1YTC

THERMODYNAMIC CYCLES AS PROBES OF STRUCTURE-FUNCTION RELATIONSHIPS IN UNFOLDED PROTEINS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Work: 0.162 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Thermodynamic cycles as probes of structure in unfolded proteins.

McGee, W.A.Rosell, F.I.Liggins, J.R.Rodriguez-Ghidarpour, S.Luo, Y.Chen, J.Brayer, G.D.Mauk, A.G.Nall, B.T.

(1996) Biochemistry 35: 1995-2007

  • DOI: 10.1021/bi951228f

  • PubMed Abstract: 
  • The relationship between structure and stability has been investigated for the folded forms and the unfolded forms of iso-2 cytochrome c and a variant protein with a stability-enhancing mutation, N52I iso-2. Differential scanning calorimetry has been ...

    The relationship between structure and stability has been investigated for the folded forms and the unfolded forms of iso-2 cytochrome c and a variant protein with a stability-enhancing mutation, N52I iso-2. Differential scanning calorimetry has been used to measure the reversible unfolding transitions for the proteins in both heme oxidation states. Reduction potentials have been measured as a function of temperature for the folded forms of the proteins. The combination of measurements of thermal stability and reduction potential gives three sides of a thermodynamic cycle and allows prediction of the reduction potential of the thermally unfolded state. The free energies of electron binding for the thermally unfolded proteins differ from those expected for a fully unfolded protein, suggesting that residual structure modulates the reduction potential. At temperatures near 50 degrees C the N52I mutation has a small but significant effect on oxidation state-sensitive structure in the thermally unfolded protein. Inspection of the high-resolution X-ray crystallographic structures of iso-2 and N52I iso-2 shows that the effects of the N52I mutation and oxidation state on native protein stability are correlated with changes in the mobility of specific polypeptide chain segments and with altered hydrogen bonding involving a conserved water molecule. However, there is no clear explanation of oxidation state or mutation-induced differences in stability of the proteins in terms of observed changes in structure and mobility of the folded forms of the proteins alone.


    Related Citations: 
    • Structure Determination and Analysis of Yeast Iso-2-Cytochrome C and a Composite Mutant Protein
      Murphy, M.E.P.,Nall, B.T.,Brayer, G.D.
      (1992) J.Mol.Biol. 227: 160
    • The Structure and Function of Omega Loop a Replacements in Cytochrome C
      Murphy, M.E.P.,Fetrow, J.S.,Burton, R.E.,Brayer, G.D.
      (1993) Protein Sci. 2: 1429


    Organizational Affiliation

    Department of Biochemistry, University of Texas Health Science Center, San Antonio 78284-7760, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
YEAST ISO-2 CYTOCHROME C
A
112Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 1 
Gene Names: CYC7 (CYP3)
Find proteins for P00045 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P00045
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
HEM
Query on HEM

Download SDF File 
Download CCD File 
A
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
M3L
Query on M3L
A
L-PEPTIDE LINKINGC9 H21 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Work: 0.162 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 36.660α = 90.00
b = 36.660β = 90.00
c = 138.920γ = 90.00
Software Package:
Software NamePurpose
R-AXISdata reduction
X-PLORphasing
X-PLORmodel building
PROLSQrefinement
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 1995-07-03 
  • Released Date: 1996-03-08 
  • Deposition Author(s): Luo, Y., Brayer, G.D.

Revision History 

  • Version 1.0: 1996-03-08
    Type: Initial release
  • Version 1.1: 2008-03-21
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2019-07-17
    Type: Data collection, Derived calculations, Other, Refinement description
  • Version 1.4: 2019-08-14
    Type: Data collection, Refinement description