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PDBsum entry 2eti
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Protein inhibitor PDB id
2eti

 

 

 

 

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Contents
Protein chain
28 a.a.
PDB id:
2eti
Name: Protein inhibitor
Title: Use of restrained molecular dynamics in water to determine three- dimensional protein structure: prediction of the three-dimensional structure of ecballium elaterium trypsin inhibitor ii
Structure: Trypsin inhibitor ii. Chain: a. Engineered: yes
Source: Ecballium elaterium. Jumping cucumber. Organism_taxid: 3679
NMR struc: 1 models
Authors: A.Heitz,L.Chiche,D.Le-Nguyen,B.Castro
Key ref: L.Chiche et al. (1989). Use of restrained molecular dynamics in water to determine three-dimensional protein structure: prediction of the three-dimensional structure of Ecballium elaterium trypsin inhibitor II. Proteins, 6, 405-417. PubMed id: 2622910
Date:
15-Jul-91     Release date:   15-Oct-91    
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
P12071  (ITR2_ECBEL) -  Trypsin inhibitor 2 from Ecballium elaterium
Seq:
Struc: 		30 a.a.
28 a.a.
Key:    PfamA domain  Secondary structure

 

 
Proteins 6:405-417 (1989)
PubMed id: 2622910  
 
 
Use of restrained molecular dynamics in water to determine three-dimensional protein structure: prediction of the three-dimensional structure of Ecballium elaterium trypsin inhibitor II.
L.Chiche, C.Gaboriaud, A.Heitz, J.P.Mornon, B.Castro, P.A.Kollman.
 
