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PDBsum entry 1pwt
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Circular permutant PDB id
1pwt

 

 

 

 

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Contents
Protein chain
61 a.a. *
Waters ×88
* Residue conservation analysis
PDB id:
1pwt
Name: Circular permutant
Title: Thermodynamic analysis of alpha-spectrin sh3 and two of its circular permutants with different loop lengths: discerning the reasons for rapid folding in proteins
Structure: Alpha spectrin. Chain: a. Fragment: sh3 domain. Synonym: pwt. Mutation: yes
Source: Gallus gallus. Chicken. Organism_taxid: 9031. Organ: brain. Cellular_location: cytoskeleton
Resolution:
1.77Å     R-factor:   0.189     R-free:   0.246
Authors: J.C.Martinez,A.R.Viguera,R.Berisio,M.Wilmanns,P.L.Mateo,V.V.Filmonov, L.Serrano
Key ref:
J.C.Martínez et al. (1999). Thermodynamic analysis of alpha-spectrin SH3 and two of its circular permutants with different loop lengths: discerning the reasons for rapid folding in proteins. Biochemistry, 38, 549-559. PubMed id: 9888794 DOI: 10.1021/bi981515u
Date:
06-Oct-98     Release date:   11-May-99    
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
P07751  (SPTN1_CHICK) -  Spectrin alpha chain, non-erythrocytic 1 from Gallus gallus
Seq:
Struc: 		 
Seq:
Struc: 		 
Seq:
Struc: 		 
Seq:
Struc: 		 
Seq:
Struc: 		2477 a.a.
61 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 

 
DOI no: 10.1021/bi981515u Biochemistry 38:549-559 (1999)
PubMed id: 9888794  
 
 
Thermodynamic analysis of alpha-spectrin SH3 and two of its circular permutants with different loop lengths: discerning the reasons for rapid folding in proteins.
J.C.Martínez, A.R.Viguera, R.Berisio, M.Wilmanns, P.L.Mateo, V.V.Filimonov, L.Serrano.
 
  ABSTRACT  
 
The temperature dependences of the unfolding-refolding reaction of a shorter version of the alpha-spectrin SH3 domain (PWT) used as a reference and of two circular permutants (with different poly-Gly loop lengths at the newly created fused loop) have been measured by differential scanning microcalorimetry and stopped-flow kinetics, to characterize the thermodynamic nature of the transition and native states. Differential scanning calorimetry results show that all these species do not belong to the same temperature dependency of heat effect. The family of the N47-D48s circular permutant (with 0-6 Gly inserted at the fused-loop) shows a higher enthalpy as happens with the PWT domain. The wild type (WT) and the S19-P20s permutant family have a more similar behavior although the second is far less stable. The crystallographic structure of the PWT shows a hairpin formation in the region corresponding to the unstructured N-terminus tail of the WT, explaining the enthalpic difference. There is a very good correlation between the calorimetric changes and the structural differences between the WT, PWT, and two circular permutants that suggests that their unfolded state cannot be too different. Elongation of the fused loop in the two permutants, taking as a reference the protein with one inserted Gly, results in a small Gibbs energy change of entropic origin as theoretically expected. Eyring plots of the unfolding and refolding semireactions show different behaviors for PWT, S19-P20s, and N47-D48s in agreement with previous studies indicating that they have different transition states. The SH3 transition state is relatively close to the native state with regard to changes in heat capacity and entropy, indicating a high degree of compactness and order. Regarding the differences in thermodynamic parameters, it seems that rapid folding could be achieved in proteins by decreasing the entropic barrier.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
19617233 A.M.Candel, E.S.Cobos, F.Conejero-Lara, and J.C.Martinez (2009).
Evaluation of folding co-operativity of a chimeric protein based on the molecular recognition between polyproline ligands and SH3 domains.
  Protein Eng Des Sel, 22, 597-606.  
18223000 E.S.Cobos, A.M.Candel, and J.C.Martinez (2008).
An error analysis for two-state protein-folding kinetic parameters and phi-values: progress toward precision by exploring pH dependencies on Leffler plots.
  Biophys J, 94, 4393-4404.  
18156472 I.E.Sánchez (2008).
Protein folding transition states probed by loop extension.
  Protein Sci, 17, 183-186.  
17251003 M.O.Lindberg, and M.Oliveberg (2007).
Malleability of protein folding pathways: a simple reason for complex behaviour.
  Curr Opin Struct Biol, 17, 21-29.  
17962401 S.S.Jaswal, and A.D.Miranker (2007).
Scope and utility of hydrogen exchange as a tool for mapping landscapes.
  Protein Sci, 16, 2378-2390.  
15978038 C.Lange, I.Luque, M.Hervás, J.Ruiz-Sanz, P.L.Mateo, and M.A.De la Rosa (2005).
Role of the surface charges D72 and K8 in the function and structural stability of the cytochrome c from Nostoc sp. PCC 7119.
  FEBS J, 272, 3317-3327.  
15459337 J.A.Knappenberger, C.M.Kraemer-Pecore, and J.T.Lecomte (2004).
Insertion of the cytochrome b5 heme-binding loop into an SH3 domain. Effects on structure and stability, and clues about the cytochrome's architecture.
  Protein Sci, 13, 2899-2908.  
15240485 J.M.Borreguero, F.Ding, S.V.Buldyrev, H.E.Stanley, and N.V.Dokholyan (2004).
Multiple folding pathways of the SH3 domain.
  Biophys J, 87, 521-533.  
15075405 Y.Bai, H.Zhou, and Y.Zhou (2004).
Critical nucleation size in the folding of small apparently two-state proteins.
  Protein Sci, 13, 1173-1181.  
12752445 G.Fernández-Ballester, J.Maya, A.Martín, S.Parche, J.Gómez, F.Titgemeyer, and J.L.Neira (2003).
The histidine-phosphocarrier protein of Streptomyces coelicolor folds by a partially folded species at low pH.
  Eur J Biochem, 270, 2254-2267.  
11179897 M.Oliveberg (2001).
Characterisation of the transition states for protein folding: towards a new level of mechanistic detail in protein engineering analysis.
  Curr Opin Struct Biol, 11, 94.  
11173498 R.Berisio, A.Viguera, L.Serrano, and M.Wilmanns (2001).
Atomic resolution structure of a mutant of the spectrin SH3 domain.
  Acta Crystallogr D Biol Crystallogr, 57, 337-340.
PDB code: 1g2b
10998048 A.M.Fernández, V.Villegas, J.C.Martínez, N.A.Van Nuland, F.Conejero-Lara, F.X.Avilés, L.Serrano, V.V.Filimonov, and P.L.Mateo (2000).
Thermodynamic analysis of helix-engineered forms of the activation domain of human procarboxypeptidase A2.
  Eur J Biochem, 267, 5891-5899.  
10429210 J.Ruiz-Sanz, A.Simoncsits, I.Törö, S.Pongor, P.L.Mateo, and V.V.Filimonov (1999).
A thermodynamic study of the 434-repressor N-terminal domain and of its covalently linked dimers.
  Eur J Biochem, 263, 246-253.  
10449376 L.Regan (1999).
Protein redesign.
  Curr Opin Struct Biol, 9, 494-499.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.

 

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