1d5e

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (07:48, 15 November 2023) (edit) (undo)
 
(14 intermediate revisions not shown.)
Line 1: Line 1:
-
{{Seed}}
 
-
[[Image:1d5e.png|left|200px]]
 
-
<!--
+
==The role of phenylalanine 8 in the stabilization of the S protein-S peptide interaction: Packing and cavities==
-
The line below this paragraph, containing "STRUCTURE_1d5e", creates the "Structure Box" on the page.
+
<StructureSection load='1d5e' size='340' side='right'caption='[[1d5e]], [[Resolution|resolution]] 2.25&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'>[[1d5e]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D5E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1D5E 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]] 2.25&#8491;</td></tr>
-
-->
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NLE:NORLEUCINE'>NLE</scene>, <scene name='pdbligand=SET:AMINOSERINE'>SET</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-
{{STRUCTURE_1d5e| PDB=1d5e | SCENE= }}
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1d5e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d5e OCA], [https://pdbe.org/1d5e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1d5e RCSB], [https://www.ebi.ac.uk/pdbsum/1d5e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1d5e ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/RNAS1_BOVIN RNAS1_BOVIN] Endonuclease that catalyzes the cleavage of RNA on the 3' side of pyrimidine nucleotides. Acts on single stranded and double stranded RNA.<ref>PMID:7479688</ref>
 +
== 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/d5/1d5e_consurf.spt"</scriptWhenChecked>
 +
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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=1d5e ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
The hydrophobic effect is widely believed to be an important determinant of protein stability. However, it is difficult to obtain unambiguous experimental estimates of the contribution of the hydrophobic driving force to the overall free energy of folding. Thermodynamic and structural studies of large to small substitutions in proteins are the most direct method of measuring this contribution. We have substituted the buried residue Phe8 in RNase S with alanine, methionine, and norleucine. Binding thermodynamics and structures were characterized by titration calorimetry and crystallography, respectively. The crystal structures of the RNase S F8A, F8M, and F8Nle mutants indicate that the protein tolerates the changes without any main chain adjustments. The correlation of structural and thermodynamic parameters associated with large to small substitutions was analyzed for nine mutants of RNase S as well as 32 additional cavity-containing mutants of T4 lysozyme, human lysozyme, and barnase. Such substitutions were typically found to result in negligible changes in DeltaC(p)() and positive values of both DeltaDeltaH degrees and DeltaDeltaS of folding. Enthalpic effects were dominant, and the sign of DeltaDeltaS is the opposite of that expected from the hydrophobic effect. Values of DeltaDeltaG degrees and DeltaDeltaH degrees correlated better with changes in packing parameters such as residue depth or occluded surface than with the change in accessible surface area upon folding. These results suggest that the loss of packing interactions rather than the hydrophobic effect is a dominant contributor to the observed energetics for large to small substitutions. Hence, estimates of the magnitude of the hydrophobic driving force derived from earlier mutational studies are likely to be significantly in excess of the actual value.
-
===The role of phenylalanine 8 in the stabilization of the S protein-S peptide interaction: Packing and cavities===
+
Thermodynamic and structural studies of cavity formation in proteins suggest that loss of packing interactions rather than the hydrophobic effect dominates the observed energetics.,Ratnaparkhi GS, Varadarajan R Biochemistry. 2000 Oct 10;39(40):12365-74. PMID:11015216<ref>PMID:11015216</ref>
 +
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 +
</div>
 +
<div class="pdbe-citations 1d5e" style="background-color:#fffaf0;"></div>
-
<!--
+
==See Also==
-
The line below this paragraph, {{ABSTRACT_PUBMED_11015216}}, adds the Publication Abstract to the page
+
*[[Ribonuclease 3D structures|Ribonuclease 3D structures]]
-
(as it appears on PubMed at http://www.pubmed.gov), where 11015216 is the PubMed ID number.
+
== References ==
-
-->
+
<references/>
-
{{ABSTRACT_PUBMED_11015216}}
+
__TOC__
-
 
+
</StructureSection>
-
==About this Structure==
+
-
1D5E is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D5E OCA].
+
-
 
+
-
==Reference==
+
-
Thermodynamic and structural studies of cavity formation in proteins suggest that loss of packing interactions rather than the hydrophobic effect dominates the observed energetics., Ratnaparkhi GS, Varadarajan R, Biochemistry. 2000 Oct 10;39(40):12365-74. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11015216 11015216]
+
[[Category: Bos taurus]]
[[Category: Bos taurus]]
-
[[Category: Protein complex]]
+
[[Category: Large Structures]]
-
[[Category: Ratnaparkhi, G S.]]
+
[[Category: Ratnaparkhi GS]]
-
[[Category: Varadarajan, R.]]
+
[[Category: Varadarajan R]]
-
[[Category: Cavity s protein]]
+
-
[[Category: S peptide]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jun 30 22:26:47 2008''
+

Current revision

The role of phenylalanine 8 in the stabilization of the S protein-S peptide interaction: Packing and cavities

PDB ID 1d5e

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1d5e"
Personal tools