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==Protein environment affects the water-tryptophan binding mode. Molecular dynamics simulations of Engrailed homeodomain mutants== | ==Protein environment affects the water-tryptophan binding mode. Molecular dynamics simulations of Engrailed homeodomain mutants== | ||
<StructureSection load='6fvc' size='340' side='right'caption='[[6fvc | <StructureSection load='6fvc' size='340' side='right'caption='[[6fvc]]' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[6fvc]] is a 1 chain structure with sequence from [ | <table><tr><td colspan='2'>[[6fvc]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Drosophila_melanogaster Drosophila melanogaster]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6FVC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6FVC FirstGlance]. <br> | ||
</td></tr> | </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=6fvc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6fvc OCA], [https://pdbe.org/6fvc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6fvc RCSB], [https://www.ebi.ac.uk/pdbsum/6fvc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6fvc ProSAT]</span></td></tr> | ||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | |||
</table> | </table> | ||
== Function == | == Function == | ||
[ | [https://www.uniprot.org/uniprot/HMEN_DROME HMEN_DROME] This protein specifies the body segmentation pattern. It is required for the development of the central nervous system. Transcriptional regulator that represses activated promoters. Wg signaling operates by inactivating the SGG repression of EN autoactivation. | ||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Water molecules can interact with aromatic moieties using either their O-H bonds or their lone-pairs of electrons. In proteins, water-pi interactions have been reported to occur with tryptophan and histidine residues, and dynamic exchange between O-Hpi hydrogen bonding and lone-pairpi interactions was suggested to take place, based on ab initio calculations. Here we used classical and QM/MM molecular dynamics simulations, complemented with an NMR study, to examine a specific water-indole interaction observed in the engrailed homeodomain and in its mutants. Our simulations indicate that the binding mode between water and indole can adapt to the potential created by the surrounding amino acids (and by the residues at the DNA surface in protein-DNA complexes), and support the model of dynamic switching between the O-Hpi hydrogen bonding and lone-pairpi binding modes. | |||
Protein environment affects the water-tryptophan binding mode. MD, QM/MM, and NMR studies of engrailed homeodomain mutants.,Spackova N, Trosanova Z, Sebesta F, Jansen S, Burda JV, Srb P, Zachrdla M, Zidek L, Kozelka J Phys Chem Chem Phys. 2018 May 9;20(18):12664-12677. doi: 10.1039/c7cp08623g. PMID:29696277<ref>PMID:29696277</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 6fvc" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: | [[Category: Drosophila melanogaster]] | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Jansen | [[Category: Jansen S]] | ||
[[Category: Kozelka | [[Category: Kozelka J]] | ||
[[Category: Srb | [[Category: Srb P]] | ||
[[Category: Trosanova | [[Category: Trosanova Z]] | ||
[[Category: Zachrdla | [[Category: Zachrdla M]] | ||
[[Category: Zidek | [[Category: Zidek L]] | ||
Revision as of 13:46, 14 June 2023
Protein environment affects the water-tryptophan binding mode. Molecular dynamics simulations of Engrailed homeodomain mutantsProtein environment affects the water-tryptophan binding mode. Molecular dynamics simulations of Engrailed homeodomain mutants
Structural highlights
FunctionHMEN_DROME This protein specifies the body segmentation pattern. It is required for the development of the central nervous system. Transcriptional regulator that represses activated promoters. Wg signaling operates by inactivating the SGG repression of EN autoactivation. Publication Abstract from PubMedWater molecules can interact with aromatic moieties using either their O-H bonds or their lone-pairs of electrons. In proteins, water-pi interactions have been reported to occur with tryptophan and histidine residues, and dynamic exchange between O-Hpi hydrogen bonding and lone-pairpi interactions was suggested to take place, based on ab initio calculations. Here we used classical and QM/MM molecular dynamics simulations, complemented with an NMR study, to examine a specific water-indole interaction observed in the engrailed homeodomain and in its mutants. Our simulations indicate that the binding mode between water and indole can adapt to the potential created by the surrounding amino acids (and by the residues at the DNA surface in protein-DNA complexes), and support the model of dynamic switching between the O-Hpi hydrogen bonding and lone-pairpi binding modes. Protein environment affects the water-tryptophan binding mode. MD, QM/MM, and NMR studies of engrailed homeodomain mutants.,Spackova N, Trosanova Z, Sebesta F, Jansen S, Burda JV, Srb P, Zachrdla M, Zidek L, Kozelka J Phys Chem Chem Phys. 2018 May 9;20(18):12664-12677. doi: 10.1039/c7cp08623g. PMID:29696277[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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