  ABSTRACT  
 
Refinement of distance geometry (DG) structures of EETI-II (Heitz et al.: Biochemistry 28:2392-2398, 1989), a member of the squash family trypsin inhibitor, have been carried out by restrained molecular dynamics (RMD) in water. The resulting models show better side chain apolar/polar surface ratio and estimated solvation free energy than structures refined "in vacuo." The consistent lower values of residual NMR constraint violations, apolar/polar surface ratio, and solvation free energy for one of these refined structures allowed prediction of the 3D folding and disulfide connectivity of EETI-II. Except for the few first residues for which no NMR constraints were available, this computer model fully agreed with X-ray structures of CMTI-I (Bode et al.: FEBS Lett. 242:285-292, 1989) and EETI-II complexed with trypsin that appeared after the RMD simulation was completed. Restrained molecular dynamics in water is thus proved to be highly valuable for refinement of DG structures. Also, the successful use of apolar/polar surface ratio and of solvation free energy reinforce the analysis of Novotny et al. (Proteins 4:19-30, 1988) and shows that these criteria are useful indicators of correct versus misfolded models.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20958922 A.Walewska, A.Jaśkiewicz, G.Bulaj, and K.Rolka (2011).
Selenopeptide analogs of EETI-II retain potent trypsin inhibitory activities.
  Chem Biol Drug Des, 77, 93-97.  
19077275 A.Heitz, O.Avrutina, D.Le-Nguyen, U.Diederichsen, J.F.Hernandez, J.Gracy, H.Kolmar, and L.Chiche (2008).
Knottin cyclization: Impact on Structure and Dynamics.
  BMC Struct Biol, 8, 54.  
18393393 C.Combelles, J.Gracy, A.Heitz, D.J.Craik, and L.Chiche (2008).
Structure and folding of disulfide-rich miniproteins: insights from molecular dynamics simulations and MM-PBSA free energy calculations.
  Proteins, 73, 87.  
18058774 O.Avrutina, H.U.Schmoldt, D.Gabrijelcic-Geiger, A.Wentzel, H.Frauendorf, C.P.Sommerhoff, U.Diederichsen, and H.Kolmar (2008).
Head-to-tail cyclized cystine-knot peptides by a combined recombinant and chemical route of synthesis.
  Chembiochem, 9, 33-37.  
16131759 R.Krätzner, J.E.Debreczeni, T.Pape, T.R.Schneider, A.Wentzel, H.Kolmar, G.M.Sheldrick, and I.Uson (2005).
Structure of Ecballium elaterium trypsin inhibitor II (EETI-II): a rigid molecular scaffold.
  Acta Crystallogr D Biol Crystallogr, 61, 1255-1262.
PDB codes: 1h9h 1h9i 1w7z
14681383 J.C.Gelly, J.Gracy, Q.Kaas, D.Le-Nguyen, A.Heitz, and L.Chiche (2004).
The KNOTTIN website and database: a new information system dedicated to the knottin scaffold.
  Nucleic Acids Res, 32, D156-D159.  
12554935 J.Aÿ, K.Hilpert, N.Krauss, J.Schneider-Mergener, and W.Höhne (2003).
Structure of a hybrid squash inhibitor in complex with porcine pancreatic elastase at 1.8 A resolution.
  Acta Crystallogr D Biol Crystallogr, 59, 247-254.
PDB code: 1mcv
10400675 S.Lu, P.Deng, X.Liu, J.Luo, R.Han, X.Gu, S.Liang, X.Wang, F.Li, V.Lozanov, A.Patthy, and S.Pongor (1999).
Solution structure of the major alpha-amylase inhibitor of the crop plant amaranth.
  J Biol Chem, 274, 20473-20478.
PDB code: 1qfd
10049306 T.Wymore, and T.C.Wong (1999).
Molecular dynamics study of substance P peptides partitioned in a sodium dodecylsulfate micelle.
  Biophys J, 76, 1213-1227.  
8805527 M.Zweckstetter, M.Czisch, U.Mayer, M.L.Chu, W.Zinth, R.Timpl, and T.A.Holak (1996).
Structure and multiple conformations of the kunitz-type domain from human type VI collagen alpha3(VI) chain in solution.
  Structure, 4, 195-209.  
8521849 A.Heitz, L.Chiche, D.Le-Nguyen, and B.Castro (1995).
Folding of the squash trypsin inhibitor EETI II. Evidence of native and non-native local structural preferences in a linear analogue.
  Eur J Biochem, 233, 837-846.  
  7540906 F.D.Sönnichsen, B.D.Sykes, and P.L.Davies (1995).
Comparative modeling of the three-dimensional structure of type II antifreeze protein.
  Protein Sci, 4, 460-471.  
8075980 I.Radhakrishnan, and D.J.Patel (1994).
Solution structure of a pyrimidine.purine.pyrimidine DNA triplex containing T.AT, C+.GC and G.TA triples.
  Structure, 2, 17-32.
PDB code: 149d
  8003965 K.J.Nielsen, D.Alewood, J.Andrews, S.B.Kent, and D.J.Craik (1994).
An 1H NMR determination of the three-dimensional structures of mirror-image forms of a Leu-5 variant of the trypsin inhibitor from Ecballium elaterium (EETI-II).
  Protein Sci, 3, 291-302.
PDB code: 2let
8210313 A.T.Brünger, and M.Nilges (1993).
Computational challenges for macromolecular structure determination by X-ray crystallography and solution NMR-spectroscopy.
  Q Rev Biophys, 26, 49.  
  8443596 D.Le-Nguyen, A.Heitz, L.Chiche, M.el Hajji, and B.Castro (1993).
Characterization and 2D NMR study of the stable [9-21, 15-27] 2 disulfide intermediate in the folding of the 3 disulfide trypsin inhibitor EETI II.
  Protein Sci, 2, 165-174.  
  8251934 J.J.Skalicky, W.J.Metzler, D.J.Ciesla, A.Galdes, and A.Pardi (1993).
Solution structure of the calcium channel antagonist omega-conotoxin GVIA.
  Protein Sci, 2, 1591-1603.  
8272423 M.W.MacArthur, and J.M.Thornton (1993).
Conformational analysis of protein structures derived from NMR data.
  Proteins, 17, 232-251.  
  1304346 C.A.Schiffer, J.W.Caldwell, R.M.Stroud, and P.A.Kollman (1992).
Inclusion of solvation free energy with molecular mechanics energy: alanyl dipeptide as a test case.
  Protein Sci, 1, 396-400.  
  1304396 J.Guenot, and P.A.Kollman (1992).
Molecular dynamics studies of a DNA-binding protein: 2. An evaluation of implicit and explicit solvent models for the molecular dynamics simulation of the Escherichia coli trp repressor.
  Protein Sci, 1, 1185-1205.  
1515547 M.A.Ech-Cherif el-Kettani, and J.Durup (1992).
Theoretical determination of conformational paths in citrate synthase.
  Biopolymers, 32, 561-574.  
1541261 W.Bode, and R.Huber (1992).
Natural protein proteinase inhibitors and their interaction with proteinases.
  Eur J Biochem, 204, 433-451.  
2326281 L.Chiche, L.M.Gregoret, F.E.Cohen, and P.A.Kollman (1990).
Protein model structure evaluation using the solvation free energy of folding.
  Proc Natl Acad Sci U S A, 87, 3240-3243.  
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 codes are shown on the right.

 

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