1di4: Difference between revisions

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{{Seed}}
[[Image:1di4.png|left|200px]]


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==ROLE OF AMINO ACID RESIDUES AT TURNS IN THE CONFORMATIONAL STABILITY AND FOLDING OF HUMAN LYSOZYME==
The line below this paragraph, containing "STRUCTURE_1di4", creates the "Structure Box" on the page.
<StructureSection load='1di4' size='340' side='right'caption='[[1di4]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
You may change the PDB parameter (which sets the PDB file loaded into the applet)
== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<table><tr><td colspan='2'>[[1di4]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DI4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DI4 FirstGlance]. <br>
or leave the SCENE parameter empty for the default display.
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
{{STRUCTURE_1di4|  PDB=1di4  |  SCENE=  }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1di4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1di4 OCA], [https://pdbe.org/1di4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1di4 RCSB], [https://www.ebi.ac.uk/pdbsum/1di4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1di4 ProSAT]</span></td></tr>
</table>
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
  <jmolCheckbox>
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/di/1di4_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
    <text>to colour the structure by Evolutionary Conservation</text>
  </jmolCheckbox>
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1di4 ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
To clarify the role of amino acid residues at turns in the conformational stability and folding of a globular protein, six mutant human lysozymes deleted or substituted at turn structures were investigated by calorimetry, GuHCl denaturation experiments, and X-ray crystal analysis. The thermodynamic properties of the mutant and wild-type human lysozymes were compared and discussed on the basis of their three-dimensional structures. For the deletion mutants, Delta47-48 and Delta101, the deleted residues are in turns on the surface and are absent in human alpha-lactalbumin, which is homologous to human lysozyme in amino acid sequence and tertiary structure. The stability of both mutants would be expected to increase due to a decrease in conformational entropy in the denatured state; however, both proteins were destabilized. The destabilizations were mainly caused by the disappearance of intramolecular hydrogen bonds. Each part deleted was recovered by the turn region like the alpha-lactalbumin structure, but there were differences in the main-chain conformation of the turn between each deletion mutant and alpha-lactalbumin even if the loop length was the same. For the point mutants, R50G, Q58G, H78G, and G37Q, the main-chain conformations of these substitution residues located in turns adopt a left-handed helical region in the wild-type structure. It is thought that the left-handed non-Gly residue has unfavorable conformational energy compared to the left-handed Gly residue. Q58G was stabilized, but the others had little effect on the stability. The structural analysis revealed that the turns could rearrange the main-chain conformation to accommodate the left-handed non-Gly residues. The present results indicate that turn structures are able to change their main-chain conformations, depending upon the side-chain features of amino acid residues on the turns. Furthermore, stopped-flow GuHCl denaturation experiments on the six mutants were performed. The effects of mutations on unfolding-refolding kinetics were significantly different among the mutant proteins. The deletion/substitutions in turns located in the alpha-domain of human lysozyme affected the refolding rate, indicating the contribution of turn structures to the folding of a globular protein.


===ROLE OF AMINO ACID RESIDUES AT TURNS IN THE CONFORMATIONAL STABILITY AND FOLDING OF HUMAN LYSOZYME===
Role of amino acid residues at turns in the conformational stability and folding of human lysozyme.,Takano K, Yamagata Y, Yutani K Biochemistry. 2000 Jul 25;39(29):8655-65. PMID:10913274<ref>PMID:10913274</ref>


From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1di4" style="background-color:#fffaf0;"></div>


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==See Also==
The line below this paragraph, {{ABSTRACT_PUBMED_10913274}}, adds the Publication Abstract to the page
*[[Lysozyme 3D structures|Lysozyme 3D structures]]
(as it appears on PubMed at http://www.pubmed.gov), where 10913274 is the PubMed ID number.
== References ==
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<references/>
{{ABSTRACT_PUBMED_10913274}}
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</StructureSection>
==About this Structure==
1DI4 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DI4 OCA].
 
==Reference==
Role of amino acid residues at turns in the conformational stability and folding of human lysozyme., Takano K, Yamagata Y, Yutani K, Biochemistry. 2000 Jul 25;39(29):8655-65. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/10913274 10913274]
[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
[[Category: Lysozyme]]
[[Category: Large Structures]]
[[Category: Single protein]]
[[Category: Takano K]]
[[Category: Takano, K.]]
[[Category: Yamagata Y]]
[[Category: Yamagata, Y.]]
[[Category: Yutani K]]
[[Category: Yutani, K.]]
[[Category: Hydrolase]]
[[Category: Mutant]]
[[Category: Stability]]
[[Category: Turn]]
 
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Retrieved from "https://proteopedia.org/1di4"