, Q.X., Zhao, M., Narayana, N., Nakagawa, S.H., Jia, W., Weiss, M.A.
      (2000) Proc Natl Acad Sci U S A 97: 1999
    • The Relationship Between Insulin Bioactivity and Structure in the NH2-terminal A-chain Helix
      Olsen, H.B., Ludvigsen, S., Kaarsholm, N.C.
      (1998) J Mol Biol 284: 477
    • Mapping the Functional Surface of Insulin by Design: Structure and Function of Novel A-chain Analogue
      Hua, Q.X., Hu, S.Q., Frank, B.H., Jia, W., Chu, Y.C., Wang, S.H., Burke, G.T., Katsoyannis, P.G., Weiss, M.A.
      (1996) J Mol Biol 264: 390
    Organizational Affiliation: 

    Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA. weiss@biochemistry.cwru.edu



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
insulin aA, C21N/AMutation(s): 1 
UniProt & NIH Common Fund Data Resources
Find proteins for P01308 (Homo sapiens)
Explore P01308 
Go to UniProtKB:  P01308
PHAROS:  P01308
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01308
Protein Feature View
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  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
insulin bB, D30N/AMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P01308 (Homo sapiens)
Explore P01308 
Go to UniProtKB:  P01308
PHAROS:  P01308
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01308
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN
Download Ideal Coordinates CCD File 
E [auth B],
F [auth D]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.204 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.652α = 90
b = 80.652β = 90
c = 37.936γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-06-20
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2021-10-27
    Changes: Advisory, Database references, Derived calculations