2eti: Difference between revisions
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==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== | ==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== | ||
<StructureSection load='2eti' size='340' side='right'caption='[[2eti | <StructureSection load='2eti' size='340' side='right'caption='[[2eti]]' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[2eti]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/ | <table><tr><td colspan='2'>[[2eti]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Ecballium_elaterium Ecballium elaterium]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ETI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ETI FirstGlance]. <br> | ||
</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2eti FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2eti OCA], [https://pdbe.org/2eti PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2eti RCSB], [https://www.ebi.ac.uk/pdbsum/2eti PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2eti ProSAT]</span></td></tr> | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr> | ||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2eti FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2eti OCA], [https://pdbe.org/2eti PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2eti RCSB], [https://www.ebi.ac.uk/pdbsum/2eti PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2eti ProSAT]</span></td></tr> | |||
</table> | </table> | ||
== Function == | == Function == | ||
[https://www.uniprot.org/uniprot/ITR2_ECBEL ITR2_ECBEL] Inhibits trypsin. | |||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
== Publication Abstract from PubMed == | == Publication Abstract from PubMed == | ||
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__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: | [[Category: Ecballium elaterium]] | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Castro | [[Category: Castro B]] | ||
[[Category: Chiche | [[Category: Chiche L]] | ||
[[Category: Heitz | [[Category: Heitz A]] | ||
[[Category: Le-Nguyen | [[Category: Le-Nguyen D]] | ||
Revision as of 19:35, 13 December 2023
USE OF RESTRAINED MOLECULAR DYNAMICS IN WATER TO DETERMINE THREE-DIMENSIONAL PROTEIN STRUCTURE: PREDICTION OF THE THREE-DIMENSIONAL STRUCTURE OF ECBALLIUM ELATERIUM TRYPSIN INHIBITOR IIUSE OF RESTRAINED MOLECULAR DYNAMICS IN WATER TO DETERMINE THREE-DIMENSIONAL PROTEIN STRUCTURE: PREDICTION OF THE THREE-DIMENSIONAL STRUCTURE OF ECBALLIUM ELATERIUM TRYPSIN INHIBITOR II
Structural highlights
FunctionITR2_ECBEL Inhibits trypsin. Publication Abstract from PubMedRefinement 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. 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.,Chiche L, Gaboriaud C, Heitz A, Mornon JP, Castro B, Kollman PA Proteins. 1989;6(4):405-17. PMID:2622910[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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